Acute lung injury (ALI) is a serious respiratory disorder for which therapy is primarily supportive once infection is excluded. Surgical lung biopsy may rule out other diagnoses, but has not been generally useful for therapy decisions or prognosis in this setting. Importantly, tissue and peripheral blood eosinophilia, the hallmarks of steroid-responsive acute eosinophilic pneumonia, are not commonly linked with ALI. We hypothesized that occult eosinophilic pneumonia may explain better outcomes for some patients with ALI.EPX-mAb) was used to assess intrapulmonary eosinophil accumulation/degranulation. Lung biopsies from ALI patients (n = 20) were identified following review of a pathology database; 45% of which  displayed classical diffuse alveolar damage (ALI-DAD). Controls were obtained from uninvolved tissue in patients undergoing lobectomy for lung cancer (n = 10). Serial biopsy sections were stained with hematoxylin and eosin (H&E) and subjected to EPX-mAb immunohistochemistry.Immunohistochemistry using a novel monoclonal antibody recognizing eosinophil peroxidase (EPX-mAb immunohistochemistry provided a >40-fold increased sensitivity to detect eosinophils in the lung relative to H&E stained sections. This increased sensitivity led to the identification of higher numbers of eosinophils in ALI patients compared with controls; differences using H&E staining alone were not significant. Clinical assessments showed that lung infiltrating eosinophil numbers were higher in ALI patients that survived hospitalization compared with non-survivors. A similar conclusion was reached quantifying eosinophil degranulation in each biopsy.EPX-mAb immunohistochemistry uniquely identified eosinophil accumulation/degranulation in patients with ALI relative to controls. More importantly, this method was a prognostic indicator of patient survival. These observations suggest that EPX-mAb immunohistochemistry may represent a diagnostic biomarker identifying a subset of ALI patients with improved clinical outcomes.The enhanced sensitivity of  ALI encompasses a spectrum of pulmonary disorders that is often accompanied by life-threatening hypoxemic respiratory failure and diffuse bilateral pulmonary infiltrates. Moreover, the origins of ALI are often complex  and not easily attributed to a defined cause -6. In itThe pathogenesis of ALI remains unclear, largely a consequence of the heterogeneity of patients coming into the ICU and the broad clinical features characteristic of ALI ,19. The For most patients with ALI, eosinophils have not been reported as a prominent histological feature, despite their potential tissue damaging capability ,28 and tEPX)-specific monoclonal antibody (EPX-mAb) visualized by immunohistochemistry. We employed this unique increase in sensitivity to detect eosinophils and evidence of tissue degranulation in a group of ALI patients. A retrospective assessment of ALI patients who had a lung biopsy taken during the course of their acute care was conducted, comparing the results of these assessments with lung tissue from control subjects. These blinded assessments revealed that the added sensitivity of EPX-mAb immunohistochemistry detected a significant increase in eosinophil accumulation/degranulation in ALI vs. control subjects. More importantly, EPX-mAb immunohistochemistry identified a subset of ALI patients who survived hospitalization, suggesting its use as a prognostic indicator may represent a previously underappreciated diagnostic strategy in the management of pulmonary patients.In this study we demonstrate that standard histological evaluation of lung biopsies significantly underestimates eosinophil accumulation when compared to assessments using a novel eosinophil peroxidase , and in compliance with HIPPA guidelines for patient privacy.(i) The presence of fibrin in the alveoli; (ii) The demonstration of an organizing pneumonia ; and (iii) Evidence of reactive airway epithelial Type II cell hyperplasia. Among these twenty ALI patients, 45%  displayed classical diffuse alveolar damage (ALI-DAD). Seven of the study group did not survive hospitalization, and of these non-surviving patients >71% (5/7) received an ALI-DAD diagnosis. A variety of co-morbid medical disorders were evident in our ALI patients, including several patients with connective tissue disorders. However, examination of the medical records and care-giver notes failed to identify elements of commonality regarding disease onset or progression. Nonetheless, the unresolved character of disease progression in these subjects was such that nineteen of the twenty patients received corticosteroid therapy during their course of treatment.An overview of the demographic data and pathological/clinical assessments of our ALI study subjects is presented in Tables Control lung samples consisted of uninvolved areas of lung tissue recovered from patients undergoing resection for a diagnosis of lung cancer Table . None ofThe twenty lung specimens obtained from patients with ALI included sixteen surgical lung biopsies and four transbronchial lung biopsies considered adequate for histologic review . All control biopsies were taken from uninvolved areas of surgically resected lung tissue removed for treatment of lung cancer. Lung tissue biopsies were fixed in 4% buffered formalin, embedded in paraffin, and serial 4 μm thick sections were cut.EPX-mAb as previously described [H&E staining was performed using an automated stain processing unit in the Mayo Clinic Arizona clinical histology unit. Immunohistochemistry was performed using a escribed . EvaluatEPX-mAb and slide 3 served as an isotype immunoglobulin negative control for the immunohistochemistry.Serial sections from each biopsy were coded by clinical histopathology laboratory personnel and in each case the middle (slide 2) of the three serial sections was stained with Hematoxylin - Eosin (H&E). Slide 1 of the series was subjected to immunohistochemical staining with 2 field of view); that is, a total area of ~3 mm2 per biopsy-investigator. The reported values are the mean ± SEM of all investigator-derived counts.The eosinophil infiltration of lung tissue using H&E staining was performed in an investigator-blinded fashion independently by an experienced pulmonary pathologist with a specialty in lung diseases (KL) and a pathology resident (PG). The slides were evaluated by each individual as a numerical average calculated from 10 randomly selected hpf ; KL and EJ - EPX-mAb assessments of eosinophil degranulation), a hospital/clinic-based pulmonary fellow (KP - EPX-mAb based eosinophil counts in lung tissue), and a PhD graduate research fellow (LW - EPX-mAb based eosinophil counts and degranulation in lung tissue). All evaluations were done at a magnification of 400x. The number of positively stained eosinophils was determined in the alveolar lung parenchyma as a numerical average calculated from 10 randomly selected hpf; that is, a total area of ~3 mm2 per biopsy-investigator. The reported values are the mean ± SEM of investigator-derived counts.Quantification of eosinophil tissue infiltration within each biopsy using 2 field of view); that is, a total area of ~3 mm2 per biopsy-investigator. Each field examined was graded using a scale that permitted stratifying the available patients based on a relatively low resolution grading scale that was easily reproduced by multiple evaluators of varying levels of experience and expertise: Level 0 = No identifiable eosinophils and/or degranulation [The level and extent of eosinophil degranulation observed within each patient biopsy was also determined by scanning 10 randomly selected hpf  were also determined between investigators reading slides as a measure of inter-rater agreement .H&E stained slides as well as lung sections subjected to EPX-mAb immunohistochemistry are shown in Figure H&E stained patient biopsies revealed little evidence of eosinophil infiltration in both control and ALI subjects . However, evaluation by the same pathology investigators of the serial slides subjected to EPX-mAb immunohistochemistry demonstrated an enhanced sensitivity to detect eosinophils in these lung tissue sections. Specifically, evaluations of the lungs of control subjects using EPX-mAb immunohistochemistry revealed a >40-fold increase in the ability to detect tissue infiltrating eosinophils relative to H&E staining .Serial biopsy sections from either control or ALI subjects were stained for evaluations of eosinophil tissue infiltration. Representative photomicrographs of EPX-mAb immunohistochemistry demonstrated that the density of pulmonary eosinophils in the collective group of ALI patients is significantly higher relative to control subjects , respectively). More importantly, further evaluations of the ALI patients .Evaluation of serial lung sections following EPX-mAb immunohistochemistry revealed that ALI patients displayed significant and varying levels of degranulation that were quantifiable. This degranulation was often observed in these patients in the absence of identifiable intact eosinophils. The photomicrographs of Figure Level 0) in a given high powered field to >50% of the field evidencing eosinophil degranulation (Level 2b). Similar to the higher levels of eosinophil infiltration observed in the collective group of ALI patients, the collective group also evidenced a >2-fold increase in the level of eosinophil degranulation compared to control subjects . More importantly, quantitative assessments of degranulation  based on EPX-mAb immunohistochemistry .Assessments of lung sections following ry Table  revealedEPX-mAb immunohistochemistry relative to H&E staining are noteworthy: EPX-mAb (i) immunohistochemistry is an easily performed assessment that provided a >40-fold enhancement to detect tissue infiltrating eosinophils. This increased sensitivity not only allowed for the greater detection of tissue infiltrating eosinophils but also corresponding increases in the speed, accuracy, and reproducibility of this determination. EPX-mAb (ii) immunohistochemistry provided a rapid and definitively quantitative assessment of eosinophil degranulation within the lung parenchyma, observable even in the absence of intact infiltrating eosinophils.Independent of any conclusions regarding our evaluation of ALI vs. control subjects, two technical observations regarding our assessments of the lung biopsies using n = 20) whose disease origins and severity vary considerably. Moreover, we did not have control over the general demographics of these ALI patients nor could we dictate why, when, or where within the lung the biopsies for study were taken relative to the course of disease and/or patient treatment. The ALI subjects of this study were also not selected on the basis of a defined and standardized medical history or a regimented treatment plan. Finally, the control subjects available to us were limited and did not include healthy volunteer biopsies or ALI patients prior to any medical interventions.Unfortunately, studies of ALI patients are often incomplete and subject to ambiguities resulting from the broad and complex character of symptoms and contributing etiologies ,37. CompEPX-mAb immunohistochemistry to distinguish ALI patients from control subjects. Specifically, eosinophils are not considered a reliable histopathological marker of ALI . Yetalities, ,8,10,19 alities, . Indeed,The studies presented in this report have identified both significant technical insights and revelations regarding eosinophils in lung biopsy samples from control and ALI patients. These observations will likely have a direct impact on the assessment of eosinophils and their role(s) in lung diseases and, more important, may lead to previously overlooked or untried diagnostic and therapeutic strategies with which to treat these problematic patients.• Immunohistochemical detection of EPX in lung tissue biopsies provides even a board certified pathologist  a >40-fold increase in sensitivity to detect tissue infiltrating eosinophils in lung tissue sectionsEPX-mAb based immunohistochemistry allows for the unique assessment of eosinophil activation  within the lung even in the absence of a demonstrable eosinophil infiltrate• EPX-mAb demonstrate that increases in lung infiltrating eosinophils and evidence of eosinophil degranulation are surprisingly characteristic features of biopsies from ALI patients relative to control subjects• The increased sensitivities afforded by EPX-mAb immunohistochemical staining may provide a potential basis to identify a subset of the ~40% of ALI patients who will not survive their hospitalization.• Assessments of lung biopsies from ALI patients following The authors declare that they have no competing interests.The corresponding author (JJL) had full access to all of the data reported in this study and had final responsibility for the decision to submit this report for publication. KP, LW, KL, JJL, designed research study; LW KP, CAP, EJ, PG, KL, and JJL performed research; CAP and NAL contributed new reagents/analytical tools; LW, CAP, RM, KL, and JJL analyzed data; and LW, KL, NAL, and JJL wrote the paper. All authors read and approved the final manuscript.


Natural killer (NK) cells are lymphocytes that play an important role in anti-tumour immunity. Their potential against brain cancer has been demonstrated in vitro and in vivo, both as a direct anti-tumour agent and in experimental therapies stimulating endogenous NK cell cytotoxicity. However, the clinical translation of these promising results requires detailed knowledge about the immune status of brain tumour patients, with focus on the NK cell population. In this report, we provide an overview of the studies investigating NK cell infiltration into the tumour, emphasizing the need of revision of the methodologies and further research in this field. We also discuss the potential of using autologous or allogeneic NK cells as effector cells in cellular therapy against brain cancer and developing immunotherapies stimulating endogenous NK cell-mediated anti-tumour response, such as blocking inhibitory killer immunoglobulin-like receptors. Combination of NK cell adoptive transfer with targeted therapies, such as anti-EGFR therapeutic antibody (CetuximAb) could also be a potent strategy. Brain tumours are intracranial neoplasms located in the brain and meninges  and they account for approximately 1.4 % of all cancers . The incNatural killer (NK) cells are large granular lymphocytes of the innate immune system. These cells are able to directly lyse infected or transformed cells without specific immunization . NK cellNK cells play an important role in anti-tumour immunity as several lines of evidence link NK cell surveillance , anti-tuNumerous studies have investigated the immune system of brain tumour patients, mainly in the context of malignant glioma. Brain tumour patients suffer from extensive immunosuppression due to lymphopenia, decreased lymphocyte proliferation , 34 and The remaining question was whether the NK cells infiltrate the tumour site. In 1988, Stevens et al. characterised the immune infiltrates in gliomas, carcinoma metastases, craniopharyngiomas and meningiomas . To idendimCD16− [Contrasting results were reported by Yang et al.  in the mdimCD16− . These r+CD16− occurs as in the other gliomas.Concerning oligodendrogliomas, Rossi et al. reported absence of NK cells in those tumours . HoweverThe most recent study focusing on meningiomas was conducted by Domingues et al.  and demoA number of in vitro and in vivo functional studies have been performed in order to investigate the role of NK cells in anti-tumour immunity in brain cancers and the potential of using them as a therapeutic agent. Alizadeh et al.  investigThe prognostic significance of NK cells’ activity has been demonstrated in patients with various solid tumours –22, 24. Therefore, using pure NK cells against solid tumours becomes an attractive alternative strategy to using LAK cells. To date, only one phase I clinical trial has been conducted, where pure autologous NK cells were used as effector cells against brain tumours . In thisThe NK cells have limited access into the nascent brain  and theyMalignant brain tumours develop multiple mechanisms of immune escape and both local, and systemic immunosuppression , 61, 62.To summarize, NK cells play an important role not only in anti-tumour immunity but they are potent effectors that may be considered for developing novel immunotherapies. However, stringent research is required to determine the impact of NK cell infiltration into the tumour site and their therapeutic efficacy in brain tumour patients. Investigating NK cells in the context of brain tumour is also essential for improving the NK cell-based immunotherapies that are increasingly investigated for clinical development for brain tumour patients.


Long-term survivors of pediatric and young adult (PAYA) cancers have a high incidence of subsequent neoplasms, but few risk factors other than cancer treatment have been identified. We aimed to describe the burden of human papillomavirus (HPV)-associated malignancies among survivors of PAYA cancers to assess whether HPV infections might be a reasonable area of future etiologic research on subsequent malignancies in this population. We used longitudinal data from 9 population-based registries of the Surveillance, Epidemiology, and End Results program collected between 1973 and 2010 to assemble a cohort of individuals who were diagnosed with any cancer between the ages of 0 and 29 years and survived at least 5 years post-diagnosis. We estimated sex-specific standardized incidence ratios (SIRs) with corresponding 95% confidence limits (CL) of HPV-associated subsequent malignancies . Our study population comprised 64,547 long-term survivors of PAYA cancers diagnosed between 1973 and 2010. Compared with females in the general US population, female PAYA cancer survivors had a 40% relative excess of HPV-associated malignancies overall . Compared with males in the general US population, male PAYA cancer survivors had a 150% relative excess of HPV-associated malignancies overall . Our findings suggest an excess of HPV-associated malignancies among PAYA cancer survivors compared with the general US population. We hypothesize that a portion of subsequent malignancies among PAYA cancer survivors may be directly attributable to HPV infection. This hypothesis warrants exploration in future studies. Long-term survivors of pediatric and young adult (PAYA) cancers have an excess incidence of subsequent malignancies in various organ systems relative to what would be expected in the general population Persistent infection with oncogenic human papillomavirus (HPV) types, particularly HPV-16 and -18, is a well-established cause of cervical cancer We used longitudinal data from 9 population-based registries of the Surveillance, Epidemiology, and End Results (SEER) program The publicly available de-identified SEER data used for this analysis are exempt from institutional review board approval  Our outcomes of interest were restricted to subsequent malignancies for which current evidence suggests an etiologic relation with HPV : cervical, vaginal, vulvar, penile, anal, oropharyngeal, tongue, and tonsillar cancers p.240–243, for the SIR when the expected number of cases was ≥5 and mid-P-value CL, a small sample method p.253–254, when the expected number of cases was <5.We used person-time and outcome data for PAYA cancer survivors to estimate the cumulative incidence of all HPV-associated subsequent malignancies based on Fine and Gray’s proportional subdistribution hazard model to account for the competing risk of death eq.19–13:A* and E* are the original unadjusted numbers, and T* is person-years. Given the SEER program’s extensive efforts to confirm diagnoses of submitted cases APAYA = A*PAYA/Se and EUS = E*US/Se p.359, and the SIRs adjusted for misclassification were computed as APAYA/EUS.PAYA cancer survivors may interact with the healthcare system more often than the general US population (e.g. 87% of 5-year survivors of pediatric cancer reported general medical contact Our study population comprised 64,547 long-term survivors of PAYA cancers diagnosed between 1973 and 2010 in the US. Our hypothesis-generating study aimed to describe the burden of HPV-associated malignancies among long-term PAYA cancer survivors. The cumulative incidence of all subsequent HPV-associated malignancies among PAYA cancer survivors was 0.71%, which suggests a modest absolute burden of disease. Our results also suggest that female and male PAYA cancer survivors have a relative excess of most HPV-associated malignancies compared with the general US population. In particular, a relative excess of head and neck malignancies compared with the general population is consistent between male and female PAYA cancer survivors. Furthermore, the relative excess of most site-specific HPV-associated malignancies persists regardless of first-course radiation status among female and male PAYA cancer survivors.Despite cervical cancer representing approximately half of all subsequent HPV-associated malignancies among female PAYA cancer survivors, our results suggest that cervical cancer incidence is similar between female PAYA cancer survivors and the general population. One plausible explanation is that cervical cancer is screen-detectable and cervical cancer screening rates are similar between female PAYA cancer survivors and females in the general US population a priori consideration included potential outcome misclassification because of differential rates of cancer detection between PAYA cancer survivors and the general population, which was explored in a sensitivity analysis. The results of our sensitivity analysis suggest that the difference in sensitivity of cancer detection would have to be at least 30% lower among females in the general US population than among female PAYA cancer survivors to nullify the relative excess of HPV-associated malignancies overall. The difference required to nullify the relative excess would have to be even more extreme than 30% between male PAYA cancer survivors and males in the general US population. We speculate that such large differences in the sensitivity of detecting HPV-associated malignancies between PAYA cancer survivors and the general US population are unlikely given that screening is available for cervical cancer and the symptoms associated with the other HPV-associated malignancies are likely to prompt medical attention. Nonetheless, the actual detection rates of HPV-associated malignancies among PAYA cancer survivors and the general US population are unknown. Consequently, the results of our sensitivity analysis offer simulated quantitative evidence that the relative excess of HPV-associated malignancies overall observed in our study is unlikely to be fully explained by outcome misclassification, particularly for male PAYA cancer survivors.Additional sources of uncertainty should be considered when interpreting our results. One The SEER data used in our analysis include information about radiation as first-course therapy, but information is unavailable about the use of radiation to treat a recurrent cancer The SEER program’s high case ascertainment rates for initial cancers within population-based coverage areas reduce the potential for underestimating the expected number of cases in the general US population when estimating an SIR In summary, our findings suggest an excess of HPV-associated malignancies among PAYA cancer survivors. This relative excess is not fully attributable to radiation therapy, particularly among males. The relative excess of subsequent malignancies such as those of the head and neck could be partly explained by factors such as smoking Given the available evidence, we hypothesize that a portion of subsequent malignancies among PAYA cancer survivors may be directly attributable to HPV infection. HPV infections, based on direct measurements among individuals, have been associated with subsequent malignancies among adult cancer survivors


Neosalanx taihuensis) diversified in response to thermal regime following introduction 25 y prior. In general, warmwater icefish variants grew faster, had larger adult body size and higher condition and fecundity, but matured at smaller sizes. Conversely, coldwater variants had smaller adult body size and lower condition, but matured at larger sizes and had larger eggs. These life-history differences strongly suggest that key ecological trade-offs exist for icefish populations exposed to different thermal regimes, and these trade-offs have driven relatively rapid diversification in the life histories of icefish within Lake Erhai. Results are surprisingly concordant with current knowledge on life-history evolution at macroecological scales, and suggest that improved conservation management might be possible by focusing on patterns operating at microgeographical, including, within-ecosystem scales.Climatic variations are known to engender life-history diversification of species and populations at large spatial scales. However, the extent to which microgeographic variations in climate  can also drive life-history divergence is generally poorly documented. We exploited a spatial gradient in water temperatures at three sites across a large montane lake in southwest China (Lake Erhai) to examine the extent to which life histories of a short-lived fish species (icefish,  Biologists have long been fascinated with how thermal habitat variations shape species evolution and life histories One of the best opportunities for expanding this work lies in the simple observation that temperature often varies widely within a single large ecosystem 2, is 42.6 km long from south to north, and has an average and maximum depth of 10.2 m and 20.7 m respectively. The lake receives inflow from two large rivers in the north and several smaller streams in the southwest. Previous limnological surveys revealed that water temperatures in the northern sections of the lake are consistently higher than temperatures in the southern sections with a typical difference of ∼1°C or more . Standing at the foot of the Cangshan Mountains, it has a surface area of 249.0 km or more . This teNeosalanx taihuensis  is a small fish species native to the middle and lower reaches of the Yangtze River basin in China. The species inhabits the pelagic zone of lakes and rivers, is zooplanktivorous, and has a short generation time (∼1 y) with few individuals capable of reaching a second year of life. Over time, icefish have been introduced into lakes and reservoirs throughout China for the purpose of commercial fisheries production Cyprinus longipectoralis, C. pellegrini, and Zacco taliensisThe icefish In this study, we document life-history variations in icefish populations at three sites along the north-south axis of Lake Erhai. We exploit the natural thermal gradient present in the lake, along with the fact that each population represents recent adaptation from a single source population, as a natural experiment to explore the effect of temperature variations on the diversification of icefish life histories.Icefish populations were sampled monthly at three sites in Lake Erhai from June 2010 to May 2011 using a lift-net . The opeTL) and mass (TM) were measured for each individual to the nearest 0.01 mm and 0.01 g. Sex and maturation score GM) and eviscerated body mass (EM) weighed to the nearest 0.1 mg. Gonad somatic index (GSI) was calculated using the equation: GSI = 100*(GMEM−1) ON, defined as the total number of oocytes in the actively spawning stage) counted for estimation of absolute fecundity (AF). Relative fecundity  was calculated using the equation: RF = OMEN−1K) was calculated using the equation: K = 105TLTM−3Total body length , log(TM), and log(K) were dependent variables, site was a fixed variable and month of collection was a random variable. Sphericity assumption was tested using Mauchly's test and degrees of freedom were adjusted using a Greenhouse-Geisser Epsilon correction when data violated the assumption of sphericity. When significant month × site interactions were observed, one-way ANOVAs with Tukey's HSD post-hoc tests were used to evaluate among site differences in each month.Statistical differences in RF data were not normally distributed, Kruskal-Wallis tests were used to evaluate statistical differences in these variables. Significant differences among-site in these response variables were evaluated using Wilcoxon post-hoc tests. AF data were normally distributed, thus analysis of covariance (ANCOVA) was used to examine among-site differences in AF (with TL as a covariate). Significant post-hoc differences between means were determined using Tukey's HSD test. GSI data were normally distributed, thus one-way ANOVA with Tukey's HSD post-hoc test was used to test differences in GSI among-sites. Logistic regressions were used to model relationships between maturity  and total length. Lengths at which 50% of individuals were sexually mature were estimated at each site using logistic regressions . A log-likelihood ratio test was used to examine differences in maturity-TL relationships among the three sites Whereas egg diameter and All the procedures described in this study were approved by the ethics committee of the Institute of Hydrobiology Chinese Academy of Sciences, Hubei Province, China. Sampling permits for each location were issued by the Lake Erhai Protection Agency of China. The study did not involve any endangered or protected species.TL and TM at all three sites over the course of the surveys , body mass  and condition factor  among all three sites.Across all months and sites, a total of 5400 individual icefish were sampled from Lake Erhai. Icefish displayed positive growth in  surveys . At eachMean total lengths and weights (averaged across the year) were highest in the warmwater northern icefish variants followed by mid-lake icefish and finally cold water southern icefish . SignifiT50L) increased from the warmest to coldest sites , respectively and log-likelihood ratio tests confirmed that differences between all three sites were significant . Thus icefish variants from the warmest site matured at significantly smaller sizes relative to icefish from the coldest site.Logistic models revealed that average size at maturity (st sites . LT50 vaTL as a covariant), there were also significant differences in absolute fecundity among all three sites . Coldwater icefish variants from the south produced the largest eggs, followed by the mid-lake site with intermediate-sized eggs, and finally the warmwater variants from the north with the smallest egg sizes (Life-history traits are basic determinants of species and population performance Ovis aries) declined by ∼20% due to direct temperature effects on metabolism and growth rate, rather than selection per se The extent to which phenotypic differences among variants observed in this study are based in genetic differences or phenotypic plasticity remains uncertain Classically, a series of well-known ecological factors combine to influence the selection and diversification of life-history strategies. Below, we discuss the potential for each of several of these factors to produce the life-history patterns observed.Cyprinus longipectoralis, C. pellegrini, Zacco taliensis) and lack carnivorous predator conspecifics Channa argus) are apparently present within Lake Erhai. However, the levels are so low as to be functionally zero, and are only found in isolated areas of the littoral zone, whereas icefish exclusively occupy pelagic habitats. In fact, during a previous study of snakehead diets in Lake Erhai, none were found to have preyed upon icefish Predation risk can exert strong selective forces on phenotypes of prey Similar to predators, variations in ecological productivity can also drive life-history diversification Under heavy exploitation pressure, fish populations are known to evolve in characteristic ways Temperature frequently varies substantially within aquatic ecosystems Life-history theory predicts that a significant thermal gradient in a large lake environment (given sufficient selection strength and isolation) could, over time, elicit the formation of predictable and divergent life-history strategies Drosophilia subobscura in the southern Palearctic, chromosomal diversity was estimated to have shifted by 18.3% in only 16 years as a result of rapid global warming in this region Rana sylvatica) underwent rapid microgeographic evolution in thermal tolerance in only 36 y following the construction of beaver ponds and corresponding alteration of thermal water regimes A variety of examples of rapid evolution exist in response to thermal and other ecological changes against which these results might be compared Ultimately, it also remains unclear whether phenotypic differences and putative genetically-based life histories were a product of true adaptive evolution or genetic drift  or a combination of both. Both processes are well-known to lead to genetic differentiation in a diverse number of taxa and situations Species introductions can also be a major driver of rapid evolution and diversification of phenotypes Previous research on life-history evolution of aquatic organisms in response to thermal-scaling laws originates primarily from macroecological studies, e.g., across species ranges or continents These findings have bearing on the conservation management of ectothermic animals in large ecosystems. For example, fisheries management in large lakes is typically conducted on lake-wide scales. Even in extremely large ecosystems , fisheries regulations can vary little system-wide. However, these data show that, within large lake environments, fish life histories can be quite different depending on the thermal characteristics of the lake section. These dynamics foreshadow new challenges for fisheries managers that require additional thought and research. For a variety of reasons, it can be unpopular to manage different lake sections under different fishing regulations. Furthermore, limited budgets and staffing issues in water-rich areas preclude collection of intense system-specific data on fish populations. Nonetheless, when life-history variants exist under a single management system, the potential for poor management of one of the variants will be present  Enhanced reproduction as a consequence of reduced body size may also be an important pattern for understanding biological response to climate change. Currently, a large amount of research is being conducted towards understanding species geographic-range shifts under various warming scenarios


Internet addiction has become increasingly recognized as a mental disorder, though its neurobiological basis is unknown. This study used functional neuroimaging to investigate whole-brain functional connectivity in adolescents diagnosed with internet addiction. Based on neurobiological changes seen in other addiction related disorders, it was predicted that connectivity disruptions in adolescents with internet addiction would be most prominent in cortico-striatal circuitry.Participants were 12 adolescents diagnosed with internet addiction and 11 healthy comparison subjects. Resting-state functional magnetic resonance images were acquired, and group differences in brain functional connectivity were analyzed using the network-based statistic. We also analyzed network topology, testing for between-group differences in key graph-based network measures.Adolescents with internet addiction showed reduced functional connectivity spanning a distributed network. The majority of impaired connections involved cortico-subcortical circuits . Bilateral putamen was the most extensively involved subcortical brain region. No between-group difference was observed in network topological measures, including the clustering coefficient, characteristic path length, or the small-worldness ratio.Internet addiction is associated with a widespread and significant decrease of functional connectivity in cortico-striatal circuits, in the absence of global changes in brain functional network topology. Internet addiction has been increasingly recognized both in public and the scientific community worldwide Resting-state fMRI is a relatively new imaging technique for investigating inter-regional correlations of spontaneous brain activity, recorded as someone lies quietly in the scanner without being engaged in a specific task In this study, we used resting-state fMRI data to map differences in functional connectivity between a comprehensive set of 90 distinct cortical and subcortical brain regions in healthy individuals and adolescents with internet addiction, focusing on individuals engaging in excessive online gaming among the proposed subtypes of this disorder Based on previous structural and functional neuroimaging findings in internet addiction This study was approved by the institutional review board for human subjects at the Seoul National University. All the adolescents and their parents provided written informed consent prior to study entry. The study was conducted in accordance with the Declaration of Helsinki.Twelve right-handed male adolescents with internet addiction and 11 right-handed and gender-matched 2; flip angle 90°; voxel size 3.0 mm×3.0 mm×3.0 mm; slices 40. The total time of the acquisition was 6 min 45 sec. A head coil was used and head motion was minimized by filling the empty space around the head with sponge material and fixing the lower jaw with a tape.Resting-state fMRI images were acquired on a 3T Siemens scanner  with the following parameters: repetition time (TR) 2700 ms; echo time (TE) 30 ms; acquisition matrix 64×64; field of view (FOV) 192×192 mmp<0.05) in the four head motion parameters recently suggested by Van Dijk et al. The preprocessing of fMRI images was conducted using the Data Processing Assistant for Resting-State fMRI (DPARSF) graph components, were then identified among the connections with a t-statistic exceeding a threshold of t = 3.0. A family-wise error (FWE)-corrected p-value was calculated for the size of each resulting component using permutation testing (20000 permutations). Each permutation involved randomly shuffling the group labels and identifying the size of the largest interconnected network, thereby yielding an empirical null distribution of maximal component sizes http://www.brain-connectivity-toolbox.net/) or NITRC (http://www.nitrc.org/projects/nbs/). To assess the reproducibility of any significant findings to alternative atlases http://www.fmrib.ox.ac.uk/fsl/data/atlas-descriptions.html) and a random parcellation comprising 120 regions The network-based statistic (NBS) Next, we tested for between-group differences in key graph-based network measures Finally, the clustering coefficient and path length were calculated locally for each of the 90 regions. A two-sided t-test was also used to test for between-group differences in these region-specific measures. The false discovery rate (FDR) All participants were right-handed males. No significant difference was found in age and IQ between the two groups, and YIAS score was significantly higher in internet addiction group .p<0.05, FWE-corrected) decreased connectivity in adolescents with internet addiction compared to controls. This affected network comprised 59 links, involving 38 different brain regions (http://www.nitrc.org/projects/bnv/).The NBS identified a single network showing significantly  (p<(1/90) = 0.011 No between-group difference was noted in the average clustering coefficient, the characteristic path length or the small-worldness ratio at any of the network densities investigated (rrected) . AdditioEvidence of decreased brain functional connectivity was found in adolescents with internet addiction. Consistent with current models emphasizing the role of cortico-subcortical pathology in addiction In this study, the NBS was used with network size measured based on its extent; that is, the total number of connections comprising the network. This size measure is not suited to detecting focal effects involving single, isolated connections that do not collectively form a network. To test for these kinds of focal between-group differences, the NBS analysis was repeated testing for differences in component mass rather than size. The mass statistic provides greater sensitivity to focal, intense effects than testing for differences in component size. In addition, we also thresholded edge-wise comparisons using the FDR, which will be very sensitive to high-intensity, focal effects. No significant between-group differences were apparent with either the FDR or mass statistics, suggesting that aberrant connectivity in internet addiction encompasses a distributed network involving several cortical and subcortical regions.Given that brain network properties are known to be sensitive to the choice of parcellation template, we investigated several alternative parcellation schemes in order to assess the reproducibility of any findings to changes in nodal definitions In contrast to the decreased strength of functional connectivity, topological parameters revealed no significant group differences. Even when we conducted further exploratory analyses based on less stringent control against type I error, the results indicated possible topological difference mainly involving the occipital lobe, which was unaffected in the NBS analysis. Thus, while internet addiction was associated with a widespread and significant decrease of functional connectivity in cortico-subcortical circuits, this decrease was not associated with a global disruption in brain functional network topology. This study demonstrates that widespread differences in functional connectivity can exist in the absence of alterations in basic topological measures. It may seem remarkable that differences in connectivity strength were so widespread in the absence of any significant topological differences. However, it is important to remark that topology and connectivity strength are distinct properties of the connectome and abnormalities in one need not imply abnormalities in the other. Similar findings have been observed in other disorders Among the 59 connections included in the altered network, 25 were interhemispheric connections and 34 were intrahemispheric, pointing to involvement of long-range as well as short-range connections throughout the brain. Given that internet addiction is a newly recognized mental health condition, with its concept and diagnostic criteria still elusive and undetermined, perhaps it might be surprising to find such an extensively affected network in the brain of these subjects. Recently, Lin et al. (2012) investigated brain white matter integrity in adolescents with internet addiction using diffusion-tensor imaging, and found a widespread decrease in fractional anisotropy (FA) throughout the brain with no area of higher FA in internet addiction group Regarding the large number of interhemispheric connections found in the altered network, efficient interhemispheric communication has long been thought to be important in brain functions Interestingly, a similar pattern of decreased resting-state functional connectivity between frontal and parietal regions was reported both in cocaine- and heroin-dependent individuals One of the most interesting findings in the current study was the strong involvement of the putamen. This brain structure is known to modulate several neurotransmitters including dopamine, and blunted striatal dopaminergic function has been strongly implicated as one of the key biological mechanisms of addiction disorders Our finding that the putamen was the most extensively involved subcortical region in the decreased functional network, sparing the caudate nucleus, is also interesting. Both structures are part of the striatum, which in turn is part of the subcortical structures. The putamen is typically considered a brain region associated with motor activity, and has less often been implicated in substance addition than the caudate. Among motor activities, a well-learned sequence of repetitive finger movements has been shown to be associated with activation in the putamen Another point worthy of discussion is the absence of any increased functional connectivity in the internet addiction group. Although we mainly expected to find decreased functional connectivity in the addiction group, in fact, we did not exclude the possibility of observing increased functional connectivity as well, particularly given the hypothesis that adolescents with internet addiction might show a practice effect due to excessive online activities The present study has some important limitations. First, the sample size was quite small, which likely limited our power to detect significant correlations between functional connectivity and YIAS scores. Thus, the current finding needs to be replicated in a larger sample of participants with internet addiction and controls. It is, however, noteworthy that our sample size was on the whole comparable to that of former functional neuroimaging studies of internet addiction. Our sample was unique, as most former studies were based on adults In summary, the results of this study suggest that adolescents with internet addiction display altered brain functional connectivity in the absence of gross disturbances of network topology. The altered network showed an extensive involvement of long-range interhemispheric connections as well as short-range intrahemispheric links throughout the brain. Subcortical brain regions may play an important role in this altered network, particularly the putamen, which showed decreased connections with all three major cerebral lobes involved.Figure S1Network of decreased brain functional connectivity in adolescents with internet addiction (using different atlases).Red dots represent stereotactic centroids of brain regions (nodes) defined by Montreal Neurological Institute (MNI) structural atlas (A) and random parcellation atlas (B), and blue lines represent suprathreshold links  comprising the affected network identified with the network-based statistic (NBS) .(TIF)Click here for additional data file.Figure S2Proportion of connections affected in internet addiction linking distinct pairs of broad cerebral divisions .The number of links involving each pair of divisions is normalized by total number of pair-wise links.(TIF)Click here for additional data file.Table S1Local clustering coefficient.This table shows trend level results with less stringent false positive correction p<(1/90) = 0.011; no result survived the standard false discovery rate correction for multiple comparisons.(DOC)Click here for additional data file.Table S2Local path length.This table shows trend level results with less stringent false positive correction p<(1/90) = 0.011; no result survived the standard false discovery rate correction for multiple comparisons.(DOC)Click here for additional data file.


Solanum with c. 1,200 species. Previous studies have established that the set of most highly variable NCPs vary between major plant families, and here we explore whether this variation extends beyond family level to genera and major clades within genera. Using full plastome data, we identify the most highly variable plastid markers in the Potato clade of Solanum. We then compare sequence variation between the Potato and the closely related Morelloid clade. Results show that whilst a narrow set of NCPs show consistently high variation, levels of sequence variation in most NCPs differ greatly between the two closely related clades. The high variation detected between closely related groups implies that repeated screening studies will be needed for individual projects despite the potential availability of results from closely related taxa, and indicates a narrower applicability of family-specific screening studies than previously thought.Rapidly evolving non-coding plastid regions (NCPs) are currently widely used in evolutionary biology especially in plant systematic studies where NCPs have become one of the most commonly used tools in clarifying species relationships. Currently, the generally small amount of sequence variation provided by NCPs compared to nuclear regions makes plastid phylogeny reconstruction challenging at the species-level, especially so in species rich clades such as  Rapidly evolving non-coding plastid regions (NCPs) are currently used in a wide range of evolutionary studies, including origin of domesticated species Despite past efforts to identify the most rapidly evolving plastid markers across land plants The advances in next generation sequencing technologies (NGS) during the past five years have brought solutions for building species-level plastid phylogenies. Whole plastid genomes can now be generated for multiple species with much reduced cost through massive parallel sequencing PinusSolanum which includes c. 1,200 species. For such species-rich clades, cost of sequencing full plastid genomes is still large, and there are clear advantages of sequencing more species with fewer base pairs compared to fewer species with full genomes in molecular systematic projects. A trade-off approach has been adopted where only a few full plastid genomes are generated, and then used for developing highly variable plastid markers that can be sequenced with traditional Sanger sequencing. Such a screening approach has thus far been used in Solanaceae, Asteraceae, and Poaceae to identify a set of most variable plastid markers Although full plastid genome sequencing has become an increasingly realistic option for molecular phylogenetic studies of relatively small genera with up to 150 species . We then compare sequence variation in the most variable regions within the Potato clade with sequence variation in the same set of markers in the relatively closely related Morelloid clade of Solanum. In addition, we screen seven NCPs which have been previously used in molecular systematic studies in Solanaceae. We discuss variation across the newly identified and previously used NCPs in the context of plastid marker selection for phylogeny reconstruction.In this paper we explore whether variation in the most highly variable plastid markers extends beyond family level to genera and major clades within genera. We specifically ask: (1) Do genera, and clades within genera, share the same hyper-variable plastid regions, and (2) Can full genome sequences of closely related species be used to find and develop new hyper-variable plastid markers for related taxa? We use the mega-diverse genus The thirteen most variable plastid markers identified from the full plastome sequences of three Solanum species included atpB-rbcL, clpP-psbB, ndhF, ndhF-rpl32, petL-psaJ (petL-petG-trnW-trnP-psaJ), petN-psbM, rpl32-trnL, rpoC1-rpoB, trnA-trnI, trnK-rps16, and ycf1 (parts 1–3) . Three ondhF-rpl32, rpl32-trnL, and trnK-rps16, ndhC-trnV) were amongst the widely used plastid markers published by Shaw et al. trnK-rps16 was identified as the most variable plastid marker in Solanum in a previous study that focused on exploring plastid variation within Solanaceae but not within Solanum in particular ndhF, has been widely used in molecular phylogenetic studies in Solanaceae [57]. The remaining regions have not been previously used in Solanaceae.Of the thirteen markers, four  in order to assure that the two repeat segments are identical, which is expected based on the fact that the two IR copies evolve in concert trnA-trnI results were scored  of the plastid genome, including e scored . We did Solanum clades when compared to variation found in the most commonly used nuclear markers ITS and waxy  , and 40 (4.2%) for the Morelloid clade . The besctively) . The difectively .Solanum plastid genomes, S. bulbocastanum and S. lycopersicum, but did not specifically aim to identify the most variable plastid regions for Solanum. Since their study, the potato plastid genome has become available, and by comparing the three plastomes, we aimed to identify the most variable plastid regions for Solanum that could be used for building robust plastid phylogenies in species-level studies.A study by Daniell et al. Solanum. In fact, most markers with high sequence variation in one clade showed more modest levels of variation in the related clade. Our results are in agreement with previous studies that have aimed to identify plastid regions that show consistently high sequence variation across a wide range of plant groups Whether measured by variable sites, or by the combination of variable sites and indels, our results show that the set of most variable plastid regions vary between the two closely related clades of Solanum clades, indicate that there is little universality in sequence variation in the plastid genome even at this close taxonomic level. The results imply that screening studies will be needed for individual projects despite the availability of results on plastid marker variability from a related group. For example, investigators working with other clades of Solanum should perform their own screening study in order to find the most variable set of plastid markers for their group of interest. Investigators working at species-level in specific clades within families for which general screening studies have been done . This indicates that considerable amount of time and money can be saved in molecular phylogenetic studies if initial screening studies are performed with additional markers.Particular markers merit special attention. One of the markers tested, Solanum. Previous studies have demonstrated failure of a single or a small set of barcodes to discriminate between closely related species e.g., Solanum, as only a subset of markers are likely to show adequate levels of sequence variation throughout individual clades. Previous studies have identified that the failure of multiple barcodes in plants has not been due to lack of sequence variation provided by the chosen barcodes Solanum.Our results have potential implications for species-level barcoding studies, especially so for studies involving large clades such as Solanum, there is great variation in the set of most highly variable markers even between closely related groups. New primers for a set of highly variable plastid markers are now available that can be used to explore and screen plastid sequence variation in molecular phylogenetic studies of Solanum and Solanaceae in general.Our study highlights the conclusions of Shaw et al. Solanum, including S. tuberosum (DQ231562), S. bulbocastanum (DQ347958), and S. lycopersicum (DQ347959) Solanum species S. tuberosum genome as a reference sequence. Sliding window analysis was run in the software DnaSP v5 http://primer3.ut.ee), whilst published primers were used for regions already in use  to compare sequence variation across regions in the two closely allied Solanum clades.All three currently available full plastome genomes for y in use . Primer Solanum which belongs to the same major clade of SolanumThe newly developed primers for the most variable plastid loci identified for the Potato clade were used to screen for the most variable regions in the closely related Morelloid clade of Solanum, a further six markers were screened. These included the trnT-L and trnL-F intergenic spacers, which are amongst the most commonly used plastid markers in molecular systematic studies in SolanumpsbK-I, which has been proposed as a plant barcoding marker trnD-T, which is a commonly used marker in species-level phylogenetic studies across angiosperm groups waxy , and the nuclear ribosomal transcribed spacer (ITS).In order to compare the variation found in the most variable regions within the Potato clade with the currently most commonly used markers in molecular systematic studies of rpl32-trnL, trnK- rps16, petL-psaJ, ndhC-trnV, trnA-trnI, and ycf1 (parts 1–2), diluted DNA (1∶10) showed higher PCR amplification success. PCR conditions were 94°C for 45 s, 30 cycles of 45 s at 94°C, 1 min at 55°C and 1 min at 72°C, followed by a final extension of 5 min at 72°C. For trnA-trnI, annealing temperature of 59.2°C was used. PCR products were purified using the Wizard® SV PCR Clean-Up System (Promega) and sequenced using the PCR primers following Big Dye chemistry. Consensus sequences were assembled using Sequencher , and aligned using ClustalW with default settings as implemented in BioEdit v7.0.9 Total genomic DNA from silica dried leaves or herbarium material was isolated using the DNeasy Plant Mini Kit (Qiagen). All primers used are listed in We measured the number and proportion of variable sites within each region. The number of PI characters was only recorded for the Morelloid clade, due to the fact that PI characters cannot be recorded for alignments with less than four sequences. Previous studies have, however, shown that the proportion of PI and variable sites is positively correlated File S1Voucher details with Genbank numbers for all sequences generated in this study.(XLSX)Click here for additional data file.File S2Aligned sequence files for the Morelloid clade.(ZIP)Click here for additional data file.File S3Aligned sequence files for the Potato clade.(ZIP)Click here for additional data file.


In silico comparative genomics approaches have been efficiently used for functional prediction and reconstruction of metabolic and regulatory networks. Riboswitches are metabolite-sensing structures often found in bacterial mRNA leaders controlling gene expression on transcriptional or translational levels.cis-regulatory RNAs have been recently classified into numerous RNA families in the Rfam database. High conservation of these RNA motifs provides a unique advantage for their genomic identification and comparative analysis.An increasing number of riboswitches and other cis-regulatory RNAs and more than 12000 target genes in 255 microbial genomes. All predicted RNA-regulated genes were classified into specific and overall functional categories. Analysis of taxonomic distribution of these categories allowed us to establish major functional preferences for each analyzed cis-regulatory RNA motif family. Overall, most RNA motif regulons showed predictable functional content in accordance with their experimentally established effector ligands. Our results suggest that some RNA motifs  are widespread and likely originated from the last common ancestor of all bacteria. However, many more analyzed RNA motifs are restricted to a narrow taxonomic group of bacteria and likely represent more recent evolutionary innovations.A comparative genomics approach implemented in the RegPredict tool was used for reconstruction and functional annotation of regulons controlled by RNAs from 43 Rfam families in diverse taxonomic groups of Bacteria. The inferred regulons include ~5200 http://regprecise.lbl.gov/).The reconstructed regulatory networks for major known RNA motifs substantially expand the existing knowledge of transcriptional regulation in bacteria. The inferred regulons can be used for genetic experiments, functional annotations of genes, metabolic reconstruction and evolutionary analysis. The obtained genome-wide collection of reference RNA motif regulons is available in the RegPrecise database ( Riboswitches are found mostly in bacterial genomes and represent genetic elements that frequently reside at the leader regions of mRNAs. Riboswitches achieve gene regulation by possessing two alternative structural states and are likened to an “on/off” switch . Direct cis-acting RNA regulatory motifs have recently been identified using a combination of comparative genomics and experimental approaches [cis-regulatory RNA elements called T-boxes is utilized for the control of transcription of amino acid metabolic genes in Bacillus subtilis and other Gram-positive bacteria [Escherichia coli and related Gram-negative bacteria utilize a different RNA-based mechanism of transcription attenuation for the control of amino acid biosynthesis operons, which involves translation of a portion of the leader sequence that codes for a specific amino acid-rich peptide [An increasing number of riboswitches and other proaches ,4,9,10. proaches . Severalproaches ,12. A spbacteria -15. T-bobacteria . In cont peptide . Finally peptide ,19.in silico reconstruction of their respective regulons [cis-regulatory RNA motifs identified in bacterial genomes are available in the Rfam database [Many classes of widespread riboswitches controlling coenzyme and amino acid metabolism have been analyzed in completely sequenced organisms by comparative genomics resulting in regulons -15,20-24database , where tdatabase  and Ribodatabase , were prdatabase . On the database ,30. HoweThe comparative genomic analysis of microbial regulons is an efficient method for functional gene annotation and metabolic pathway reconstruction, especially when combined with traditional approaches of genome context analysis . As mostcis-regulatory RNA motif detection to elucidate the metabolic capacities of RNA-mediated gene regulation in bacteria. We combined the inference of regulatory RNAs and their operon analysis in completely sequenced bacterial genomes to evaluate the regulatory networks for different Rfam families of cis-regulatory RNA motifs. As a result, 43 RNA families including all known and candidate riboswitches, the ribosomal and amino acid operon leaders and T-boxes were analyzed in the respresentative subset of genomes from 24 taxonomic groups of Bacteria. Our results show that relatively few RNA motifs originated in the last common ancestor of Bacteria and bring into question the notion that the riboswitch is a remnant of the RNA world. Instead, many RNA motifs probably arose recently as they are restricted to a few closely related taxonomic groups. Functional analysis of reconstructed RNA motif regulons in diverse taxonomic lineages of bacteria revealed the lineage-specific metabolic gene content preferences and identified major trends in the evolution of their regulons. A large number of regulatory interactions from the inferred RNA motif regulons contribute to genome-wide transcriptional regulatory networks and metabolic models of bacterial cells.In this study, we combine genome context analysis with cis-regulatory RNA motifs that are currently available in the Rfam database [cis-regulatory RNA motifs termed ‘leaders’ that reside in the leader regions of ribosomal and amino acid biosynthesis operons. For the comparative analysis of these RNA motif regulons, we selected a set of 255 representative genomes from 24 diverse taxonomic lineages of Bacteria , metal ions (ykoK), secondary messengers (cyclic di-GMP), and unknown substrates , as well as the PyrR binding motif controlling the pyrimidine metabolism. In group C, we include RNA motifs that are restricted to no more than three taxonomic groups. The group C contains riboswitches that are specific for amino acids and derivatives , cofactors , ions (Mg sensor), and unknown substrates . In addition, we classified the cis-regulatory RNA leaders that control the ribosomal protein operons  and the amino acid biosynthesis operons  into groups D and E, respectively. T-box RNA motifs also control the amino acid metabolism, however since these cis-regulatory RNAs utilize a unique mechanism involving uncharged tRNA, we classified them into the separate group F 1. Cobalamin  and B12 , as well as isofunctional enzymes that provide alternatives to B12-dependent enzymes, have been previously found to be subject to regulation by cobalamin riboswitches in bacterial genomes [12 biosynthesis, (ii) B12 and precursor transporters, (iii) cobalt transporters, and (iv) isozymes of B12-dependent enzymes  and one group of γ-proteobacteria , both representing pathogenic species with reduced biosynthetic capacities  that still retains the complete B12 biosynthetic pathway despite the absence of a cobalamin riboswitch. This fact suggests that the riboswitch-dependent control of cognate metabolic pathways is not ubiquitous. The cobalamin riboswitch regulons are the largest in the dataset. Altogether this dataset includes 535 RNA sites that control over 2400 genes in 197 genomes , suggesting they are either constitutive or regulated by a different mechanism.We used the SFC classification to understand functional preferences for the genes regulated by cobalamin riboswitches across all taxonomic groups Figure . There i2. TPP (thiamin pyrophosphate)Lactobacillus helveticus, Bartonella quintana, Desulfovibrio magneticus, Lawsonia intracellularis and two Chlorobium spp.). It should be noted that some of the above species  possess the thiamin biosynthesis genes but not TPP riboswitches in their genomes, again indicating that there are exceptions from almost universal regulation by coenzyme-sensing riboswitches. Altogether we annotated 564 TPP RNA sites that control near 1800 genes in 249 genomes. On average, these numbers correspond to 7 regulated genes per genome or 3.2 genes per riboswitch.The TPP riboswitch had previously been found to control various biosynthetic enzymes and known and predicted transporters involved in the synthesis and salvage of thiamin and its metabolic precursors, hydroxymethylpyrimidine and hydroxyethylthiazole . For funthiC, which encodes an essential thiamin biosynthesis enzyme. Among TPP-regulated genes, thiamin biosynthesis genes dominate the SFC categories in the majority of lineages, accounting for over 65% in most cases. The thiamin and thiamin precursor transporter genes constitute the next most abundant SFC and can be found in almost all the studied lineages except Burkholderia, Caulobacterales, Chlorobiales, Cyanobacteria, and Ralstonia. On average, the transporter genes represent 30% of TPP-regulated genes. However, the thiamin transporters dominate over the biosynthesis genes in Chloroflexi, Lactobacillaceae, Pasteurellales, and Streptococcaceae, accounting for over the half of the total regulated genes. The abundance of various TPP-regulated transporters in this species correlates with their predicted thiamin auxotrophic phenotypes, caused by the absence of thiamin biosynthetic genes.Despite the wide distribution of TPP motifs, there is a large variation in the number of regulated genes per genome Figure . Vibrion3. FMN (Flavin mononucleotide)Similarly to TPP regulons, the FMN riboswitch regulons were classified into two SFCs: (i) riboflavin biosynthesis, and (ii) riboflavin transporters, that include seven and five functional gene orthologs, respectively  represent the largest proportion of regulated genes. In contrast, most species from the Proteobacterial phylum, as well as two Chlorobia spp, have a single FMN-controlled gene involved in riboflavin biosynthesis (ribB or ribH2). In contrast to cobalamin and TPP, transporters specific for riboflavin are not as widely distributed and can only be found in 7 taxonomic groups . Interestingly, the riboflavin transporter pnuX is the only FMN-regulated gene in Corynebacteria.Based on the analysis of distribution of FMN riboswitch-regulated genes Figure , roughly4. GlycineThe glycine riboswitch-regulated genes were classified into three SFCs: (i) glycine metabolism, (ii) glycine transporters, and (iii) serine metabolism that include twelve, three and three functional gene orthologs, respectively  were introduced in this work to facilitate the functional content analysis of reconstructed RNA regulons Table . OFCs prWhen all RNA motif regulons were combined, the coenzyme metabolic category appeared to be the most abundant OFC, ranging from ~20% to over 50% across different taxonomic lineages Figure . ExceptiykkC-yxkD and mini-ykkC RNA motifs are fairly well-distributed with many taxonomic overlaps  when compared to the ykkC-yxkD regulons (17%). A similar situation was observed between the preQ1 and preQ1-II riboswitches for queuosine metabolism and uptake. preQ1 regulates a small proportion of genes related to coenzyme uptake (27%), whereas the remaining target genes are classified as the coenzyme metabolic OFC. In contrast, preQ1-II exclusively regulates genes from the coenzyme uptake OFC.When analyzed according to RNA motif family, most regulons showed predictable OFC content Figure . For inscis-regulatory sequences in bacterial genomes, there have been few attempts at analyzing their overall distributions or even the operon contents of individual RNA-regulated operons across different microbial genomes. In this study we established regulatory capacities of different cis-regulatory RNAs and used comparative genomics to describe potential functions for many previously uncharacterized genes in RNA regulons.While much effort has been put into discovering novel RNA Analysis of RNA motif abundances and diversity allowed us to make certain predictions regarding the origins of some of these regulators. Among the most widespread group of RNA motifs (Group A), many riboswitches are specific for cofactors such as TPP, cobalamin, and FMN Figure . As thesykkC-yxkD. For instance, the SAM riboswitch  controlling methionine metabolism is widely distributed in three lineages of Firmicutes and is also present in diverse species from eight other phyla, suggesting an ancient origin. Within the Firmicutes phylum, the loss of SAM riboswitches in Streptococcaceae and almost all Lactobacillus genomes is correlated with the emergence of several novel regulatory systems for the control of cysteine and methionine metabolism including two transcription factors (CymR and MtaR), the Smk-box RNA motif, and the expansion of methionine-specific T-boxes [Clostridium-like Firmicute [The occurrences of many riboswitches from group B in taxonomically distant organisms suggest two possible scenarios for their evolutionary histories  riboswitch regulates a variety of genes in several phyla, and the difference in operon contents may be influenced by lifestyle and/or habitat of individual species. For instance, Bacteroidaceae species are part of the human intestinal microflora, and the ability to synthesis B12 may be replaced by B12 transporters or transporters with multiple specificities  and the riboflavin transporter genes, s Figure . On the de novo production of glycine. The regulatory differences observed between glycine biosynthetic and transporter genes may reflect the different metabolic needs of these organisms. Although the regulatory mechanisms for glycine and serine metabolic genes were expected to be similar, given the ease of conversion between these two amino acids, serine metabolic genes were largely absent in most of glycine riboswitch regulons. Even in those lineages in which serine metabolic genes were found, they constitute a small proportion of overall regulated genes. Our findings may reflect the ways these two amino acids are utilized inside a cell. For example, serine may be more valuable as a precursor for energy production in glycolysis than as a precursor for other amino acids, but under most circumstances, glycine may better serve as a building block.Even though only glycine transporter genes were found to be regulated by glycine riboswitches in Streptococcaceae and certain γ-proteobacteria, glycine biosynthetic genes exist elsewhere in the genomes of these organisms for iunH and folE from genomes of many Firmicutes. The ydaO-yuaA riboswitch regulates a wide variety of transporters, which may all play roles in osmoregulation; in addition, regulated cell wall remodeling enzymes like COG0791 and COG3773 from Corynebacteriaceae and Clostridiaceae may serve similar roles. ykkC-yxkD and the functionally equivalent mini-ykkC riboswitches both have been proposed previously to function in regulating efflux pumps and other detoxification mechanisms; however, our findings also yielded genes (COG3382 and COG731 from Clostridiaceae) that function in capacities other than transport. For SAH riboswitches, some novel genes (PF04020 and PF04993) were predicted in Ralstonia although their functional contribution to SAM/SAH homeostasis is unknown.In contrast to group A, group B RNA motifs are responsible for regulating a wide variety of metabolic processes including the transport of amino acids, cofactors, nucleotides and metal ions. Still, many regulate genes with unknown cellular functions. The fact that frequent horizontal transfer probably occurred in this group of RNA motifs suggests peripheral metabolic functions that, when incorporated, confer certain survival benefits. Many novel genes were also found associated with other group B motifs, and their functions can be putatively assigned based on their regulators. For example, various genes found in Bacillales, Clostridiaceae, and Chloroflexi under SAM riboswitch regulation are probably involved in cysteine and methionine metabolism or the transport of corresponding substrates. Similarly, many genes regulated by GEMM RNA motifs can be assigned to cellular motility, virulence and biofilm formation. Some preQ1 riboswitch regulated genes of unknown function may function in the queuosine biosynthesis or salvage pathways; examples of this include Group C RNA motifs are phylogenetically confined to a few closely related taxonomic groups. Their limited distribution points to their recent invention and, as a consequence, their existence in these few taxa may have been the result of vertical transmission. Their regulon contents are also highly conserved with little variation between genomes, thus providing additional evidence for vertical transmission.E. coli and B. subtilis reported that most of these RNA structures were narrowly distributed in γ-proteobacteria and Bacilli, respectively, and that many distinct ribosomal RNA motifs may yet to be identified in bacteria [For group D RNA motifs, even though ribosomal subunits are highly conserved between different bacterial lineages, their regulatory regions appear to exhibit greater variation than the coding sequences. Four studied motifs  that regulate the large ribosomal subunits appear to be confined to all lineages of Firmicutes but were also identified in Thermotogales. It is plausible that these four RNA motifs were originated in Firmicutes, and that the L20 and L21 motifs in Thermotogales were horizontally acquired from Firmicutes. The L10 and S15 motifs have wider taxonomic distributions, being identified in 13 and 10 lineages, respectively , and their substrate specificities are currently restricted to histidine, leucine, threonine and tryptophan, as only these four RNA motifs were available in the Rfam database. In addition to these four motifs, a couple of other amino acid attenuator motifs specific to isoleucine/valine and phenylalanine were previously characterized ; howeverGeobacter spp. [For group F, despite the ubiquity of tRNAs and their associated genes in bacteria, the distribution of T-box RNA motifs is rather limited to Firmicutes, Actinobacteria, Chloroflexi and the Thermus/Deinococcus group. In addition, T-boxes have been previously found in ter spp. , which bter spp. -15. Aminter spp. . Many cater spp. .In this study, we performed a comprehensive comparative genomics analysis of RNA regulons controlled by 43 Rfam motifs including metabolite-sensing riboswitches, ribosomal and amino acid operon leaders, and T-boxes. As result, 5204 RNA regulatory sites were identified in 255 complete genomes demonstrating a high variability in the genomic distributions of numbers and types of RNA sites across diverse taxonomic groups of bacteria. We further performed reconstruction and functional annotation of 3251 RNA regulons controlling over 12,000 genes. Each regulon was defined as a set of genes in a single genome controlled by RNA regulatory sites from the same Rfam family. To facilitate the comparative analysis of this large number of regulons, we used the regulog approach implemented in the RegPredict web server. All studied organisms were subdivided into 24 taxonomic groups, and the analyses of RNA regulons were performed independently in each lineage, resulting in reconstruction of 393 regulogs. Based on taxonomic distribution of the obtained regulogs, each known or putative riboswitch was assigned to one of three groups, whereas the ribosomal and amino acid leaders and T-boxes were classified independently. Further, we introduced a two-level functional classification of genes controlled by each analyzed RNA motif. Specific functional categories (SFCs) allowed us to analyze functional preferences for each individual RNA motif family across taxonomic groups. Overall functional categories (OFCs) provided an overview of biological processes controlled by RNA motifs by taxonomy and also according to RNA motif family.cis-regulatory RNA regulation and the ease of horizontal transmission for these regulators, the preservation of other regulators appears necessary for normal metabolism in other organisms. Our functional annotations of many of regulated genes will allow researchers to validate our initial predictions.Our analyses allowed inferences of possible evolutionary pathways for many of the examined RNA regulatory elements as well as functional annotations to the regulated genes. Our results suggested that some RNA motifs may have arisen in the last common ancestor of most or all bacteria, but far more may have arisen relatively recently. Additional analyses of the metabolic pathways from organisms missing the corresponding RNA motifs suggested that functionally equivalent regulators are also widespread. Despite the simplicity of The results of this study suggest that many metabolic RNA motif regulons evolve rapidly in microbial lineages to adapt to changes in habitats and lifestyles. The reconstructed RNA regulons obtained for the reference collection of genomes will provide the basis for computational propagation of these regulons to new genomes. An expanded set of genomes with mapped RNA motif regulons will enable more detailed studies on the co-evolution of these regulatory RNAs and their cognate metabolic pathways.cis-regulatory RNAs in the uploaded genomes were performed using covariance models of 43 RNA motifs uploaded from the Rfam database [http://regpredict.lbl.gov) [255 complete genomes of bacteria analyzed in this study   to perfoThe RegPredict tool allows simultaneous analysis of multiple microbial genomes and integrates information on location of regulatory sites, gene orthologs, operon predictions, and functional gene annotations. Each RNA motif regulon was independently analyzed in each of the 24 selected groups of closely-related genomes. The genome scanning procedure implemented in RegPredict utilizes the pre-computed files with genomic coordinates and scores of candidate RNA sites from each Rfam family. The genome scan parameters were set up to reduce the chance of nonfunctioning sequences from being detected. Specifically, positions of RNA sites were set between 500 nucleotides upstream and 100 nucleotides downstream of a gene start codon. The maximum intergenic distance for an operon boundary was set to 200 nucleotides under ‘Operon definition’, and the ‘coding region overlap’ option was chosen. After genome scanning and filtering, the RNA motif regulons were clustered into groups termed Clusters of co-Regulated Orthologous operoNs (CRONs) in RegPredict . This aphttp://regprecise.lbl.gov) [Biological functions of regulated genes were predicted and annotated in RegPredict by a combination of a sequence similarity search against the Swiss-Prot section of the UniProtKB database , domain lbl.gov) , where tlbl.gov) .SAM: S-adenosylmethionine; SAH: S-adenosylhomocysteine; tRNA: Transfer RNA; ECF: Energy-coupling factor; SFC: Specific functional category; OFC: Overall functional category; TPP: Thiamin pyrophosphate; FMN: Flavin mononucleotide; MOCO: Molybdenum cofactor; THF: Tetrahydrofolate; CRON: Cluster of co-regulated orthologous operons.The authors declare that they have no competing interests.DAR and PSN conceived and designed the research project. EIS and DAR wrote the manuscript. EIS and SAL performed comparative genomic analysis for reconstruction of regulons. DAR also provided the quality control as a curator. MDK computed RNA regulatory sites in microbial genomes. MHS contributed to the development of the project and writing of the manuscript. All authors read and approved the final manuscript.The inferred content of 42 RNA motif regulons in microbial genomes from 24 taxonomic groups. Each cell contains all genes and operons predicted to be regulated by a particular RNA motif in a genome. Multiple candidate operons are separated by semicolons. In the operon description, dashes separate neighboring genes but are omitted for genes sharing the same locus mnemonic. Parentheses indicate fused genes.Click here for fileThe inferred content of 19 amino acid-specific T-box regulons in microbial genomes from 9 taxonomic groups. Each cell contains all genes and operons predicted to be regulated by a particular RNA motif in a genome. Multiple candidate operons are separated by semicolons. In the operon description, dashes separate neighboring genes but are omitted for genes sharing the same locus mnemonic. Parentheses indicate fused genes.Click here for fileDistribution of RNA motifs in microbial genomes. Riboswitches are arranged in six groups according to abundance and substrate types.Click here for fileTotal number of genes controlled by predicted RNA motif regulons in 24 taxonomic groups of Bacteria. Riboswitches are arranged in six groups according to abundance and substrate types.Click here for fileClassification of identified RNA motif-regulated genes by specific and overall functional categories (SFC and OFC). Only genes with annotated functional roles in the RegPrecise database are shown under ‘gene name’; number of gene families indicates the total types of different orthologues found.Click here for fileDistribution of Specific Functional Categories regulated by each RNA motif family across 24 analyzed taxonomic groups. SFC number for individual riboswitch family is listed in each row, with averaged proportion listed in the last column; ‘per genome’ values and listed at the bottom.Click here for fileComparative genomics analysis of functional regulon content for RNA motifs from groups B and C, ribosomal and amino acid operon leaders (groups D and E), and T-boxes (group F). Additional text describes detailed analyses of the remaining RNA motif families that were not included in the main manuscript text.Click here for fileSupporting figures S1-17 for Additional file Click here for file


A commentary onA theory of cerebellar cortexby Marr, D. (1969). J. Physiol. 202, 437–470.A commentary onA theory of cerebellar functionby Albus, J. S. (1971). Math. Biosci. 10, 25–61.Four decades ago, Marr and Albus suggested that the climbing fiber (CF) pathway from the inferior olive (IO) to the cerebellum instructs the cellular changes necessary for motor learning Marr, . Subsequin vivo evidence that indirectly supports it  or long-term potentiation (LTP), is different at each site Figure . The besIn an effort to better understand the mechanistic details of how CFs participate in cerebellar learning, we have exploited optogenetic and pharmacological approaches to selectively manipulate CF signals. Using adeno-associated viral delivery of ChR2-eYFP to IO neurons we are able to transfect CFs with high efficiency and specificity in the rat Figure . Optical+ channels, or ZD 7288, an inhibitor of hyperpolarization activated cation channels) were each demonstrated to prolong the post-complex spike pause (Maiz et al., in vitro (Pugh and Raman, In complimentary experiments we have used specific pharmacological tools to manipulate a component of the CF signal, the post-complex spike pause in simple spike firing rate. Two very different compounds (1-EBIO, a positive modulator of calcium activated K“When you teach your son, you teach your son's son.” Future experiments utilizing a wide breadth of classical and novel techniques, like those mentioned here will be required to determine just how paternalistic the CF is, and whether it broadens its influence in an analogous way.A critical step in understanding cerebellar learning is to explain how CFs, or other teaching signals, coordinate learning-related changes within the circuit. The experiments described here address important questions about the biology of the CF and how it might operate as a teaching signal. Related questions include whether CFs give rise to distinctive postsynaptic signals at those sites in the circuit where they have been hypothesized as teachers, and whether CFs trigger heterosynaptic, associative forms of plasticity that might contribute to learned motor behaviors. The striking anatomical organization of the cerebellar cortex coupled with the remarkable properties of the CF contact on PNs led to the insightful conjecture of Marr and Albus more than 40 years ago. Our observations are consistent with CFs exerting control over multiple sites within the cerebellar circuit, in part through indirect actions read out by MLIs or groups of PNs, a picture that brings to mind the aphorism from the Talmud,


In plants, efficient immune responses against microbial infection depend on the ability to rapidly couple pathogen recognition to downstream signaling responses. In this context, plant immunity requires highly dynamic responses that involve multiple organelles during the recognition and signaling events associated with defense. Nuclear dynamics play a critical role in plant immunity based on the growing number of reports revealing that nuclear localization of pathogen effectors, plant disease resistance proteins, and key plant components, including transcription factors and regulators, are essential for immunity. This Research Topic provides an overview of the current knowledge about the importance of nuclear components—both from the “microbial side” and from the “plant side”—and nuclear dynamics during the establishment of plant immune responses.Mutations in plant cellular factors involved in the transport of macromolecules through the nuclear envelope compromise plant resistance signaling, underlining the importance of nucleocytoplasmic trafficking during plant innate immunity. The Mini-Review article by Gaouar and Germain  describeFusarium oxysporum is required to trigger I2-mediated resistance in tomato plants, whereas Stam et al. (Phytophthora infestans. Finally, the Opinion article by Noël et al. (Xanthomonas.Following their delivery into plant cells, a significant number of effector proteins from different pathogenic microorganisms, including viruses, oomycetes, fungi, nematodes, and bacteria, are targeted to the nucleus by co-opting the host nuclear import machinery. This suggests that effectors may manipulate host transcription or directly target essential host nuclear components for the benefit of the pathogen. Indeed, pathogen-induced transcriptional regulation in host cells plays a crucial role in the establishment of plant defense and associated plant cell death responses. Several articles in this Research Topic highlight these ideas. Quentin et al.  describem et al.  show thel et al.  discusseArabidopsis genes are transcriptionally regulated in response to pathogen infection and a significant number of transcription factors are involved in the defense gene regulation. Raffaele and Rivas (Arabidopsis MYB protein AtMYB30, which is a positive regulator of disease resistance. The Review article by Gimenez-Ibanez and Solano (It has been estimated that about 25% of nd Rivas  review od Solano  discusseArabidopsis WRKY domain-containing immune receptor RRS1 contributes to temperature-conditioned autoimmune responses conferred by a second nuclear immune receptor, RPS4. These data suggest that RPS4 engages RRS1 to direct defence signaling.Spatial restriction of immune receptors and defense regulators by the nuclear envelope as well as their stimulus-induced nuclear translocation provide an important mechanism for defense regulation, as their level of nuclear accumulation determines the magnitude of the defense response. In addition, nuclear translocation of effectors may also affect subcellular localization of their cognate resistance proteins in a process that is essential for plant immunity. Bhattacharjee et al.  review nIn summary, recent findings from our rapidly evolving field situate the nucleus at the forefront of the mutual recognition between plants and pathogens. Integrating the knowledge on immunity-associated nuclear events within the outlook of whole cellular dynamics represents an exciting perspective for future research.


RNA-dependent processes are essential to determine when, where, and how much of a protein is synthesized. In eukaryotes, these processes start with transcription in the nucleus and end with mRNA translation at distinct cytoplasmic sites followed by mRNA degradation Ustilago maydisDue to the central importance of RNA biology in regulating protein synthesis, it is not surprising that fungal pathogens intensely rely on RNA-dependent processes to control infection. Here, we focus on RNA biology in fungal plant pathogenesis, which is best studied in the corn smut U. maydis, a major pathogenicity determinant is the homeodomain transcription factor bW/bE that triggers a cascade of transcriptional responses essential for full virulence clp1 is a direct target gene of bW/bE, which is induced early during formation of infectious filaments. However, the Clp1 protein is only synthesized later at the specific stage of plant penetration when it acts as an antagonist of bW/bE clp1 mRNA by a currently unknown mechanism  protein RBP35 causes defects in virulence and development. Protein interaction studies revealed that RBP35 functions as a novel auxiliary protein of the polyadenylation machinery of plant pathogens  is an important mechanism to control endogenous and foreign RNA in most organisms. Noteworthily, genome comparison with U. maydis the ELAV -type protein Rrm4 functions in long-distance mRNA transport, a process that is specifically important during formation of infectious unipolar filaments In higher eukaryotes, active microtubule-dependent transport of mRNAs by molecular motors functions in spatial protein expression during developmental and neuronal processes ubi1 and rho3, encoding ubiquitin fused to ribosomal protein Rpl40 and the small GTPase Rho3, respectively rrm4 deletion strains are disturbed in septum formation. Hence, microtubule-dependent transport of rho3 mRNA might act in correct septal localization of Rho3, which could promote septum insertion in infectious filaments Rrm4 transports specific mRNAs such as C. albicansIn summary, endosomal mRNA transport along microtubules is a novel aspect of RNA biology and this posttranscriptional process is particularly important during early infection. Since the RNA-binding protein She3 functions in actin-dependent mRNA transport during infection of U. maydis, which is usually localized in the cytoplasm. However, 10% of its mRNA is alternatively spliced, generating an enzyme with a C-terminal peroxisomal targeting sequence (PTS1 type). This results in peroxisomal localization of GAPDH, a process termed cryptic peroxisomal targeting  of argeting  [21]. Siargeting . The appThe importance of RNA biology in fungal infection is further underlined by the fact that posttranscriptional regulation is targeted during host defense. Plants react to infection by producing antimicrobial peptides (AMPs) that are proposed to degrade the fungal cell wall or to permeabilize the membrane. Some AMPs also enter the cell to exert their function U. maydis secretes ribonucleases that might function as virulence factors in degrading host RNAs Pseudomonas syringae that is essential for virulence on Arabidopsis thalianaIntriguingly, the opposite is true as well: pathogens interfere with posttranscriptional control of the host to promote infection. Although this has so far only been shown for bacterial and oomycete phytopathogens vice versa pathogen effectors suppress host RNA silencing during plant protection.Moreover, microbial effectors interfere with plant microRNA activity. miR393, for instance, targets the F-box auxin receptor TIR1 and thereby represses auxin signaling, a process involved in plant immunity The different levels of RNA biology such as alternative splicing, 3′ end processing, endosomal mRNA transport, and translational regulation are essential to orchestrate plant infection of fungal pathogens. RNA-binding proteins are key components in executing these functions. After improving transcriptome-wide approaches such as iCLIP


The tumor suppressor promyelocytic leukemia protein (PML) is located primarily in the nucleus, where it is the scaffold component of the PML nuclear bodies (PML-NBs). PML-NBs regulate multiple cellular functions, such as apoptosis, senescence, DNA damage response, and resistance to viral infection. Despite its nuclear localization, a small portion of PML has been identified in the cytoplasm. The cytoplasmic PML (cPML) could be originally derived from the retention of exported nuclear PML (nPML). In addition, bona fide cPML isoforms devoid of nuclear localization signal (NLS) have also been identified. Recently, emerging evidence showed that cPML performs its specific cellular functions in tumorigenesis, glycolysis, antiviral responses, laminopothies, and cell cycle regulation. In this review, we will summarize the emerging roles of cPML in cellular functions. The. promyelocytic leukemia protein (PML) was initially identified in the acute promyelocytic leukemia (APL), a disease largely associated with t chromosomal translocation, which results in the fusion protein of PML and the retinoic acid receptor alpha (RARα)  as described by Jensen et al.  Figure . PML I tin vitro, while Pml−/− cells grow faster than wild-type counterparts  is a glycolytic enzyme that catalyzes the dephosphorylation of phosphoenolpyruvate (PEP) to produce pyruvate, which will be converted into lactate rapidly. PKM2 is critical for aerobic glycolysis and expressed in proliferating cells during embryogenesis and tumorigenesis . A receTwo recent reports revealed that PML regulates fatty acid oxidation (FAO)  play an important role in the antiviral responses. Upon viral infection, the cells release IFNs, which then bind to the cell surface specific receptors and activate downstream signaling to combat virus infection [reviewed in , the lymphocytic choriomeningitis virus (LCMV) and the human immunodeficiency virus type 1 (HIV-1)  in HSV-1 infected cells  is found in the laminopathy cells and the number of these particles increases with disease severity (Houben et al., The redistribution of nPML to cytoplasm has also been described in the laminopathy diseases characterized by in vivo, cPML specific animal models such as cPML knockin mice or nPML knockin mice are needed. Another remaining question is how cPML is regulated to orchestrate downstream events. Given that PML undergoes distinct posttranslational modifications [reviewed in (Carracedo et al., The emerging evidence we discussed in this review revealed that cPML exhibits multiple cellular functions Figure . The cPMThe authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.