Gene duplication is one of the major driving forces shaping genome and organism evolution and thought to be itself regulated by some intrinsic properties of the gene. Comparing the essential genes among mouse and human, we observed that the essential genes avoid duplication in mouse while prefer to remain duplicated in humans. In this study, we wanted to explore the reasons behind such differences in gene essentiality by cross-species comparison of human and mouse. Moreover, we examined essential genes that are duplicated in humans are functionally more redundant than that in mouse. The proportion of paralog pseudogenization of essential genes is higher in mouse than that of humans. These duplicates of essential genes are under stringent dosage regulation in human than in mouse. We also observed slower evolutionary rate in the paralogs of human essential genes than the mouse counterpart. Together, these results clearly indicate that human essential genes are retained as duplicates to serve as backed up copies that may shield themselves from harmful mutations. Gene duplication was thought to be one of the major driving factors stimulating genome and organism evolution –4, as itEssential genes are indispensable to an organism and cause severe reduction in its fitness like sterility or lethality upon deletion . These gGene essentiality was widely studied across model organisms and shown to bear a complex relationship with gene duplication . In loweTill date, all the studies regarding essential genes were carried in yeast and mouse due to unavailability of human gene essentiality data. In a previous study, researchers attempted to explore the properties of human orthologs of mouse essential genes . HoweverHomo sapiens) and mouse (Mus musculus) were obtained from the Online Gene Essentiality (OGEE) database (http://ogeedb.embl.de)  whereas, in humans, among 7563 singleton genes, 486 genes exist as essential (6.43%) and among 10837 duplicated genes, 984 are essential (9.08%) . The overall proportion of essentiality is higher in mouse, which may be due to the fidelity of the methods applied to detect essential genes  or the uAnother possible bias in our dataset may arise due to the age of the duplicates. Previous studies showed that the genes originated from old duplications are more likely to be essential than singletons . TherefoOur study contradicted the previous study of Liao and Zhang  which enTo investigate whether the diversification supports the fixation of duplicate copies of essential genes in the human genome, or the duplicates are maintained as a backup system under stringent dosage-regulatory mechanism, we compared the essential genes and their paralogs between mouse and humans.-6, Mann-Whitney U test) functional distance value in human duplicated essential genes  than in mouse duplicated essential genes . However, the Czekanowski—Dice distance formula we used here is sensitive to the number of go terms associated with a gene, which may vary from species to species. Therefore, for an unbiased cross-species comparison of functional distance, we binned our dataset into three groups containing according to their go id count , which may be due to the low proportion of pseudogene occurrence in both species . This result suggests that mouse essential genes’ paralogs can become pseudogenized more easily. In other words, human essential genes retain their functionality more readily, which in turn can help them to serve as functional backup copies, as we have previously shown that they are functionally more similar to their ancestral genes.Although we observed that human essential duplicates are functionally less diverged than mouse, we were curious to understand the occurrence of pseudogenized paralogs among essential genes of both species. As our main dataset contains essential genes of human and mouse, no occurrence of pseudogene was observed. However, among the paralogs, we did not find any significant difference between mouse (0.82%) and human (0.50%) micro-RNA target sites in duplicated essential genes of human  than in mouse , suggesting the robust regulation by micro-RNAs after the duplication of essential genes enables humans to maintain the redundant copies.The human essential genes in our study were observed to show lower functional divergence. Thus, we hypothesize that the essential gene duplicates are functionally redundant and they may be maintained as backup copies. However, the maintenance of newly synthesized duplicates is very crucial and often performed by micro-RNA mediated post-transcriptional regulation, which may give support to the backed up essential genes by reducing their expression . Therefohuman = 0.101, dN/dSmouse = 0.128, P = 2.53×10-5, Mann Whitney U test, Nmouse = 2931, Nhuman = 1651), indicated by their lower dN/dS ratio [We observed the human essential duplicate genes mostly prefer to remain functionally redundant and can be maintained as backup copies, being able to escape the dosage imbalance. However, as the gene duplication is the mean of providing raw materials for genome evolution , we weredS ratio . This inGene duplication generates multiple copies of a gene that are initially functionally redundant, and their retention demands either functional diversification or regulation of the protein dosage. In this study we showed that human essential genes are mostly retained as duplicates, a trend which is different from mouse, with the duplicated copies being functionally more redundant in humans. Consistent with this, the evolutionary rate of these redundant human paralogs of essential genes is lower than that in mouse. We showed that these redundant human duplicates can be maintained due to the presence of more efficient dosage-regulation. Our study sheds light on the importance of the backup copies to restore the fitness effect of gene deletion, thereby increasing the fitness in humans. This study opens the future direction for in depth analysis of duplicated essential genes and their role in the human protein evolution.S1 DatasetThis dataset contains the essentiality, duplicability, involvement in development and phyletic age data of mouse and human genes.(XLSX)Click here for additional data file.S2 DatasetThis dataset contains the duplicate pairs for mouse and human genes used for functional distance measurement.(XLSX)Click here for additional data file.S3 DatasetThis dataset contains the pseudogene annotation for all mouse and human genes under study.(XLSX)Click here for additional data file.


The number of depressed patients treated with deep brain stimulation (DBS) is relatively small. However, experience with this intervention now spans more than 10 years at some centers, with study subjects typically monitored closely. Here we describe one center’s evolving impressions regarding optimal patient selection for DBS of the subcallosal cingulate (SCC) as well as observations of short- and long-term patterns in antidepressant response and mood reactivity. A consistent time course of therapeutic response with distinct behavioral phases is observed. Early phases are characterized by changes in mood reactivity and a transient and predictable worsening in self ratings prior to stabilization of response. It is hypothesized that this characteristic recovery curve reflects the timeline of neuroplasticity in response to DBS. Further investigation of these emerging predictable psychiatric, biological, and psychosocial patterns will both improve treatment optimization and enhance understanding and recognition of meaningful DBS antidepressant effects. The DBS target with the most experience is the subcallosal cingulate white matter, alternatively referred to as subgenual or Area 25 DBS (SCC; Mayberg et al., Screening and evaluating hundreds of participants with in-depth assessments Table  has shapA typical history for those participants who respond to DBS starts with a depressive episode in their 20s that responded to antidepressant medication with symptomatic and functional recovery. In subsequent episodes, more aggressive antidepressant treatment was required and more medication failures were experienced. Most underwent electroconvulsive therapy, with an initial good response that could not be recaptured when symptoms later returned. Puigdemont et al.  reportedAll subjects must meet a minimum severity score on a standardized rating scale for study inclusion Table . HoweverIntraoperative testing of DBS contacts is conducted in awake subjects to explore acute stimulation effects, assess safety, and confirm electrode placement. In the SCC target, acute effects to stimulation including “lightness” and “connectedness” were initially reported and replicated in subsequent studies (Mayberg et al., Our observations led us to take a more systematic approach to intraoperative testing, which confirmed predictable, reproducible, contact-specific responses in most subjects (Riva-Posse et al., The acute behavioral effects seen with intraoperative stimulation and described above are typically reproducible within the immediate post-operative period. In the days following intraoperative stimulation, it is not uncommon for our patients to experience some persisting symptom relief even though stimulation is off. This effect is strongest in the days after surgery and fades within 3 weeks. Repeating acute stimulation 1 month after surgery may reproduce the effects in attenuated form, or they may be absent. These intraoperative responses are now being evaluated as initial antidepressant effects, as biomarkers to confirm proper electrode placement, and as a probe of initial antidepressant physiological responses.A 1-month post-operative recovery period, during which stimulation is off, is followed by 6 months of continuous stimulation during which no medication changes are allowed and only limited adjustments to stimulation parameters are made. In our observations, the full antidepressant response evolves through stereotypic early and late subacute phases before settling into stable long-term recovery.In the first weeks of chronic stimulation, patients generally report minimal change, though outside observers notice more dynamic affect, movement, and speech. Anecdotally, family members comment that the patient “looks younger” or “is more like her old self.” Within the first month, patients report an increase in activity and may notice more things in their environment. They report little subjective change in mood, although depression ratings are usually decreasing. Patients begin to notice that they are having more emotions, including brief positive moods, before endorsing any significant or lasting lifting of their depression. Others have similarly observed that significant subjective improvement in mood may not be reported for several weeks of active stimulation (Lozano et al., Having chosen the contacts for chronic stimulation on the basis of tractography and intraoperative effect, we typically do not make changes to stimulation parameters as this clinical process unfolds. While it is not uncommon for programming changes to be required over time in neurodegenerative diseases like Parkinson’s disease, it is not clear that this level of tuning is necessary or helpful in depression (Bewernick et al., The relatively smooth and progressive improvement in depressive symptoms seen in the first weeks tends to destabilize roughly 10–12 weeks after initiation of chronic stimulation. What follows is a temporary period of subclinical emotional dysregulation characterized by increased negative affect, especially flares of anger and irritability, mood swings, and disproportionate negative emotional reactivity to environmental stressors. This is often concurrent with increased activity outside the home and increased frequency and complexity of interpersonal interactions. This period tends to last around 4 weeks. During this time, patients may report a return of depressive symptoms with increases in depression rating scores, although generally they no longer meet criteria for a major depressive episode. In the Emory experience, these fluctuations resolve without changes in stimulation parameters. At a similar time point after starting DBS, Puigdemont et al.  reportedAfter 6 months of chronic stimulation, emotional hypersensitivity usually abates. Depression rating scale scores again decrease. Global Assessment of Function scores increase, as patients become more active and connected with others. They are able to imagine life further into the future and entertain longer-term goals, such as a return to employment or other productive activities. Relationships with loved ones, especially partners, change in response to the patient’s decreased dependency. Patients report an increased ability to tolerate setbacks in life and relationships. We see gradual improvement in mood and resilience through the first year and beyond, suggesting ongoing plasticity effects. Long-term follow-up studies have typically shown that the response at 1 year may continue to improve in subsequent years (Kennedy et al., Interestingly, even those considered non-responders by study criteria may nevertheless report meaningful improvement in their lives and choose to continue the treatment even when offered discontinuation and device removal, as has been the experience with other stimulation targets (Bewernick et al., Once therapeutic contacts and parameter settings have been established, they are typically maintained over the years. Medications are generally not changed significantly once stimulation is initiated. In some instances, doses have been reduced, but generally not eliminated. However, since the protocol does not allow medication changes until after 6 months, it is possible that DBS becomes entrained with the pharmacological milieu instantiated at the time that DBS effects evolved. That said, patients do not appear to require medication to enable a DBS effect as patients on no medications can achieve clinical response and remission, although this is uncommon.In our experience, patients with the best response to SCC DBS are those who have a history of treatment-responsive depressive episodes with good inter-episode recovery, but undergo a malignant transformation and no longer respond to standard therapies. The antidepressant response to SCC DBS may be best described in acute, subacute, and chronic phases. Acute stimulation of appropriately positioned electrodes is frequently associated with feelings of relief or increased awareness. These responses are specific to each individual and highly reproducible with repeated testing in the intraoperative and perioperative period.That said, with chronic stimulation, initial changes are noticed first by others. Patients notice increased activity and become more aware of their environment before they notice improved mood. As patients experience more sustained improvement in mood and more critically, increased emotional range, they move from a state of relative stability around a low negative to relative instability, with heightened emotional sensitivity and reactivity. Close follow-up and reassurance during this period of emotional recalibration is warranted, though frequent stimulation parameter adjustments are not. This intermediate stage of recovery, generally lasting several weeks, gives way to increased stability and resilience manifest by progressive improvement in depressive symptoms that are maintained over months and years. While the steepest improvement tends to be seen in the first 6 months, DBS responders report continued gradual improvement over one or more years of treatment. Discontinuation of stimulation during this recovery phase nonetheless leads to a gradual return of symptoms over several weeks. Current studies are exploring how rehabilitative strategies may best synergize with these distinct phases of recovery.The gradual and predictably bumpy recovery curve in SCC DBS for depression stands in contrast to the response to DBS observed in Parkinson’s disease and essential tremor, where the effect is apparent immediately, maximal effect is reached within hours, and with discontinuation, primary symptoms return immediately (Hristova et al., It is hoped that knowledge gained from these small, open-label, mechanistic investigations will inform the design of larger scale efficacy trials for DBS. Those who would design such trials face significant challenges. The heterogeneity of depression may be obscuring subsets of patients who are the most appropriate candidates for DBS at each anatomical target. Inability to effectively quantify the desired patient characteristics creates a problem for clinical trials, where everything must be operationalized. Allowances must be made in treatment decision algorithms for discrepancies between clinical impression and standardized rating scores. During the transient period of emotional hypersensitivity in the subacute phase, depression ratings may worsen, which may trigger protocol-defined parameter changes that interrupt the natural course of recovery thus confusing the clinical picture and ultimately, the demonstration of efficacy. Development of next-generation closed-loop DBS systems that are capable of monitoring and responding to changes in neuronal signals may further improve the conduct of future clinical trials (Afshar et al., Dr. Crowell has received funding from the American Psychiatric Association’s Psychiatric Research Fellowship Award funded by Eli Lilly and Company and the National Institutes of Health Loan Repayment Program. Dr. Mayberg has received funding from the Dana Foundation, Woodruff Fund, Stanley Medical Research Institute, and the Hope for Depression Research Foundation and consulting and intellectual licensing fees from St. Jude Medical Inc. All other authors report no commercial or financial relationships that could be construed as a potential conflict of interest.


Arabidopsis arenosa, that support this hypothesis.Whole genome duplication is a prominent feature of many highly evolved organisms, especially plants. When duplications occur within species, they yield genomes comprising multiple identical or very similar copies of each chromosome (“autopolyploids”). Such genomes face special challenges during meiosis, the specialized cellular program that underlies gamete formation for sexual reproduction. Comparisons between newly formed (neo)-autotetraploids and fully evolved autotetraploids suggest that these challenges are solved by specific restrictions on the positions of crossover recombination events and, thus, the positions of chiasmata, which govern the segregation of homologs at the first meiotic division. We propose that a critical feature in the evolution of these more effective chiasma patterns is an increase in the effective distance of meiotic crossover interference, which plays a central role in crossover positioning. We discuss the findings in several organisms, including the recent identification of relevant genes in The online version of this article (doi:10.1007/s00412-015-0571-4) contains supplementary material, which is available to authorized users. Most eukaryotic organisms have diploid genomes. However, in some cases, a genome contains more than two homologous copies of each chromosome. This condition, known as “polyploidy,” occurs in many species, notably plants but also many animals Astaurov . PolyploPolyploids generally fall into two broad categories, albeit with a range of intermediate states ; sister chromatids then segregate at the second division of meiosis (MII). For full fertility in polyploid meiosis, the MI must still somehow result in a regular segregation of equal numbers of parental chromosomes to each pole, despite the fact that there are now multiple copies of each chromosome present. This challenge is particularly stark for autopolyploids, because the different versions of each chromosome are very similar or indistinguishable in DNA sequence and thus provide no special intrinsic cues to guide equi-partitioning during the segregation process. For allopolyploids, in contrast, the presence of homology can be (and is) used to solve this problem, as shown by the fact that more homologous chromosomes preferentially segregate from one another  are oriented towards opposite poles, in preparation for segregation during the ensuing anaphase Fig. . At thisThese connections are essential for the regular segregation of homologs to opposite poles, analogous to the way in which a physical connection of sister chromatids ensures bipolar orientation and segregation during mitosis and metaphase/anaphase of the second meiotic division  acquire at least one CO (and thus chiasma). This feature is often called the “obligatory CO.” Many diploid species exhibit only one or two COs/chiasmata per bivalent  occur indiscriminately among these copies in all pairwise combinations. This situation compromises both of the features required for regular two-by-two segregation.First, newly arising autotetraploids exhibit complex arrays of chiasma configurations  Fig. . Sets ofSecond, neo-autotetraploid chromosomes exhibit extensive numbers of chromosomal associations that appear to be comprised of both multivalents and entanglements , and interstitial positions as seen from MI configurations and confirmed by molecular analysis of CO-correlated Mlh1 foci along prophase chromosomes . On the other hand, the occurrence of chiasmata near chromosome ends  is positively correlated with regular quadrivalent segregation  might explain how newly formed autotetraploids evolve the specific chiasma configurations needed to support regular two-by-two MI segregation? Since CO positions are determined during prophase, evolutionary forces are presumably acting on events that occur during this period, long before chiasmata are actually required to mediate chromosome alignment and segregation.Universally, meiosis involves the initiation of recombination via a large number of programmed double-strand breaks (DSBs) which interact primarily with homolog partners to give a large number of early recombinational interactions Hunter . A minorWe have proposed a specific model for how CO patterning might occur Fig. , has twoCaenorhabditis elegans; Martinez-Perez and Colaiacovo Schistocerca gregaria . Given this situation, the final array of COs will be determined by three factors: the position(s) of early recombination interactions along the chromosomes, the strength of the CO designation process in relation to the inhibitory effects of interference, and the distance over which CO interference acts. In an extreme case, where the interference distance is longer than the length of the chromosome, each homolog pair will acquire one and only one CO, regardless of the number and positions of early recombination interactions. In diploid species, this situation occurs both genome wide  and by studies of axis relationships in autotetraploids, where coalignment of multiple axes has been observed prior to and after synaptonemal complex (SC) formation. Such complex partner interactions are common in newly formed autotetraploids  interference distance will reduce the total number of COs/chiasmata. It will also specifically generate exactly the chiasma configurations observed in evolved autotetraploids. The effectiveness of this change is a direct consequence of the basic logic of the CO patterning process (above). The efficiency of CO designation will ensure that every chromosome copy acquires at least one CO/chiasma, thus eliminating “zero-CO” univalents in general and trivalent-plus-univalent configurations in particular. Concomitantly, operation of interference over a sufficiently long distance can ensure that no chromosome becomes connected to more than two partners and, more specifically, that such two-partner connections will occur near the ends of the chromosomes. These effects are illustrated below Fig. .If CO interference acts over a distance longer than the length of a particular chromosome, a first CO designation will always preclude the occurrence of a second CO designation anywhere else on either of the two participating homologs, even in regions where they are paired to other partners. A second CO designation will then occur only on one of the other two homologs. The result would be a pair of bivalents, each linked by only a single CO. In this situation, the COs in question could occur anywhere along the lengths of the chromosomes.If the first CO designation occurs at an interstitial location, it will preclude CO designations anywhere else on the involved chromosome pair, thus ensuring that other CO designations involve the other pair to create a pair of bivalents. The second pair might also acquire a single interstitial CO; however, if the second CO designation is near a chromosome end, the third CO designation could occur at the opposite end, generating a bivalent with a pair of terminal COs  also increases in these situations remains to be determined.One way to increase the effective interference distance would be to decrease chromosome length (above). In accordance with this possibility, evolved autotetraploids in the three well-defined cases have been shown to have shorter prophase chromosomes than the diploids from which they evolved. This is true in the sand cress  or during DSB-mediated coalignment process prior and prerequisite to CO designation. This may seem unlikely in view of the complex patterns of associations that are seen at leptotene/zygotene in evolved tetraploid lines as well as their newly formed counterparts ESM 2(DOCX 733 kb)Below is the link to the electronic supplementary material.


Arguably the most popular of international fungal genetics conferences, the Asilomar meeting reached its registration cap 2 days before the early bird deadline, with 910 participants from 35 countries.The 28th Fungal Genetics Conference was held March 17−22, 2015, at the Asilomar Conference Center in Pacific Grove, California  the hashtag #Fungal15 racked up 3456 tweets from 349 participants, and tweets were seen by more than 3 million others.One striking feature of this year’s meeting was the high level of Twitter participation. On the basis of analytics from the health care social media analytics company Symplur  and Antonio Di Pietro  invited the top tweeters to join us in picking highlights of the 28th Fungal Genetics Conference. Even so, these highlights were not able to cover all the terrific science at the meeting.http://www.scienceismetal.com). The education and outreach session also featured a number of talks that highlighted the use of fungi as tools in undergraduate teaching and useful online resources, including the Genetics Society of America peer-reviewed education portal (http://www.genetics-gsa.org/education/).Perhaps not surprisingly, several of the top tweeters mentioned participation in the twitter subculture  as a meeting highlight, noting that active use of Twitter during the meeting actually provided an additional venue for scientific discussion and sharing of ideas. This type of access was especially useful during concurrent sessions, allowing followers of #Fungal15 to get a taste of talks they were unable to attend. Twitter also was the subject of a talk in the education and outreach session from Cat Adams , who pointed out that academic tweets are nine times more likely to be rebroadcast and that 30% of tweets sent by academics contain a link to a peer-reviewed resource. Because Twitter can be intimidating to new users, Adams thoughtfully provided newbie tips for effective communication , whose group is studying patterns of microbial diversity in the surface-associated communities that make up the rind of major types of cheeses—edible biofilms. High-throughput sequencing of 137 different rind communities across 10 cheese-loving countries revealed 24 widely distributed and culturable genera of bacteria and fungi as dominant community members. Intriguingly, highly reproducible community types evolved independent of geographic location of production. Microbial communities of cheese rinds and other fermented foods represent an experimentally tractable system for defining ecological and genetic mechanisms that influence microbial community assembly and function.@KSBruno9Dutton’s talk also inspired one of the more unique hashtags of the meeting #96wellcheeseplate; from Ken Bruno Saccharomyces whole-genome duplication arose after hybridization of two species rather than genome doubling of a single species. He presented compelling evidence for the existence of a coetaneous interspecies hybridization, providing a new perspective for interpreting the origin and consequences of genome expansions.Several presentations focused on genome structure, evolution, and links to epigenetics. Toni Gabaldón  postulated that the Leptosphaeria maculans , Zymoseptoria tritici , and Verticillium dahliae  provided new tools for analyzing sequence and structural polymorphisms and their links to pathogenicity in populations of these species. For example, comparative analysis of V. dahliae genomes revealed recent segmental duplications that established lineage-specific regions, suggesting that evolution is linked to segmental genome duplications and rearrangements mediated by improperly repaired DNA breaks.High-quality genome assemblies in Neurospora crassa, the role of epigenetics in pathogenicity is actively being investigated. So far, it appears that repeat-rich areas show increased marks of methylation. Mark Gijzen (Agriculture and Agri-Food Canada) reported on effector gene silencing in Phytophthora. Intriguingly, his results suggest strain-specific epigenetic modifications enable the pathogen to evade plant immune recognition while the effector gene itself is maintained.Although epigenetic marks have been poorly characterized in filamentous fungi outside the model species In vivo Imaging of Host-pathogen Interactions” illustrated what technologies are available to observe these interactions in real time for both plant and animal pathogens (#zebrafish); some great tools and ideas were shared in the education and outreach session, particularly with respect to navigating social media; and finally the “Synthetic Biology” session featured probably one of the hottest new techniques—the CRISPR/cas9 system as presented by Christina Noedvig , which was #standingroomonly—and highlighted our ability to advance fungal biology in new and exciting ways.A highlight throughout the meeting was the sharing of new tools and techniques in a variety of fungal systems. Many concurrent sessions were organized around these themes: “Fungal Biotechnology” focused on mining fungi for enzymes; “Environmental Metagenomics” showed us how next-generation sequencing technologies are providing insight to the microbial world beyond just bacteria; “Aureobasidium pullulans, that thrive in a variety of extreme environments and most surprisingly are commonly found in dishwashers.Many talks and presentations presented a perspective on fungal biology beyond the model filamentous and yeast systems. In her plenary session talk, Emily Troemel  described her laboratory’s work on Microsporida parasites of worms. Her studies are building an understanding of the biology of Microsporidia through genomic comparisons, identifying unique patterns in gene families like hexokinases that may be important in host cell reprogramming. The “Extremophilic Fungi” concurrent session offered a plethora of speakers covering fungi that excel in hot, arid, or salty environments. For example, Nina Gunde-Cimerman  reported on a group of halotolerant and human pathogenic fungi, such as Paramicrosporidium saccamoeba that are parasites of Amoeba nuclei by Alisha Quandt (University of Michigan), and genome analysis of Nosema cernae, revealing recent population expansion by Nicolas Coradi . Yet another highlight was the talk by Olga Lastovetsky (Cornell University) on fungal-bacterial symbioses between Rhizopus and endosymbiotic Burkholderia bacteria, revealing extensive signaling that precedes the establishment of symbiosis. In her plenary talk, Rosa Ruiz-Vazquez  presented the mechanisms of RNA silencing in the Zygomycete Mucor circinelloides, an opportunistic pathogen of humans, and reported exciting results on the presence of a second Dicer-independent RNAi pathway in the Zygomycetes.The “Early Diverging Fungi” session included many talks that highlighted how genomic technologies are providing new looks at these enigmatic species. Mary Berbee  presented a novel hypothesis about the evolution of pectinases in chytrid fungi and the implicated role in the metabolism and trophism of these fungi. Alisha Quandt (University of Michigan) introduced work using single-cell genomics to sequence the genomes of Cryptomycota lineages that are parasites of other fungi and protists. Other notable talks included phylogenomics of the Zygomycetes from Jason Stajich , studies of Saccharomyces cerevisiae populations to laboratory evolution. Taking samples of the populations for analysis via flow cytometry, high-throughput sequencing, and freezer storage , his group showed that patterns of sequence evolution are driven by a balance between chance events and the deterministic action of selection on individual mutations, thus favoring parallel evolutionary solutions in replicate populations. As sequencing technology continues to improve and sequencing cost to decrease, we are likely to see a striking increase in our ability to test fundamental questions in evolutionary biology of additional fungal model systems, such as N. crassa, in the laboratory.Many laboratories currently are leveraging a combination of experimental evolution and high-throughput sequencing methods to study the molecular basis of adaptation and the reproducibility of evolutionary outcomes across a variety of model systems. This was elegantly highlighted in a Chair′s Choice talk by Gregory Lang (Lehigh University), who combined the awesome power of yeast genetics with robotics, subjecting hundreds of isogenic @MRoerdamCan’t help feeling that the talk from the Lang lab should have had standing ovations at #Fungal15 Awesome science! Mikael R. Andersen in vitro reconstitution. She illustrated how the construction of 3D artificial cargos helps to dissect the mechanism of bi-directional, microtubule-based transport. Berl Oakley (Kansas State University) showed that microtubule nucleator gamma tubulin has roles controlling the cell cycle, likely through localization of spindle assembly checkpoint and other regulatory proteins. In an elegant dissection of appressorium development in the rice blast fungus Magnaporthe oryzae, Nick Talbot  showed that appresorium formation is controlled by the cell cycle. By recreating classic cell-cycle mutations, his group demonstrated that appresorium morphogenesis requires passage through the G2/M transition and the DNA replication checkpoint. Nicholas Buchler (Duke University) presented a thought-provoking analysis of the evolution of cell-cycle control in eukaryotes, showing that the SBF transcription factor, a major regulator of the G1/S transition, was likely introduced into fungi by horizontal gene transfer from a DNA virus.Several plenary talks highlighted the cytoskeleton and cell cycle. Samara Reck-Peterson (Harvard) gave a beautiful overview of microtubule-based intracellular transport, a fundamental process in all eukaryotic cells. Transport of the molecular motor dynein by a kinesin to the start of the microtubule plus end was shown by the use of N. crassa. Fleissner showed that the composition of the plasma membrane is critical for proper cell−cell interaction and that mutants accumulating specific ergosterol precursors exhibit defects in the fusion program. Glass showed that self and nonself interactions during germling fusion are linked, that an interplay between these two systems is important in the regulation of chemotropic interactions and cell fusion, and that genes involved in cell fusion are highly polymorphic.Andre Fleissner  and Louise Glass  provided two nicely complementary plenary talks on the mechanisms underlying cell−cell communication and hyphal fusion in RNAse-Like Proteins in Haustoria (RALPH), whose structure is highly similar to that of microbial RNAses and which interact with nucleic acids and with host proteins. Yet another type of secreted virulence effector was introduced by Antonio Di Pietro, : Fusarium Rapid ALkalinization Factor  was likely horizontally acquired from plants and affects local pH during infection to promote host colonization. Yasin Dagdas  and Elodie Gaulin  reported on functional analyses of oomycete effectors that interfere with defense responses, either by targeting autophagosomes or by triggering host DNA damage in plant and animal cells. Gero Steinberg  presented a spectacular Chair’s Choice talk on long-distance endosome trafficking that drives fungal effector production, whereas Alga Zuccaro’s  plenary lecture provided novel insights into the molecular mechanisms driving endophytic interactions in plants, obtained from genomic studies in sebacinoid root endophytes.Several talks introduced new functions for effectors of filamentous pathogens. Bart Thomma  and Tim Friesen (USDA-ARS and North Dakota State University) showed that LysM effectors are produced by various plant pathogens to protect them against host chitinases and suppress chitin-triggered immunity. Pietro Spanu  presented a novel class of effector proteins in cereal powdery mildews named Phytophthora acts as a haustorial targeting domain that is cleaved and N-acetylated before effector secretion, similar to a related motif in host-translocated effectors of plasmodia. This evokes a model in which RXLR is involved in pre-secretory sorting rather than host translocation per se. However, the topic remains controversial since Qunqing Wang (Oregon State University) reported experimental evidence arguing against effector cleavage during infection. Future breakthroughs in this field may originate from new host-translocation assays. Libera Lo Presti  reported promising progress on a BirA biotin ligase based assay of pathogen-dependent effector translocation.The ways in which effectors of oomycete and fungal pathogens translocate into plant cells remains an unsolved mystery. Stephan Wawra  proposed that the Arg-Xaa-Leu-Arg (RXLR) translocation motif of In the closing Perkins/Metzenberg Lecture, Michael Hynes  gave a sharp, entertaining, and highly personal view of his scientific career, including sound advice to early career scientists: read, think, talk to your peers; be generous with your ideas and time; be realistic, flexible and do not neglect your work-family life balance.@sau916@fmartin1954@eupathdb@mycomancy@drvalleyfever@team_thomma@kamounlab@hyphaltip@jchrispires@mcmomanyWe are all here because at some time in the past we chose to work on fungi or organisms with fungal lifestyles. Some of us chose fungi because they are exquisite models. We wanted to answer fundamental biological questions using the systems that gave the world one gene-one enzyme and gamma tubulin, that helped to unravel the control of cell cycle and circadian rhythms.Some chose fungi because of their massive potential for damage and a desire to stop it. Every year fungal disease kills as many people as malaria or tuberculosis. Perhaps even more stunning, every year 20% of agricultural crops are lost with most of that loss caused by fungi. That lost food is especially important, given our ever-growing population.Some chose fungi not because of their destructive potential, but because of their great capacity to make and secrete products, a capacity that is a direct result of the fungal hallmark of extracellular digestion. Every year industry uses 1.2 million tons of citric acid in products such as soft drinks. Those 1.2 million tons are made by a fungus. And, of course, fungi were using plants for biofuel long before it was trendy.Some did not choose fungi for their power as models or their ability to destroy or to make products. They chose fungi for their fascinating and unique biology. Members of the fungal kingdom range from microscopic unicellular yeasts to macroscopic basidiomycetes with mycelia that cover acres. What drives the evolution of such diversity? What drives interactions with the environment and other organisms? With 500 sequenced genomes and hundreds more in the pipeline we can answer such questions at an unprecedented level of detail, a level not even imagined just ten years ago.Regardless of why you are here, we welcome you and sincerely hope that you will be amazed and inspired at this 28th Fungal Genetics Conference.-Michelle Momany, Scientific Co-Chair


In nature, most plants are resistant to a wide range of phytopathogens. However, mechanisms contributing to this so-called nonhost resistance (NHR) are poorly understood. Besides constitutive defenses, plants have developed two layers of inducible defense systems. Plant innate immunity relies on recognition of conserved pathogen-associated molecular patterns (PAMPs). In compatible interactions, pathogenicity effector molecules secreted by the invader can suppress host defense responses and facilitate the infection process. Additionally, plants have evolved pathogen-specific resistance mechanisms based on recognition of these effectors, which causes secondary defense responses. The current effector-driven hypothesis is that NHR in plants that are distantly related to the host plant is triggered by PAMP recognition that cannot be efficiently suppressed by the pathogen, whereas in more closely related species, nonhost recognition of effectors would play a crucial role. In this review we give an overview of current knowledge of the role of effector molecules in host and NHR and place these findings in the context of the model. We focus on examples from filamentous pathogens (fungi and oomycetes), discuss their implications for the field of plant-pathogen interactions and relevance in plant breeding strategies for development of durable resistance in crops. In nature, successful pathogens are the exception, as the majority of plants are resistant to most pests and pathogen species. This form of disease resistance is known as nonhost resistance (NHR) and can be defined as resistance exhibited by an entire plant species to all genetic variants of a non-adapted pathogen species or forma specialis (f. sp.). Multiple factors contribute to NHR to unadapted pathogens, including constitutive defenses and induced defense mechanisms that result in plant immunity .Plant structure and chemistry form the first barriers encountered by any filamentous plant pathogen. The pathogen must locate a potential host. Variation in chemical compounds released by the plants can affect the attraction process . Once inR) genes, mainly nucleotide-binding – leucine-rich repeat (NB-LRR) proteins which upon activation, lead to effector-triggered immunity  by host cell surface pattern recognition receptors (PRRs) which activate pattern-triggered immunity PTI; . PAMPs aity ETI; . The ETIR genes  flanking chromosomal breakpoints. These LS are enriched for retrotransposons and other repetitive sequence elements  allows targeted sequencing, focusing on the NB-LRR composition. Using RenSeq, the number of predicted R genes present in the potato genome increased from 438 predicted in the original genome sequence, to 755 after enrichment . A screen of 54 P. infestans RXLR proteins in pepper revealed that many effectors are recognized in various pepper lines leading to a HR  showed recognition of multiple effectors  and in distantly related nonhost plant  induction triggered by the PAMP flg22 in tomato. Interestingly, only three of the eight maintained this activity in Arabidopsis, suggesting the failure of the remaining five effectors to successfully manipulate their targets in the nonhost plant. Unfortunately, the effector targets in this case are yet not known.In order for an effector to achieve its function and promote virulence, it is expected to manipulate one or more host target proteins or processes. One of the main ways effectors are thought to act is by suppressing defense responses activated during PTI. While there is a lot of evidence in the literature for effectors of filamentous pathogens suppressing immunity in host plants  very litP. infestans and P. mirabilis, evolved to specifically inhibit proteases from the distantly related plants tomato and four o’clock flower  respectively. Cysteine proteases are involved in immunity and cell death signaling in plants  is under diversifying selection compared to PiEPIC1. The genes corresponding to the equivalent proteases of tomato RCR3 were cloned from potato and four o’clock flower  and the inhibitory activity of each effector was analyzed. PiEPIC1 was able to efficiently suppress potato and tomato RCR3 activity but not MRP2 and the opposite was observed for PmEPIC1  genes  genes . Modificifficult .NHR is by definition more durable than host resistance; we have summarized here the recent findings supporting the idea that NHR is likely to be governed by multiple recognition events. However, effector recognition in distantly related nonhost plants has not frequently been observed. Taken together, the recent studies presented here rather support the original model of NHR proposed by The 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.


Neurocognitive functioning (NCF) has been increasingly recognized as an important contributor to quality of life in patients with cerebral neoplasms. Accordingly, studies of NCF in this population have grown tremendously over the past few decades, and performance-based neuropsychological measures assessing diverse NCF domains are now routinely included in brain tumor clinical trials . HoweverThe article by Dwan and colleagues highlights method variance as another important contributor to the variability in rates of NCF impairment reported. The authors adeptly point to a substantial lack of consistency in impairment classification schemas throughout the literature. Utilizing a few of the more commonly employed classification strategies in a sample of patients with brain tumors, they also demonstrate that classification of impairment based upon intra-individual comparison to estimated premorbid intellectual function differs from classification using published norms or matched controls. The authors then conclude that “this supports the need to interpret individuals’ neuropsychological test results in the context of their estimated premorbid IQ.” While we agree with Dwan et al. that consideration of premorbid functioning is important when interpreting neuropsychological test results, we believe that the approach utilized in their report may be prone to misclassification for reasons discussed below, and we briefly suggest an alternative that is potentially more statistically sound and robust.In the analyses under discussion, the authors classify a test score as “impaired” if it falls at least one SD below the patient’s own premorbid intellectual function estimate, as determined by performance on a word-reading task. This method is economical and demands minimal statistical sophistication, making it attractive for use in clinical and research settings alike. However, as the authors briefly acknowledge, the approach risks elevating false positive (Type I) error rates for individuals at the upper tail of the premorbid intellectual distribution, as well as false negative errors (Type II) for those at the lower end of the distribution. Importantly, risk of error tends to increase with the number of tests included in a battery, which are numerous in routine neuropsychological practice, and when comparisons are made at the individual test level rather than domain level. A related issue involves differences between correlations among tests. Since tests of NCF vary in sensitivity, ceiling/floor levels, and domains of specificity, uniform correlations between measures of premorbid intellectual function and other tests are unlikely. This is problematic since it cannot be assumed that low-average estimated premorbid intellectual function entails that visual memory, processing speed, executive function, and performances within other domains should also be low average.Fortunately, various methods exist to address aspects of these concerns. While a comprehensive delineation of the numerous techniques is beyond the scope of this paper, one popular method involves calculation of regression-based norms from healthy control data . With thWhile this method has its own limitations and is by no means the only viable alternative, it has been shown to improve test sensitivity . AdditioThe 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. The Associate Editor Kerrie Leanne McDonald and the Reviewer Eng-Siew Koh declare that, despite being affiliated to the same institution as author Joanna E. Fardell, the review process was handled objectively and no conflict of interest exists.


Angina which is refractory to conventional medical therapy and revascularisation with bypass surgery and/or percutaneous coronary intervention is extremely challenging to manage with limited treatment options and a pressing need to establish effective therapy.Lipoprotein(a) [Lp(a)], a genetically determined form of LDL-cholesterol, is an independent cardiovascular risk factor which is felt to increase risk by promoting thrombosis; enhancing intimal lipoprotein deposition, and by potentially affecting myocardial perfusion, micro-vascular function, plasma viscosity and endothelial function. Lipoprotein apheresis is currently the most effective treatment available for raised Lp(a). Increasing evidence suggests that aggressive Lp(a) reduction may improve cardiovascular outcomes, although much more prospective research is required to confirm this.We are conducting a prospective, blinded randomised controlled cross-over study of patients with refractory angina and raised Lp(a), randomised to undergoing lipoprotein apheresis or ‘sham' apheresis with assessment of the impact of treatment on myocardial perfusion, carotid atherosclerosis, endothelial function, thrombogenesis, oxidised phospholipids, exercise capacity, angina and quality of life.Our primary hypothesis is that lipoprotein apheresis improves quantitative myocardial perfusion assessed by Myocardial Perfusion Reserve (MPR) detected by stress/rest Cardiovascular Magnetic Resonance (CMR), in patients with refractory angina and raised Lp(a).At least 20 patients with refractory angina and elevated Lp(a) will be recruited and randomly assigned to either a treatment arm who will undergo lipoprotein apheresis weekly for three months, or to a control group who will receive placebo ‘sham' sessions weekly for three months. All patients will have CMR at baseline assessing functional parameters, first-pass quantitative perfusion at stress and rest and late gadolinium enhancement (LGE), and quantitative assessment of carotid atherosclerosis. Following the three month period of either active or sham therapy all baseline tests will be repeated to determine the net treatment effect. After a wash-out period of at least 1 month, patients will cross-over to the opposite treatment arm with the process repeated.The trial is currently in progress. Analysis of quantitative myocardial perfusion and carotid indices will be performed fully blinded with results expected by the end of 2015.We are conducting a randomised controlled cross-over trial using CMR to assess whether lipoprotein apheresis is beneficial in patients with refractory angina and raised Lp(a). Our research will confirm whether raised Lp(a) should be a therapeutic target in patients with refractory angina and will provide valuable insights into the mechanistic role of Lp(a) in cardiovascular disease.This project is supported by the NIHR Cardiovascular Biomedical Research Unit of Royal Brompton and Harefield NHS Foundation Trust and Imperial College London. Apheresis equipment being used has been provided by Kaneka Pharma.


Altogether, our results suggest that some observed comorbidities between phenotypically different diseases could be due to a shared protein involved in unrelated biological processes.Moonlighting proteins are a subset of multifunctional proteins characterized by their multiple, independent, and unrelated biological functions. We recently set up a large-scale identification of moonlighting proteins using a protein-protein interaction (PPI) network approach. We established that 3% of the current human interactome is composed of predicted moonlighting proteins. We found that disease-related genes are over-represented among those candidates. Here, by comparing moonlighting candidates to non-candidates as groups, we further show that  ACO1 gene, is an enzyme of the tricarboxylic acid cycle (TCA cycle) which turns into a translation regulator upon a conformational change, when the iron concentration is low  from a protein-protein interaction (PPI) network  . We still observed this enrichment when considering MF-CAN and MCNC separately   are enriched in proteins involved in diseases   Figure . This, t) Figure  suggestsDifferent OMIM diseases caused by the dysregulation of a same gene can affect the same body organs or have similar phenotypic manifestations  and MONO . This result shows that MF-CAN proteins are involved in disease affecting distinct body parts. Therefore, this led us to evaluate the phenotypic similarity between disease pairs by computing the Sorensen-Dice distance based on their HPO annotation terms (see Methods for details). For each pair of diseases in which a same gene is involved, we have compared their phenotypic descriptions to assess their similarity aiming at grasping possible differences. We indeed found that those pairs associated with MF-CAN are significantly different . We obtained similar results using semantic similarity measures . These results could be due to the fact that multifunctional candidates (MF-CAN and MCNC) are acting in several biological processes, and are therefore involved in different diseases and phenotypes.To do so, we mapped OMIM diseases to the Human Phenotype Ontology (HPO) , whereas MONO are significantly depleted in such pairs (P = 1.1 × 10−5).In order to estimate whether moonlighting candidates could explain some comorbidity patterns, we used the list of comorbid diseases established by Park et al. , based oOur results therefore indicate that EMF proteins involved in several diseases can contribute to comorbidity, probably through the unrelated biological processes in which they participate.in vivo studies on mice harboring humanized AR alleles showed that long polyQ may be involved in late-onset PC and influence hormone sensitivity  is one of the MF-CAN proteins associated to a disease pair showing a comorbidity pattern  the fact that diseases in which an EMF is involved can occur in a same individual and (ii) our hypothesis that comorbidity can be due their involvement.Moreover, we found that a significant fraction of these EMF candidates represents a possible molecular link between comorbid diseases. Nevertheless, although a gene/protein may be involved in different diseases, these diseases are not necessarily co-occurring within a single individual. Our finding that comorbid diseases identified from Medicare records are enriched among EMF candidates therefore reinforces (i) we previously showed that EMFs are enriched in SLiMs compared to MCNC  a recent report showed that disease mutations occur more likely within SLiMs than neutral missense mutations in intrinsically disordered regions (Uyar et al., Diseases associated to EMF proteins display different phenotypes according to HPO, independently of the location of the mutations in the protein sequence, within or outside known protein domains. This raises several possibilities. First, these mutations may occur in existing domains not yet discovered. Indeed, current tools may not have detected some domains, since they are below the detection thresholds, or differing from the model used by the prediction tools. Second, this lack of difference may also be explained by the fact that disease mutations occur in SLiMs, short stretches of amino acids sequences that represent potential regulatory sites and are located mostly in intrinsically disordered regions (van Roey et al., In an early study on co-occurring metabolic diseases, Barabasi and colleagues (Lee et al., It should be noted that our observations cross and link several integrated functional levels (Brun et al., Finally, grounded on our computational identification of moonlighting candidates, this work represents, to our knowledge, the first effort toward the elucidation of the convoluted relationships between moonlighting protein functions, disease phenotypes and comorbidities. Overall, although much remains to be learned, our analysis underlined the necessity of identifying moonlighting proteins and to better understand their role in human diseases, particularly in the context of drug development to avoid side effects. Indeed, knowing that the different diseases in which a protein is involved, are due to the dysregulation of different processes may help choosing specific interactions to inhibit in order to act on one disease and not the other. In addition, a drug inhibiting an unsuspected moonlighting protein may cause side effects if it also impairs the secondary function of the protein. Therefore, the identification of candidate moonlighting proteins can be useful to gain a deeper understanding of disease molecular details and to design more effective therapeutic strategies.The 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.


Declarative memory—long-term memory for events and facts—is a key form of cognition that depends on distributed neural coding. Given the rich, multifaceted nature of life events, their neural representations (episodic memory “engrams”) typically incorporate a broad set of cortical and subcortical regions whose coding properties underlie event features  and across relevant cortical and subcortical regions, creates challenges for measurement of mnemonic content across various stages of memory encoding and retrieval. By combining non-invasive imaging techniques  with multivariate pattern-analyses (MVPA), such representational content can be decoded from distributed patterns of brain activity —with the hippocampus at its core—is the most prominently studied region in memory research , a prefrontal region intimately connected with the hippocampus and suggested to be involved in the building of knowledge structures , and suggest future research directions.Reinstatement of a previously learned memory during new encoding may build associations between overlapping experiences  are dissociable from those associated with separation processes in both the hippocampus and mPFC  giving rise to between-trace interference or weakening of its associations, either or both of which would result in episodic details loss, but also (b) allowing for incorporating the new experience into a semantic memory engram Dudai, . With coThis perspective motivates new questions about the nature of mnemonic processing, questions that also can be answered using MVPA techniques. For example, instead of asking whether one memory is stronger or weaker than another, we can ask whether and how both new and existing memories change with integration, at both the neural and cognitive level: (a) Do they become more alike (Milivojevic et al., Better understanding of how memories build on each other to construct integrated or semantic memory engrams is of central importance in settings where they benefit our daily lives. For example in educational situations, where students are taught to construct knowledge through a specific training regimen, neuroscientific insights into the biological mechanisms underlying our learning abilities and interactions with prior knowledge are very valuable Goswami, . Such inThe use of multivariate decoding and similarity techniques to inform memory research is rapidly advancing. Because of the distributed nature of episodic and semantic memory representations, MVPA-analyses are promising techniques for delineating how distinct mnemonic representations interact. Researchers have provided novel evidence for memory alterations that occur through mnemonic reinstatement during learning–changes that may serve to facilitate construction of integrated, generalizable knowledge about our world. However, when such integration occurs, it may come at the expense of episode-specific distinctions in memory. Insights from MVPA may help bridge perspectives on how knowledge structures form with constructs such as integrative encoding and mnemonic interference. Understanding neural and cognitive mechanisms contributing to memory integration may inform learning in real-world settings such as education, where efficient knowledge construction is imperative for success.All authors listed, have made substantial, direct and intellectual contribution to the work, and approved it for publication.This research is funded by a Rubicon fellowship from the Netherlands Organisation for Scientific Research and the Wallenberg Network Initiative on Culture, Brain, and Learning.The 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.


Eukaryotic whole genome sequences are accumulating at an impressive rate. Effective methods for comparing multiple whole eukaryotic genomes on a large scale are needed. Most attempted solutions involve the production of large scale alignments, and many of these require a high stringency pre-screen for putative orthologs in order to reduce the effective size of the dataset and provide a reasonably high but unknown fraction of correctly aligned homologous sites for comparison. As an alternative, highly efficient methods that do not require the pre-alignment of operationally defined orthologs are also being explored.A non-alignment method based on the Singular Value Decomposition (SVD) was used to compare the predicted protein complement of nine whole eukaryotic genomes ranging from yeast to man. This analysis resulted in the simultaneous identification and definition of a large number of well conserved motifs and gene families, and produced a species tree supporting one of two conflicting hypotheses of metazoan relationships.Our SVD-based analysis of the entire protein complement of nine whole eukaryotic genomes suggests that highly conserved motifs and gene families can be identified and effectively compared in a single coherent definition space for the easy extraction of gene and species trees. While this occurs without the explicit definition of orthologs or homologous sites, the analysis can provide a basis for these definitions. Several methods have been developed for the detailed global comparison of multiple whole genomes and the production of global phylogenies. Most of these methods require the prior identification and selection of a reasonably small subset of putative orthologs within which individual homologous sites are identified with some degree of confidence using alignment -7. FrequThough generally less developed, many non-alignment methods, considered initially by Blaisdell , are curThe nine eukaryotic genomes compared in this analysis are listed in Table All the proteins in the dataset were recoded as overlapping tetrapeptide frequency vectors and the resulting data matrix was decomposed by the SVD. A total of 437 singular triplets were obtained as output. The "protein" vectors provided in the "right" factor matrix are known to provide reduced dimensional definitions for all proteins in the dataset as linear combinations of the orthogonal "right" singular vectors (rsv's). Conversely, the right singular vectors themselves frequently represent "ideal" versions of proteins defining a given gene family ,14 Proteth singular vector). Those provided by negative vector values are followed by an "a" (e.g. 277a). Its worth noting at this point that protein family definitions provided by the SVD necessarily account for not only "what is there" (tetrapeptides that form the motifs that define the family), but also "what is not there" .Each right singular vector can potentially define two distinct gene families. In this case, the highest positive elemental values within a vector identify proteins associated with one protein family, while the highest negative values identify proteins associated with an anti-correlated family (i.e. proteins that rarely share the same tetrapeptides). Frequently, however, strong family definitions are provided for just one protein family. In this case, the anti-correlated proteins are seen to be derived from a mixture of two or more families. Since the choice of sign is arbitrary, strong family definitions are equally likely to be provided by either the positive or the negative values within a vector. Family definitions provided by positive vector values are denoted below using the simple vector index  comprising a given singular triplet. The lsv's describe these copep motifs as linear combinations of the 160,000 possible tetrapeptides. Those with high positive values identify peptides found with high probability in the conserved motif of a given subfamily, while those with a high negative value identify peptides excluded with high probability. Therefore, like the rsv's, the lsv's frequently describe two distinct anti-correlated entities (in this case motifs rather than protein families) using either positive or negative values within the vector. Using essentially the same procedure described above for any given rsv, the tetrapeptides having the largest positive or largest negative projections on any given lsv were identified in order to provide a focused summary of the motifs described by that vector. For motif extraction, however, an arbitrary cut-off value  was used to identify dominant tetrapeptides.In most cases, it is possible to cluster the resulting short list of dominant tetrapeptides into several uninterrupted copep strings formed by tetrapeptides that overlap in 3 of 4 consecutive amino acid positions. Using this procedure, one long copep string was identified for each of the singular triplets listed in Table Figure Instead of simply providing restricted motif summaries using the most dominant elements of the left singular vectors, we have also attempted to examine entire vectors in order to gain a better understanding of the motifs (and associated protein families) they describe. A reasonably efficient method for depicting left singular vectors is presented in Figure The detailed comparative information contained within the hundreds of singular vectors and their corresponding motifs and gene families was subsequently used to build a species phylogeny by summing all the SVD-derived right protein vectors separately for each organism and then comparing the relative orientation of the resulting species vectors . Figure Use of the "successive, delete-one" jackknife procedure as a species tree branch statistic is justified by the fact that SVD provides singular triplets in order of their "dominance" in explaining the data set . MathemaWhile our SVD-based analysis technically considers all proteins present within all nine genomes of the data set, it is likely that accurate vector definitions are provided for only a small fraction of these proteins. Theoretically, the 437 singular triplets could effectively describe as many as 2 × 437 = 874 protein families. However, many of these vectors appear to best describe particular subfamilies of larger groups of closely related proteins. Thus, the 58 protein families listed in Table 3 proteins removed) resulted in 22% bootstrap and 100% modified jackknife support for the coelomate lineage, but 0% support for the ecdysozoan lineage. Removal of a much higher fraction of poorly described proteins  produced an equivalent result. Hence, poorly described proteins contribute little to the support that our analysis provides for the coelomate model.In an attempt to increase the fraction of well described proteins used to define species, proteins having poor projections on all 437 right singular vectors were ignored during the summation process. Arbitrary vector magnitude cut-off values of 0.005 or 0.05 were applied to reduce the number of poorly described proteins used to build species trees. Even though the highest and most stringent cut-off value removed the majority of proteins during summation, both new species trees had identical topologies to that of the tree shown in Figure As demonstrated above, an SVD-based analysis of multiple genomes automatically interprets proteins from input genomes as potential members of a limited list of hierarchically defined protein families and subfamilies. Each subfamily is defined in detail by one or more singular vectors as linear combinations of a large number of peptides . Potentially, a large number of proteomes lacking annotation can be directly interpreted using this method, assuming a sufficient number of annotated proteomes are included in the analysis. Although most of the genomes used in the present analysis were already accompanied by detailed protein annotations, formal annotations of the Frub and Agam proteins were not readily available. Nevertheless, our SVD-based analysis was able to provide precise protein motif descriptions and subfamily affiliations, not only for the six Frub or Agam proteins shown in Figure Our method bears partial resemblance to a recently described graph-theoretic method for rapidly clustering massive datasets of whole genome protein sequence . In thisAlthough our descriptive analysis of singular triplets , three output matrices were obtained, consisting of 437 singular triplets . Each left singular vector produced by the SVD defines one or two conserved motifs within the dataset as particular linear combinations of tetrapeptides [Each protein sequence in the dataset was recoded as a high dimensional vector containing raw frequencies for each of the 160,000 possible tetrapeptides. Previous work has established that although tripeptides work well for estimating similarities between highly divergent proteins contained within small sets of viral genomes , tetrapepeptides ,14. Simi"Dominant" vector elements  were extracted from the left singular vectors and summarized using the C++ program "Copepx" . These vDistance matrices were derived by summing all the SVD-derived right protein vectors for a given organism and then comparing the relative orientation of the resulting species vectors using the program Cosdist ,14. SpecHomo Sapiens (Hsap), Mus musculus (Mmus), Rattus Norvegicus (Rnov), Anopheles gambiae (Agam), Drosophila melanogaster (Dmel), Caenorhabditis elegans (Cele), Plasmodium falciparum , and Saccharomyces cerevisiae (Scer), Fugu rubripes (Frub), correlated peptide (copep), correlated protein (coprot), right singular vector (rsv), left singular vector (lsv).GS conceived the study, gathered the input data, provided primary interpretation of the output, and drafted the manuscript. MB wrote and adapted software, performed computational analysis on the input data, and provided manuscript modifications. All authors read and approved the final manuscript.Copep Motifs. Long copep strings identified within the left singular vectors of a given s-triplet.Click here for file


New York Times bestseller list and winning accolades from the likes of Jimmy Carter. A wide range of inherited disorders falls under the rubric of muscular dystrophy, but all involve some form of progressive muscle wasting. Stepanek's condition impaired nearly all of his body's functions, but other more common forms, including Emery-Dreifuss muscular dystrophy (EDMD), selectively target skeletal muscle and induce cardiac abnormalities.In June, muscular dystrophy patients lost one of their most passionate advocates to a rare form of this degenerative neuromuscular disorder—thirteen-year-old Mattie Stepanek. In his short life, Stepanek wrote five volumes of inspirational poetry, topping the EDMD is caused by mutations in either of two genes: one encodes lamin A, a structural protein associated with the nucleus, and the other encodes a nuclear membrane protein called emerin. Lamins, a major component of the structural network that supports the nuclear envelope, help the nuclear envelope maintain structural integrity and absorb mechanical stress without rupturing.  Emerin binds to proteins that regulate gene transcription. Emerin and lamins are found in most cell types, yet EDMD attacks only skeletal muscles, major tendons, and the cells that regulate cardiac muscle contraction. So where does this tissue specificity come from?One theory suggests that emerin selectively targets proteins that specifically regulate gene expression in EDMD-affected tissues. Another theory proposes that emerin provides structural support to the nuclear envelope and that emerin mutations are most destructive in tissues subjected to mechanical stress—like skeletal muscle and tendons. Current evidence supports both models. Recent studies suggest that emerin forms complexes with actin—the mother of all structural proteins. Actin proteins can join together (polymerize) to form a variety of filaments. However, given longstanding doubts that actin exists in the nucleus, let alone functions there, researchers were unsure what the findings might indicate. Now James Holaska, Amy Kowalski, and Katherine Wilson propose that emerin not only functions as a structural protein in the nucleus but that it does so by interacting with actin.Evidence that emerin and lamin A can form multiprotein complexes comes primarily from experiments in test tubes. To get a sense of the physiological significance of these findings, Wilson and colleagues purified emerin-binding proteins from the nuclei of living cells. They found that emerin binds to polymerized actin and, in fact, appears to stimulate polymerization. By binding and “capping” a specific end of the actin filament, emerin prevents filament de-polymerization (disassembly), effectively increasing the rate of actin polymerization by four- to twelve-fold. The authors propose that emerin “promotes the formation of a nuclear actin cortical network,” which could serve to anchor membrane proteins and lamin filaments to the inner nuclear membrane and thus enhance the structural integrity of the nuclear envelope. Whether emerin also interconnects the lamin and actin filament networks at the nuclear envelope—which could significantly reinforce its mechanical strength—will have to await further study.Muscle contraction places enormous stress on cell membranes. These results suggest that actin-based networks, in addition to lamin networks, support the structural integrity of the nuclear envelope. Defects in proteins involved in either network could compromise nuclear structure, which could in turn disrupt the cell's gene expression program, for example, or rupture the cell membrane, killing the cell. Subtle defects in proteins important for muscle cell integrity can cause several forms of muscular dystrophy. Now it appears that emerin defects could cause EDMD in part by compromising the mechanical integrity of nuclei in muscle cells and tendons.


How does your brain pass the time while you're sleeping? If you've ever wrestled the demons of insomnia, you know what sleepless nights can do to your mental agility. Sleep cycles in mammals are characterized by two distinct, successive sleep stages: slow wave and rapid eye movement (REM). Both stages of sleep have uniquely associated electrical activity in the brain, which neuroscientists can measure by placing elec-trodes on the brain during sleeping and waking states. What neuroscientists can't easily measure is the purpose of these two sequential sleep stages.The notion that sleep helps to improve memory was introduced over 80 years ago. Since then, several studies have demonstrated that sleep deprivation following the acqui-sition of a new memory strongly impairs its consolidation. Insight into the mechanisms underlying this effect came from the observation that neuronal activity patterns detected during waking reappear during ensuing sleep, suggesting that newly acquired “memory traces” may be replayed in the brain to solidify neural connections and thus “consolidate” memory. These reverberating patterns of activity have been observed in both mammals and birds, pointing to a very general biological phenomenon.Still, the relationship between brain reverberation and memory consolidation remains unclear for a number of reasons. First, studies to date have observed only subtle, short-lived reverberations lasting less than an hour and can't explain the memory-disrupting effects of sleep deprivation applied several hours and even days after initial memory encoding. And since brain reverberation in mammals has only been investigated in the hippocampus and cerebral cortex, it is unclear whether the phenomenon is specific to this neural circuit or is a more general property of the brain. Furthermore, reverberation studies have so far relied on neural activity measured in animals that were highly trained on specific laboratory tasks and therefore may simply not be representative of the acquisition of new memories. Finally, experience-dependent neural reverberation has been detected in both phases of sleep as well as waking, but no quantitative comparison of the different contributions of each state has been established.In a study designed to address these concerns, Sidarta Ribeiro and his colleagues at Duke University in Durham, North Carolina, recorded over a hundred neurons continuously over the course of the normal sleep--wake cycle in rats, focusing on four major forebrain areas that are essential for rodent-specific behaviors. Halfway through the recording time, animals were transiently allowed to explore four strictly novel objects, each of them designed to provide different spatial and sensory cues. The researchers found that in all the forebrain areas examined the neuronal firing patterns recorded when the rats initially explored the new objects reverberated for up to 48 hours after these objects were removed. The reverberation of neuronal activity sampled when rats explored familiar environs was insignificant. Reverberation was most significant during slow-wave sleep (a state that accounts for nearly 40% of a rat's life), decreased during waking periods, and was highly variable during REM sleep.In this study, Ribeiro et al. demonstrate that long-lasting neuronal reverberation following novel waking experiences can occur in several forebrain sites and is strongly enhanced during slow-wave sleep. Because neuronal reverberations are sustained for long periods, this may provide a mechanism to recall and amplify memories until they are effectively stored. On the basis of differences observed between REM and slow-wave sleep in this and previous studies, the authors propose that the two phases of sleep play separate and complementary roles in memory consolidation. Thus, the two stages of sleep give the brain a chance to process the novel events of the day in peace.


Acquired resistance to chemotherapy is a major obstacle to successful cancer treatment. Understanding the mechanisms by which tumors become resistant to a particular agent is key to identifying new drugs or combination regimens.Kinases are signaling molecules that control many aspects of cell behavior, including cell proliferation, i.e., whether and how fast cells divide. Abnormally active kinases promoting tumor growth are found in many cancers and are a focus of rational cancer drug design. One target for kinase inhibitors is the epidermal growth factor receptor (EGFR). Two EGFR inhibitors, gefitinib and erlotinib, showed therapeutic benefits in a subset of patients with non-small cell lung cancer. Recent work has helped us understand why some patients respond and some don't: responsive tumors usually harbor activating mutations in the EGFR gene, which somehow make the tumors sensitive to treatment. Nearly all patients whose tumors initially respond to EGFR inhibitors, however, eventually become resistant to the drugs and progress despite continued therapy.William Pao and colleagues examined tumors from six patients with non-small cell lung cancer who initially responded to gefitinib or erlotinib but subsequently relapsed. Tumors from all six patients carried activating mutations in the EGFR gene. In addition, in three out of the six cases, the resistant tumor cells carried an identical second mutation in the EGFR gene. Whereas the activating mutation was present in tumor cells before treatment with erlotinib or gefitinib, the second mutation was not found in pre-treatment biopsies from these patients, nor in over 150 lung cancer samples from patients who had not been treated with either drug. Additional cell culture studies supported the notion that the secondary mutation causes resistance to gefitinib or erlotinib. It is clear, though, that this is only one mechanism of resistance, because in the three other cases resistance occurred in the absence of the second mutation. What caused the resistance in those tumors is not known.10.1371/journal.pmed.0020075), the initial identification three years ago of resistance mutations against imatinib led to the rapid development of alternative kinase inhibitors that work even against tumors with the resistance mutation. Similarly, the results by Pao and colleagues should help researchers develop second generation drugs for lung cancer.All kinases share some common features, and a resistance mutation very similar to the one identified here has also been found in other kinase genes from tumors with acquired resistance to imatinib, another kinase inhibitor. As Gary Gilliland and colleagues point out in an accompanying Perspective (DOI:


Large-scale quantitative analysis of transcriptional co-expression has been used to dissect regulatory networks and to predict the functions of new genes discovered by genome sequencing in model organisms such as yeast. Although the idea that tissue-specific expression is indicative of gene function in mammals is widely accepted, it has not been objectively tested nor compared with the related but distinct strategy of correlating gene co-expression as a means to predict gene function.PWP1 is widely expressed across different tissues but is co-expressed with many RNA-processing genes; we show that the uncharacterized yeast homolog of PWP1 is required for rRNA biogenesis.We generated microarray expression data for nearly 40,000 known and predicted mRNAs in 55 mouse tissues, using custom-built oligonucleotide arrays. We show that quantitative transcriptional co-expression is a powerful predictor of gene function. Hundreds of functional categories, as defined by Gene Ontology 'Biological Processes', are associated with characteristic expression patterns across all tissues, including categories that bear no overt relationship to the tissue of origin. In contrast, simple tissue-specific restriction of expression is a poor predictor of which genes are in which functional categories. As an example, the highly conserved mouse gene We conclude that 'functional genomics' strategies based on quantitative transcriptional co-expression will be as fruitful in mammals as they have been in simpler organisms, and that transcriptional control of mammalian physiology is more modular than is generally appreciated. Our data and analyses provide a public resource for mammalian functional genomics. Caenorhabditis elegans has established that coordinate transcriptional regulation of functionally related genes occurs on a broader scale than was previously recognized, encompassing at least half of all cellular processes in yeast Click here for additional data file175 lists of genes that are expressed in individual tissues, highest in individual tissues, or specific to individual tissuesClick here for additional data file


Every spring and fall, billions of songbirds fly thousands of miles between their summer breeding grounds in North America and their wintering grounds in the more hospitable climes of southern California, Mexico, and Central and South America. While some birds fly during the day, most, including the white-crowned sparrow, fly under cover of night. Many aspects of this remarkable voyage remain obscure, especially if, and how, nocturnal migrators get any sleep at night.A tracking study of the Swainson's thrush found that the roughly seven-inch birds flew up to seven hours straight on six of seven nights, racking up over 930 miles. While the study didn't track their daytime behavior, the birds' migratory pace—as well as the increased activity required to sustain migrations—suggests little time for sleep. Yet field observations indicate that presumably sleep-deprived fliers appear no worse for wear, foraging, navigating, and avoiding predators with aplomb. Researchers are left trying to reconcile this observation with the vast body of evidence linking sleep deprivation to impaired neurobehavioral and physiological function. How do songbirds cope with so little sleep? Do they take power naps? Have they taken “sleep walking” to new heights? Or have they managed to selectively short-circuit the adverse effects of sleep deprivation during migratory stints?To investigate these questions, Ruth Benca and colleagues studied cognitive and sleep behaviors in captive white-crowned sparrows over the course of a year. The sparrows fly nearly 2,700 miles twice a year between their Alaska and southern California homes. In laboratory cages, the birds' migratory instincts manifest as increased restlessness at night during the migratory season, with lots of hopping around and wing flapping.Niels Rattenborg et al. characterized the birds' activity levels with motion-detection measurements and video recordings, and placed sensors on their brains to monitor their seasonal sleep patterns. The brain recordings showed a marked seasonal difference in both the amount and type of sleep during a 24-hour period: migrating birds spent roughly two-thirds less time sleeping than nonmigratory birds and fell into REM sleep  much sooner. Birds displaying active migratory behavior appeared completely awake during such activity. Cognitive tests—birds performed a task that involved pecking a key in exchange for seed—revealed that birds in the nonmigrating state suffered cognitive deficits when sleep-deprived but displayed an “unprecedented” ability to maintain cognitive function in the face of ongoing sleep loss in the migratory state.These results suggest that wild songbirds drastically reduce sleep time during migration, though Benca and colleagues concede it's impossible to know for sure without recording the birds in action. And it is unclear what molecular mechanisms jumpstart the migratory mindset. Such an ability to temporarily circumvent the need for sleep, however, could prove useful for humans in situations that demand continuous performance. Some studies link migration with increased neuroendocrine activity, which is in turn associated with sleep disruption, accelerated timing of REM cycles, and mood disorders in humans. “Like migrating sparrows,” the authors note, “both depressed and manic patients show reduced latency to REM sleep, loss of slow-wave sleep, and reduced amounts of total sleep.” Given the parallels between migratory behaviors and bipolar illness, it's possible that similar mechanisms may be involved in both.Whatever the mechanism, the unprecedented imperviousness of migrating songbirds to sleep deprivation, the authors conclude, clearly warrants further testing. But it also raises interesting questions about the role of sleep, which recent studies suggest is required to incorporate novel perceptions into the brain's memory banks. If this is true, how do songbirds consolidate memories of migratory events with so little sleep? Understanding the mechanisms that power the sleepless flight of songbirds promises to unravel one of the longstanding mysteries of their improbable journey. It may also shed light on the origins of sleep-related seasonal disorders and the much-debated role of sleep itself.


At a fundamental level, the continuity of life depends on cell division. Humans generate many millions of cells per second just to stay alive, with most cell types dividing and multiplying repeatedly during a lifetime. Details of cell division vary from cell to cell and organism to organism, but certain features are universal, including what is arguably a cell's most crucial task: the faithful duplication and segregation of its genetic material.During mitosis, a cell copies its nuclear DNA, then splits into two identical daughter cells, a process that involves moving the replicated chromosomes  toward opposite ends of the cell. After chromosomes replicate, a protein complex called cohesin binds the sister chromatids together. Cohesion helps the cell distinguish between the copies, which in turn aids proper distribution. Improper sister chromatid segregation can yield an abnormal number of chromosomes  in the daughter cells, a condition associated with cancer. During meiosis—the cell division that produces egg and sperm cells—aneuploidy causes a number of congenital disorders, including Down's syndrome.To end up in their appropriate positions, sister chromatids must establish attachments to tentacle-like protein polymers called spindle microtubules, which emanate from spindle poles at opposite ends of a cell. Cohesion between the chromatids makes these bipolar attachments possible and keeps sister chromatids from separating after they attach to the spindle. Cohesion occurs along the length of a chromosome and is particularly strong around centromeres, the pinched region of a chromosome. Centromeres, in turn, assemble another protein complex called the kinetochore, which mediates the attachment of chromosomes to spindle microtubules; together, they guide chromosomes to their respective destinations.Saccharomyces cerevisiae, a favorite system for cell biologists. In the first paper, Jennifer Gerton and colleagues generated a map for the entire yeast genome of locations where cohesin binds to chromosomes during meiosis and mitosis. In the second paper, Paul Megee and colleagues found that centromeres attract large concentrations of cohesin to their flanks and that the assembly of these cohesin domains is mediated by centromere–kinetochore complexes.Cohesin's binding locations were discovered by removing chromatin—the mass of DNA and proteins that forms chromosomes—from cells, and purifying the regions associated with cohesin. These studies looked at cohesin's binding distribution either genome-wide or at select regions of a few chromosomes. Here, two research groups use a similar approach to provide a broader picture in their analysis of cohesin binding in the budding yeast Gerton's group reports that large regions surrounding centromeres have “intense” cohesin binding. These binding sites correlate with DNA base composition—DNA is composed of four chemical bases, or nucleotides, that are referred to as A, C, G, and T—showing a strong association with AT-rich regions. In meiotic chromosomes, cohesin binding sites are interspersed between the DNA double-strand breaks that initiate the exchange of genetic information characteristic of meiosis, perhaps keeping the chromatids attached without interfering with genetic recombination.Most striking, the authors note, is the observation that cohesin binding changes according to the cell's gene transcription program. Cohesin prefers DNA that lies between active transcription zones and is unceremoniously displaced from regions where RNA transcripts are being made . This suggests that elongation through a region and cohesion binding may be incompatible. These observations support previous work indicating that DNA sequences required for the replication and segregation of chromosomes must be protected from transcription to function properly. Whatever the explanation, this finding begs the question of how more complicated genomes can accommodate these two seemingly contradictory processes.Megee's group investigated whether all yeast chromosomes have these large centromere-flanking cohesin regions and whether the centromeres and DNA sequences that surround them somehow facilitate the assembly of cohesin complexes. By removing centromeres and generating cells incapable of assembling kinetochores, the researchers show that the assembly of these cohesin regions is mediated solely by the centromere–kinetochore complex.What's more, inserting centromeric DNA sequences in abnormal chromosomal locations produced new cohesin-assembling regions around these “neo” centromeres. The kinetochores' influence appears to stretch over tens of thousands of DNA bases and serves chromatid segregation in two crucial ways: by recruiting high levels of cohesin to centromeres' sides, which attaches chromatids to their bipolar spindles, and by attaching chromatids to microtubules, which provides their passage to the cell's opposite sides. The maintenance of genomic integrity, the authors conclude, likely relies on the coordination of these essential functions.