Candida albicans show an overexpression of Cdr1p and/or CaMdr1p belonging to ABC and MFS superfamilies, respectively. Hence, azole resistant isolates display reduced accumulation of therapeutic drug due to its rapid extrusion and that facilitates its survival. Considering the importance of major antifungal transporters, the focus of recent research has been to understand the structure and function of these proteins to design inhibitors/modulators to block the pump protein activity so that the drug already in use could again sensitize resistant yeast cells. The review focuses on the structure and function of ABC and MFS transporters of Candida to highlight the recent advancement in the field.It is now well-known that the enhanced expression of ATP binding cassette (ABC) and major facilitator superfamily (MFS) proteins contribute to the development of tolerance to antifungals in yeasts. For example, the azole resistant clinical isolates of the opportunistic human fungal pathogen  Candida, Aspergillus and Cryptococcus  proteins are primary active transporters that employ energy from the hydrolysis of ATP to drive the efflux of drugs, those belonging to major facilitator superfamily (MFS) are secondary active transporters that utilize the electrochemical gradient of protons across the plasma membrane to efflux substrates , CaSnq2p, and Ca4531  followed by a highly hydrophobic transmembrane domain (TMD)  Figure . The NBDDespite the overall conservation of the domain architecture of TMDs, their primary sequences are variable among similar transporters. Thus, the extent of conservation is very poor among TMSs of fungal ABC transporters as compared to NBDs which are highly conserved domains (discussed later). The promiscuity toward substrates is a characteristic feature of most ABC drug transporters and hence makes their functionality all the more complex to understand. Therefore, considerable attention is being devoted toward assessment of the structural and functional features in Cdr1p which could explain its diverse substrate specificity spectrum. Understanding the structure activity relationship (SAR) between drug transporter protein and host of xenobiotics they export is expected to improve therapeutic strategies. For this, already there have been concerted efforts to understand the basis of promiscuity of multidrug resistance transporters. Several studies have been undertaken to identify the drug binding site(s) to elucidate the molecular attributes required for substrate/transporter interactions as described below.Saccharomyces cerevisiae, a close homologous protein of Cdr1p, has offered significant information about the requirement of substrate binding sites. The study by Golin et al. . Identifying the characteristic molecular descriptors is a prerequisite for these computational modeling approaches which have been successfully used in case of human ortholog of the organic cation transporter (hOCT1). The work on Pdr5p of n et al.  concludeUnderstanding, how transport protein recognizes such diverse nature of substrate remains a challenge. In an effort to understand the molecular basis of drug recognition, binding and release, several studies have been done to elucidate the location and biophysical properties of the drug-binding sites in Cdr1p. One such study, characterized, three drug binding sites in Cdr1p, one for the binding of rhodamine 6G and azoles such as ketaconazole, miconazole, and itraconazole, second for only fluconazole and third site for iodoarylazido prazosin   replaced with an alanine  and conserved Lys901 (K901C) in the Walker A motif of C-NBD were replaced  on extracellular face and four intracellular loops (ICL1-4) on the cytosolic face of plasma membrane Figure . The strS. cerevisiae led to the identification of several point mutations that caused significant changes in drug specificity which were found to be distributed throughout the length of Pdr5p, particularly, in the extracellular, transmembrane or cytoplasmic regions of the transporter , while Cdr3p, which is not involved in drug resistance, carries out-to-in translocation (flippase activity) of phospholipids between the two monolayers of plasma membrane  proteins are another class of major drug transporters which are involved in the development of multidrug resistance in yeasts. MFS transporters, like ABC transporters, belong to a large superfamily of membrane proteins from bacteria to higher eukaryotes which include symporters, antiporters, and uniporters of various substrates  family, which effluxes drugs in exchange with one or more H+ with a substrate molecule G(×3)GP(×2)GP(×2)G]) as depicted in Figure The bacterial MFS drug/H+antiporters, which have a unique antiporter motif, also called motif “C” [G(X8)G(X3)GP(X2)GG], is necessary for the drug/H+antiporter activity GP. The conservation of a residue is calculated from the amino acid frequency distribution in the corresponding column of a MSA. However, the physicochemical conservation is not necessarily responsible for a protein's structure and function but could reflect a more general function such as membrane localization. Thus, conservation alone is not sufficient to distinguish between residues responsible for the protein function and membrane localization. Membrane proteins differ from soluble proteins because of their inter-TM hydrophilic and TM hydrophobic propensities, which have allowed the development of efficient membrane protein TM prediction methods and of membrane protein specific substitution matrices. Recent study employed a membrane environment based computational approach to predict the functionally critical residues of CaMdr1p. For this, DHA1 (antiporters) family was contrasted with sugar porter family (SP) (symporters) to identify residues selectively conserved in DHA1 family vis-à-vis the SP family. The residues with highest cumulative relative entropy (CRE) were short-listed for analysis and were predicted to impart functional specificity to the DHA1 members. The functional relevance of these high-CRE scoring residues of CaMdr1p was evaluated by employing site directed mutagenesis. However, only those positions were mutated to alanine or leucine wherein the CaMdr1p residue matched with the most frequent amino acid at a particular alignment position of DHA1members. Most of the mutant variants displayed complete drug susceptibility while few were selectively susceptible to tested drugs Figure . The enhLacY (lactose permease of Escherichia coli) transporter  family , the promiscuity with regard to their ability to transport variety of structurally unrelated compounds, of the two families of transporters is most common striking feature. This promiscuity of such proteins makes it a big challenge in dissecting their structure and function. From the recent studies, it is evident that lot of efforts are devoted in resolving the mechanisms of drug transport. It is confirmed that TMSs of these transporters harbors drug binding sites and critical amino acid residues align and make up a large drug binding pocket which can accommodate diverse compounds to export. The challenge lies in dissecting participation of important residues responsible for single or select drug transport. Unlike MFS transporetrs, several ABC drug transporters are phospholipid translocators which may reflect their normal physiological function. But understanding how phospholipids and drug are transported by these proteins is a challenge. Nonetheless, resolving such issues will pave the way in rationally designing inhibitors/modulators for making drug exporters transport incompetent so that they could chemosensitize the drug resistant cells.Rajendra Prasad: drafting the work and revising it critically for important intellectual content; and final approval of the version to be published. Manpreet K. Rawal: contributed in drafting the work.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.


Human apurinic/apyrimidinic endonuclease 1 (APE1) functions mainly in DNA repair as an enzyme removing AP sites and in redox signaling as a coactivator of various transcription factors. Based on these multifunctions of APE1 within cells, numerous studies have reported that the alteration of APE1 could be a crucial factor in development of human diseases such as cancer and neurodegeneration. In fact, the study on the combination of an individual's genetic make-up with environmental factors (gene-environment interaction) is of great importance to understand the development of diseases, especially lethal diseases including cancer. Recent reports have suggested that the human carcinogenic risk following exposure to environmental toxicants is affected by APE1 alterations in terms of gene-environment interactions. In this review, we initially outline the critical APE1 functions in the various intracellular mechanisms including DNA repair and redox regulation and its roles in human diseases. Several findings demonstrate that the change in expression and activity as well as genetic variability of APE1 caused by environmental chemical  and physical carcinogens (ultraviolet and ionizing radiation) is likely associated with various cancers. These enable us to ultimately suggest APE1 as a vital marker for the prediction of environmental carcinogenesis risk. Escherichia coli Xth and Saccharomyces cerevisiae APN2 which is APE1 endonuclease activity pyrene, a major constituent of CSC, enhanced APC-mediated accumulation of abasic DNA lesions, leading to increased neoplastic transformation of breast epithelial cells [Several studies have reported that cigarette smoke condensate (CSC) increased expression of adenomatous polyposis coli (APC) and blocked long-patch base excision repair (LP-BER) in human breast epithelial cells , 181. Inal cells . Smokingal cells  demonstrA number of epidemiological studies have evaluated the relationship among polymorphisms of APE1, smoking, and the risk of lung cancer. Several reports have suggested that APE1 genotypes were not major determinants of lung cancer susceptibility among smokers , 86, whiUltraviolet (UV) can induce DNA repair process directly or indirectly through the photoproducts generation or the ROS accumulation. Indeed, Izzotti et al.  reported In vitro findings revealed that the mammalian cells exposed to X-rays caused change in the expression and activity as well as polymorphism of APE1 [Ionizing radiation (IR) is a widely used therapy for treating various types of cancers. However, it causes damage to normal cells of living tissue vicinity to tumors, resulting in mutation, radiation sickness, cancer, and ultimately death , 184. Se of APE1 , 94–96. There is no doubt of critical roles of APE1 in maintenance of genomic stability against endogenous and exogenous stresses. APE1 possesses powerful biological capacities in various cellular processes such as DNA repair, redox regulation, cell cycle, and RNA modulation. Because of the widely known APE1 multifunction, there are many reports that deal with the importance of APE1 in human disease developments. In particular, previous cell-based, animal model, and epidemiological studies suggested that the genetic variation  of APE1 as well as the alteration of APE1 localization, expression, and activity can be possible causes of lethal disease, including cancer . AlthougSince several studies showed that APE1 malfunction enhances the risk of disease development when a person is exposed to harmful substances, we attempted to suggest APE1 as an important modulator in human disease caused by various environmental factors considering gene-environment interactions. Heavy metals such as arsenic, cadmium, and lead are widespread environmental pollutants and cause detrimental health effects including cancer, even at low doses. Although the molecular mechanisms of toxicity and carcinogenicity of these heavy metals remain poorly understood, commonly suggested mechanisms involve induction of oxidative DNA damage and the inhibition of DNA repair. It is well known that these heavy metals can change the expression and activity of APE1 and such APE1 malfunction is a vital factor related to severe human diseases. Nevertheless, as shown in


Membrane-bound organelles such as mitochondria, peroxisomes, or the endoplasmic reticulum (ER) create distinct environments to promote specific cellular tasks such as ATP production, lipid breakdown, or protein export. During recent years, it has become evident that organelles are integrated into cellular networks regulating metabolism, intracellular signaling, cellular maintenance, cell fate decision, and pathogen defence. In order to facilitate such signaling events, specialized membrane regions between apposing organelles bear distinct sets of proteins to enable tethering and exchange of metabolites and signaling molecules. Such membrane associations between the mitochondria and a specialized site of the ER, the mitochondria associated-membrane (MAM), as well as between the ER and the plasma membrane (PAM) have been partially characterized at the molecular level. However, historical and recent observations imply that other organelles like peroxisomes, lysosomes, and lipid droplets might also be involved in the formation of such apposing membrane contact sites. Alternatively, reports on so-called mitochondria derived-vesicles (MDV) suggest alternative mechanisms of organelle interaction. Moreover, maintenance of cellular homeostasis requires the precise removal of aged organelles by autophagy—a process which involves the detection of ubiquitinated organelle proteins by the autophagosome membrane, representing another site of membrane associated-signaling. This review will summarize the available data on the existence and composition of organelle contact sites and the molecular specializations each site uses in order to provide a timely overview on the potential functions of organelle interaction. In eukaryotic cells sophisticated membrane-bound organelles have evolved which enable the cell to compartmentalize specialized biochemical reactions in specific locations within the cell Figure . HistoriAs an introduction to the Frontiers research topic on “Molecular mechanisms and physiological significance of organelle interactions and cooperation” this review aims at providing a general and timely overview of the new and fascinating mechanisms which convey the cellular plasticity required to react to metabolic and environmental changes in a spatial and temporal manner. We address processes of organelle interaction with a particular focus on membrane contact sites emerging at the cross roads of organelle research and intracellular signaling. In addition, we highlight novel findings on the functional aspects of organelle interaction with a special emphasis on mitochondria and peroxisomes. We particularly focus on organelle interplay in mammals but where appropriate also refer to recent discoveries in plants and fungi.2+ dynamics between the extracellular space and the ER, which is the dominant Ca2+ storage compartment of the cell. In this respect the plasma membrane of T-tubules is enriched in voltage gated ion channels which activate juxtaposed ryanodine receptors in the PAM to elicit Ca2+ into the cytosol , which interacts with the plasma membrane Ca2+ channel Orai1 at ER/plasma membrane contact sites in order to replenish ER Ca2+ concentrations .In striated muscle cells a close apposition between peripheral ER and the plasma membrane, now well known as the T-tubule system required for excitation-contraction coupling, was reported as early as the 1950's by the pioneers of cell biological research, Keith Porter and George Palade  have been described in the ER of dendritic spines  , the PAM is also supposed to be involved in the transfer of lipids to the opposing plasma membrane. While the MAM delivers phosphatidylserine to mitochondria [see Section The Mitochondria-associated Membrane of the ER (MAM)], the PAM is involved in the transport of sterol compounds between the ER and the plasma membrane  are conserved in higher eukaryotes  , dynamin-related protein 1 (DRP1), calnexin, autophagy-related protein 14 (ATG14), the oxidoreductase Ero1α and IP3R, reveals that the MAM is a multifunctional compartment which is involved in several metabolic but also regulatory pathways of the cell. In this respect, the MAM is currently supposed to be involved in the processes of (1) phospholipid synthesis and transfer, (2) calcium signaling, (3) mitochondrial fission, (4) mitophagy, (5) ER-stress response, (6) regulation of apoptosis, and (7) inflammatory/antiviral responses  which release calcium into the local surrounding cytosol in response to IP3 signaling . In this process the ER stops protein translation and activates chaperones assisting protein folding  in delivery of phospholipids and some specific PMPs, such as Pex3.in vitro cell-free system  to phosphatidylethanolamine (PE) was artificially targeted to peroxisomes , Interplay between Peroxisomes and Mitochondria, and Lysosomal Interactions and Autophagy for details and Prinz,  for a coAs initially indicated, ER-peroxisome contacts are extensively observed in mammalian cells and likely represent functionally specialized contact sites comparable to the MAM or PAM described above. However, it remains to be determined if these numerous appositions between both organelles predominantly mirror the process of peroxisome biogenesis or if they mainly contribute to several other cellular processes including exchange of metabolites, such as precursors of ether phospholipids, polyunsaturated fatty acids and cholesterol or even regulation of viral defence (see Section Interplay between Peroxisomes and Mitochondria). Thus, their contribution to peroxisome biogenesis is just one aspect of their multiple functions and it will be challenging to unravel their actual function in different experimental models and set ups.In recent years, convincing evidence for a close connection between peroxisomes and mitochondria has been obtained . The size of the organelle is a critical factor for the efficient engulfment by the sequestering compartment, the phagophore. Organelle fission is critical for the efficient elimination of mitochondria  are specialized organelles involved in the storage of neutral lipids, mainly triacylglycerols, and sterol esters, for energy and membrane homeostasis. LDs have been found in all eukaryotic and some prokaryotic cells, since lipids are essential for life and the capacity to store lipids confer an evolutionary advantage to the organism. The concept that LDs are simple, inert lipid-storage containers has now been dismissed. Today it is widely accepted that LDs are dynamic organelles which are involved in multiple cellular processes including lipid metabolism, but also protein sequestration/degradation and pathogen replication  by delivering them to the lysosome  the pexophagy receptor is Atg30, which interacts with peroxisomal membrane proteins Pex3, Pex14, and Atg37  p62Also, for mammalian cells a two-step model for priming mitochondria for mitophagy has been proposed: RING-between-RING E3 ubiquitin ligase Parkin dependent or Parkin independent , The Peroxisome-ER Connection, Interplay between Peroxisomes and Mitochondria, Lipid Droplets, and Lysosomal Interactions and Autophagy, clearly illustrate that subcellular organelles are integrated in cooperating cellular networks. Although intimate physical contacts between organelles were described some time ago, we are just beginning to reveal the key components involved and their physiological importance. A major role of organelle interaction is clearly in metabolite exchange, but exciting new functions in organelle distribution and membrane dynamics have been discovered. Furthermore, increasing evidence points to an important function in signaling and the assembly of dynamic signaling platforms according to cellular requirements. In this respect, higher ordered complexes between more than two organelles may exist as exemplified by antiviral signaling via MAVS involving the ER, mitochondria and peroxisomes. A common principle may be the involvement of structurally similar or overlapping protein complexes for the physical tethering of different organelle membranes. Future studies will reveal if organelle interplay and cooperation is primarily mediated via those hubs, or if indirect mechanisms via the cytosol are more prevalent.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.


In this case report, the feasibility and precision of tridimensional (3D) virtual planning in one patient with craniofacial microsomia is tested using Nemoceph 3D-OS software  to predict postoperative outcomes on hard tissue and produce CAD/CAM (Computer Aided Design/Computer Aided Manufacturing) surgical splints.  The clinical protocol consists of 3D data acquisition of the craniofacial complex by cone-beam computed tomography (CBCT) and surface scanning of the plaster dental casts. The ''virtual patient'' created underwent virtual surgery and a simulation of postoperative results on hard tissues. Surgical splints were manufactured using CAD/CAM technology in order to transfer the virtual surgical plan to the operating room. Intraoperatively, both CAD/CAM and conventional surgical splints are comparable. A second set of 3D images was obtained after surgery to acquire linear measurements and compare them with measurements obtained when predicting postoperative results virtually.It was found a high similarity between both types of surgical splints with equal fitting on the dental arches. The linear measurements presented some discrepancies between the actual surgical outcomes and the predicted results from the 3D virtual simulation, but caution must be taken in the analysis of these results due to several variables. The reported case confirms the clinical feasibility of the described computer-assisted orthognathic surgical protocol. Further progress in the development of technologies for 3D image acquisition and improvements on software programs to simulate postoperative changes on soft tissue are required. Comprehensive visualization and records of the craniofacial complex are important goals in orthodontic imaging which have been conventionally achieved by means of plaster dental casts, photographs and radiographs. However, cone-beam computed tomography (CBCT) has gained considerable acclaim worldwide as a viable tridimensional 3D) imaging modality.D imagingThe first computer-based cephalometric systems appeared in the late 1970s, and since then several two-dimensional (2D) computer-assisted imaging systems were created, allowing for a combination of photographs, tracings, and radiographs. These computer-assisted programs permit rapid measurements and treatment planning, but the validity and reliability of these systems are limited by their 2D nature when dealing with a 3D structure.In a reconstruction of a CBCT scan, the skin is untextured and the dental structures may contain streak artifacts caused by restorations or orthodontic fixed appliances. Therefore, it is necessary to superimpose a textured facial soft tissue surface  and upgrade the dental images , thereby improving the visualization of the interocclusal relationship with precise dental morphology of the surfaces and cusps.,In orthognathic surgery, the repositioning of skeletal constructs is conventionally guided by the surgical splint technique obtained through time-consuming and imprecise model surgery.,,In the traditional method, in order to achieve a precise diagnosis of the dentoskeletal deformity and create a treatment plan intraoperatively reproducible, it is necessary to collect data from different sources, such as photographs, cephalograms, dental casts, physical examination along with face bow record and its transfer to semi-adjustable articulators, and measurement of plaster casts movement, according to the surgical simulation.,,As a result of developments in 3D imaging technology, surgeons are provided with extra information that could not be obtained from lateral cephalogram alone, thus improving the quality of preoperative planning.In this case report, the feasibility and precision of 3D virtual planning in one patient with craniofacial microsomia is tested using Nemoceph 3D-OS software  to predict postoperative outcomes on hard tissue and produce CAD/CAM surgical splints.A 19-year-old female presented with left craniofacial microsomia Pruzansky IIA associated with diminished left jugal soft tissues, a unilateral cleft lip and macrostomia, maxillary and mandibular retrusion and vertical maxillary excess, requiring combined orthodontic-orthognathic surgery treatment. Extraoral and intraoral initial status, previous to orthodontic treatment, can be seen in Preoperative orthodontic treatment was performed with a multibracket appliance  and extraction of mandibular first premolars for correction of dental compensations, enabling the occlusal coordination of both dental arches . SurgicaTM device, version 17-19  with a FOV set to a height of 17 cm and a diameter of 23 cm. The radiological parameters used were 120 kV of tube voltage, 5 mA of tube current and exposure of 37.10 mAs, with a voxel size of 0.3 x 0.3 x 0.3 mm. The images obtained using CBCT were stored in DICOM format and sent to Nemotec CAD/CAM Centre  together with patient's dental plaster casts and digital facial photographs . Upper and lower dental plaster casts were scanned using a surface laser scanner and incorporated in the 3D image by means of a semi-automatic procedure (Two CBCT scans were obtained: one preoperative (two months prior to orthognathic surgery) and one postoperative (one month after surgery), using the i-CATrocedure . SegmentAt first, the whole skull data set was manually aligned to natural head position (NHP), using patient's photographs  which were generated in the computer and fabricated by a milling machine milling the surgical splints on polymethyl methacrylate (PMMA) .Bimaxillary surgery was performed under general anesthesia, with Le Fort I and BSSO osteotomies. Intraoperative registration of the correct condylar position within the glenoid fossa was performed using the initial splint , and the reposition of the osteotomized maxilla and mandible was guided by the CAD/CAM surgical splints using fixation plates and screws . MaxilloThe CAD/CAM splints were clinically evaluated by an experienced clinician regarding its adaptation, passivity and occlusal scheme. There was no need for adjustments, as a perfect fit was obtained during splints try-in performed in the patient's mouth before surgery.Conventional intermediate and final acrylic splints try-ins were also performed intraoperatively, after reposition and fixation of the jaws with CAD/CAM splints, and an equal fitting was verified with both types of splints, demonstrating that both splints were able to transfer the same surgical plan to the patient at the time of surgery.Measurements were performed in the 3D simulation using Nemoceph 3D-OS software for assessment of quantitative changes between the preoperative and the postoperative simulated positions of selected dental and bone landmarks A. A full,Modern 3D virtual planning for orthognathic surgery has critical advantages compared to conventional treatment planning. Simulating the operation on plaster dental casts is difficult, especially in cases of complicated two-jaw surgery, as it requires many laboratory-based steps that are time-consuming and may lead to potential errors.,,-,,,,,Surgical splints can be manufactured with rapid prototyping techniques in order to transfer the virtual plan to the operating room. The accuracy of rapid prototyping procedures for orthognathic surgery is now beyond all question, and the reliability of these CAD/CAM-generated splints has already been validated. Treatment outcome evaluation is possible through techniques of voxel-based rigid registration and superimposition on a 3D reference system.,,,Using this methodology, treatment plans can be stored in the computer where patient's records are instantly available, and the dental casts can be discarded after digitalization, saving the space normally taken up by physical elements used in conventional planning.,,,,Regarding the limitations of this technique, the most problematic inconvenience is probably the fact that although there are advanced 3D imaging techniques capable of individually displaying the facial skeleton, dentition, and soft tissues, there is currently no single imaging technique that can accurately capture the complete triad with optimal quality for orthognathic surgery planning.,,,Considering the postsurgical prediction results in this clinical case, the linear measurements shown in In order to enable this paradigm shift in routine planning of orthognathic surgery, both image acquisition systems and 3D virtual planning software must become user-friendly, easily accessible and available at a relatively low cost.The reported case confirms the clinical feasibility of a computer-assisted orthognathic surgical protocol incorporating virtual planning and its transfer to the operating room using CAD/CAM fabricated surgical splints. Further progress is required in the development of technologies for 3D image acquisition and improvements on software programs to simulate postoperative changes on soft tissues.


These additional signalling roles of desmoglein 3 may not be associated to its adhesive function in desmosomes but rather function outside of the junctions, acting as a key regulator in the control of actin based cellular processes. This review will discuss recent advances which support the role of desmoglein 3 in cancer progression.Desmoglein 3 is one of seven desmosomal cadherins that mediate cell-cell adhesion in desmosomes. Desmosomes are the intercellular junctional complexes that anchor the intermediate filaments of adjacent cells and confer strong cell adhesion thus are essential in the maintenance of tissue architecture and structural integrity. Like adherens junctions, desmosomes function as tumour suppressors and are down regulated in the process of epithelial-mesenchymal transition and in tumour cell invasion and metastasis. However, recently several studies have shown that various desmosomal components, including desmoglein 3, are up-regulated in cancer with increased levels of expression correlating with the clinical stage of malignancy, implicating their potentiality to serve as a diagnostic and prognostic marker. Furthermore,  N-terminal head domain of the Plakin family protein, desmoplakin (Dp), which links the stress-bearing intermediate filaments of the cytoskeleton to desmosome via its C-terminal domain, forming the inner dense plaque [Desmosomal cadherins constitute the adhesive interface at the core domain of desmosome junctions (DSMs), which in principle function to anchor the intermediate filaments of neighbouring cells to sites of adhesion to form the desmosome-intermediate filament complex essential in the maintenance of tissue architecture and integrity . Since ce plaque ,5. Anothe plaque ,7.in vitro studies based on overexpression of human Dsg3 in cancer cell lines have shed light on its signalling role that regulates a variety of cellular processes including cell cohesion and migratory behaviour. This review will focus on recent advances with regard to the role of Dsg3 in cancer progression and metastasis.The tumour suppressor function of DSMs is believed to be achieved through mediating strong cell-cell adhesion and sequestering desmosomal components, some of which may have oncogenic potential, to enforce adhesion and to prevent epithelial to mesenchymal transition (EMT) and tumour development ,9. ParadIntercellular junctions are conventionally accepted to function as tumour suppressors by restricting cell growth through contact-mediated inhibition of cell proliferation and locomotion ,21. DisrThe mechanisms by which DSMs suppress tumour formation are as diverse as the molecules that attribute to their function. Many studies suggest that this may be achieved by regulating the availability of desmosomal components with oncogenic potential, such as Pg and Pkps, to suppress tumour development ,9. PlakoThe newly characterised desmosomal component Perp has emerged as a crucial mediator in tumour suppression through its function on DSM formation as well as its ability to induce apoptosis . This isEvidence of the Dsg3 down-regulation in the context of cancer development and progression is comparatively less. However, a reduction of Dsg3 expression has been observed in moderately or poorly differentiated oral SqCC compared with normal oral epithelia  and immoOur understanding of Dsg3 function is largely based on studies in Pemphigus Vulgaris (PV), a rare autoimmune blistering disorder. Characterised by the loss of keratinocyte cohesion in the oral mucosa and epidermis, PV is caused by cell surface binding of auto-antibodies (PV-IgGs) that target mainly the extracellular domain of Dsg3 and trigger a range of cellular and molecular events. Such studies have uncovered the fundamental role of Dsg3 in cell-cell adhesion as well as in signal transduction. The addition of PV-IgGs to keratinocyte culture has been shown to promote rapid re-organisation of cortical actin filaments ,47 and tetc. [in vitro and in vivo [Despite the traditional view of DSMs as tumour suppressors and the contribution of Dsg3 in desmosomal adhesive function, recent studies have discovered that Dsg3 is upregulated in SqCC of the head and neck, lung, skin and oesophagus etc. ,17,18,19etc. ,16,55, setc. ,57,58. T in vivo ,43,59.Cell migration is a highly integrated multistep process initiated by actin based membrane morphological changes, specifically membrane protrusions . The driThe special regulation of actin based processes requires orchestration in order to achieve a global cellular response . Ezrin, The Src family of non-receptor tyrosine kinases, of which Src, Yes and Fyn are ubiquitously expressed, is a group of enzymes that propagate a diverse spectrum of receptor-induced biological activities through their ability to engage with different classes of cellular receptors and numerous cellular targets . ActivatAlthough it has been demonstrated that Dsg3 is capable of regulating Src activity it remains unclear how this could be achieved. Emerging evidence suggests that this regulatory pathway may involve caveolin-1, a major constituent of caveolae. Caveolae are a special type of lipid raft of the plasma membrane with a flask-like structure which functions as a regulator in endocytosis and exocytotic vesicle trafficking, cell adhesion and motility ,104. It et al. suggests that Dsg3 negatively regulates Wnt/β-catenin signalling in a Pg-dependent manor, most likely by sequestering Pg preventing its nuclear translocation and suppression of LEF/TCF transcriptional activity [et al. showed that Dsg3 silencing in head and neck SqCC increased the translocation of Pg to the nucleus where it interacts with and inhibits TCF/LEF transcription activity, to suppress tumour growth and invasion [in vitro study based on cancer cell lines shows that Dsg3 overexpression increases the tyrosine phosphorylation and activity of β-catenin as well as a reduction of E-cadherin [In attempt to elucidate the molecular mechanism of Dsg3-dependent tumour cell migration a recent study by Chen activity . In suppactivity ,39. LEF/activity ,113,114.invasion . Correspinvasion . Thus, tinvasion . In linecadherin ,116. Botcadherin .N-terminal residues inhibits DNA binding of cJun homodimers [Activator protein-1 (AP-1) is a dimeric transcription factor with an expansive transcriptional repertoire propagated by its diverse homo- and hetero-dimeric compositional array of Jun, Atf, Fos and Maf bZIP protein families. The activity of AP-1 is regulated at multiple levels; transcriptionally the abundance of AP-1 components can be influenced by various extracellular signals transduced through MAPK cascade. For example, the activation of JNK in turn activates ternary complex factors (TCFs) to induce the cFos expression  whereas modimers , while tmodimers .AP-1 is known to regulate a vast array of cellular processes including development, proliferation, apoptosis, immune and stress responses ,124,125.−/− and Dsg3+/− keratinocytes was examined in immune-compromised scid mice. A reduction in tumour formation and growth was observed in mice injected with Dsg3−/− keratinocytes compared with control group injected with Dsg3+/− keratinocytes [Dsg3/−− mice alongside their wild type counterpart. This approach revealed no significant difference in tumour latency, size and multiplicity between the two cohorts [Although Dsg3 is shown to play a positive role in oncogenesis evidence suggests that Dsg3 may not function as a main driver in cancer formation but rather as a factor that promotes cancer progression. The miss-expression of Dsg3 in the epidermis of transgenic mice driven by the K1 promoter provokes hyper-proliferation, abnormal differentiation and parakeratosis of the epidermis . While tinocytes . In the  cohorts . Collect cohorts ,55,142.With more than 90% of cancer related deaths attributed to metastasis rather than the primary tumour , the impWith respect to head and neck SqCC regional lymph node metastasis is common and represents the strongest prognostic factor pertinent to disease staging and treatment strategy selection ,151,152.In addition to head and neck SqCC, Dsg3 has also been shown to be of value in the diagnosis of pulmonary SqCC. Treatment selection for patients diagnosed with lung cancer is predominantly guided by separating lung carcinomas into small cell and non-small cell lung cancers  and the stage of diseases ,171,172.Although Dsg3 has been proposed as a potential therapeutic target in oral SqCC currently limited studies has been reported in the literature. Nevertheless, it was demonstrated by a group of researchers that the RNAi mediated Dsg3 silencing in head and neck SqCC lines reduces tumour growth and metastasis in xenograft studies in BALB/C nude mice ,59 indicAlthough a large body of study regarding Dsg3/PVA has been documented in the literature in pemphigus research highlighting its critical role in cell cohesion, recent advances in the last decade have discovered Dsg3 as a potential oncogene and a positive biomarker of SqCC. There is no doubt that Dsg3 functions as a cell-cell adhesion receptor in DSMs. However, accumulating data suggest that Dsg3 also acts as an important surface regulator for various signal pathways that are involved in actin based cell adhesion, morphological change and locomotion. Like Src and some other signalling molecules, Dsg3 seems to act as a pleiotropic gene having influence on both cell-cell adhesion and cell locomotion depending on the context in study. In normal epithelial cells Dsg3 may function to facilitate cell-cell adhesion but in transformed cells where DSM function is impaired, the overexpression of Dsg3 may favour its oncogenic signalling activity that causes pronounced membrane protrusions and accelerated cell locomotion. However, there are still many questions unanswered. For example, it remains unclear the precise function of Dsg3 in tumour cell biology and whether it acts as a driver in tumour formation? What mechanism regulates its gene expression in normal and cancer cells? Are there any other environmental factors/cues in addition to calcium? Does the overexpression of Dsg3 in cancer involve post-translational regulation, like E-cadherin? As for the Dsg3 signalling, it remains unclear what triggers its activation? Does Dsg3 signalling occur on the cell surface and also in the cytoplasm and if it is on the surface, is it triggered by homophilic ligation, such as trans- and/or cis-binding? It might well be that certain transitional structural conformation of Dsg3 or protein dimerisation on the surface is required for its signalling action and when DSMs are established this structural conformation has undergone a different rearrangement. While this review outlines the potential participation of Dsg3 in cancer cell migration and invasion in a non-adhesive fashion, this by no means negates its role of cell-cell adhesion in collective cell migration and invasion which is an important aspect of the metastatic process ,177. Nevin vivo investigation in transgenic model with Dsg3 overexpression will particularly benefit by providing new insights into how exactly this gene is involved in cancer development and progression.It is well established that Dsg3 is targeted by pemphigus autoantibodies and plays a crucial role in pemphigus pathogenesis. Recent studies have shed light that Dsg3 also acts as a key regulator in various intracellular signal pathways that are likely hijacked in cancer and promote cancer cell invasion and dissemination. However, our understanding on the functions of this gene in tumour cell biology remains limited. Further study of Dsg3 in cancer cells and their microenvironment is required to advance our knowledge. Furthermore,


This review provides an overview of the role played by UCP1 and UCP3 in mitochondrial uncoupling/functionality as well as EM and suggests that they are a potential therapeutic target for treating obesity and its related diseases such as type II diabetes mellitus.Understanding the metabolic factors that contribute to energy metabolism (EM) is critical for the development of new treatments for obesity and related diseases. Mitochondrial oxidative phosphorylation is not perfectly coupled to ATP synthesis, and the process of proton-leak plays a crucial role. Proton-leak accounts for a significant part of the resting metabolic rate (RMR) and therefore enhancement of this process represents a potential target for obesity treatment. Since their discovery, uncoupling proteins have stimulated great interest due to their involvement in mitochondrial-inducible proton-leak. Despite the widely accepted uncoupling/thermogenic effect of uncoupling protein one (UCP Mitochondria are the major regulators of cellular energy metabolism (EM). Alterations of mitochondrial functionality have been linked to the pathogenesis of some metabolic disorders, including obesity and type II diabetes mellitus (T2DM).2, obtained from oxidizable molecules  supply electrons to the electron transport chain (ETC) and result in a final reduction of molecular oxygen to water. Electron transfer through the ETC controls pumping of protons (H+) from the matrix to the intermembrane space, thus creating a proton-motive force (Δp), whose energy is used by ATP synthase for the phosphorylation of ADP.The principal function of mitochondria is ATP production. Reduced cofactors, such as NADH and FADHp dissipates as heat by the re-entry of H+ into the matrix, through pathways independent of ATP synthase (proton-leak). Proton-leak is the sum of two processes: basal- and inducible proton-leak   and UCP3 due to their expression in brown adipose tissue (BAT) and skeletal muscle (SkM), respectively, which significantly contributes to EM.The present review discusses the relevance of UCPs on influencing EM. In particular, it focuses on uncoupling protein one  are thermogenic-competent  conditions, whereas beige adipocytes only express these genes in response to activators, such as β-adrenergic and peroxisome proliferator-activated receptor-γ agonists  mitochondria number and size, (ii) UCP1 gene transcription and translation, and (iii) UCP1 thermogenic activity through activation of lipolysis and release of acute regulators of UCP1, such as free fatty acids.Cold and overfeeding are physiological stimuli that influence BAT thermogenesis through the enhancement of sympathetic overflow to BAT  failed to show an enhanced obesity predisposition compared to their wild-type counterparts  to maintain body temperature  from the circulation /computed tomography (CT)] together with histological methods has unequivocally identified the presence of UCP1 are associated with fat metabolism, obesity, and diabetes. Among the UCP1 polymorphisms, the A3826G SNP in the promoter region has been associated with obesity, weight gain, and resistance to weight loss  higher expression of UCP3 is not always associated with increased mitochondrial uncoupling  seems to be activated by specific cofactors, with FFA and reactive oxygen species (ROS) playing crucial and interrelated roles , out of the matrix. This mechanism would reduce or eliminate LOOH from the inner leaflet of the MIM, which could otherwise trigger a cascade of oxidative damage to mitochondrial DNA and enzymes as well as other critical mitochondrial matrix-localized components  suggest a protective role for this protein in obesity and T2DM  UCP3 transgenic mice are less efficient in metabolism than wild-type controls  has been observed in obesity-resistant mice compared to obesity-prone mice  section]. Therefore, the occurrence of compensatory thermogenic mechanisms in UCP−/−3 mice could have masked the possible role of the protein in EM.More experimental evidence supports a role of UCP3 also shows a protective role in T2DM. However, when studies were performed on transgenic mice, a clear involvement of the protein was evident when UCP3 overexpressing animals were used as a model , insulin sensitivity has been reported to be unaffected   could be a promising therapeutic strategy to combat obesity and its co-morbidities (such as T2DM). The uncoupling proteins have several hypothesized functions including thermogenesis in certain tissues, protection from ROS, mediation of fatty acids oxidation and export of fatty acids, which are all related to the above pathologies. Hence, an understanding of the mitochondrial processes that lead to uncoupling and, in particular, the elucidation of the exact role played by UCPs at the mitochondrial level and in EM may provide an attractive therapeutic target for diseases rooted in metabolic imbalance.1, and by expanding the tissue, through drugs or other methods, provide a promising approach for enhancing energy expenditure and combating obesity comorbidities. Recent evidence, indicating that brown and beige adipocyte can be recruited by different stimuli, raises the possibility that they may represent separate and distinct targets for therapeutic intervention. Although the roles of UCP3 are not completely clear, current data in human subjects  suggest a possible involvement of this protein in EM as well as in counteracting obesity, insulin resistance, and T2DM (Figure 1 and UCP3 represent promising therapeutic targets for treating pathologies that result from energy unbalance.In this context, the recruitment of thermogenic brown and/or beige adipocytes through activation of UCPThe 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.


Plants form belowground associations with mycorrhizal fungi in one of the most common symbioses on Earth. However, few large-scale generalizations exist for the structure and function of mycorrhizal symbioses, as the nature of this relationship varies from mutualistic to parasitic and is largely context-dependent. We announce the public release of MycoDB, a database of 4,010 studies (from 438 unique publications) to aid in multi-factor meta-analyses elucidating the ecological and evolutionary context in which mycorrhizal fungi alter plant productivity. Over 10 years with nearly 80 collaborators, we compiled data on the response of plant biomass to mycorrhizal fungal inoculation, including meta-analysis metrics and 24 additional explanatory variables that describe the biotic and abiotic context of each study. We also include phylogenetic trees for all plants and fungi in the database. To our knowledge, MycoDB is the largest ecological meta-analysis database. We aim to share these data to highlight significant gaps in mycorrhizal research and encourage synthesis to explore the ecological and evolutionary generalities that govern mycorrhizal functioning in ecosystems. As a result, ecosystem functions and the vital services humans derive from them  are fundamentally dependent on the interactions plants have with symbionts. Although symbioses are common, our knowledge of their impact on ecosystem functions and services is relatively incomplete. Broad generalizations about the relationships between plants and their symbionts are limited due to the context-dependent nature of such symbioses, which exist along a continuum of possible outcomes, from mutualistic to parasitic. Examining the results of many experiments through meta-analysis allows for larger-scale generalizations than individual experiments can provide independently and can lead to synthesis-generated evidence2. Furthermore, including phylogenetic information in meta-analyses can account for correlated evolutionary relationships among taxa used in multiple studies. Understanding ecological outcomes of symbioses, and the environmental and evolutionary context contributing to such outcomes, is crucial to maintaining and restoring the ecosystem functions and services upon which humans depend.Plant performance is largely a function of the plant-symbiotic microbiome4. The host plant and associated fungi form a trading partnership where the fungi increase the effective absorptive capabilities of the plant, delivering nutrients and water in exchange for plant-derived photosynthates5. Since most plants associate with mycorrhizal fungi, the outcome of this symbiosis can influence ecosystem structure, function, and services mediated by plant productivity. Several empirical studies have individually demonstrated how host plant traits and identities, fungal partners, soil biotic and abiotic conditions, and experimental conditions can alter the structure and function of mycorrhizal symbioses6–9. The important role of mycorrhizal fungi in global change dynamics such as N deposition, climate change, and invasive species has also been documented10–12 as well as the key role that mycorrhizal fungi play in the restoration and conservation management of ecosystems13–15. Understanding the generality of how environmental context impacts the relationship of plants with their mycorrhizal symbionts should also affect how we manage terrestrial ecosystems.Mycorrhizal fungi form an ancient symbiosis with most plants on Earth16–18, facilitating computational analytic approaches to studying global patterns of mycorrhizal symbioses. Large datasets with multiple moderators are vital to such approaches because ecological meta-analyses based on small datasets can be vulnerable to spurious interpretations resulting from unbalanced data distributions, correlated moderators, and unavailable information regarding potentially important predictors. For example, a meta-analysis of 51 studies19 suggested the absence of synergy between mycorrhizal fungi and nitrogen-fixing bacteria likely resulted from an overrepresentation of annual and agricultural species in the meta-analysis database; by contrast, separate tests of late successional legumes demonstrated strong synergism20. Another meta-analysis21 suggested that the paradoxical result of declining plant growth response to mycorrhizal inoculation with nitrogen but not phosphorus fertilization was due to the overrepresentation of studies in the dataset with high soil phosphorus and the potential correlation among moderators. The problem of spurious interpretations within ecological meta-analyses can be reduced by simultaneous testing of multiple predictors, which is made possible by larger databases.Statistical methods to simultaneously examine multiple ecological and evolutionary factors in a meta-analysis framework have been recently developedHere we present MycoDB, a large database of mycorrhizal inoculation experiments, linked with plant and fungal phylogenies (Data Citation 1), to facilitate tests on the ecological and evolutionary contexts in which the addition of mycorrhizal fungi is beneficial or parasitic to plant hosts. MycoDB focuses on studies of two dominant types of mycorrhizal fungi, ectomycorrhizal (EM) fungi and arbuscular mycorrhizal (AM) fungi, because they predominate among published studies on mycorrhizal symbioses. MycoDB contains data on plant productivity response to mycorrhizal fungi from 4,010 studies (from 438 unique publications) and is organized in a hierarchical fashion such that a single publication can contain multiple discrete experiments and a single experiment can contain multiple studies. The ecological and evolutionary context of studies can be explored with 24 additional explanatory variables . From this initial list, 134 publications were selected, in random order, as having met our inclusion criteria for meta-analysis such as reporting plant biomass response, use of a mycorrhizal addition treatment, and inclusion of a non-inoculated control (see ‘Criteria for inclusion’ below). More publications from the initial list of 1852 publications likely met our criteria, but were excluded from Phase I of database construction because of time constraints. Data from 49 additional publications on EM fungi were added from a previous meta-analysis22 to reduce dominance of the data by studies on AM symbioses. This process resulted in a total of 183 publications summarized in MycoDB during Phase I. In 2010, as part of an NCEAS  Distributed Graduate Seminar conducted across nine institutions, we began Phase II of the data collection to dramatically increase the size of MycoDB with several targeted literature searches. On September 21, 2010, we conducted searches of the ISI Web of Science database using the following search terms: (1) (mycorrhiz* or ectomyc* or endomyc* or arbuscul* or vesicular*) and inocul* resulting in 4,013 papers; (2) search terms from (1) AND restoration or rehabilitation or reclamation or revegetation or reforestation resulting in 305 papers; (3) search terms from (1) AND local adaptation or strain or isolate or genotype or ecotype or geograph* resulting in 627 papers; (4) search terms from (1) AND tissue P or tissue N or shoot P or shoot N or leaf P or leaf N resulting in 793 papers; (5) search terms from (1) AND Gigaspor* or Acaulospor* or Scutellospora or Archaeospora resulting in 387 papers. Searches 2–5 were designed to enrich the database in studies relevant to restoration ecology, local adaptation, influences of nutrients, and AM fungi besides Glomus, because these topics were identified either as being of interest for planned focused meta-analyses  or as under-represented in the Phase I search results . The results from all five searches were collated, duplicates  were removed, and papers were selected that appeared in at least one of the four focused searches (2–5), resulting in a list of 1,768 publications. Again, from this larger list, 255 publications were selected, in random order, as having met our inclusion criteria for meta-analysis such as reporting plant biomass response, use of a mycorrhizal addition treatment, and inclusion of a non-inoculated control (see below ‘Criteria for inclusion’), and their data were added to MycoDB. After Phase II, MycoDB contained data from a total of 4,010 studies from 438 publications. Phase III of the creation of MycoDB consisted of extensive data validation and the creation of phylogenetic trees for all plant species and fungal genera in the database.MycoDB (Data Citation 1) contains data from three main phases of data collection and validation. Phase I occurred in 2005, when we identified 1852 publications by conducting an initial literature search of the ISI Web of Science database using the key words 21. Different subsets of these data have been used to explore local adaptation among plants, mycorrhizal fungi, and soils  as well as how partner identity, colonization levels, and P fertilization impact plant host response to EM associations22.A subset of MycoDB was used to study how edaphic properties, plant functional groups, and microbial community complexity determine the outcome of mycorrhizal symbioses23. Data on additional explanatory variables  were also extracted from the publication text when available or looked up using supplementary peer-reviewed resources. Both lab studies and field studies are included in MycoDB and coded separately using the variable LOCATION  to a non-inoculated control. In other words, studies must compare plant response for some addition of mycorrhizal fungi to no addition. The method of inoculation varies among studies in MycoDB and can include the addition of spores, roots, mycelia, pot culture, field soil, or any combination thereof. Studies that apply mycorrhizal fungi to all treatments, eliminate fungal presence , or otherwise manipulate ecological factors to promote or suppress fungi were not included. We included studies with unsterilized background soil, many of which likely contained propagules of mycorrhizal fungi in all treatments, though this could not be confirmed because fungal colonization data was not consistently reported. If an experiment contained the manipulation of a factor in addition to mycorrhizal fungi , the results are included in MycoDB as separate studies within the same experiment. All studies report mean plant biomass data as the response variable. Studies could report shoot biomass, total biomass, or root biomass and shoot biomass. Studies must report means, but were still included if measures of dispersion  were not given as was the case in 91% of studies. If sample size was not given, the associated parameter ‘n’ was coded as 1 for both inoculated treatments and non-inoculated controls, reducing the weight of the study relative to what it would be if the sample size was known. Data presented in tables were extracted directly, but data presented in figures were extracted using Engauge Digitizer software version 4.126. For plant phylogeny, we derived phylogenetic topology from existing ‘supertrees’ and assigned well-supported divergence times to all possible internal bifurcations (evolutionary divergence event) using TimeTree27 as a source of published divergence times. The remaining unknown branch lengths were rooted with known divergence dates28 and arbitrarily set and scaled to yield an ultrametric tree wherein all extant species were lined up at the present date. In cases where taxonomic nomenclature has changed since the creation of the original ‘supertrees’ or publication of papers used in the database, names were changed manually to reflect current consensus taxonomy. Pairwise shared branch-lengths were then used to calculate a variance-covariance matrix, which can be used in mixed multifactor meta-analyses.We constructed plant and fungal phylogenetic trees for all the species in MycoDB using a composite phylogeny approach, which combines taxonomic and phylogenetic information into a single tree29; however, because of ambiguity in species identification of AM fungi, we only included fungal taxonomic identification to the genus level. Even so, some taxa formerly named Glomus could not be placed definitively within current genera and were therefore left as Glomus. In the case of the AM fungal phylogenetic branch, the composite tree topologies between different genera of this clade were informed by taxonomic position of the type species of each genus (when possible) in relationship with the taxonomic position of the other type species of another genus29–31. For EM fungi, the position of each species in the phylogenetic tree follows the online version of Index Fungorum (www.indexfungorum.org) and recent taxonomic literature. The phylogenetic framework and tree topology were based on the 2007 AFTOL classification of Fungi32 and other recent efforts in fungal systematics34.For the fungal composite phylogeny, we manually reconstructed the evolutionary relationships among different genera based on known or commonly accepted taxonomy using information from previously published reports. Fungal taxonomy, particularly of AM fungi, has undergone major revisions during the duration of the compilation of MycoDB. We traced the evolution of fungal taxa into current consensus systematics35 (version 3.0.2), the ape package in R36, Phylocom37, and Phylomatic37. The files contain the fungal and plant composite phylogenies in the Newick tree format. The FungalTree_version1.txt file (Data Citation 1) represents the evolutionary relationships among different fungal genera that exist in the MycoDB database. Similarly, the PlantTree_version1.txt file (Data Citation 1) represents the evolutionary relationships between different plant species that exist in this database, with each node of the plant’s composite tree labeled with corresponding higher taxonomic classification.Construction and manipulation of composite phylogenies was conducted using R Statistical SoftwarePinus pinaster (maritime pine) inoculated with species from the EM fungal genus Pisolithus (106 studies). The two inlay graphs represent the most common plant species in MycoDB, separated by mycorrhizae type (AM vs EM). Lines to plant species indicate the number of fungal genera in association with each plant species. For example, the most common plant species in MycoDB are Zea mays  and Eucalyptus globulus , in association with AM fungi and EM fungi, respectively. Pisolithus fungi. For AM fungi, hotspots occur within the Poaceae, Solanaceae, and Fabaceae grown in association with Rhizoglomus and Funneliformis fungi. As these plant families are important to forestry and agriculture, their prevalence in the literature makes sense, but the tropics and thus a large portion of plant and fungal biodiversity are underrepresented. Data in MycoDB are organized in a hierarchical manner as a single publication often contained data from multiple discrete experiments and studies  on multiple plant hosts. As such, the 438 publications in MycoDB contain data for 4,010 studies (Data Citation 1). A study is defined as a comparison of average plant performance between plants that were inoculated with mycorrhizal fungi  and plants that were not inoculated. 38, the majority of which likely associate with mycorrhizal fungi. Moreover, as might be expected, the plant taxa represented are heavily biased toward species important for agriculture and forestry . Similarly, the fungal taxa that are best represented in the database are taxa that have been commercially marketed, such as the ectomycorrhizal fungus Pisolithus tinctorius39. Given this uneven representation of plant and fungal species and potential correlations among closely related plant and fungal species, it is important to analyze these data using phylogenetic mixed models even when testing environmental moderators of plant responsiveness to mycorrhizal fungal inoculation.Although this database represents the efforts of over 80 people distributed over 10 years, these data still only represent a fraction of the total available data on plant response to mycorrhizal fungi. The number of papers published each year that fit our search criteria has grown exponentially in the time since our initial search. The 351 plant species in our database represent a small proportion of the 450,000 total plant species on Earth18. Similarly, multiple estimates may represent contrasts of different treatments that are compared against a common control condition, leading to statistical dependencies in the estimates due to reuse of information from the control condition40. Hence, identification of estimates that share a common control condition is of crucial importance  encountered in meta-analyses. In particular, a difficulty in many ecological meta-analyses is the lack of independence of the estimates. Multiple estimates (‘studies’) extracted from the same publication may be more similar to each other than those arising from different publications due to similarities in experimental methods or context within the same publication. Multilevel meta-analytic models (with estimates nested within publications) can be used to account for such correlated data structuresAs the largest database concerning this important symbiosis, MycoDB may prove particularly useful for the development of meta-analysis educational curriculum or statistics tutorials using ecological data. In a classroom setting, for example, the database could be used in demonstrations of single predictor meta-analyses, which could then be followed up with comparison of multiple moderator meta-analyses to demonstrate the consequences of correlated predictors. Subsets of the data could support investigation of the advantages of larger datasets in overcoming problems of correlated predictors, thereby promoting exploration of context-dependency in future meta-analyses.The database file in csv format, titled ‘MycoDB_version1.csv’ , was uploaded to the Dryad Digital Repository (Data Citation 1). Detailed meta-data for each column is located in The phylogenetic tree of mycorrhizal fungal genera present in Data record 1, in txt format and titled ‘FungalTree_version1.txt’ , was uploaded to the Dryad Digital Repository (Data Citation 1). The file contains the fungal genera composite phylogeny in the Newick tree format.The phylogenetic tree of plant hosts present in Data record 1, in txt format and titled ‘PlantTree_version1.txt’ , was uploaded to the Dryad Digital Repository (Data Citation 1). The file contains the plant composite phylogeny in the Newick tree format.24. This approach also allowed data collection to be conducted simultaneously and remotely by multiple users. After front-end data entry by users, database administrators conducted back-end database content management to validate data integrity by examining distributions and outliers as well as iteratively hand-checking random subsets of papers for accuracy. We used the United States Department of Agriculture PLANTS Database44 and The Plant List version 1.145 to verify and update scientific names and life histories for each species included in MycoDB. Database administrators hand checked outliers and returned to original papers when data were missing, as well as added moderator variables and edited moderator levels to facilitate specific meta-analyses. Finally, for the local adaptation study subset of MycoDB, all entries were compared with the original paper and corrected when necessary. The data validation methods used to create MycoDB satisfy all data-related compliance criteria designed to promote methodological quality in ecological meta-analyses46.We devised several layers of methods to ensure the quality of the data in MycoDB. First, random sampling of publications that resulted from our initial searches was conducted to reduce bias in which data were included in the database. Second, on the front end, data collection was conducted using a web-based custom data entry system with organized fields and drop down menus to reduce data entry errorhttp://dx.doi.org/10.5061/dryad.723m1 and publicly available under the CC0 public domain dedication, given proper scholarly citation of the version used and this data descriptor. We recommend that, prior to publication, users validate data subsets against original publications.MycoDB is deposited in the Dryad Digital Repository at How to cite this article: Chaudhary, V. B. et al. MycoDB, a global database of plant response to mycorrhizal fungi. Sci. Data 3:160028 doi: 10.1038/sdata.2016.28 (2016).


Nonalcoholic fatty liver disease (NAFLD) is a serious health problem in developed countries. We documented the effects of feeding with a NAFLD-inducing, methionine- and choline-deficient (MCD) diet, for 1–4 weeks on rat liver oxidative stress, with respect to a control diet. Glycogen, neutral lipids, ROS, peroxidated proteins, and SOD2 were investigated using histochemical procedures; ATP, GSH, and TBARS concentrations were investigated by biochemical dosages, and SOD2 expression was investigated by Western Blotting. In the 4-week-diet period, glycogen stores decreased whereas lipid droplets, ROS, and peroxidated proteins expression  increased. SOD2 immunostaining decreased in poorly steatotic hepatocytes but increased in the thin cytoplasm of macrosteatotic cells; a trend towards a quantitative decrease of SOD expression in homogenates occurred after 3 weeks. ATP and GSH values were significantly lower for rats fed with the MCD diet with respect to the controls. An increase of TBARS in the last period of the diet is in keeping with the high ROS production and low antioxidant defense; these TBARS may promote protein peroxidation around lipid droplets. Since these proteins play key roles in lipid mobilization, storage, and metabolism, this last information appears significant, as it points towards a previously misconsidered target of NAFLD-associated oxidative stress that might be responsible for lipid dysfunction. Nonalcoholic fatty liver disease (NAFLD), the most recurrent liver disorder in Western countries, is commonly associated with obesity and progression of metabolic syndrome –6. NAFLDFor investigating the etiology and regulation of NAFLD and NASH and for testing potential therapeutic approaches, several experimental models were developed. These are based on the application of a diet, on the administration of drugs to laboratory animals, or on the exposure of hepatic cell lines to these drugs; genetically modified rodents or zebrafish have also been introduced –12. Wherβ-oxidation was demonstrated in MCD diet fed rats compared to controls ). in situ the behavior of single cells in a complex organ  for 5 min and then visualized by ChemiDoc XRS+ System (Bio-Rad Laboratories), to get digital images.40 mg of liver was lysed in 1 mL of RIPA buffer  of each band was calculated following the manufacturer's instructions. The OD values of SOD2 were normalized versus own relative band of The liver of rats fed, for two weeks, with a diet isocaloric with the MCD diet but containing methionine and choline was considered representative and herewith described as “control.”Glycogen deposits, evidenced by a fuchsia precipitate with the PAS reaction, were present in hepatocytes throughout the lobule; they were particularly abundant in periportal and centrolobular cells .Small neutral lipid droplets, evidenced by the yellow-gold fluorescence induced by Nile Red, were present in all hepatocytes; these were polarized towards the sinusoidal domains .Lobular zonation of ROS, demonstrated by a blue precipitate with the Mn-DAB-Co reaction, was observed. The reaction was particularly intense in the cytoplasm of hepatocytes in the periportal/midzone region, where it was polarized towards the sinusoidal domains, and very low in the pericentral region. Occasional sinusoidal cells displayed strong staining .Resulting dinitrophenyl (DNP) groups were demonstrated with an immunoperoxidase method giving a brown final reaction product. Intense immunoreactivity was seen in sinusoidal and canalicular membrane domains of hepatocytes; diffuse lighter staining was also seen in the cytoplasm of periportal cells .Immunoreactivity for SOD2 was present in hepatocytes throughout the lobule, being intense in periportal and pericentral cells and moderate in hepatocytes of the midzone; it was present as a granular brown product in the cytoplasm partially polarized towards sinusoidal and canalicular domains .β-actin bands as equal loading of liver homogenates from rats fed with control diet or MCD diet for 1–4 weeks; β-actin OD) with respect to control. A trend towards a decrease of SOD2 expression in the last weeks is detected.A marked decrease in the hepatic levels of ATP and GSH was found already at the 1st week in rats fed with a MCD diet as compared with the control group Figures . The ATPThe high content of glycogen in hepatocytes is in keeping with the high caloric diet (45% sucrose) to which the animals were submitted.The droplets emitting bright-yellow fluorescence are ascribed to intracellular triacylglycerols (TAGs) depots and/or to lipoproteins , 32. Lip2+ to Mn3+, which in turn oxidizes DAB, causing its polymerization; intensification of the colored polymer is achieved by Co3+ ions. This reaction proved to demonstrate mainly superoxide anion (O2−) and singlet oxygen (O2(1ΔG)) ).ker rats , which wker rats ; the latker rats .The immunohistochemical analysis of SOD2 revealed a change in protein expression pattern in hepatocytes along the 4-week period of the MCD diet that was similar, in particular in the last weeks, to that of ROS and peroxidated proteins patterns. In particular, large steatotic cells showed intense immunoreactivity in the thin rim of cytoplasm surrounding the lipid droplets. The correspondence between strong ROS production and intense SOD2 expression in the same areas of the lobule suggests an antioxidant attempt to compensate for the high ROS production. Such attempt, associated with the fact that GSH concentration was much lower than normal, might not be entirely successful, thus explaining the formation of peroxidated proteins in the same areas where the ROS production was high. The general trend towards decrease of SOD2 expression of liver homogenates in the last 2 weeks detected by Western Blotting is here ascribed to the much lower cytoplasm area occupied by the enzyme as hepatocytes acquire an adipocyte-like morphology.As concerns the GSH concentration, though we found it to be not significantly different along the 4-week period of the diet, it is much lower with respect to the control. These data are in keeping with data reported in the literature concerning depletion of antioxidant defenses and in particular of GSH in NAFLD , 78, in  in situ the induced alteration of hepatocyte morphology, glycogen stores, lipid droplet behavior, ROS production, and expression of the antioxidant enzyme SOD2. In particular, it points towards chemical modifications of proteins involved in lipid maintenance and metabolism.In conclusion, the histochemical approach herewith illustrated and whose main results are summarized in


Increasing evidence suggests that ion channels and pumps not only regulate membrane potential, ion homeostasis, and electric signaling in excitable cells but also play important roles in cell proliferation, migration, apoptosis and differentiation. Consistent with a role in cell signaling, channel proteins and ion pumps can form macromolecular complexes with growth factors, and cell adhesion and other signaling molecules. And while cancer is still not being cataloged as a channelopathy, as the non-traditional roles of ion pumps and channels are being recognized, it is increasingly being suggested that ion channels and ion pumps contribute to cancer progression. Cancer cell migration requires the regulation of adhesion complexes between migrating cells and surrounding extracellular matrix (ECM) proteins. Cell movement along solid surfaces requires a sequence of cell protrusions and retractions that mainly depend on regulation of the actin cytoskeleton along with contribution of microtubules and molecular motor proteins such as mysoin. This process is triggered and modulated by a combination of environmental signals, which are sensed and integrated by membrane receptors, including integrins and cadherins. Membrane receptors transduce these signals into downstream signaling pathways, often involving the Rho GTPase protein family. These pathways regulate the cytoskeletal rearrangements necessary for proper timing of adhesion, contraction and detachment of cells in order to find their way through extracellular spaces. Migration and adhesion involve continuous modulation of cell motility, shape and volume, in which ion channels and pumps play major roles. Research on cancer cells suggests that certain ion channels may be involved in aberrant tumor growth and channel inhibitors often lead to growth arrest. This review will describe recent research into the role of ion pumps and ion channels in cell migration and adhesion, and how they may contribute to tumor development. Cancer is a leading cause of death worldwide. According to the American Cancer Society, more than 1.6 million new cases were diagnosed in 2013, and one in four deaths in the US is cancer related. Most cancers are treated with surgery, chemotherapy, and/or radiation therapy. Although these clinical measures have proven their efficacy in many cases, patients often experience debilitating side effects that significantly reduce their quality of life. Moreover, cancer relapse with treatment resistance underscores the urgent need to identify novel molecular targets for the development of alternative therapies. Recently, the role of ion channels in driving malignant cancer cell behavior has been revealed and much has been learned from brain tumors Figure  and haveThe proteins that transport ions across cell membranes fall into two general classes: ion channels, through which ions move down their concentration and electrical gradients, and ion pumps that use energy to actively move ions against those gradients Gadsby, . About 1V1.1 is seen in medulloblastoma  are lower in glioblastoma multiforme and in malignant brain tumors than in normal brain tissue, and expression of the EAG1 channel is inversely related to malignancy of the tumor  are the largest subset of potassium channels, and they are gated by changes in membrane potential. Calcium-activated potassium channels (KCa) are activated by intracellular calcium. According to their conductance, KCa channels can be further divided into big conductance (BK), intermediate conductance (IK), and small conductance (SK) channels. KV and KCa channels share a similar structure—they are composed of four pore-lining α-subunits, each with six transmembrane domains and one pore-forming region, except for the BK channel, which has one additional transmembrane segment in the N terminus. Transmembrane regions 1–4 represent the voltage-sensing domains for Kv channels  coding for the pore-forming α-subunits. There are also four auxiliary β-subunits, of which one or two at a time can associate with an α-subunit and modulate channel expression and activity in the plasma membrane. Recently, VGSCs have been found to have relatively high expression levels in a range of cell types that are considered non excitable, including immune cells, fibroblasts and cancer cells  are responsible for the rising phase of the action potential in the majority of electrically excitable cells and are therefore important in impulse generation and propagation. VGSCs comprise a multi-gene family of at least nine different functional members (Na+/H+ exchanger (NHE1), the Na+, +, K+, 2Cl− cotransporter (NKCC). All of these proteins utilize the Na+ electrochemical gradient to drive the transport of other ions, and they are all important in maintaining cellular pH. The NHE1 is a ubiquitously expressed transporter that contributes to cell volume regulation and cytoplasmic pH homeostasis. In cancer NHE1 is upregulated and/or overexpressed in various tumors and plays a fundamental role in malignant invasion by altering the metabolic environment and cell invasiveness  channels are distinct classes of chloride channels. Functions of chloride channels range from ion homeostasis to cell volume regulation and regulation of excitable cells. These channels have 10–12 transmembrane domains, and are found both in the plasma membrane and the membranes of various organelles. Dysregulation of chloride channels has been reported in multiple cancer types. Expression of CLCA1 and CLCA2 is downregulated in human colorectal cancer, revealing a possible tumor suppressor role for these proteins  or mitochondria. Calcium channels not only allow facilitated diffusion of Ca2+ down its concentration gradient, they also provide for the flow of Ca2+ out of the ER into the cell cytosol through ER Ca2+ channels. Plasma membrane channels involved in the influx of Ca2+ into the cell include voltage-gated Ca2+ and transient receptor potential (TRP) ion channels. There are multiple types of calcium channels that are differentially regulated in various cancer types. TRPC3 is elevated in some breast and ovarian tumors, and its silencing reduces ovarian cancer cell line proliferation in vitro and tumor formation in vivo  channel can form a macromolecular complex with vascular endothelial growth factor receptor (VEGFR)-1 and β1-integrin, and assembly of this complex confers a pro-migratory phenotype in leukemia , respectively  cells, and it enhances adhesion while inhibiting migration in a transwell assay -induced migration of a lung cancer cell line and inhibited basal migration of the cells in the absence of EGF  cells induced lamellipodia and suppressed motility in a phosphatidylinositol 3-kinase (PI3-kinase) dependent manner, and protein kinase C was involved upstream of PI3-kinase in the suppression of β1-subunit mediated cell motility in carcinoma cells  contain an Arginine-Glycine-Aspartate (RGD) sequence on their extracellular loop. RGD sequences mediate interaction between ECM proteins and integrins and are absent on the extracellular side of other K+ channels. Further evidence showed that β1 integrin associates with the Na,K-ATPase and voltage gated Ca2+ channels , the tyrosine kinase Src, and GTPases such as Ras and Rho Brown, . Evidenc1-subunit suppresses cell motility by cross talk between the two subunits of Na,K-ATPase with the PI3-kinase signaling pathway , multiple intracellular signaling pathways are activated, including the Epidermal growth factor receptor (EGFR)/Src-Ras-Erk pathway and the PI3K-PDK-Akt pathway  decreased proliferation in vitro and slowed tumor formation in xenografts, with cells arrested at G0/G1 phase of the cell cycle  mediated calcium efflux reduced proliferation of MCF-7 breast cancer cells. An antisense construct directed towards PMCA lead to changes in cell cycle control kinetics, with a prolonged G2 phase that occurs with reduced Ca2+ efflux (Lee et al., in vitro and in vivo (Chigurupati et al., Calcium signaling also plays an important role in regulation of the cell cycle. Cells progressing from G1 to S require both extracellular calcium and functional membrane calcium channels in order to activate downstream signaling (Taylor et al., V1.5 channel, a neonatal form of VGSC, was upregulated in human brain astrocytoma and positively correlated with the degree of malignancy while reduced nNaV1.5 expression significantly suppressed the proliferation of astrocytoma cells (Xing et al., In addition, changes in sodium channels impact tumor cell proliferation. For example, the nNaV10.1 EAG1 channel has been closely studied as a target for cancer therapy, since EAG1 overexpression is associated with tumorigenic potential, and its expression is correlated with poor patient survival in multiple cancer types (Pardo and Stühmer, in vitro and in vivo (Downie et al., 2+ channels have also been suggested as a potential therapeutic target for certain brain tumors. Mibefradil, a calcium channel inhibitor, was found to inhibit proliferation in human glioma and neuroblastoma cells, and overexpression of T-type Ca2+ channel protein doubled the proliferation rate while antisense treatment reduced the proliferation rate of these cells (Panner et al., 2- and α3-subunits compared to TMZ-sensitive cells and astrocytes. These cells were also sensitive to ouabain at low concentrations, and knockdown of the α3-subunit sensitized the cells to TMZ (Chen et al., Most cancers are treated by surgical resection, chemotherapy, and radiation therapy. However due to the prevalence of cancer relapse with treatment resistance, novel molecular targets must be identified for the development of alternative therapies. Despite the growing evidence of aberrant expression and function of ion channels in oncology, development of cancer treatment using ion channel targeting compounds is still at an early stage. Studies have shown that some VGSC blockers can inhibit cell behaviors associated with metastasis. For example, the anticonvulsant phenytoin suppressed migration of prostate cancer cells (Fraser et al., Increasing evidence suggests that ion channels and pumps are involved in the regulation of cell proliferation and migration, and channel proteins have been shown to form macromolecular complexes with cell adhesion molecules and other signaling proteins. As these roles of ion channels and pumps are further elucidated, it is being increasingly suggested that regulation of ion channels and pumps could contribute to cancer progression. Here we discussed that aberrant expression and function of several types of ion channels and pumps have been found in multiple cancers including brain cancer, and in particular, glioblastoma. Knowing that these proteins are involved in multiple malignant characteristics of multiple cancers, ion channels and pumps could be potential targets for therapy.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.