Biology subjects

Kinch, L. N.

Publications and source records attributed to Kinch, L. N..

14 recordsLinked to original sources

bioRxiv2026

Vibrio parahaemolyticus metabolically adapts while tempering the host immune response during host cell invasion.

Vibrio parahaemolyticus (V. para) is an enteric pathogen that establishes a protected intracellular niche using its second type III secretion system. However, how this bacterium adapts to the host cytoplasm while overcoming cellular defenses has remained unclear. To define these mechanisms, we performed dual-transcriptomic profiling of both pathogen and host during invasion, intracellular replication, and late infection. Our analyses revealed extensive metabolic reprogramming by V. para, including induction of diverse nutrient transporters and metabolic pathways. We discovered that because mammalian cells are auxotrophic for aromatic amino acids, V. para must activate its own unique biosynthetic machinery, a requirement that proved essential for intracellular growth. Infected host cells mounted a sustained NF-kappaB response. Both heightened NF-kappaB activation and disruption of canonical NF-kappaB signaling restricted bacterial expansion, indicating that V. para exploits a finely tuned Goldilocks level of immune signaling to promote survival and replication. Together, these findings uncover fundamental metabolic and immune adaptations that drive pathogenesis.

microbiology↗

bioRxiv2026

Dual Control of LDL-cholesterol Levels by ANGPTL3 and ANGPTL8

BACKGROUNDInactivation of ANGPTL3 (angiopoietin-like protein 3, A3) is a proven therapeutic strategy for lowering plasma lipid levels independently of the LDL receptor (LDLR), yet the optimal approach to inactivate A3 remains unclear. A3 is proteolytically cleaved and circulates as full-length (A3-FL), N-terminal (A3-Nter) and C-terminal (A3-Cter) fragments. The specific contribution of each form of A3, and of its paralog, ANGPTL8 (A8), in modulating circulating levels of ApoB-Containing Lipoproteins (ABCLs) remain poorly defined. Clarifying these relationships will inform next-generation A3-directed therapies. METHODSWe performed liver perfusion studies to directly compare the number and composition of VLDL particles secreted from mice with and without A3. To amplify effects on cholesterol metabolism, we generated Ldlr-/- mice expressing wildtype A3 (A3-WT), A3-FL or A3-Nter, with or without co-expression of A8, and analyzed plasma lipids, circulating A3 and A8 complexes, and intravascular lipase activities. Complementary in vitro assays and structural modeling were used to assess relative endothelial lipase (EL) inhibition by A3 alone or in complex with A8. RESULTSLiver perfusion studies revealed that A3 inactivation does not alter the rates of hepatic secretion of VLDL in wildtype or Ldlr-/- mice. Inactivation of A8 alone lowered plasma LDL-cholesterol (C) levels by [~]20%, an effect dependent upon the expression of both EL and A3. Maximal inhibition of lipoprotein lipase (LPL) required co-expression of A8 plus both A3-FL and A3-Nter, indicating that A3 cleavage, in addition to A8 expression, is essential for maximal LPL inhibition. In contrast, A8 expression, but not A3 cleavage, was required for optimal EL inhibition. CONCLUSIONSA8 acts in concert with A3 to differentially modulate LPL- and EL-mediated lipolysis, which antagonizes hepatic clearance of newly-secreted atherogenic ABCLs. This mechanistic framework refines our understanding of A3-targeted lipid lowering and highlights the therapeutic potential of dual A3- plus A8-directed strategies to treat dyslipidemia and prevent atherosclerotic cardiovascular disease. Clinical perspectiveO_ST_ABSWhat is new?C_ST_ABSO_LIInactivation of A3 lowers circulating ABCL levels without altering hepatic secretion rates of VLDL-ApoB or -TG. C_LIO_LIProteolytic cleavage of A3 is required for maximal inhibition of LPL. C_LIO_LIInactivation of A8 lowers LDL-C levels through an A3- and EL-dependent, but LDLR-independent, mechanism. C_LI What are the clinical implications?O_LICombining A8 inhibition with A3-inactivating therapies offers a strategy to achieve greater reduction in LDL-C levels and atherosclerotic cardiovascular risk. C_LI

molecular biology↗

bioRxiv2024

Genetic and microbial analysis of invasiveness for Escherichia coli strains associated with inflammatory bowel disease

Background & AimsThe adherent-invasive Escherichia coli (AIEC) pathotype is implicated in inflammatory bowel disease (IBD) pathogenesis. AIEC strains are currently defined by phenotypic measurement of their pathogenicity, including invasion of epithelial cells. This broad definition, combined with the genetic diversity of AIEC across IBD patients, has complicated the identification of virulence determinants. We sought to quantify the invasion phenotype of clinical isolates from IBD patients and identify the genetic basis for their invasion into epithelial cells. MethodsA pangenome with core and accessory genes (genotype) was assembled using whole genome sequencing of 168 E. coli samples isolated from 13 IBD patients. A modified assay for invasion of epithelial cells (phenotype) was established with consideration of antibiotic resistance phenotypes. Isolate genotype was correlated to invasiveness phenotype to identify genetic factors that co-segregate with invasion. ResultsPangenome-wide comparisons of E. coli clinical isolates identified accessory genes that can co-segregate with invasion phenotype. These correlations found the acquisition of antibiotic resistance genes in clinical isolates compromised the traditional gentamicin protection assays used to quantify invasion. Therefore, an alternate assay, based on amikacin resistance, identified genes co-segregating with invasion. These genes encode an arylsulfatase, a glycoside hydrolase, and genetic islands carrying propanediol utilization and sulfoquinovose metabolism pathways. ConclusionsThis study highlights the importance of incorporating antibiotic resistance screening for invasion assays used in AIEC identification. Accurately screened invasion phenotypes identified accessory genome elements among E. coli IBD isolates that correlate with their ability to invade epithelial cells. These results help explain why single genetic markers for the AIEC phylotype are challenging to identify. SynopsisWe established a pangenome of Escherichia coli isolates from inflammatory bowel disease patients using whole genome sequencing. The genotypes were correlated with a newly developed measurement of invasion phenotype to identify co-segregating genes.

microbiology↗

bioRxiv2024

PNPLA3(148M) Promotes Hepatic Steatosis by Interfering with Triglyceride Hydrolysis Through a Gain-of-Function Mechanism

Background & AimsPNPLA3(148M) (patatin-like phospholipase domain-containing protein 3) is the most impactful genetic risk factor for steatotic liver disease (SLD), thus motivating a search for therapeutic modulators of its expression. A key unresolved issue is whether PNPLA3(148M) confers a loss- or gain-of-function. Here we used multiple approaches to further test the hypothesis that PNPLA3 causes steatosis by sequestering ABHD5 (/{beta} hydrolase domain containing protein 5), the cofactor of ATGL (adipose TG lipase), thus limiting mobilization of hepatic triglyceride (TG). MethodsWe quantified the physical interactions between ABHD5 and PNPLA3/ATGL in cultured hepatocytes using NanoBiT complementation assays. Immunocytochemistry was used to compare the relative binding of PNPLA3 and ATGL to ABHD5 and to determine if PNPLA3 must associate with lipid droplets (LDs) to inhibit ATGL. Adenoviruses and adeno-associated viruses were used to express PNPLA3 in liver-specific Atgl-/- mice and ABHD5 in livers of Pnpla3148M/M mice, respectively. We used purified recombinant proteins to compare the TG hydrolytic activities of PNPLA3 and ATGL in the presence and absence of ABHD5. ResultsABHD5 interacted preferentially with PNPLA3 relative to ATGL in cultured hepatocytes and in vitro, with no differences observed between PNPLA3(WT) or PNPLA3(148M). PNPLA3(148M)-associated inhibition of TG hydrolysis required localization of PNPLA3 to LDs and the presence of ATGL. Finally, overexpression of ABHD5 reversed the hepatic steatosis in Pnpla3M/M mice. ConclusionsThese findings support the premise that PNPLA3(148M) promotes hepatic steatosis by accumulating on LDs and inhibiting ATGL-mediated lipolysis in an ABHD5-dependent manner. Our results predict that reducing, rather that increasing PNPLA3 expression will be the best strategy to treat PNPLA3(148M)-associated SLD. Impact and implicationsSteatotic liver disease (SLD) is a common complex disorder associated with both environmental and genetic risk factors. PNPLA3(148M) is the most impactful genetic risk factor for SLD and yet its pathogenic mechanism remains controversial. Here we provide evidence that PNPLA3(148M) promotes triglyceride (TG) accumulation by sequestering ABHD5, thus limiting its availability to activate ATGL. Although the substitution of methionine for isoleucine reduces the TG hydrolytic activity of PNPLA3, the loss-of-function is only indirectly related to the steatotic effect of the variant. Here we provide evidence that PNPLA3(148M) confers a gain-of-function by interfering with ATGL-mediated TG hydrolysis. These findings have implications for the design of potential PNPLA3-based therapies. Reducing, rather than increasing, PNPLA3 levels is predicted to reverse steatosis in susceptible individuals. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/606015v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@1dd7acaorg.highwire.dtl.DTLVardef@1a869dborg.highwire.dtl.DTLVardef@1bde743org.highwire.dtl.DTLVardef@99effc_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIABHD5 binds preferentially to PNPLA3 relative to ATGL. C_LIO_LIPNPLA3(WT) and PNPLA3(148M) compete similarly for binding and inhibition of ATGL. C_LIO_LIABHD5 activates the triglyceride lipase activity of PNPLA3, as well as ATGL. C_LIO_LIThe steatotic effect of PNPLA3(148M) requires expression of ATGL. C_LIO_LIOverexpression of ABHD5 can rescue the steatosis associated with PNPLA3(148M). C_LI

cell biology↗

bioRxiv2024

Structure classification of the proteins from Salmonella enterica pangenome revealed novel potential pathogenicity islands

Salmonella enterica is a pathogenic bacterium known for causing severe typhoid fever in humans, making it important to study due to its potential health risks and significant impact on public health. This study provides evolutionary classification of proteins from Salmonella enterica pangenome. We classified 17,238 domains from 13,147 proteins from 79,758 Salmonella enterica strains and studied in detail domains of 272 proteins from fourteen characterized Salmonella pathogenicity islands (SPIs). Among SPIs-related proteins, 90 proteins function in the secretion machinery. 41% domains of SPI proteins have no previous sequence annotation. By comparing clinical and environmental isolates, we identified 3682 proteins that are overrepresented in clinical group that we consider as potentially pathogenic. 69 of them overlap with SPI proteins. Among domains of potentially pathogenic proteins only 50% domains were annotated by sequence methods previously. Moreover, 36% (1330 out of 3682) of potentially pathogenic proteins cannot be classified into Evolutionary Classification of Protein Domains database (ECOD). Among classified domains of potentially pathogenic proteins the most populated homology groups include helix-turn-helix (HTH), Immunoglobulin-related, and P-loop domains-related. Functional analysis revealed overrepresentation of these protein in biological processes related to viral entry into host cell, antibiotic biosynthesis, DNA metabolism and conformation change, and underrepresentation in translational processes. Analysis of the potentially pathogenic proteins indicates that they form 119 clusters (islands) within the Salmonella genome, suggesting their potential contribution to the bacteriums virulence. Overall, our analysis revealed that identified potentially pathogenic proteins are poorly studied. ECOD hierarchy of classified Salmonella enterica domains is available online: http://prodata.swmed.edu/ecod/index_salm.php Author SummarySalmonella enterica is a dangerous bacterium known for causing severe typhoid fever in humans, posing significant health risks. Our study focuses on understanding the proteins of this bacteriums genetic composition, unraveling their evolutionary classification. Analyzing a vast collection of strains, we identified and classified over 17,000 protein domains, with special focus on 272 proteins within Salmonella pathogenicity islands (SPIs). By comparing strains from clinical and environmental sources, we pinpointed 3,682 proteins overrepresented in clinical samples, signifying potential pathogenicity. Surprisingly, half of these proteins domains were not identified previously using sequence-based approaches. Our analysis identified these proteins forming 119 clusters within the Salmonella genome, suggesting their involvement in its virulence. Our study underscores the insufficient understanding of these potentially pathogenic proteins, highlighting the need for further investigation into their roles and implications in Salmonella-related illnesses.

bioinformatics↗

bioRxiv2024

FicD Sensitizes Cellular Response to Glucose Fluctuations in Mouse Embryonic Fibroblasts

During homeostasis, the endoplasmic reticulum (ER) maintains productive transmembrane and secretory protein folding that is vital for proper cellular function. The ER-resident HSP70 chaperone, BiP, plays a pivotal role in sensing ER stress to activate the unfolded protein response (UPR). BiP function is regulated by the bifunctional enzyme FicD that mediates AMPylation and deAMPylation of BiP in response to changes in ER stress. AMPylated BiP acts as a molecular rheostat to regulate UPR signaling, yet little is known about the molecular consequences of FicD loss. In this study, we investigate the role of FicD in mouse embryonic fibroblast (MEF) response to pharmacologically and metabolically induced ER stress. We find differential BiP AMPylation signatures when comparing robust chemical ER stress inducers to physiological glucose starvation stress and recovery. Wildtype MEFs respond to pharmacological ER stress by downregulating BiP AMPylation. Conversely, BiP AMPylation in wildtype MEFs increases upon metabolic stress induced by glucose starvation. Deletion of FicD results in widespread gene expression changes under baseline growth conditions. In addition, FicD null MEFs exhibit dampened UPR signaling, altered cell stress recovery response, and unconstrained protein secretion. Taken together, our findings indicate that FicD is important for tampering UPR signaling, stress recovery, and the maintenance of secretory protein homeostasis. Significance StatementThe chaperone BiP plays a key quality control role in the endoplasmic reticulum, the cellular location for the production, folding, and transport of secreted proteins. The enzyme FicD regulates BiPs activity through AMPylation and deAMPylation. Our study unveils the importance of FicD in regulating BiP and the unfolded protein response (UPR) during stress. We identify distinct BiP AMPylation signatures for different stressors, highlighting FicDs nuanced control. Deletion of FicD causes widespread gene expression changes, disrupts UPR signaling, alters stress recovery, and perturbs protein secretion in cells. These observations underscore the pivotal contribution of FicD for preserving secretory protein homeostasis. Our findings deepen the understanding of FicDs role in maintaining cellular resilience and open avenues for therapeutic strategies targeting UPR-associated diseases.

molecular biology↗

bioRxiv2022

Molecular Determinants for Differential Activation of the Vibrio parahaemolyticus Bile Acid Receptor

Bile acids are important for digestion of food and for antimicrobial activity. Pathogenic Vibrio parahaemolyticus senses bile acids via the co-component signal transduction system receptor VtrA/VtrC, an obligate membrane heterodimer. Intestinal bile acids bind to the periplasmic domain of the VtrA/VtrC complex, activating a DNA-binding domain in VtrA that induces expression of another membrane protein, VtrB. VtrB induces expression of the pathogenic Type III Secretion System 2. The bile acid taurodeoxycholate (TDC) activates VtrA/VtrC-induced VtrB expression, while others such as chenodeoxycholate (CDC) do not. This study demonstrates both CDC and TDC bind to the VtrA/VtrC periplasmic heterodimer using isothermal titration calorimetry (ITC). The crystal structure of the VtrA/VtrC heterodimer bound to CDC revealed it binds in the same hydrophobic pocket as TDC, but differently. Mutation of the binding pocket caused a decrease in bile acid binding affinity with exception of the S123A mutant, which bound with a similar affinity as the wild-type protein. The S123A mutant decreased TDC-induced T3SS2 activation, providing a molecular explanation for the selective activation of the T3SS2 by bile acids.

microbiology↗

bioRxiv2022

Enzymatic Specificity of Conserved Rho GTPase Deamidases Promotes Invasion of Vibrio parahaemolyticus at the Expense of Infection

Vibrio parahaemolyticus is among the leading causes of bacterial seafood-borne acute gastroenteritis. Like many intracellular pathogens, V. parahaemolyticus invades host cells during infection by deamidating host small Rho GTPases. The Rho GTPase deamidating activity of VopC, a type three secretion system (T3SS) translocated effector, drives V. parahaemolyticus invasion. The intracellular pathogen uropathogenic Escherichia coli (UPEC) invades host cells by secreting a VopC homolog, the secreted toxin cytotoxic necrotizing factor one (CNF1). Because of the homology between VopC and CNF1, we hypothesized topical application of CNF1 during V. parahaemolyticus infection could supplement VopC activity. Here, we demonstrate that CNF1 improves the efficiency of V. parahaemolyticus invasion, a bottleneck in V. parahaemolyticus infection, across a range of doses. CNF1 increases V. parahaemolyticus invasion independent of both VopC and the T3SS altogether, but leaves a disproportionate fraction of intracellular bacteria unable to escape the endosome and complete their infection cycle. This phenomenon holds true in the presence or absence of VopC, but is particularly pronounced in the absence of a T3SS. The native VopC, by contrast, promotes a far less efficient invasion, but permits the majority of internalized bacteria to escape the endosome and complete their infection cycle. These studies highlight the significance of enzymatic specificity during infection, as virulence factors (VopC and CNF1 in this instance) with similarities in function (bacterial uptake), catalytic activity (deamidation), and substrates (Rho GTPases) are not sufficiently interchangeable for mediating a successful invasion for neighboring bacterial pathogens. IMPORTANCEMany species of intracellular bacterial pathogens target host small Rho-GTPases to initiate invasion, including the human pathogens Vibrio parahaemolyticus and uropathogenic Eschericia coli (UPEC). The type three secretion system (T3SS) effector VopC of V. parahaemolyticus promotes invasion through the deamidation of Rac1 and CDC42 in the host, whereas the secreted toxin cytotoxic necrotizing factor one (CNF1) drives UPECs internalization through the deamidation of Rac1, CDC42, and RhoA. Despite these similarities in the catalytic activity of CNF1 and VopC, we observed the two enzymes were not interchangeable. Although CNF1 increased V. parahaemolyticus endosomal invasion, most intracellular V. parahaemolyticus aborted their infection cycle and remained trapped in endosomes. Our findings illuminate how the precise biochemical fine-tuning of T3SS effectors is essential for efficacious pathogenesis. They moreover pave the way for future investigations into the biochemical mechanisms underpinning V. parahaemolyticus endosomal escape, and more broadly, the regulation of successful pathogenesis.

microbiology↗

bioRxiv2022

Co-Component Signal Transduction Systems: fast-evolving virulence regulation cassettes discovered in enteric bacteria

Bacterial signal transduction systems sense changes in the environment and transmit these signals to control cellular responses. The simplest one-component signal transduction systems include an input sensor domain and an output response domain encoded in a single protein chain. Alternately, two-component signal transduction systems transmit signals by phosphorelay between input and output domains from separate proteins. The membrane tethered periplasmic bile acid sensor that activates the Vibrio parahaemolyticus type III secretion system adopts an obligate heterodimer of two proteins encoded by partially overlapping VtrA and VtrC genes. This co-component signal transduction system binds bile acid using a lipocalin-like domain in VtrC and transmits the signal through the membrane to a cytoplasmic DNA-binding transcription factor in VtrA. Using the domain and operon organization of VtrA/VtrC, we identify a fast-evolving superfamily of co-component systems in enteric bacteria. Accurate machine learning-based fold predictions for the candidate co-components support their homology in the twilight zone of rapidly evolving sequence and provide mechanistic hypotheses about previously unrecognized lipid-sensing functions. Significance statementUsing the domain and operon organization of VtrA/VtrC, combined with fold predictions, we identify new co-component signal transduction systems in enteric bacteria that likely regulate virulence. We observe that the heterodimeric VtrA/VtrC periplasmic bile acid receptor controlling Vibrio parahaemolyticus T3SS2 is a distant homolog of the ToxR/ToxS master regulator of virulence and has evolved beyond confident sequence recognition. Exploiting the newly developed machine learning methods for structure prediction, we observe a VtrC-like lipocalin fold for both the ToxS periplasmic domain and for other detected periplasmic sensor components. This structure prediction supports the divergent evolution of VtrA/VtrC-like co-component signal transduction systems and suggests a role for lipid sensing in regulating virulence in enteric bacteria.

evolutionary biology↗

bioRxiv2021

Accurate prediction of protein structures and interactions using a 3-track network

DeepMind presented remarkably accurate protein structure predictions at the CASP14 conference. We explored network architectures incorporating related ideas and obtained the best performance with a 3-track network in which information at the 1D sequence level, the 2D distance map level, and the 3D coordinate level is successively transformed and integrated. The 3-track network produces structure predictions with accuracies approaching those of DeepMind in CASP14, enables rapid solution of challenging X-ray crystallography and cryo-EM structure modeling problems, and provides insights into the functions of proteins of currently unknown structure. The network also enables rapid generation of accurate models of protein-protein complexes from sequence information alone, short circuiting traditional approaches which require modeling of individual subunits followed by docking. We make the method available to the scientific community to speed biological research. One-Sentence SummaryAccurate protein structure modeling enables rapid solution of structure determination problems and provides insights into biological function.

bioinformatics↗

bioRxiv2020

Manipulation of IRE1-dependent MAPK signaling by a Vibrio agonist-antagonist effector pair

Diverse bacterial pathogens employ effector delivery systems to disrupt vital cellular processes in the host (1). The type III secretion system 1 of the marine pathogen, Vibrio parahaemolyticus, utilizes the sequential action of four effectors to induce a rapid, pro-inflammatory cell death uniquely characterized by a pro-survival host transcriptional response (2, 3). Herein, we show that this pro-survival response is caused by the action of the channel-forming effector VopQ that targets the host V-ATPase resulting in lysosomal deacidification and inhibition of lysosome-autophagosome fusion. Recent structural studies have shown how VopQ interacts with the V-ATPase and, while in the ER, a V-ATPase assembly intermediate can interact with VopQ causing a disruption in membrane integrity. Additionally, we observe that VopQ-mediated disruption of the V-ATPase activates the IRE1 branch of the unfolded protein response (UPR) resulting in an IRE1-dependent activation of ERK1/2 MAPK signaling. We also find that this early VopQ-dependent induction of ERK1/2 phosphorylation is terminated by the VopS-mediated inhibitory AMPylation of Rho GTPase signaling. Since VopS dampens VopQ-induced IRE1-dependent ERK1/2 activation, we propose that IRE1 activates ERK1/2 phosphorylation at or above the level of Rho GTPases. This study illustrates how temporally induced effectors can work as in tandem as agonist/antagonist to manipulate host signaling and reveal new connections between V-ATPase function, UPR and MAPK signaling. ImportanceVibrio parahaemolyticus (V. para) is a seafood-borne pathogen that encodes two Type 3 Secretion Systems (T3SS). The first system T3SS1 is thought to be maintained in all strains of V. para to to maintain survival in the environment, whereas the second sytem T3SS2 is linked to clinical isolates and disease in humans. Herein, we find that first system targets evolutionarily conserved signaling systems to manipulate host cells, eventually causing a rapid, orchestrated cells death within three hours. We have found that the T3SS1 injects virulence factors that temporally manipulate host signaling. Within the first hour of infection, the effector VopQ acts first by activating host surval signals while diminishing the host cell apoptotic machinery. Less than an hour later, another effector VopS reverses activation and inhibition of these signaling systems ultimately leading to death of the host cell. This work provides example of how pathogens have evolved to manipulate the interplay between T3SS effectors to regulate host signaling pathways.

microbiology↗

bioRxiv2020

A combined RAD-Seq and WGS approach reveals the genomic basis of yellow colour variation in bumble bee Bombus terrestris

BackgroundIn the model bumble bee species B. terrestris, both males and females exhibit black coloration on the third thoracic and first metasomal segments. We discovered a fortuitous lab-generated mutant in which this typical black coloration is replaced by yellow. As this same color variant is found in several sister lineages to B. terrestris within the Bombus s.s. subgenus, this could be a result of ancestral allele sorting. ResultsUtilizing a combination of RAD-Seq and whole-genome re-sequencing approaches, we localized the color-generating variant to a single SNP in the protein-coding sequence of a homeobox transcription factor, cut. Sanger sequencing confirmed fixation of this SNP between wildtype and yellow mutants. Protein domain analysis revealed this SNP to generate an amino acid change (Ala38Pro) that modifies the conformation of coiled-coil structural elements which lie outside the characteristic DNA binding domains. We found all Hymenopterans including B. terrestris sister lineages possess the non-mutant allele, indicating different mechanism(s) are involved in the same black to yellow transition in nature. ConclusionsCut is a highly pleiotropic gene important for multiple facets of development, yet this mutation generated no noticeable external phenotypic effects outside of setal characteristics. Reproductive capacity was observed to be reduced, however, with queens being less likely to mate and produce female offspring, in a manner similar to workers. Our research implicates a novel developmental player in pigmentation, and potentially caste as well, thus contributing to a better understanding of the evolution of diversity in both of these processes.

genomics↗

bioRxiv2019

Mutation severity spectrum of rare alleles in the human genome is predictive of disease type

The human genome harbors a variety of genetic variations. Single-nucleotide changes that alter amino acids in protein-coding regions are one of the major causes of human phenotypic variation and diseases. These single-amino acid variations (SAVs) are routinely found in whole genome and exome sequencing. Evaluating the functional impact of such genomic alterations is crucial for diagnosis of genetic disorders. We developed DeepSAV, a deep-learning convolutional neural network to differentiate disease-causing and benign SAVs based on a variety of protein sequence, structural and functional properties. Our method outperforms most stand-alone programs and has similar predictive power as some of the best available. We transformed DeepSAV scores of rare SAVs observed in the general population into a mutation severity measure of protein-coding genes. This measure reflects a genes tolerance to deleterious missense mutations and serves as a useful tool to study gene-disease associations. Genes implicated in cancer, autism, and viral interaction are found by this measure as intolerant to mutations, while genes associated with a number of other diseases are scored as tolerant. Among known disease-associated genes, those that are mutation-intolerant are likely to function in development and signal transduction pathways, while those that are mutation-tolerant tend to encode metabolic and mitochondrial proteins.

bioinformatics↗

bioRxiv2019

Genomics reveals the origins of ancient specimens

Centuries of zoological studies amassed billions of specimens in collections worldwide. Genomics of these specimens promises to rejuvenate biodiversity research. The obstacles stem from DNA degradation with specimen age. Overcoming this challenge, we set out to resolve a series of long-standing controversies involving a group of butterflies. We deduced geographical origins of several ancient specimens of uncertain provenance that are at the heart of these debates. Here, genomics tackles one of the greatest problems in zoology: countless old, poorly documented specimens that serve as irreplaceable embodiments of species concepts. The ability to figure out where they were collected will resolve many on-going disputes. More broadly, we show the utility of genomics applied to ancient museum specimens to delineate the boundaries of species and populations, and to hypothesize about genotypic determinants of phenotypic traits.

zoology↗