Biology subjects

Krishnan, A.

Publications and source records attributed to Krishnan, A..

At least 73 records · Page 4Linked to original sources

bioRxiv2022

Zebrafish screen of high-confidence targets at insomnia GWAS loci implicates MEIS1, SKIV2L, and ARFGAP2 as conserved regulators of sleep-wake behaviors

Recent large-scale human genome-wide association studies (GWAS) for insomnia have identified more than 200 significant loci. The functional relevance of these loci to the pathogenesis of insomnia is largely unknown. GWAS signals are typically non-coding variants, which are often arbitrarily annotated to the nearest protein-coding gene; however, due to 3D chromatin structure, variants can interact with more distal genes driving their function. The distal gene may, therefore, represent the true causal gene influencing the phenotype. By integrating our high-resolution chromatin interaction maps from neural progenitor cells with phenotypic data from a Drosophila RNAi screen, we prioritized candidate genes that we hypothesized would have deep phylogenetic conservation of sleep function. To determine the conservation of these candidate genes in the context of vertebrate sleep and their relevance to insomnia-like behaviors, we performed CRISPR-Cas9 mutagenesis in larval zebrafish for six highly conserved candidate genes and examined sleep-wake behaviors using automated video-tracking. CRISPR mutation of zebrafish orthologs of MEIS1 and SKIV2L produced insomnia-like behaviors, while mutation of ARFGAP2 impaired activity and development in our larval zebrafish model, demonstrating the importance of performing functional validation of GWAS-implicated effector genes to reveal genes influencing disease-relevant mechanisms.

genetics↗

bioRxiv2022

Personalized transcranial alternating current stimulation improves sleep quality: Initial Findings

Insufficient sleep is a major health issue. Inadequate sleep is associated with an array of poor health outcomes, including cardiovascular disease, diabetes, obesity, certain forms of cancer, Alzheimers disease, depression, anxiety, and suicidality. Given concerns with typical sedative hypnotic drugs for treating sleep difficulties, there is a compelling need for added alternative interventions. Here, we report results of a non-invasive electrical brain stimulation approach to optimizing sleep involving transcranial alternating current stimulation (tACS). A total of 25 participants (mean age: 46.3, S.D. {+/-}12.4, 15 females) were recruited for a null-stimulation controlled (Control condition), within subjects, randomized crossed design, that included two variants of an active condition involving 15 minutes pre-sleep tACS stimulation. To evaluate the impact on sleep quality, the two active tACS stimulation conditions were designed to modulate sleep-dependent neural activity in the theta/alpha frequency bands, with both stimulation types applied to all subjects in separate sessions. The first tACS condition used a fixed stimulation pattern across all participants, a pattern composed of stimulation at 5Hz and 10Hz. The second tACS condition used a personalized stimulation approach with the stimulation frequencies determined by each individuals peak EEG frequencies in the 4-6Hz and 9-11Hz bands. Personalized tACS stimulation increased sleep quantity (duration) by 22 minutes compared to a Control condition (p=.04), and 19 minutes compared to Fixed tACS stimulation (p=.03). Fixed stimulation did not significantly increase sleep duration compared to Control (mean: 3 minutes; p=0.75). For sleep onset, the Personalized tACS stimulation resulted in reducing the onset by 28% compared to the Fixed tACS stimulation (6 minutes faster, p=.02). For a Poor Sleep sub-group (n=13) categorized with Clinical Insomnia and with a high insomnia severity, Personalized tACS stimulation improved sleep duration by 33 minutes compared to Fixed stimulation (p=0.02), and 30 minutes compared to Control condition (p<0.1). Together, these results suggest that Personalized stimulation improves sleep quantity and time taken to fall asleep relative to Control and Fixed stimulation providing motivation for larger-scale trials for Personalized tACS as a sleep therapeutic, including for those with insomnia.

neuroscience↗

bioRxiv2022

Bill shape imposes biomechanical tradeoffs in cavity-excavating birds

Organisms are subject to a host of physical forces that influence morphological evolution. Birds, for instance, use their bills as implements to perform various functions, each exerting unique physical demands and selective influences on bill morphology. For example, birds that use their bills to excavate nesting or roosting cavities must resist a range of mechanical stresses to prevent fracture. However, the contribution of bill geometry and material composition to excavation stress resistance remains poorly understood. Here, we study the biomechanical consequences of bill diversification in two clades of cavity-excavating, frugivorous birds, the paleotropical barbets. Using multilayered finite element models and beam theory, we compare the excavation performance of different maxillary geometries for two loading regimes experienced by barbet bills during cavity excavation-dorsoventral impact and torsion. We find that deeper and wider maxillae perform better for impact loads than for torsional loads, with the converse for narrower maxillae. This results in a tradeoff between impact and torsion resistance imposed by bill geometry. Analytical beam models validate this prediction, showing that this relationship holds even when maxillae are simplified to solid elliptical beams. Finally, we find that composite bill structures broadly exhibit lower stresses than homogenous structures of the same geometry, indicating a functional synergy between the keratinous rhamphotheca and bony layers of the bill. Overall, our findings demonstrate the strong link between morphological evolution, behavior, and functional performance in organisms.

ecology↗

bioRxiv2022

Climate influences bill shape diversification in cavity-excavating birds

The remarkable structural and functional diversity of the avian bill serves as an ideal system to understand how ecological and environmental factors influence morphological diversification under physically demanding tasks. For example, in cavity-excavating birds where the bill experiences tremendous physical stresses, climate and habitat affect the mechanical properties of available nesting substrates and therefore can potentially influence the shape and performance of bills. Few studies have focused on the entire avian bill, a complex structure consisting of the rhamphotheca and bony core of the upper and lower mandibles, which may evolve as independent modules or as a single integrated unit. Here, we examined patterns and drivers of bill shape diversification in barbets using micro-computed tomography of museum study skins. We employed landmark-based geometric morphometrics and phylogenetic comparative methods to study the influence of climatic conditions, integration and phylogenetic constraints on bill shape diversification. Asian and African barbets have explored distinct maxillary shape spaces without corresponding change in mandibular shape after correcting for phylogenetic non-independence. Additionally, maxillary shape for both rhamphotheca and bony components was significantly correlated with climate variables and exhibited signatures of allometric scaling. All four bill components, however, covaried with each other and have evolved in a gradual and integrated fashion, exhibiting late-stage shape disparity. Through these findings, our study offers crucial insights into how ecological behaviors impact morphological evolution of complex, multifunctional features.

evolutionary biology↗

bioRxiv2022

Higher-order dialectic variation and syntactic convergence in the complex warble song of budgerigars

Dialectic signatures in animal acoustic signals are key in identification and association with group members. Complex vocal sequences may also convey information about behavioral state, and may thus vary according to social environment. Many bird species learn and modify their complex acoustic signals throughout their lives. However, the structure and function of vocal sequences in perennial vocal learners remains understudied. Here, we examined vocal sequence variation in the warble song of budgerigars, and how these change upon contact between social groups. Budgerigars are perennial vocal learners which exhibit fission-fusion flock dynamics in the wild. We found that two captive colonies of budgerigars exhibited colony-specific differences in the syntactic structure of their vocal sequences. Individuals from the two colonies differed in the propensity to repeat certain note types, forming repetitive motifs which served as higher-order signatures of colony identity. When the two groups were brought into contact, their vocal sequences converged within months of contact, and these colony-specific repetitive patterns disappeared, with males from both erstwhile colonies now producing similar sequences with similar syntactic structure. Our data suggests that budgerigars can encode substantial information in the higher-order temporal arrangement of notes/vocal units, which is modified throughout life by social learning as groups of birds continually associate and dissociate. Our study sheds light on the importance of examining signal structure at multiple levels of organisation, and the potential for psittaciform birds as model systems to examine the influence of learning and social environment on acoustic signals.

animal behavior and cognition↗

bioRxiv2022

The topological shape of gene expression across the evolution of flowering plants

Since they emerged ~125 million years ago, flowering plants have evolved to dominate the terrestrial landscape and survive in the most inhospitable environments on earth. At their core, these adaptations have been shaped by changes in numerous, interconnected pathways and genes that collectively give rise to emergent biological phenomena. Linking gene expression to morphological outcomes remains a grand challenge in biology, and new approaches are needed to begin to address this gap. Here, we implemented topological data analysis (TDA) to summarize the high dimensionality and noisiness of gene expression data using lens functions that delineate plant tissue and stress responses. Using this framework, we created a topological representation of the shape of gene expression across plant evolution, development, and environment for the phylogenetically diverse flowering plants. The TDA-based Mapper graphs form a well-defined gradient of tissues from leaves to seeds, or from healthy to stressed samples, depending on the lens function. This suggests there are distinct and conserved expression patterns across angiosperms that delineate different tissue types or responses to biotic and abiotic stresses. Genes that correlate with the tissue lens function are enriched in central processes such as photosynthetic, growth and development, housekeeping, or stress responses. Together, our results highlight the power of TDA for analyzing complex biological data and reveal a core expression backbone that defines plant form and function. Significance statementA grand challenge in biology is to link gene expression to phenotypes across evolution, development, and the environment, but efforts have been hindered by biological complexity and dataset heterogeneity. Here, we implemented topological data analysis across thousands of gene expression datasets in phylogenetically diverse flowering plants. We created a topological representation of gene expression across plants and observed well-defined gradients of tissues from leaves to seeds, or from healthy to environmentally stressed. Using this framework, we identified a core and deeply conserved expression backbone that defines plant form and function, with key patterns that delineate plant tissues, abiotic, and biotic stresses. Our results highlight the power of topological approaches for analyzing complex biological datasets.

plant biology↗

bioRxiv2022

Accurately modeling biased random walks on weighted networks using node2vec+

MotivationAccurately representing biological networks in a low-dimensional space, also known as network embedding, is a critical step in network-based machine learning and is carried out widely using node2vec, an unsupervised method based on biased random walks. However, while many networks, including functional gene interaction networks, are dense, weighted graphs, node2vec is fundamentally limited in its ability to use edge weights during the biased random walk generation process, thus under-using all the information in the network. ResultsHere, we present node2vec+, a natural extension of node2vec that accounts for edge weights when calculating walk biases and reduces to node2vec in the cases of unweighted graphs or unbiased walks. Using two synthetic datasets, we empirically show that node2vec+ is more robust to additive noise than node2vec in weighted graphs. Then, using genome-scale functional gene networks to solve a wide range of gene function and disease prediction tasks, we demonstrate the superior performance of node2vec+ over node2vec in the case of weighted graphs. Notably, due to the limited amount of training data in the gene classification tasks, graph neural networks such as GCN and GraphSAGE are outperformed by both node2vec and node2vec+ Contactarjun.krishnan@cuanschutz.edu Code Availabilityhttps://github.com/krishnanlab/node2vecplus_benchmarks Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2022

Temporal Characteristics of Neonatal Chick Retinal Ganglion Cell Responses: Effects of Luminance, Contrast, and Color

We perform microelectrode array recordings of neonatal chick retina explants and report stimulus-dependent response properties of different retinal ganglion cell (RGC) types to various luminance and contrast adaptation conditions. The isolated single units indicate wavelength-sensitive response properties for all the retinal ganglion cell types recorded from. Responses to different luminance and contrast conditions investigated as a function of wavelength indicates a combination of adaptation and sensitization features in the recorded population of RGCs. We further demonstrate the presence of complementary response properties in most of the RGCs to blue (450 nm) and green (530 nm) light input and infer that luminance, contrast and color information are encoded in a wide variety of metrics such as latency, response event duration and pairwise correlations.

neuroscience↗

bioRxiv2022

Chlamydomonas reinhardtii triose-phosphate/phosphate translocator3 (TPT3): A major chloroplast shunt for the export of fixed carbon and reductant

Modulation of export of photoassimilates from the chloroplast is essential for controlling the distribution of fixed carbon in the cell and maintaining optimum photosynthetic rates. In this study we identified chloroplast triose phosphate/phosphate translocators 2 and 3 (CreTPT2 and CreTPT3) in the green alga Chlamydomonas reinhardtii that exhibited similar substrate specificities but were differentially expressed over the diel cycle. We focused mostly on analyzing CreTPT3 because of its high level of expression and the severe phenotype exhibited by tpt3 relative to the tpt2 mutants. Null mutants for CreTPT3 had a pleiotropic phenotype that impacted growth, photosynthetic activities, metabolite profiles, carbon partitioning, and organelle-specific accumulation of H2O2. These analyses demonstrated that CreTPT3 is a dominant conduit on the chloroplast envelope for the transport of photoassimilate. In addition, CreTPT3 can serve as a safety valve that moves excess reductant out of the chloroplast and appears to be essential for preventing the cells from experiencing oxidative stress and accumulating of reactive oxygen species, even under low/moderate light intensities. Finally, our studies indicate subfunctionalization of the CreTPT transporters and suggest that there are differences in managing the export of photoassimilates from the chloroplasts of Chlamydomonas and vascular plants.

plant biology↗

bioRxiv2022

PyGenePlexus: A Python package for gene discovery using network-based machine learning

PyGenePlexus is a Python package that enables a user to gain insight into any gene set of interest based on a molecular interaction network using supervised machine learning. PyGenePlexus provides predictions of how associated every gene in the network is to the input gene set, offers interpretability by comparing the model trained on the input gene set to models trained on thousands of known gene sets, and returns the network connectivity of the top predicted genes. Availability and Implementationhttps://pypi.org/project/geneplexus/ and https://github.com/krishnanlab/PyGenePlexus Contactarjun@msu.edu

bioinformatics↗

bioRxiv2022

Allopatric montane wren-babblers exhibit similar song notes but divergent vocal sequences

The songs of passerine birds consist of notes temporally arranged into vocal sequences following syntactic structures, and function both in courtship and territorial defense. Geographic barriers are important drivers of avian speciation, and also influence the divergence of song. However, there is relatively little quantitative study of the relationship between geographic barriers and the syntactic structure of vocal sequences. Here, we investigate interspecific divergence in song notes and syntax within a genus of allopatric montane Asian wren-babblers (Spelaeornis). Employing a robust quantitative analytical framework and song recordings from publicly accessible databases, we find that Spelaeornis appear to have undergone diversification in song syntax without divergence in note parameters. Broadly, we find three different syntactic structures across the eight species in the genus, each occurring in a different geographic region in Asia, with two species apparently exhibiting intermediate syntax. Species within the genus appear to possess similar song notes, but subgroups confined to different geographic regions (eg: hills south of the Brahmaputra river) arrange these notes according to different syntactic rules to construct songs. Our computational framework to examine signal structure and diversification across multiple scales of signal organization has potential implications for our understanding of speciation, signal evolution and more broadly in fields such as linguistic diversification.

animal behavior and cognition↗

bioRxiv2022

Modeling clonal evolution and oncogenic dependency in vivo in the context of hematopoietic transformation

Cancer evolution is a multifaceted process involving the acquisition of somatic mutations and progressive epigenetic dysregulation of cellular fate. Both cell-intrinsic mechanisms and environmental interactions provide selective pressures capable of promoting clonal evolution and expansion, with single-cell and bulk DNA sequencing offering increased resolution into this process1-4. Advances in genome editing, single-cell biology and expressed lentiviral barcoding have enabled new insights into how transcriptional/epigenetic states change with clonal evolution5,6. Despite the extensive catalog of genomic alterations revealed by resequencing studies7,8, there remain limited means to functionally model and perturb this evolutionary process in experimental systems9. Here we integrated multi-recombinase (Cre, Flp, and Dre) tools for modeling reversible, sequential mutagenesis from premalignant clonal hematopoiesis to acute myeloid leukemia. We demonstrate that somatic acquisition of Flt3 activating mutations elicits distinct phases of acute and chronic activation resulting in differential cooperativity with Npm1 and Dnmt3a disease alleles. We next developed a generalizable allelic framework allowing for the reversible expression of oncogenic mutations at their endogenous loci. We found that reversal of mutant Flt3 resulted in rapid leukemic regression with distinct alterations in cellular compartments depending upon co-occurring mutations. These studies provide a path to model sequential mutagenesis and deterministically investigate mechanisms of transformation and oncogenic dependency in the context of clonal evolution.

cancer biology↗

bioRxiv2022

A network-based drug repurposing approach identifies new treatment opportunities for the systemic chronic inflammation underlying multiple complex diseases

Complex diseases are associated with a wide range of cellular, physiological, and clinical phenotypes. To advance our understanding of disease mechanisms and our ability to treat these diseases, it is critical to delineate the molecular basis and therapeutic avenues of specific disease phenotypes, especially those that are associated with multiple diseases. Inflammatory processes constitute one such prominent phenotype, being involved in a wide range of health problems including ischemic heart disease, stroke, cancer, diabetes mellitus, chronic kidney disease, non-alcoholic fatty liver disease, and autoimmune and neurodegenerative conditions. While hundreds of genes might play a role in the etiology of each of these diseases, isolating the genes involved in the specific phenotype (e.g., inflammation "component") could help us understand the genes and pathways underlying this phenotype across diseases and predict potential drugs to target the phenotype. Here, we present a computational approach that integrates gene interaction networks, disease-/trait-gene associations, and drug-target information to accomplish this goal. We apply this approach to isolate gene signatures of complex diseases that correspond to chronic inflammation and prioritize drugs to reveal new therapeutic opportunities.

bioinformatics↗

bioRxiv2021

CXCL8/CXCR2 signaling mediates bone marrow fibrosis and represents a therapeutic target in myelofibrosis

Pro-inflammatory signaling is a hallmark feature of human cancer, including in myeloproliferative neoplasms (MPNs), most notably myelofibrosis (MF). Dysregulated inflammatory signaling contributes to fibrotic progression in MF; however, the individual cytokine mediators elicited by malignant MPN cells to promote collagen-producing fibrosis and disease evolution remain yet to be fully elucidated. Previously we identified a critical role for combined constitutive JAK/STAT and aberrant NF-{kappa}B pro-inflammatory signaling in myelofibrosis development. Using single-cell transcriptional and cytokine-secretion studies of primary MF patient cells and two separate murine models of myelofibrosis, we extend this previous work and delineate the role of CXCL8/CXCR2 signaling in MF pathogenesis and bone marrow fibrosis progression. MF patient hematopoietic stem/progenitor cells are enriched in a CXCL8/CXCR2 gene signature and display dose-dependent proliferation and fitness in response to exogenous CXCL8 ligand in vitro. Genetic deletion of Cxcr2 in the hMPLW515L adoptive transfer model abrogates fibrosis and extends overall survival, and pharmacologic inhibition of the CXCR1/2 pathway improves hematologic parameters, attenuates bone marrow fibrosis, and synergizes with JAK inhibitor therapy. Our mechanistic insights provide a rationale for therapeutic targeting of the CXCL8/CXCR2 pathway in MF patients at risk for continued fibrotic progression.

cancer biology↗

bioRxiv2021

Seasonality and interspecific temporal partitioning in a semiarid grassland bat assemblage

Arid and semiarid environments of the world are prone to dramatic seasonal changes that affect the availability of scarce, patchily distributed resources such as water. In response to these changes, animals migrate or partition resources to minimize competition, resulting in temporal patterns within assemblages across multiple scales. Here, we demonstrate that the winter dry season bat assemblage in a semiarid grassland of northwest India exhibits both seasonal changes in composition and temporal avoidance between coexisting species at water bodies. Using a passive acoustic monitoring framework to quantify activity patterns at different points in the season, we show that two species (Rhinolophus lepidus and Tadarida aegyptiaca) exhibit seasonal differences in activity, being more frequently detected in the early and late parts of the dry season respectively. Two other species (Pipistrellus tenuis and Scotophilus heathii) do not exhibit seasonal changes in activity, but structure their diel activity patterns to minimize temporal overlap (and thus competition) at water bodies. These data, some of the first on bats from this region, demonstrate the complex temporal patterns structuring bat assemblages in arid and semiarid biomes. Our results hold promise for monitoring efforts, as a baseline to ascertain how climate change may influence the behavior and ecology of desert and grassland organisms.

ecology↗

bioRxiv2021

Toxoplasma gondii phosphatidylserine flippase complex ATP2B-CDC50.4 critically participates in microneme exocytosis

Regulated microneme secretion governs motility, host cell invasion and egress in the obligate intracellular apicomplexans. Intracellular calcium oscillations and phospholipid dynamics critically regulate micronemes exocytosis. Despite its importance for the lytic cycle of these parasites, molecular mechanistic details about exocytosis are still missing. Some members of the P4-ATPases act as flippases, changing the phospholipid distribution by translocation from the outer to the inner leaflet of the membrane. Here, the localization and function of the repertoire of P4-ATPases was investigated across the lytic cycle of Toxoplasma gondii. Of relevance, ATP2B and the non-catalytic subunit cell division control protein 50.4 (CDC50.4) form a stable heterocomplex at the parasite plasma membrane, essential for microneme exocytosis. This complex is responsible for flipping phosphatidylserine (PS), which presumably acts as a lipid mediator for the organelle fusion with the plasma membrane. DOC2.1, a previously described key egress and invasion factor, is shown here to be affected in its function in egress upon mutation on residues putatively involved in calcium binding. This study points toward the importance of PS in microneme exocytosis and unveils subtle differences in the signaling cascades leading to organelle secretion between intracellular and extracellular parasites to ensure egress and invasion, respectively. Author SummaryBiological membranes display diverse functions, including membrane fusion, which are conferred by a defined composition and organization of proteins and lipids. Apicomplexan parasites possess specialized secretory organelles (micronemes), implicated in motility, invasion and egress from host cells. Microneme exocytosis is already known to depends on phosphatidic acid for its fusion with the plasma membrane. Here we identify a type P4-ATPase and its CDC50 chaperone (ATP2B-CDC50.4) that act as flippase and contribute to the enrichment of phosphatidylserine (PS) in the inner leaflet of the parasite plasma membrane. PS and the previously described C2-containing protein DOC2.1 differentially participate in microneme exocytosis in the context of environmental changes. Overall, our results shed light on the importance membrane homeostasis and lipid composition in controlling microneme secretion.

cell biology↗

bioRxiv2021

Pantothenate biosynthesis is critical for chronic infection by the neurotropic parasite Toxoplasma gondii

Coenzyme A (CoA) is an essential molecule acting in metabolism, post-translational modification, and regulation of gene expression. While all organisms synthesize CoA, many, including humans, are unable to produce its precursor, pantothenate. Intriguingly, like most plants, fungi and bacteria, parasites of the coccidian subgroup of Apicomplexa, including the human and animal pathogen Toxoplasma gondii, possess all the enzymes required for de novo synthesis of pantothenate. Here, the importance of CoA and pantothenate biosynthesis for the acute and chronic stages of T. gondii infection was dissected through genetic, biochemical and metabolomic approaches, revealing that CoA synthesis is essential for T. gondii tachyzoites, due to the parasites inability to salvage CoA or intermediates of the pathway. In contrast, de novo pantothenate synthesis was only partially active in T. gondii tachyzoites, making the parasite reliant on Pan uptake. However, Pan synthesis proved to be crucial for the establishment of chronic infection, offering a promising target for intervention against the persistent stage of T. gondii.

microbiology↗

bioRxiv2021

Patterns of morphological diversification in the Ramphastoidea reveal the dramatic divergence of toucans from a conserved morphotype

BackgroundMorphological traits offer insights into an organisms ecological niche, species interactions, and patterns of community organisation. Pantropical lineages - animals and plants distributed across the three tropical continental regions of Asia, Africa, and America - provide a way to test how different environments and communities influence morphological diversification. Here, we examined a monophyletic group of frugivorous birds, the barbets and toucans (Ramphastoidea), which diversified independently on three continents, to investigate whether clades in each region exhibit similar (phylogenetically constrained) or distinct (ecologically influenced) patterns of morphological diversification. ResultsOur results show that despite differences in community dynamics in these regions, lineage accumulation patterns through time on all three continents are broadly similar, putatively due to phylogenetic niche conservatism. We quantified morphological variation in light of phylogenetic relatedness to further reveal that all barbet lineages across continents occupy a conserved region of morphospace after correcting for variation in size. However, in the Neotropics, one lineage, the toucans, have diverged dramatically from typical barbet space and converged toward (yet are distinct from) the trait space occupied by the distantly related hornbills in Asia and Africa. Additionally, we found no link between climatic variables and morphological traits. We conclude that barbets exhibit a conserved morphotype across continents and have diversified by scaling mainly in body size. However, the absence of other large frugivorous birds may have allowed toucans to diversify into a different region of morphospace of increased bill/wing to tail/wing ratios. ConclusionsA combination of photographic and specimen measurements enabled us to demonstrate the presence of a globally conserved barbet morphotype across three tropical continents. By examining different continental lineages of a single monophyletic bird group, we shed light on the contrasting effects of regional ecological factors and phylogenetic constraints on morphological diversification.

ecology↗