Biology subjects

Kumar, M.

Publications and source records attributed to Kumar, M..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

Microevolution of clade II isolates of Candida auris highlights multifaceted intra-clade heterogeneity in acquiring resistance towards amphotericin B

Candida auris exhibits high-level resistance to amphotericin B (AmB). Mechanisms such as ergosterol biosynthesis malfunction, oxidative damage mismanagement, and increased drug efflux contribute to AmB resistance in C. auris. In this study, we experimentally evolved two East Asian drug-susceptible clade II isolates of C. auris (P2428 and CBS10913T) isolated from different geographical locations to develop resistance against AmB. We analysed alterations in karyotype, genome sequence, and gene expression profiles to uncover the mechanisms driving AmB resistance. The independently evolved clade II adaptors displayed up to 4-16-fold higher MIC50, as compared to the parental cells. AOX2 (alternative oxidase) and the cell wall integrity pathway have been identified as critical in the development of AmB resistance. However, we noted certain intra-clade heterogeneity in the associated mechanisms. While in P2428 adaptors (P-lines), the ergosterol and sphingolipid pathways appear to play a crucial role, this was not the case for CBS10913T adaptors (A-lines), which acquired resistance independent of lipid-associated changes. The transcriptomic, WGS, and phenotypic analyses also confirm that the evolved AmB-resistant isolates follow distinct trajectories for adaptation, Furthermore, unlike the fluconazole-resistant isolates, as reported previously, changes in ploidy do not seem to contribute to the differential mechanisms of AmB resistance. Overall, this study not only provides insights into the mechanisms and pathways involved in AmB resistance but also highlights intra-clade-heterogeneity that exists within clade II of C. auris. ImportanceCandida auris demonstrates significant resistance to amphotericin B (AmB) that stems from factors like alteration of ergosterol biosynthesis, perturbation of the oxidative damage response, etc. A comprehensive understanding of underlying mechanisms can be studied in a holistic manner by subjecting resistant as well as susceptible clinical isolates to a comparative genome-level analysis. An alternate and more dynamic approach is to expose susceptible isolates to a certain concentration of drug which is not lethal but can trigger the resistance mechanisms. In the present study, we evolved C. auris towards AmB and observed novel and differential mechanisms of resistance development, in two different isolates despite belonging to the same clade. This study provides insights into the intra-clade heterogeneous behavior of C. auris towards AmB.

microbiology↗

bioRxiv2023

Genomic consequences of isolation and inbreeding in an island dingo population

Dingoes come from an ancient canid lineage that originated in East Asia around 8000-11,000 years BP. As Australias largest terrestrial predator, dingoes play an important ecological role. A small, protected population exists on a world heritage listed offshore island, Kgari (formerly Fraser Island). Concern regarding the persistence of dingoes on Kgari has risen due to their low genetic diversity and elevated inbreeding levels. However, whole-genome sequencing data is lacking from this population. Here, we include five new whole-genome sequences of Kgari dingoes. We analyze a total of 18 whole genome sequences of dingoes sampled from mainland Australia and Kgari to assess the genomic consequences of their demographic histories. Long (>1 Mb) runs of homozygosity (ROH) -- indicators of inbreeding -- are elevated in all sampled dingoes. However, Kgari dingoes showed significantly higher levels of very long ROH (>5 Mb), providing genomic evidence for small population size, isolation, inbreeding, and a strong founder effect. Our results suggest that, despite current levels of inbreeding, the Kgari population is purging strongly deleterious mutations, which, in the absence of further reductions in population size, may facilitate the persistence of small populations despite low genetic diversity and isolation. However, there may be little to no purging of mildly deleterious alleles, which may have important long-term consequences, and should be considered by conservation and management programs. SIGNIFICANCEA long-standing question in conservation genetics is whether long-term isolation and elevated levels of inbreeding always leads to inevitable population extinction. Here we conduct the first-ever whole-genome analysis of a population of dingoes living in long-term isolation on an island off the coast of Australia (Kgari). We show that these animals are beset by very low genetic diversity, likely the result of extensive inbreeding, and an elevated number of deleterious homozygotes. However, our results suggest that these dingoes are likely purging highly deleterious alleles, which may have allowed them to persist long term despite their extremely small population (<200 individuals).

evolutionary biology↗

bioRxiv2023

iATPSnFR2: a high dynamic range fluorescent sensor for monitoring intracellular ATP

We developed a significantly improved genetically encoded quantitative adenosine triphosphate (ATP) sensor to provide real-time dynamics of ATP levels in subcellular compartments. iATPSnFR2 is a variant of iATPSnFR1, a previously developed sensor that has circularly permuted super-folder GFP inserted between the ATP-binding helices of the{varepsilon} -subunit of a bacterial F0-F1 ATPase. Optimizing the linkers joining the two domains resulted in a [~] 5-6 fold improvement in the dynamic range compared to the previous generation sensor, with excellent discrimination against other analytes and affinity variants varying from 4 M to 500 M. A chimeric version of this sensor fused to either the HaloTag protein or a suitably spectrally separated fluorescent protein, provides a ratiometric readout allowing comparisons of ATP across cellular regions. Subcellular targeting of the sensor to nerve terminals reveals previously uncharacterized single synapse metabolic signatures, while targeting to the mitochondrial matrix allowed direct quantitative probing of oxidative phosphorylation dynamics. Significance StatementAdenosine triphosphate (ATP) is a key metabolite necessary for cellular life. Here we develop a next-generation genetically encoded ratiometric fluorescent ATP sensor that allows subcellular tracking of ATP levels in living cells. The large dynamic range makes it possible to follow the dynamics of this metabolite across cells and subcellular regions under different metabolic stressors. We expect that iATPSnFR2 will provide researchers with exciting new opportunities to study ATP dynamics with temporal and spatial resolution that has, until now, been unavailable.

biochemistry↗

bioRxiv2023

Systematic discovery of protein interaction interfaces using AlphaFold and experimental validation

Structural resolution of protein interactions enables mechanistic and functional studies as well as interpretation of disease variants. However, structural data is still missing for most protein interactions because we lack computational and experimental tools at scale. We thoroughly assessed AlphaFold-Multimer accuracy for structure prediction of interactions involving folded domains binding to short linear motifs from the ELM database. The structure predictions were highly sensitive but not very specific when using small protein fragments. Sensitivity decreased substantially when using long protein fragments or full length proteins with intrinsically disordered regions. We delineated a fragmentation strategy to optimize sensitivity and applied it to interactions between proteins associated with neurodevelopmental disorders. This enabled prediction of highly confident and likely disease-related novel interfaces, but also resulted in many high scoring false positive predictions. Experiments supported predicted interfaces between CREBZF-HCFC1, FBXO23-STX1B, STX1B-VAMP2, ESRRG-PSMC5, PEX3-PEX19, PEX3-PEX16, and SNRPB-GIGYF1 providing novel molecular insights for diverse biological processes. Our work highlights exciting perspectives, but also reveals clear limitations and the need for future developments to maximize the power of Alphafold-Multimer for interface predictions.

systems biology↗

bioRxiv2023

Interaction of SCoV-2 NSP7 or NSP8 alone may cause constriction of the RNA entry channel in NSP12: Implications for novel RdRp inhibitor drug discovery

RNA-dependent RNA polymerase (RdRP) is a critical component of the RNA virus life cycle, including SCoV-2. Among the Coronavirus-encoded proteins, non-structural protein 12 (NSP12) exhibits polymerase activity in collaboration with one unit of NSP7 and two units of NSP8, constituting the RdRp holoenzyme. While there is abundant information on SCoV-2 RdRp-mediated RNA replication, the influence of interplay among NSP12, NSP7, and NSP8 on template RNA binding and primer extension activity remains relatively unexplored and poorly understood. Here, we recreated a functional RdRp holoenzyme in vitro using recombinant SCoV-2 NSP12, NSP7, and NSP8, and established its functional activity. Subsequently, molecular interactions among the NSPs in the presence of a variety of templates and their effects on polymerase activity were studied, wherein we found that NSP12 alone exhibited notable polymerase activity that increased significantly in the presence of NSP7 and NSP8. However, this activity was completely shut down, and the template RNA-primer complex was detached from NSP12 when one of the two cofactors was present. Through computational analysis, we found that the template RNA entry channel was more constricted in the presence of one of the two cofactors, which was relatively more constricted in the presence of NSP8 compared to that in the presence of NSP7. In conclusion, we report that NSP7 and NSP8 together synergise to enhance the activity of NSP12, but antagonise when present alone. Our findings have implications for novel drug development, and compounds that obstruct the binding of NSP7 or NSP8 to NSP12 can have lethal effects on viral RNA replication.

molecular biology↗

bioRxiv2023

Length-dependent RNA foci formation and RAN translation are associated with SCA12 disorder

Spinocerebellar ataxia type-12 (SCA-12) is a neurodegenerative disease caused by tandem CAG repeat expansion in the 5-UTR/non-coding region of PPP2R2B. Molecular pathology of SCA12 has not been studied in the context of CAG repeats and no appropriate models exist. We found in human SCA12-iPSC derived neuronal lineage that expanded CAG in PPP2R2B transcript forms nuclear RNA foci and were found to sequester variety of proteins. Further, the ectopic expression of transcript containing varying length of CAG repeats exhibits non-canonical Repeat Associated Non-AUG (RAN) translation in multiple frames in HEK293T cells, which was further validated in patient-derived neural stem cells using specific antibodies. mRNA sequencing of the SCA12 and control neurons have shown a network of crucial transcription factors affecting neural fate, in addition to alteration of various signaling pathways involved in neurodevelopment. Altogether, this study identifies the molecular signatures of spinocerebellar ataxia type-12 disorder using patient-derived neuronal cell lines.

neuroscience↗

bioRxiv2023

Defects in Mitochondrial Biogenesis Drive Mitochondrial Alterations in PINK1-deficient Human Dopamine Neurons

Mutations and loss of activity in the protein kinase PINK1 play a role in the pathogenesis of Parkinsons disease (PD). PINK1 regulates many aspects of mitochondrial quality control including mitochondrial autophagy (mitophagy), fission, fusion, transport, and biogenesis. Defects in mitophagy are though to play a predominant role in the loss of dopamine (DA) neurons in PD. Here we show that, although there are defects in mitophagy in human DA neurons lacking PINK1, mitochondrial deficits induced by the absence of PINK1 are primarily due to defects in mitochondrial biogenesis. Upregulation of PARIS and the subsequent down regulation of PGC-1 accounts for the mitochondrial biogenesis defects. CRISPR/Cas9 knockdown of PARIS completely restores the mitochondrial biogenesis defects and mitochondrial function without impacting the deficits in mitophagy due to the absence of PINK1. These results highlight the importance mitochondrial biogenesis in the pathogenesis of PD due to inactivation or loss of PINK1 in human DA neurons.

neuroscience↗

bioRxiv2023

Non-micellar ganglioside GM1 induces an instantaneous conformational change in Aβ42 leading to the modulation of the peptide amyloid-fibril pathway

Alzheimers disease is a progressive degenerative condition that mainly affects cognition and memory. Recently, distinct clinical and neuropathological phenotypes have been identified in AD. Studies revealed that structural variation in A{beta} fibrillar aggregates correlates with distinct disease phenotypes. Moreover, environmental surroundings, including other biomolecules such as proteins and lipids, have been shown to interact and modulate A{beta} aggregation. Model membranes containing ganglioside (GM1) clusters are specifically known to promote A{beta} fibrillogenesis. This study unravels the modulatory effect of non-micellar GM1, a glycosphingolipid frequently released from the damaged neuronal membranes, on A{beta}42amyloid fibril formation. Using far-UV circular dichroism experiments, we observed a spontaneous change in the peptide secondary structure from random-coil to {beta}-turn with subsequent generation of predominantly {beta}-sheet-rich species upon interaction with GM1. Thioflavin-T (ThT) fluorescence assays further indicated that GM1 interacts with the amyloidogenic A{beta}42 primary nucleus leading to a possible formation of GM1-modified A{beta}42 fibril. Statistically, no significant difference in toxicity to RA-differentiated SH-SY5Y cells was observed between A{beta}42 fibrils and GM1-tweaked A{beta}42 aggregates. Moreover, GM1-modified A{beta}42 aggregates exhibited prion-like properties in catalyzing the amyloid fibril formation of both major isomers of A{beta}, A{beta}40, and A{beta}42.

biophysics↗

bioRxiv2023

Guild and Niche Determination Enable Targeted Alteration of the Microbiome

Microbiome science has greatly contributed to our understanding of microbial life and its essential roles for the environment and human health1-5. However, the nature of microbial interactions and how microbial communities respond to perturbations remains poorly understood, resulting in an often descriptive and correlation-based approach to microbiome research6-8. Achieving causal and predictive microbiome science would require direct functional measurements in complex communities to better understand the metabolic role of each member and its interactions with others. In this study we present a new approach that integrates transcription and translation measurements to predict competition and substrate preferences within microbial communities, consequently enabling the selective manipulation of the microbiome. By performing metatranscriptomic (metaRNA-Seq) and metatranslatomic (metaRibo-Seq) analysis in complex samples, we classified microbes into functional groups (i.e. guilds) and demonstrated that members of the same guild are competitors. Furthermore, we predicted preferred substrates based on importer proteins, which specifically benefited selected microbes in the community (i.e. their niche) and simultaneously impaired their competitors. We demonstrated the scalability of microbial guild and niche determination to natural samples and its ability to successfully manipulate microorganisms in complex microbiomes. Thus, the approach enhances the design of pre- and probiotic interventions to selectively alter members within microbial communities, advances our understanding of microbial interactions, and paves the way for establishing causality in microbiome science.

microbiology↗

bioRxiv2023

Lipidome unsaturation affects the morphology and proteome of the Drosophila eye.

While the proteome of an organism is largely determined by the genome, the lipidome is shaped by a poorly understood interplay of environmental factors and metabolic processes. To gain insights into the underlying mechanisms, we analyzed the impacts of dietary lipid manipulations on the ocular proteome of Drosophila melanogaster. We manipulated the lipidome with synthetic food media that differed in the supplementation of an equal amount of saturated or polyunsaturated triacylglycerols. This allowed us to generate flies whose eyes had a highly contrasting length and unsaturation of glycerophospholipids, the major lipid class of biological membranes, while the abundance of other membrane lipid classes remained unchanged. By bioinformatically comparing the resulting ocular proteomic trends and contrasting them with the impacts of vitamin A deficiency, we identified ocular proteins whose abundances are differentially affected by lipid saturation and unsaturation. For instance, we unexpectedly identified a group of proteins that have muscle-related functions and increase their abundances in the eye upon lipidome unsaturation but are unaffected by lipidome saturation. Moreover, we identified two differentially lipid-responsive proteins involved in stress responses, Turandot A and Smg5, whose abundances decrease with lipid unsaturation. Lastly, we discovered that the ocular lipid class composition is robust to dietary changes and propose that this may be a general homeostatic feature of the organization of eukaryotic tissues, while the length and unsaturation of fatty acid moieties is more variable to compensate environmental challenges. We anticipate that these insights into the molecular responses of the Drosophila eye proteome to specific lipid manipulations will guide the genetic dissection of the mechanisms that maintain visual function when the eye is exposed to dietary challenges.

neuroscience↗

bioRxiv2023

Computational and experimental hunt for expansion prone tandem CNG repeats in human genomes

IntroductionSpinocerebellar ataxias (SCA) are a group of clinically and genetically heterogeneous neurodegenerative disorders. Tandem repeat expansion is the pathogenic mutation in most of SCA cases. The pathophysiology of SCAs is still not completely defined due to the lack of genetic mutation in around 50% of cases worldwide. These uncharacterized cases must be genetically diagnosed for a better understanding and future treatment purposes. In this study, we tried a combination of computational and experimental approaches to find out novel CNG repeat loci that may be associated with SCAs. MethodologyWe investigate the human reference genome (hg-37) to find out all the possible CNG repeats present in more than 3 continuous uninterrupted units and annotated their functional locations. For experiment purposes, we targeted 52 loci from exonic and UTR regions and screened them in our 100 control samples through fragment analysis to know their polymorphic status. All the highly polymorphic loci were further investigated in 100 patient samples to know any large repeat expansion. ResultsThere are 15069 CNG repeat loci present in the human genome. After the examination of 52 loci in the control samples, 19 loci showed a highly polymorphic repeat pattern and were screened in patients. The 1000 genome different population data also suggested the polymorphic status in the available 15 loci data. From the GTEx database, 18 loci proposed the expression in the brain, suggesting any variation in these genes may cause neurological disorders. ConclusionWe tried a different kind of approach to find out tandem repeat expansion mutation in a cost-effective manner. Although we were unable to identify any disease-causing mutation in our patient cohort recently, various studies from different populations of the world have vouched for the genetic changes in these genes like GLS, RAI1, GIPC1, and CNKSR2 resulted in neurological disorders. Moreover, publications on the same identified repeats in GIPC1 for OPMD and GLS for ataxia with developmental delay, confirm the hypothesis to evaluate these repeat loci in different populations and other neurological disorders to identify novel targets.

genetics↗

bioRxiv2023

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses

The COVID-19 pandemic has seen large-scale pathogen genomic sequencing efforts, becoming part of the toolbox for surveillance and epidemic research. This resulted in an unprecedented level of data sharing to open repositories, which has actively supported the identification of SARS-CoV-2 structure, molecular interactions, mutations and variants, and facilitated vaccine development and drug reuse studies and design. The European COVID-19 Data Platform was launched to support this data sharing, and has resulted in the deposition of several million SARS-CoV-2 raw reads. In this paper we describe (1) open data sharing, (2) tools for submission, analysis, visualisation and data claiming (e.g. ORCiD), (3) the systematic analysis of these datasets, at scale via the SARS-CoV-2 Data Hubs as well as (4) lessons learned. As a component of the Platform, the SARS-CoV-2 Data Hubs enabled the extension and set up of infrastructure that we intend to use more widely in the future for pathogen surveillance and pandemic preparedness.

bioinformatics↗

bioRxiv2023

Structural insights into TRPV4-Rho GTPase signaling complex function and disease

Crosstalk between ion channels and small GTPases is critical during homeostasis and disease1, but little is known about the structural underpinnings of these interactions. TRPV4 is a polymodal, calcium-permeable cation channel that has emerged as a potential therapeutic target in multiple conditions2-5. Gain-of-function mutations also cause hereditary neuromuscular disease6-11. Here, we present cryo-EM structures of human TRPV4 in complex with RhoA in the apo, antagonist-bound closed, and agonist-bound open states. These structures reveal the mechanism of ligand-dependent TRPV4 gating. Channel activation is associated with rigid-body rotation of the intracellular ankyrin repeat domain, but state-dependent interaction with membrane-anchored RhoA constrains this movement. Notably, many residues at the TRPV4-RhoA interface are mutated in disease and perturbing this interface by introducing mutations into either TRPV4 or RhoA increases TRPV4 channel activity. Together, these results suggest that the interaction strength between TRPV4 and RhoA tunes TRPV4-mediated calcium homeostasis and actin remodeling, and that disruption of TRPV4-RhoA interactions leads to TRPV4-related neuromuscular disease, findings that will guide TRPV4 therapeutics development.

biophysics↗

bioRxiv2023

Ketogenic diet prevents sucrose withdrawal-induced anxiety-like behaviour in male mice

Sugar bingeing has been shown to induce withdrawal effects when sugar is no longer available in the diet. In this study, we investigated the sex differences in sugar-addiction-like behaviour and the effects of the ketogenic diet on these outcomes. We used the two-bottle sucrose choice paradigm as a pre-clinical sucrose overeating and withdrawal model. Female mice consumed more sucrose than males when given free access to water and 10% sucrose for four weeks. One week of sucrose withdrawal after four weeks of consecutive sucrose overeating showed anxiety-like behaviour in male mice. However, the ketogenic diet did not affect sucrose overconsumption in males and females but prevented the sucrose withdrawal-induced anxiety-like behaviour in male mice with a concomitant increase in cFos mRNA in the prefrontal cortex. These findings provide evidence of sex differences in sucrose addiction-like behaviour and also indicate that a ketogenic diet may prevent sucrose withdrawal-induced anxiety-like behaviour in males. However, further research is needed to explore the underlying molecular mechanisms driving sex differences in sugar-addiction-like behaviour and the anxiolytic effects of the ketogenic diet.

neuroscience↗

bioRxiv2023

Eye proteome of Drosophila melanogaster

The Drosophila melanogaster eye is a popular model to elucidate the molecular mechanisms that underlie the structure and function of the eye as well as the causes of retinopathies. For instance, the Drosophila eye has been used to investigate the impacts of ageing and environmental stresses such as light-induced damage or dietary deficiencies. Moreover, large-scale screens have isolated genes whose mutation causes morphological and functional ocular defects, which includes key components of the phototransduction cascade. However, the proteome of the Drosophila eye is poorly characterized. Here, we used GeLC-MS/MS to quantify 3516 proteins he adult Drosophila melanogaster eye and provide a generic and expandable resource for further genetic, pharmacological, and dietary studies.

neuroscience↗

bioRxiv2023

Eggplant's chlorogenic acid provides resistance against the tropical armyworm

Lepidopteran pests are the major crop devastators. Farmers have to resort to heavy synthetic pesticide application for their control. It increases the pesticide residue contamination on produce and causes health hazards. Synthetic pesticides also endanger beneficial insects and pollute the environment. Therefore, the use of safe and eco-friendly botanicals as biopesticides is rapidly increasing. Despite their high demand, only a few botanicals are commercially available. Consequently, biopesticide discovery research boomed in the last decade. Spodoptera litura Fabricius (armyworm) is a polyphagous multi-insecticide-resistant lepidopteran pest. It is a serious concern for several commercially important crops. In this study, we employed a chemical ecology approach to discover a biopesticide against it. As a biopesticide source, we explored secondary metabolite-rich Solanum melongena L. (eggplant), one of the armyworms hosts. We found that the armyworm larvae show differential occurrence on seven eggplant varieties; the Himalayan eggplant variety RC-RL-22 (RL22) showed no armyworm infestation. When reared in a no-choice condition on RL22, larval mortality was two-fold higher, and mass was three-fold lower than the varieties showing high infestation. We tested whether RL22s secondary metabolite(s) were associated with this hampered larval performance. Using LC-ESI-QTOF-based non-targeted metabolomics of eggplant varieties, we identified candidate metabolites. 5-O-caffeoylquinic acid (chlorogenic acid; CGA) showed a strong negative correlation (r= -0.88; p= 0.008) with the larval performance. CGA-spiked (average physiological concentration) artificial diet (CGA-AD)-fed larvae showed a three-fold mass reduction and two-fold mortality increase than the control artificial diet (AD)-fed larvae; pupation and eclosion also significantly reduced (1.3-fold and 1.4-fold, respectively) in the CGA-ingested larvae. We used a reverse genetics approach to assess the in planta insecticidal potential of CGA. When RL22s CGA biosynthesis gene hydroxycinnamoyl-CoA quinate transferase (SmHQT) was silenced using virus-induced gene silencing (VIGS), CGA levels decreased by three-fold. This CGA depletion rendered RL22 two-fold armyworm-susceptible than controls. Foliar CGA application restored RL22s armyworm resistance. Overall, this study showed that CGA exhibits larvicidal properties against the armyworm. It is also safe for beneficial organisms. CGA is a well-known dietary supplement and an antioxidant for humans. Thus, it is safe for human consumption. Together, high CGA-containing varieties can be used to reduce the armyworm infestation risk. CGA is a promising biopesticide candidate for the field trial phase against the lepidopteran pests, especially armyworm. If successful, it can be integrated into the pest control measures.

plant biology↗

bioRxiv2023

Genomic signatures of bottleneck and founder effects in dingoes

Dingoes arrived in Australia during the mid-Holocene and are the native top-order terrestrial predator on the mainland and some offshore islands. Although dingoes subsequently spread across the continent, the initial founding population(s) could have been small. To investigate this hypothesis, we examined the potential signatures of bottlenecks and founder effects in dingoes by sequencing the whole genomes of three dingoes and also obtaining the genome data from nine additional dingoes and 56 canines, including wolves, village dogs and breed dogs, and examined the signatures of bottlenecks and founder effects. We found that the nucleotide diversity of dingoes was low, and 36% less than highly inbred breed dogs and 3.3 times lower than wolves. The number of runs of homozygosity (RoH) segments in dingoes was 1.6 to 4.7 times higher than in other canines. Whilst examining deleterious mutational load, we observed that dingoes carried elevated ratios of nonsynonymous-to-synonymous diversities, significantly higher numbers of homozygous deleterious Single Nucleotide Variants (SNVs), and increased numbers of loss of function SNVs, compared to breed dogs, village dogs, and wolves. These results suggest dingoes experienced a severe bottleneck, potentially caused by the limited number of founding individuals. While many studies observe less diversity and a higher number of deleterious mutations in domesticated populations compared to their wild relatives, we observed the opposite - .i.e. wild dingoes have lower diversity and a greater number of harmful mutations than domesticated dogs. Our findings can be explained by bottlenecks and founder effects during the establishment of dingoes on mainland Australia. These findings highlight the need for conservation-based management of dingoes and need for wildlife managers to be cognisant of these findings when considering the use of lethal control measures across the landscape.

evolutionary biology↗

bioRxiv2023

Constrained dynamics of oligonucleotides in the phase-separated droplets

Phase-separated droplets are excellent means of compartmentalizing functional molecules and have been shown as excellent models for protocells. Although complex functions based on oligonucleotides have been studied, we still lack an understanding of how the oligonucleotide dynamics are affected by the condensed internal environment of these droplets. Particularly, we lack high-resolution experimental measurements of the dynamical parameters that control oligonucleotide diffusion inside the phase-separated droplets. In addition, there is no clarity on how these dynamical parameters differ in the charged (coacervates) vs non-charged (aqueous two-phase system, ATPS) environment of these droplets. In this study, using fluorescence correlation spectroscopy (FCS), we demonstrate the constrained dynamics of oligonucleotides inside membraneless phase-separated droplets at an unprecedented resolution. We further compare transport properties at different lengths of oligonucleotides as well as salt concentrations. We observe that among all the parameters the oligonucleotides caging (spatial restriction in the movement) inside the matrix has a considerable impact on the diffusive dynamics. Our study provides a way of unravelling, quantifying and understanding physical parameters governing the polymer transport dynamics inside the phase-separated droplets.

biophysics↗