Biology subjects

Sharma, A.

Publications and source records attributed to Sharma, A..

At least 253 records · Page 14Linked to original sources

bioRxiv2023

qTAG: An adaptable CRISPR-based endogenous tagging protocol using optimized repair cassettes

Endogenous tagging makes it possible to study a proteins localization, dynamics, and function within its native regulatory context. This is typically accomplished via CRISPR, which involves inserting a sequence encoding a functional tag into the reading frame of a gene. However, this process is often inefficient. Here, we introduce the "quickTAG," or qTAG system, a versatile collection of optimized repair cassettes designed to make CRISPR-mediated tagging more accessible. By including a desired tag sequence linked to a selectable marker in the cassette, integrations can be quickly isolated post-editing. The core sequence scaffold within these constructs incorporates several key features that enhance flexibility and ease of use, such as: specific cassette designs for N- and C-terminus tagging; standardized cloning sequences to simplify the incorporation of homology arms for HDR or MMEJ-based repairs; restriction sites next to each genetic element within the cassette for easy modification of tags and selectable markers; and the inclusion of lox sites flanking the selectable marker to allow for marker gene removal following integration. We showcase the versatility of these cassettes with a diverse range of tags, demonstrating their applications in fluorescence imaging, proximity-dependent biotinylation, epitope tagging, and targeted protein degradation. The adaptability of this scaffold is also exhibited by incorporating novel tags such as mStayGold, which offer enhanced brightness and photostability, reconciling prolonged live-cell imaging of proteins at their endogenous levels. Finally, by leveraging the restriction sites, entirely distinct cassette structures and editing schemes were developed. These enabled scenarios that included conditional expression tagging, selectable knockout tagging, and safe-harbor expression. Our existing and forthcoming collection of plasmids will be accessible through Addgene. It includes ready-to-use constructs targeting common subcellular marker genes, as well as an assortment of tagging cassettes for the tagging of genes of interest. The qTAG system offers an accessible framework to streamline endogenous tagging and will serve as an open resource for researchers to adapt and tailor for their own experiments.

molecular biology↗

bioRxiv2023

A possible mechanistic insight on how Compromised Hydrolysis of Triacylglycerol 7 (CHT7) restrains the involvement of it's DNA binding CXC domain from quiescence repression

CHT7 is a regulator of quiescence repression and TAG degradation between the nitrogen deprived and the nitrogen replenished states in Chlamydomonas reinhardtii. Initially it was thought that the CHT7s repression activity is managed by its DNA binding CXC domain which is a tandem repeat of two cysteine rich subdomains. Later, it was found that the CXC (CHT7_CXC) domain is effectively dispensable for CHT7s activities. Rather, CHT7s predicted protein binding domains are proposed to be involved in gene regulation activities by binding through other repressors in the cell. Yet, it remains unclear why and how CHT7 manages to refrain its own CXC domain from participating in any transcriptional activities. The question becomes more intriguing, because CXC binding regions are available in promoter regions of some of the misregulated genes in the CHT7 mutant (cht7). Through the combination of biophysical experiments and molecular dynamics approaches, we have studied the DNA recognition behavior of CHT7_CXC. The results show that CHT7_CXC domain is highly selective towards DNA sequences and this selectivity is imparted due to the differential binding abilities of the CXC subdomains. Further, to understand if the case is - that CXC looses its DNA binding capabilities in the vicinity of other repressor molecules, we carried out CHT7_CXCs DNA binding stability test by simulating the spatial constraint conditions using the AsLOV2- CXC fusion. Our test results show limited ability of CHT7_CXC to withstand steric forces and provide insights to why and how algal cells may hold back CHT7_CXCs indulgence in quiescence repression. SignificanceMicroalgae, under nutrient rich conditions, provide biomass. Whereas, nutrient deprivation leads to accumulation of biofuel feedstock, but cells enter quiescence. Net enhancement in feedstock, therefore relies on the precision of the quiescence regulator. In Chlamydomonas reinhardtii, CHT7 is a central regulator of quiescence. Surprisingly, rather than using its own DNA binding domain (DBD) for the regulatory activities, CHT7 recruits external transcriptional regulators using its non DBDs. To ensure smooth functioning, CHT7s DBD must rapidly switch to inactive form. Modifications in DNA binding profiles of DBDs due to non DBDs are seen in transcription factors of many organisms. The switching mechanism discussed could therefore be a generic approach of timely regulation of individual components of the complex transcriptional machineries.

biophysics↗

bioRxiv2023

Spontaneous network transitions predict somatosensory perception

Sensory perception is essential for transforming incoming information in the brain into targeted behavior. Our brains are everlastingly active, and variations in perception are ubiquitously associated with human behavioral performance. Previous studies indicate that changes in spontaneous neural activity within local sensory areas correlate with the perception of ambiguous stimuli. However, the contribution of whole brain spontaneous networks to perception is not well understood. Using an ambiguous tactile temporal discrimination task, we demonstrate that the interaction between wholebrain networks in the seconds of the spontaneous pre-stimulus period also contributes to perception during the task. Transitions to a frontal and a multi-frequency network across the brain are essential for the correct percept. Conversely, incorrect percepts are mainly preceded by transitions to an alphaparietal network. Brain transitions occur faster during the period before stimulus presentation for correct stimuli detection, suggesting the need for enhanced network flexibility during this phase. Significance statementOur brain is constantly engaged in processing sensory input and translating it into sensory perceptions. When confronted with ambiguous sensory information, individuals do not always have the same perceptual experience. We demonstrate that brain network transitions to frontal areas are essential for the correct percept. Conversely, incorrect percepts are mainly preceded by transitions to an alpha-parietal network. Correct stimuli detections are characterized by faster transitions, suggesting the need for enhanced network flexibility. These results extend our knowledge of perception by pointing to the relevance of whole-brain spontaneous networks and their dynamic properties.

neuroscience↗

bioRxiv2023

Acid Ceramidase Inhibitor LCL-805 Antagonizes Akt Signaling and Promotes Iron-Dependent Cell Death in Acute Myeloid Leukemia

Acute myeloid leukemia (AML) is an aggressive hematologic malignancy requiring urgent treatment advancements. Ceramide is a cell death-promoting signaling lipid that plays a central role in therapy-induced cell death. Acid ceramidase (AC), a ceramide-depleting enzyme, is overexpressed in AML and promotes leukemic survival and drug resistance. The ceramidase inhibitor B-13 and next-generation lysosomal-localizing derivatives termed dimethylglycine (DMG)-B-13 prodrugs have been developed but remain untested in AML. Here, we report the in vitro anti-leukemic efficacy and mechanism of DMG-B-13 prodrug, LCL-805, across AML cell lines and primary patient samples. LCL-805 inhibited AC enzymatic activity, increased total ceramides, and reduced sphingosine levels. A median EC50 value of 11.7 M was achieved for LCL-805 in cell viability assays across 32 human AML cell lines. As a single agent tested across a panel of 71 primary AML patient samples, a median EC50 value of 15.8 M was achieved. Exogenous ceramide supplementation with C6-ceramide nanoliposomes, which is entering phase I/II clinical trial for relapsed/refractory AML, significantly enhanced LCL-805 killing. Mechanistically, LCL-805 antagonized Akt signaling and led to iron-dependent cell death distinct from canonical ferroptosis. These findings elucidated key factors involved in LCL-805 cytotoxicity and demonstrated the potency of combining AC inhibition with exogenous ceramide.

cancer biology↗

bioRxiv2023

Efficient axonal trafficking of endolysosomes depends on the balanced ratio of microtubule tyrosination and detyrosination

In neurons, the microtubule (MT) cytoskeleton forms the basis for long-distance protein transport from the cell body into and out of dendrites and axon. To maintain neuronal polarity, the axon initial segment (AIS) serves as a physical barrier, separating the axon from the somatodendritic compartment and acting as a filter for axonal cargo. Selective trafficking is further instructed by axonal enrichment of MT post-translational modifications, which affect MT dynamics and the activity of motor proteins. Here, we compared two knockout mouse lines lacking the respective enzymes for MT tyrosination and detyrosination and we found that both knockouts led to a shortening of the AIS. Neurons from both lines also showed an increased immobile fraction of endolysosomes present in the axon, whereas mobile organelles displayed shortened run distances in the retrograde direction. Overall, our results highlight the importance of maintaining the balance of tyrosinated/detyrosinated MT for proper AIS length and axonal transport processes. Summary StatementDespite opposite effects on microtubule dynamics, shifting the balance of microtubule tyrosination/detyrosination in either direction resulted in surprisingly similar defects in axonal organelle transport.

neuroscience↗

bioRxiv2023

Telomeres control regulation of the human Telomerase (hTERT) gene through non-telomeric TRF2 and independent of Telomere looping

The function of the human telomerase reverse transcriptase (hTERT) in the synthesis and maintenance of chromosome ends, or telomeres, is widely understood. Whether and how telomeres, on the other hand, influence hTERT regulation is relatively less studied. We found hTERT was transcriptionally altered depending on telomere length (TL). This resulted from TL-dependent binding of TRF2 between telomeres and the hTERT promoter. hTERT promoter-bound TRF2 was non-telomeric and did not involve the looping of telomeres to the hTERT promoter. Cell lines from different tissue types (fibrosarcoma (HT1080), colon cancer (HCT116), and breast cancer (MDA-MB-231), engineered for either telomere elongation/shortening gave increase/decrease in hTERT, respectively. Mechanistically, we show hTERT promoter-bound non-telomeric TRF2 recruits the canonical PRC2-complex inducing repressor histone H3K27-trimethylation in a TL-dependent fashion. This was further supported by TL-dependent promoter activity from an exogenously inserted hTERT reporter. Increase in TL over days followed by gradual decline, resulted in activation followed by repression of hTERT in a concerted manner, further implicating TL as a key factor for hTERT regulation. Notably on reprogramming primary fibroblasts to induced pluripotent stem cells (iPSCs), TRF2 loss from the hTERT promoter was evident along with telomere elongation and hTERT upregulation. Conversely, on telomere shortening in iPSCs, hTERT promoter-bound TRF2 was restored with marked reduction in hTERT further supporting the causal role of TL in hTERT transcription. Mechanisms of tight control of hTERT by TL shown here are likely to have major implications in telomere-related physiologies, particularly, cancer, ageing and pluripotency. TeaserTelomere length controls hTERT expression by modulating TRF2 distribution and PRC2-mediated repression, highlighting a self-regulatory mechanism in cancer.

cancer biology↗

bioRxiv2023

Alpha-synuclein expression in neuron modulates the Japanese encephalitis virus infection

Japanese encephalitis virus (JEV) stands as a prominent vector-borne zoonotic pathogen, displaying neurotropism and eliciting Parkinsons disease (PD)-like symptoms among most symptomatic survivors. A characteristic feature of PD is aggregation of mutated -synuclein (-syn) that damages the dopaminergic neurons. Considering this link between JEV-induced PD-like symptoms and -syn pathogenesis, we explored the role of -syn in JEV infectivity in neuronal cells. Our investigation revealed significant increase in endogenous -syn expression in JEV-infected cells. Additionally, treatment with exogenous -syn (Exo-syn) led to a substantial reduction in JEV replication, suggesting its anti-JEV effect. Furthermore, Exo-syn treatment led to the upregulation of superoxide dismutase 1 (SOD1) and reduction in reactive oxygen species (ROS). The results were validated by endogenous -syn-silencing, that decreased SOD1 level and raised ROS level in neuronal cells. Similarly, the SOD1 inhibition via LCS-1 also intensified ROS and JEV infection. Overall, our results suggest that -syn exerts an anti-JEV effect by regulating protein involved in oxidative stress inside neuronal cells. This study contributes valuable insights into the interplay between -syn expression and JEV infectivity, shedding light on avenues to further investigate the potential role of -syn in JEV pathogenesis. ImportanceJapanese encephalitis virus (JEV) poses significant threat particularly to children. Despite extensive research efforts, the development of effective treatments against JEV has been impeded. One of the major setbacks is a lack of comprehensive understanding of neurotropism. The study focuses on alpha synuclein (-syn), a neuronal protein, and aims to determine its role in JEV pathogenesis. Present study reveals that host cell upregulates -syn in response of JEV infection. -syn restrains JEV propagation by modulating superoxide dismutase 1 (SOD1) expression which further blocks JEV-induced ROS generation. Endogenous -syn silencing led to decrease in SOD1 expression and increased viral titer. -syn plays crucial role in counteracting oxidative stress through SOD1, which is essential for limiting JEV replication. This study provides broader implications for antiviral strategies and its possible role in neurodegenerative diseases; however, there is still much to explore, particularly regarding its aggregation kinetics in JEV infection.

microbiology↗

bioRxiv2023

Predicting Long and Short Duration Beta Bursts from Subthalamic Nucleus Local Field Potential Activity in Parkinson's Disease

Neural activities within the beta frequency range (13-30 Hz) are not stationary, but occur in transient packets known as beta bursts. Parkinsons disease (PD) is characterized by the occurrence of beta bursts of increased duration and amplitude within the cortico-basal ganglia network. The pathophysiological importance of beta bursts is exemplified by the fact that they serve as a clinically useful feedback signal in beta amplitude triggered adaptive Deep Brain Stimulation (aDBS). Prolonged duration beta bursts are closely associated with motor impairments in PD, whilst bursts of shorter duration may have a physiological role. Consequently, we aimed to develop a deep learning-based pipeline capable of predicting long (> 150ms) and short (< 150ms) duration beta bursts from subthalamic nucleus local field potential (LFP) recordings. Our approach achieved promising accuracy values of 87% and 85.2% in two patients implanted with a DBS device that was capable of long-term wireless LFP sensing. Our findings highlight the feasibility of prolonged beta burst prediction and could inform the development of a new type of intelligent DBS approach with the capability of delivering stimulation only during the occurrence of prolonged bursts.

bioengineering↗

bioRxiv2023

Circulating Platelets Modulate Oligodendrocyte Progenitor Cell Differentiation During Remyelination

Revealing unknown cues that regulate oligodendrocyte progenitor cell (OPC) function in remyelination is important to optimise the development of regenerative therapies for multiple sclerosis (MS). Platelets are present in chronic non-remyelinated lesions of MS and an increase in circulating platelets has been described in experimental autoimmune encephalomyelitis (EAE) mice, an animal model for MS. However, the contribution of platelets to remyelination remains unexplored. Here we show platelet aggregation in proximity to OPCs in areas of experimental demyelination. Partial depletion of circulating platelets impaired OPC differentiation and remyelination, without altering blood-brain barrier stability and neuroinflammation. Transient exposure to platelets enhanced OPC differentiation in vitro, whereas sustained exposure suppressed this effect. In a mouse model of thrombocytosis (CALRHET), there was a sustained increase in platelet aggregation together with a reduction of newly-generated oligodendrocytes following toxin-induced demyelination. These findings reveal a complex bimodal contribution of platelet to remyelination and provide insights into remyelination failure in MS.

neuroscience↗

bioRxiv2023

Deep Learning for Protein Peptide bindingPrediction: Incorporating Sequence, Structural andLanguage Model Features

Protein-peptide interactions play a crucial role in various cellular processes and are implicated in abnormal cellular behaviors leading to diseases such as cancer. Therefore, understanding these interactions is vital for both functional genomics and drug discovery efforts. Despite a significant increase in the availability of protein-peptide complexes, experimental methods for studying these interactions remain laborious, time-consuming, and expensive. Computational methods offer a complementary approach but often fall short in terms of prediction accuracy. To address these challenges, we introduce PepCNN, a deep learning-based prediction model that incorporates structural and sequence-based information from primary protein sequences. By utilizing a combination of half-sphere exposure, position specific scoring matrices, and pre-trained transformer language model, PepCNN outperforms state-of-the-art methods in terms of specificity, precision, and AUC. The PepCNN software and datasets are publicly available at https://github.com/abelavit/PepCNN.git.

bioinformatics↗

bioRxiv2023

De novo genome assembly of the saw-scaled viper Echis carinatus, a medically important venomous snake in the Indian Subcontinent

Echis carinatus is a widely distributed venomous snake in the Indian subcontinent. It is one of the "Big Four" snake species responsible for mortality and severe health complications caused by envenomations. Given the significance of the species for human health, we assembled and annotated the whole genome of E. carinatus. Using long reads for assembly and short reads for correction, we achieved a highly contiguous 1.57Gb assembly, with a contig N50 of 17.1 Mb and scaffold N50 of 23.5 Mb. We could map 96.58% of our reads back to the assembled genome, and Benchmarking Universal Single-Copy Orthologs (BUSCO) score of 97.4%, indicates near completeness. 48.59% of the genome had repeat elements. The predominant types of repeats include retrotransposons (LINEs, SINEs and LTR elements), DNA transposons and satellite DNA (SSRs). Additionally, we conducted a gene prediction analysis, identifying a total of 26,711 protein-coding genes. These genes included alternatively spliced products, leading to the prediction of 31,106 proteins, 77.6% of which were successfully annotated using Blastp and InterProScan. Out of the total predicted gene set, we identified 119 toxin-coding genes, crucial for venom toxin production in the species. The acquisition of toxin sequence-based information resulted in a valuable dataset of genes that are involved in venom production in E. carinatus. This dataset advances our understanding of the biological processes underlying venom production and lays the foundation for the development of new antivenom formulations.

genomics↗

bioRxiv2023

Rho of plant GTPases with geranylgeranylation motif modulate monoterpene indole alkaloid biosynthesis in Catharanthus roseus

Rho Of Plant (ROP) GTPases function as molecular switches that control signaling processes essential for growth, development, and defense. However, their role in specialized metabolism is poorly understood. Previously, we demonstrated that inhibition of protein geranylgeranyl transferase (PGGT-I) negatively impacts the biosynthesis of monoterpenoid indole alkaloids (MIA) in Catharanthus roseus, indicating the involvement of prenylated proteins in signaling. Here, we show through biochemical, molecular and in planta approaches that specific geranylgeranylated ROPs modulate C. roseus MIA biosynthesis. Among the six C. roseus ROP GTPases (CrROPs), only CrROP3 and CrROP5, having a C- terminal CSIL motif, were specifically prenylated by PGGT-I. Additionally, both of their transcripts showed higher expression in most parts compared to other CrROPs. Protein- protein interaction studies revealed that both CrROP3 and CrROP5, but not CrROP2 (lacking CSIL motif), interacted with CrPGGT-I. Further, CrROP3 and CrROP5 exhibited nuclear localization, whereas CrROP2 was localized to plasma membrane. In planta functional studies revealed that silencing of CrROP3 and CrROP5 negatively affected MIA biosynthesis, while their overexpression upregulated MIA formation. In contrast, silencing and overexpression of CrROP2 had no effect on MIA biosynthesis. Moreover, overexpression of {Delta}CrROP3 and {Delta}CrROP5 mutants lacking the CSIL motif failed to enhance MIA biosynthesis. Taken together, these results implicate that CrROP3 and CrROP5 have positive regulatory role on MIA biosynthesis and thus shed light on how geranylgeranylated ROP GTPases mediate the modulation of specialized metabolism in C. roseus.

plant biology↗

bioRxiv2023

Proteomic profiling of regenerated urinary bladder tissue with stem cell seeded scaffold composites in a non-human primate bladder augmentation model

Urinary bladder insult can be caused by environmental, genetic, and developmental factors. Depending upon insult severity, the bladder may lose its ability to maintain capacity and intravesical pressures resulting in renal deterioration. Bladder augmentation enterocystoplasty (BAE) is employed to increase bladder capacity to preserve renal function using autologous bowel tissue as a "patch." To avoid the clinical complications associated with this procedure, we have engineered composite grafts comprised of autologous bone marrow mesenchymal stem cells (MSCs) with CD34+ hematopoietic stem/progenitor cells (HSPCs) co-seeded onto a pliable synthetic scaffold [POCO; poly(1,8-octamethylene-citrate-co-octanol)] or a biological scaffold (SIS; small intestinal submucosa) to regenerate bladder tissue in a baboon bladder augmentation model. We set out to determine the protein expression profile of bladder tissue that has undergone regeneration with the aforementioned stem cell seeded scaffolds along with baboons that underwent BAE. Data demonstrate that POCO and SIS grafted animals share high protein homogeneity between native and regenerated tissues while BAE animals displayed heterogenous protein expression between the tissues following long-term engraftment. We posit that stem cell seeded scaffolds can recapitulate tissue that is almost indistinguishable from native tissue at the protein level and may be used in lieu of procedures such as BAE. Significance of StudyBladder augmentation enterocystoplasty has been used for decades as the gold-standard surgical procedure to treat severely dysfunctional bladders. Unfortunately, bowel (typically ileum) used for augmentation is an anatomical and physiological mismatch to bladder tissue and results in numerous complications including bladder perforation, secondary and tertiary redo surgeries, metabolic imbalances, excess mucus production, and increased risk of cancer. This is in part due to the intestinal protein expression that serves as a starting point and subsequent foundation in the optimization of pseudo bladder tissue. Within the context of this study, we demonstrate that autologous, bone marrow derived mesenchymal stem cells along with primitive hematopoietic stem/progenitor cells can used to regenerate bladder tissue in a large deficit, non-human primate bladder augmentation model. Data demonstrate that this synergistic cellular combination facilitates the promotion of a protein tissue landscape that is nearly identical to native bladder tissue.

bioengineering↗

bioRxiv2023

Simian Immunodeficiency Virus and Storage Buffer: Field-friendly preservation methods for RNA viral detection in primate feces

Wild non-human primates carry many types of RNA viruses, including simian immunodeficiency virus (SIV), simian foamy virus, simian T-cell leukemia virus, and hepatitis C virus. These viruses can also infect humans via zoonotic transmission through handling and consumption of primate bushmeat. Characterizing viral prevalence and shedding in natural hosts is critical to understand infection and transmission risks within and between primate species. Here, we sought to identify a robust "field-friendly" method (i.e., without freezing or refrigeration) for preserving viral RNA, specifically SIV, in primate fecal samples. Fecal samples were collected from a mantled guereza colobus (Colobus guereza) housed at the Columbus Zoo and Aquarium. Samples were homogenized and inoculated with three concentrations (low, medium, high) of inactivated SIV virus and preserved in four different storage buffers (DNA/RNA Shield, RNAlater, 95% Ethanol, and Viral Transport Medium). SIV viral RNA was then extracted from samples at four time points (1 week, 4 weeks, 8 weeks, and 12 weeks) to determine the efficacy of each buffer for preserving SIV RNA. Quantitative RT-PCR was used for detection and quantification of viral RNA. At all concentrations, DNA/RNA Shield yielded the highest average SIV virion concentrations. We then successfully validated this approach using fecal samples from known SIV-positive and SIV-negative sooty mangabeys (Cercocebus atys) housed at Emory National Primate Research Center. Our results indicate that DNA/RNA shield is an optimal "field-friendly" buffer for preserving SIV RNA in fecal samples over time, and may also be effective for preserving other RNA viruses in feces. ImportanceHuman immunodeficiency virus (HIV) was introduced into human populations through zoonotic transmission of SIV from African primates, leading to a global epidemic and ongoing worldwide public health issue. SIV occurs naturally in over 40 primate species in sub-Saharan Africa and these viruses have crossed species barriers on multiple occasions, leading to the spread of HIV-1 and HIV-2. Quantifying RNA viruses in wild primate populations can be challenging as invasive sampling is often not feasible, and many field stations lack ready access to a freezer for storing biological samples. This study compares SIV RNA preservation and recovery across multiple storage buffers to identify a robust field-friendly option for RNA viral detection in noninvasively collected feces. Our results will inform future fieldwork and facilitate improved approaches to characterizing prevalence, shedding, and transmission of RNA viruses like SIV in natural hosts including wild-living nonhuman primates.

microbiology↗

bioRxiv2023

Multi-representation DeepInsight: an improvement on tabular data analysis

Tabular data analysis is a critical task in various domains, enabling us to uncover valuable insights from structured datasets. While traditional machine learning methods have been employed for feature engineering and dimensionality reduction, they often struggle to capture the intricate relationships and dependencies within real-world datasets. In this paper, we present Multi-representation DeepInsight (abbreviated as MRep-DeepInsight), an innovative extension of the DeepInsight method, specifically designed to enhance the analysis of tabular data. By generating multiple representations of samples using diverse feature extraction techniques, our approach aims to capture a broader range of features and reveal deeper insights. We demonstrate the effectiveness of MRep-DeepInsight on single-cell datasets, Alzheimers data, and artificial data, showcasing an improved accuracy over the original DeepInsight approach and machine learning methods like random forest and L2-regularized logistic regression. Our results highlight the value of incorporating multiple representations for robust and accurate tabular data analysis. By embracing the power of diverse representations, MRep-DeepInsight offers a promising avenue for advancing decision-making and scientific discovery across a wide range of fields.

bioinformatics↗

bioRxiv2023

Hundreds of independent midsize deletions mediate DNA loss in wild relatives of Red Jungle Fowl

Small and midsize deletions and insertions (InDels) are major events that play a crucial role in the evolution of genome size and contribute to the genetic and phenotypic diversity of species. In recent years, considerable attention has been given to studying small indels associated with various developmental, growth, and production traits in domestic chicken breeds. Additionally, small and midsize indels have been studied between chicken and phylogenetically more distant species such as duck, turkey, rock pigeon, and other passerine birds. However, the investigation of small and midsize deletions in the wild relatives of chickens has been relatively overlooked until now. To address this gap, our study aimed to identify the presence and distribution of midsize deletions (> 1 Kb) in the wild relatives of chickens. We conducted a comparative genomic analysis using high-quality genomic data from four species belonging to the Gallus genus. Our analysis revealed the existence of more than 125 midsize deletions in the three other species compared to Gallus gallus (red junglefowl). These midsize deletions were found to be distributed in intergenic regions and within introns of various protein-coding genes but not in the exonic regions of protein-coding genes. Furthermore, we observed a trend between the number of midsize deletions and the phylogenetic distance in the phylogeny of the Gallus genus. The most ancestral species, Gallus varius (green junglefowl), exhibited the highest deletions, followed by Gallus lafayettii (Ceylon junglefowl) and Gallus sonneratii (grey junglefowl). Some protein-coding genes harboring deletions in their introns and upstream regions were associated with body development, production, growth traits, abdominal fat deposition, behavioral patterns such as stress, fear, anxiety, plumage color, and adaptation to extreme climatic conditions. Our study finds that the midsize deletions identified in wild relatives of red junglefowl contribute less than 1% of DNA loss with a rate of 8-44 Kb/My during the evolution of the Gallus genus.

genomics↗

bioRxiv2023

Pathogenic aggregates alter actin organization and cellular viscosity resulting in stalled clathrin mediated endocytosis

Protein aggregation is a common underlying feature of neurodegenerative disorders. Cells expressing neurodegeneration-associated mutant proteins show altered uptake of ligands, suggestive of impaired endocytosis, in a manner as yet unknown. Using live cell imaging, we show that clathrin-mediated endocytosis (CME) is affected due to altered actin cytoskeletal organization in the presence of Huntingtin aggregates. Additionally, we find that cells containing Huntingtin aggregates are stiffer and less viscous than their wild-type counterparts due to altered actin conformation, and not merely due to the physical presence of aggregate(s). We further demonstrate that CME and cellular viscosity can be rescued by overexpressing Hip1, Arp2/3 or transient LatrunculinA treatment. Examination of other pathogenic aggregates revealed that only a subset of these display defective CME, along with altered actin organization and increased stiffness. Together, our results point to an intimate connection between functional CME, actin organization and cellular stiffness in the context of neurodegeneration.

cell biology↗

bioRxiv2023

Machine Learning Made Easy (MLme): A Comprehensive Toolkit for Machine Learning-Driven Data Analysis

BackgroundMachine learning (ML) has emerged as a vital asset for researchers to analyze and extract valuable information from complex datasets. However, developing an effective and robust ML pipeline can present a real challenge, demanding considerable time and effort, thereby impeding research progress. Existing tools in this landscape require a profound understanding of ML principles and programming skills. Furthermore, users are required to engage in the comprehensive configuration of their ML pipeline to obtain optimal performance. ResultsTo address these challenges, we have developed a novel tool called Machine Learning Made Easy (MLme) that streamlines the use of ML in research, specifically focusing on classification problems at present. By integrating four essential functionalities, namely Data Exploration, AutoML, CustomML, and Visualization, MLme fulfills the diverse requirements of researchers while eliminating the need for extensive coding efforts. To demonstrate the applicability of MLme, we conducted rigorous testing on six distinct datasets, each presenting unique characteristics and challenges. Our results consistently showed promising performance across different datasets, reaffirming the versatility and effectiveness of the tool. Additionally, by utilizing MLmes feature selection functionality, we successfully identified significant markers for CD8+ naive (BACH2), CD16+ (CD16), and CD14+ (VCAN) cell populations. ConclusionMLme serves as a valuable resource for leveraging machine learning (ML) to facilitate insightful data analysis and enhance research outcomes, while alleviating concerns related to complex coding scripts. The source code and a detailed tutorial for MLme are available at https://github.com/FunctionalUrology/MLme. Key PointsO_LIMLme is a novel tool that simplifies machine learning (ML) for researchers by integrating Data Exploration, AutoML, CustomML, and Visualization functionalities. C_LIO_LIMLme improves efficiency and productivity by streamlining the ML workflow and eliminating the need for extensive coding efforts. C_LIO_LIRigorous testing on diverse datasets demonstrates MLmes promising performance in classification problems. C_LIO_LIMLme provides intuitive interfaces for data exploration, automated ML, customizable ML pipelines, and result visualization. C_LIO_LIFuture developments aim to expand MLmes capabilities to include support for unsupervised learning, regression, hyperparameter tuning, and integration of user-defined algorithms. C_LI

bioinformatics↗