Biology subjects

Das, A.

Publications and source records attributed to Das, A..

At least 109 records · Page 6Linked to original sources

bioRxiv2024

Paused Polymerase synergises with transcription factors and RNA to enhance the transcriptional potential of promoters

Regulated pausing of RNA polymerase II (Pol II) is essential for enabling rapid and coordinated transcriptional responses to signalling cues. Pausing also contributes to the formation of nucleosome-free regions with the help of chromatin remodellers. However, if these nucleosome-free regions engage with transcription factors to stimulate the transcription potential of paused promoters is not known. In this study, we demonstrate that ligand-induced estrogen receptor-alpha (ER) binding is stabilized at Pol II-paused sites. This stabilization results from an increased dwell time of ER on chromatin, as revealed by single molecule tracking (SMT) experiments. Notably, short chromatin-associated RNAs generated by the paused Pol II contribute to enhancing ER binding at paused promoters. We also observe that pausing increases histone H3K27 acetylation (H3K27ac) levels, which primes paused promoters for robust transcriptional activation upon release. Collectively, these findings suggest that paused Pol II plays a central role in enhancing transcription factor binding through an RNA-dependent mechanism. This, in turn, results in a more vigorous transcriptional response following pausing release, thus contributing to the fine-tuning of ER-mediated gene regulation.

molecular biology↗

bioRxiv2024

Prefoldin 5 is a microtubule-associated protein that suppresses Tau-aggregation and neurotoxicity

Tauopathies represent a major class of neurodegenerative disorders associated with intracellular aggregates of the microtubule-associated protein Tau. To identify molecular modulators of Tau toxicity, we used a genetic screen to identify protein chaperones whose RNAi-mediated knockdown could modulate hTauV337M-induced eye-ommatidial degeneration in Drosophila. This screen identified the Prefoldins Pfdn5 and Pfdn6 as strong modifiers of hTauV337M cytotoxicity. Consistent with the known function of Pfdn as a cotranslational chaperone for tubulin, Pfdn5 mutants showed substantially reduced levels of tubulin monomer. However, additional microtubule-related functions were indicated by the robust unexpected association of Pfdn5 with axonal microtubules in vivo, as well as binding with stabilized microtubules in biochemical assays. Loss of Pfdn5 resulted in neuromuscular junctions (NMJ) defects similar to those previously described in hTau-expressing flies: namely, increased supernumerary boutons and fewer microtubule loops within mature presynaptic boutons. Significantly, synaptic phenotypes caused by hTauV337M overexpression were also strongly enhanced in a Pfdn5 mutant background. Consistent with a role in modulating Tau toxicity, not only did loss of Pfdn5 result in increased accumulations of Tau-aggregates in hTauV337M expressing neurons, but also neuronal overexpression of Prefoldin strikingly ameliorated age-dependent neurodegeneration and memory deficits induced by pathological hTau. Together, these and other observations described herein: (a) provide new insight into Prefoldin-microtubule interactions; (b) point to essential posttranslational roles for Pfdn5 in controlling Tau-toxicity in vivo; and (c) demonstrate that Pfdn5 overexpression is sufficient to restrict Tau-induced neurodegeneration.

neuroscience↗

bioRxiv2024

Identification of a novel basal body-localized epsilon-tubulin in Leishmania

Epsilon-tubulins are unconventional isoforms of the tubulin family, found in only a few organisms so far. We identified a novel epsilon-tubulin in Leishmania major (Lme-tubulin) that exhibits significant sequence similarity and conservation of functional domains with its known counterparts. Lme-tubulin was found to be constitutively expressed in both the extracellular promastigote form of the parasite and the amastigotes residing within infected macrophages. For localization studies, we generated a Leishmania strain expressing mNeonGreen-tagged Lme-tubulin using CRISPR-Cas9-mediated endogenous protein tagging method. Imaging studies with this strain revealed Lme-tubulin to be localized near the kinetoplast and at the flagellar base, indicating a basal body localization. That Lme-tubulin is indeed localized at the basal body and not a part of the microtubular network was confirmed when its localization was found to remain unaltered upon treatment with nocodazole, a microtubule disruptor. This is the first experimental finding of an e-tubulin not only in the genus Leishmania but in the entire Trypanosomatidae family and is likely to incite further research to uncover the physiological role of this intriguing tubulin in this group of protozoan parasites. Summary StatementWe report for the first time an epsilon-tubulin in Leishmania parasite. This nocodazole-insensitive unconventional tubulin is expressed constitutively and found to be localized in the basal body.

cell biology↗

bioRxiv2024

Early hominin arrival in Southeast Asia triggered the evolution of major human malaria vectors

Understanding the evolution of anthropophily, the preference of mosquitoes to feed on humans, offers insights into current and future human disease transmission. Some species of the Leucosphyrus Group of Anopheles mosquitoes in Southeast Asia are highly anthropophilic and efficient vectors of human malaria parasites, while others primarily feed on non-human primates and transmit non-human primate malaria parasites. Through phylogenomic analysis of 11 out of 20 recognized species, we studied the biogeography and evolutionary history of anthropophily in this group. Molecular dating and ancestral state reconstruction revealed that anthropophily evolved during the late Pliocene/early Pleistocene in Sundaland, likely in response to early hominins. This finding provides independent non-archaeological evidence supporting the limited fossil record of early hominin colonization in Southeast Asia around 1.8 million years ago.

evolutionary biology↗

bioRxiv2024

The binary protein interactome mapping of the Giardia lamblia proteasome lid reveals extra proteasomal functions of GlRpn11

Giardia lamblia does not encode Rpn12 and Sem1, two proteins crucial for assembling the proteasome lid. To understand how the interactions between the giardial proteasome lid subunits may have changed to compensate for their absence, we used the yeast two-hybrid assay to generate a binary protein interaction map of the Giardia lid subunits. Most interactions within the Giardia proteasome lid are stronger than those within the Saccharomyces cerevisiae lid. These may compensate for the absence of Rpn12 and Sem1. A notable exception was the weaker interaction between GlRpn11 and GlRpn8, compared to the strong interaction between Rpn11-Rpn8 of yeast. The Rpn11-Rpn8 dimer provides a platform for lid assembly and their interaction involves the insertion of a methionine residue of Rpn11 into a hydrophobic pocket of Rpn8. Molecular modeling indicates that GlRpn8s pocket is wider, reconciling the experimental observation of its weak interaction with GlRpn11. This weaker interaction may have evolved to support extra proteasomal functions of GlRpn11, which localizes to multiple subcellular regions where other proteasome subunits have not been detected. One such location is the mitosome. Functional complementation in yeast shows that GlRpn11 can influence mitochondrial function and distribution. This, together with its mitosomal localization, indicates that GlRpn11 functions at the mitosome. Thus, this parasites proteasome lid has a simpler subunit architecture and structural attributes that may support dual functionalities for GlRpn11. Such parasite-specific proteasome features could provide new avenues for controlling the transmission of Giardia. 1 Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/613619v1_ufigs1.gif" ALT="Figure 0"> View larger version (33K): org.highwire.dtl.DTLVardef@989e69org.highwire.dtl.DTLVardef@1c8134aorg.highwire.dtl.DTLVardef@6a9794org.highwire.dtl.DTLVardef@5ac20_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIGiardia genome does not encode two proteasomal lid subunits: Rpn12 and Sem1 C_LIO_LIUnique interactions within the lid may compensate for the absence of these two C_LIO_LIGlRpn8:GlRpn11 weakly interacts to support GlRpn11s extra-proteasomal distribution C_LIO_LIGlRpn11 localizes at mitosomes, OZ of VD, and to the VFP C_LIO_LIThe 182-218 fragment of GlRpn11 may regulate mitosomal function C_LI

cell biology↗

bioRxiv2024

Enantiomeric histidine-rich peptide coacervates enhance antigen delivery to T cells

Peptides and peptidomimetics that self-assemble via LLPS have recently emerged as building blocks for fabricating functional biomaterials due to their unique physicochemical properties and dynamic nature. One of lifes most distinctive signatures is its selectivity for chiral molecules and, to date, coacervates comprised of D-amino acids have not been reported. Here, we demonstrate that histidine-rich repeats of (GHGXY)4 (X=L/V/P) and their enantiomers undergo LLPS opening new avenues for enhancing coacervate stability. Through a series of biophysical studies, we find that LLPS kinetics, droplet size, fusion, and encapsulation efficiency are dictated by the primary sequence. Further, these coacervates can encapsulate therapeutic cargo which are then internalized via endocytic mechanisms. Finally, we show that the coacervates enhance antigen presentation to CD4+ and CD8+ T cells resulting in robust proliferation and production of functional cytokines. Collectively, our study describes the development and characterization of enantiomeric peptide coacervates as attractive vaccine delivery vehicles with tunable physicochemical properties. HIGHLIGHTSO_LID amino acid-peptides were used for the first time to construct phase separating coacervates C_LIO_LIChirality does not restrict LLPS or modulate other coacervate properties C_LIO_LIAntigen delivery using chiral coacervates enhances and prolongs presentation to T cells C_LI PROGRESS AND POTENTIALPeptides can undergo self-assembly via liquid-liquid phase separation (LLPS) to result in solute-rich coacervates that can serve as biomaterials. Using histidine-rich peptide repeats, this work demonstrates that peptides composed of entirely D-amino acids can form functional coaceravtes. The kinetics of LLPS and bulk properties of the droplets can be controlled through simple amino acid substitutions. The coacervates, while immunologically inert, exert an adjuvanting effect and enhance antigen presentation to T cells leading to proliferation and functional cytokine production. The materials showcased here possess high translational potential for combined delivery of immunomodulators and antigens for vaccine delivery against infectious diseases or cancer. The deliverables from this study will also inspire the development of chiral systems that will contribute to the knowledge of cellular processes associated with phase changes integral to both physiology and pathology.

bioengineering↗

bioRxiv2024

Neural population dynamics during sleep in a songbird vocal circuit resemble sharp wave ripple activity

Similar to motor skill learning in mammals, vocal learning in songbirds requires a set of interconnected brain areas that make up an analogous basal ganglia-thalamocortical circuit known as the anterior forebrain pathway (AFP). Although neural activity in the AFP has been extensively investigated during awake singing, very little is known about its neural activity patterns during other behavioral states. Here, we used chronically implanted Neuropixels probes to investigate spontaneous neural activity in the AFP during natural sleep and awake periods in male zebra finches. We found that during sleep, neuron populations in the pallial region LMAN (lateral magnocellular nucleus of the nidopallium) spontaneously exhibited synchronized bursts that were characterized by a negative sharp deflection in the local field potential (LFP) and a transient increase in gamma power. LMAN population bursts occurred primarily during non-rapid eye movement (NREM) sleep and were highly reminiscent of sharp-wave ripple (SWR) activity observed in rodent hippocampus. We also examined the functional connectivity within the AFP by calculating the pairwise LFP coherence. As expected, delta and theta band coherence within LMAN and Area X was higher during sleep compared to awake periods. Contrary to our expectations, we did not observe strong coherence between LMAN and Area X during sleep, suggesting that the input from LMAN into Area X is spatially restricted. Overall, these results provide the first description of spontaneous neural dynamics within the AFP across behavioral states. Significance statementAlthough cortical and basal ganglia circuits are known to be required for learning in both mammals and birds, little is known about the ongoing spontaneous activity patterns within these circuits, or how they are modulated by behavioral state. Here we prove the first description of cortical-basal ganglia network activity during sleep and awake periods in birds. Within the pallial area LMAN, we observed population-wide bursting events that were highly reminiscent of hippocampal sharp-wave ripple (SWR) activity, suggesting that large-scale population events have diverse functions across vertebrates.

neuroscience↗

bioRxiv2024

Di-HAMP domains of a cytoplasmic chemoreceptor modulate nucleoid array formation and downstream signalling

In bacterial chemosensing, environmental cues are typically sensed by bacterial transmembrane receptors known as methyl accepting chemotaxis proteins (MCPs). MCPs form highly organized arrays using the bacterial membrane as a scaffold, which amplify the signals and transduce them into a cellular response. The FrzCD cytoplasmic receptor from Myxococcus xanthus is unique due to its ability to bind DNA and use the nucleoid as a scaffold to form arrays. In this study, we identified two HAMP (histidine kinase, adenylyl cyclase, MCP and phosphatase) domains located between the DNA binding and signaling domains of FrzCD. In vitro experiments demonstrate that these HAMP domains restrict FrzCD to a dimeric form in solution and modulate FrzCDs affinity for DNA, whereas the signaling domain stabilizes higher-order oligomeric assemblies upon DNA binding. Through fluorescence microscopy and analyses on Myxococcus social behavior, we demonstrate that the impact of FrzCD HAMP domains on DNA binding and oligomerization significantly influences group motility and development. Our results suggest that HAMP domains might have roles not only in signal transduction but also in the plasticity of chemosensory arrays. These observations illustrate mechanisms of regulation of a DNA-bound cytoplasmic array formed by a diffusible MCP. Significance StatementOur study identifies the presence of tandem HAMP domains in a cytoplasmic chemoreceptor, FrzCD, from Myxococcus xanthus, and highlights their role in dynamic receptor oligomerization on a DNA scaffold. By controlling receptor oligomerization and subsequently the array formation on the nucleoid, the tandem HAMP domains impart plasticity to the receptor arrays. Such plasticity governs cellular responses to external signals and dictate bacterial social behavior in group motility and multicellular structure formation.

microbiology↗

bioRxiv2024

Altered Copper Transport in Oxidative Stress-Dependent Brain Endothelial Barrier Dysfunction Associated with Alzheimer's Disease

Oxidative stress and blood-brain barrier (BBB) disruption due to brain endothelial barrier dysfunction contribute to Alzheimers Disease (AD), which is characterized by beta-amyloid (A{beta}) accumulation in senile plaques. Copper (Cu) is implicated in AD pathology and its levels are tightly controlled by several Cu transport proteins. However, their expression and role in AD, particularly in relation to brain endothelial barrier function remains unclear. In this study, we examined the expression of Cu transport proteins in the brains of AD mouse models as well as their involvement in A{beta}42-induced brain endothelial barrier dysfunction. We found that the Cu uptake transporter CTR1 was upregulated, while the Cu exporter ATP7A and/or ATP7B were downregulated in the hippocampus of AD mouse models, and in A{beta}42-treated human brain microvascular endothelial cells (hBMECs). In the 5xFAD AD mouse model, Cu levels (assessed by ICP-MS) were elevated in the hippocampus. Moreover, A{beta}42-induced reactive oxygen species (ROS) production, ROS-dependent loss in barrier function in hBMEC (measured by transendothelial electrical resistance), and tyrosine phosphorylation of VE-cadherin were all inhibited by either a membrane permeable Cu chelator or by knocking down CTR1 expression. These findings suggest that dysregulated expression of Cu transport proteins may lead to intracellular Cu accumulation in the AD brain, and that A{beta}42 promotes ROS-dependent brain endothelial barrier dysfunction and VE-Cadherin phosphorylation in a CTR1-Cu-dependent manner. Our study uncovers the critical role of Cu transport proteins in oxidative stress-related loss of BBB integrity in AD. HighlightsO_LIUpregulation of the Cu importer CTR1 and downregulation of the Cu exporter ATP7A in the hippocampus of AD mouse models C_LIO_LIA{beta}42 increases CTR1 expression while reduces ATP7A and ATP7B levels in human brain microvascular ECs. C_LIO_LIA{beta}42 triggers increased reactive oxygen species (ROS) production in human brain microvascular ECs through a CTR1- and Cu-dependent manner. C_LIO_LIA{beta}42 induces endothelial barrier dysfunction in human brain microvascular ECs through a CTR1-Cu-ROS-pendent manner. C_LI

neuroscience↗

bioRxiv2024

DAMP-inducing Peptide Nanofibers and PAMP Combination Adjuvants Boost Functional Lung Tissue-resident Memory CD4+ T Cell Responses

Vaccine adjuvants are typically composed of pathogen-associated molecular patterns (PAMPs) or danger-associated molecular patterns (DAMPs) that activate innate immune cells. Advances in basic immunology have demonstrated the need for various types of protective immunity, which are difficult to achieve with a single adjuvant. The FDA approval of multiple PAMP-DAMP combinations for clinical use has led to an increased momentum in the area in recent years. Here we report the use of DAMP-inducing peptide nanofibers (PNFs) and CL429 (PAMP) combinations as subunit boosters for Bacille Calmette-Guerin (BCG). We demonstrate that pulmonary boosting with PNFs and CL429 enhances the lung-resident memory phenotype, effector cytokine profiles, and transcription factor bias of antigen-specific CD4+T cell populations compared to PNFs alone. Importantly, the combination significantly improved the frequency of tissue-resident memory T (TRM) cells which, have been shown to provide superior protection compared to circulating memory T cells. Interestingly, the T helper (Th) subset profile was driven in part driven by the route of vaccination resulting in a Th17 bias via a mucosal route or a Th1 bias when delivered intravenously. We show that following pulmonary administration, lung-resident antigen presenting cells (APCs) efficiently internalize PNFs and upregulate important co-stimulatory markers that drive T cell priming and activation. Our findings suggest that heterologous booster vaccines composed of DAMP-inducing PNFs and PAMP combinations can engage innate and adaptive immunity for generating TRM cells that protect against TB and potentially other respiratory diseases.

bioengineering↗

bioRxiv2024

Unravelling a mechanistic link between mitophagy defect, mitochondrial malfunction, and apoptotic neurodegeneration in MPS VII

Progressive neurodegeneration and cognitive disability are prominent symptoms of MPS VII, a lysosomal storage disorder caused by {beta}-glucuronidase enzyme deficiency. Yet, the mechanism of neurodegeneration in MPS VII remains elusive thereby limiting the scope of targeted intervention. To address this, we recently developed a {beta}-glucuronidase-deficient (CG2135-/-) Drosophila model of MPS VII. The CG2135-/- flies exhibited signs of neuromuscular degeneration, including loss of dopaminergic neurons, and accumulated engorged lysosomes, ubiquitinated proteins and mitochondria in their brains. These observations, coupled with our current finding that the CG2135-/- flies were highly susceptible to starvation, prompted us to investigate potential defects in the autophagy-lysosomal clearance machinery in the brain. We found that both autophagy induction and lysosome-mediated autophagosomal turnover were impaired in the CG2135-/- fly brain. This was evidenced by lower Atg8a-II levels, reduced Atg1 and Ref(2)P expression along with accumulation of lipofuscin-like inclusions and multilamellar bodies. Interestingly, mitophagy was also found to be defective in their brain, causing buildup of enlarged mitochondria with distorted cristae and reduced membrane potential. This, in turn, affected mitochondrial function as reflected by drastically reduced brain ATP levels. Energy depletion triggered apoptosis in neuronal as well as non-neuronal cells of the CG2135-/- fly brain, where we also detected apoptotic dopaminergic neurons. Resveratrol treatment, previously found to protect against loss of dopaminergic neurons in the CG2135-/- flies, has now been shown act by correcting the mitophagy defect and preventing ATP depletion. Collectively, our study establishes a causal link between mitophagy defect, mitochondrial malfunction, and apoptotic neurodegeneration in MPS VII.

cell biology↗

bioRxiv2024

EMMPRIN confers metabolic advantage for monocytes and macrophages to promote disease in a model of multiple sclerosis

Monocytes and monocyte-derived macrophages have important roles in the initiation and progression of multiple sclerosis (MS). These cells undergo metabolic reprogramming to generate immunophenotypes that promote leukocyte infiltration, axonal degeneration and demyelination, worsening MS pathology. The mechanisms that dictate metabolic programs in monocytes and macrophages in MS remain unclear. We previously reported that extracellular matrix metalloproteinase inducer (EMMPRIN, CD147), a glycoprotein that acts as a chaperone of monocarboxylate transporter 4 (MCT4), assisted with glycolysis-driven pro-inflammatory phenotype in macrophages in experimental autoimmune encephalomyelitis (EAE), an animal model of MS. Using newly-generated CCR2CreERT2:EMMPRINfl/fl (CCR2:EMMP) mice, we report that presymptomatic deletion of EMMPRIN in CCR2+ monocytes prevented or reduced clinical disability of EAE. This was correspondent with decreased infiltration of leukocytes into the CNS. Single cell RNA-seq of blood monocytes from EAE and proteomics analysis of macrophages from CCR2:EMMP-/- mice revealed significant alterations in metabolic programs, particularly reduced glycolysis and elevated mitochondrial electron transport and fatty acid oxidation, which were linked to their reduced pro-inflammatory traits. Our findings implicate EMMPRIN as a key regulator of metabolic pathways that exacerbate pro-inflammatory functions of monocytes in MS.

immunology↗

bioRxiv2024

Colorimetric CRISPR Biosensor: A Case Study with Salmonella Typhi

There is a critical need to implement a sensitive and specific point-of-care (POC) biosensor that addresses the instrument limitations and manufacturing challenges faced in resource-constrained contexts. In this paper we focus on enteric fever which is a highly contagious and prevalent infection in low- and middle-income countries. Although easily treatable, its ambiguous symptoms paired with a lack of fast, accurate and affordable diagnostics lead to incorrect treatments which exacerbate the disease burden, including increasing antibiotic resistance. In this study, we develop a readout module for CRISPR-Cas12a that produces a colorimetric output that is visible to the naked eye and can act as a cascade signal amplifier in any CRISPR assay based on trans-cleavage. We achieve this by immobilizing an oligo covalently linked to a {beta}-galactosidase (LacZ) enzyme, which is cleaved in the presence of DNA target-activated CRISPR-Cas12a. Upon cleavage, the colorimetric enzyme is released, and the supernatant transferred to an environment containing X-Gal producing an intense blue color. This method is capable of detecting amplified bacterial genomic DNA and has a lower limit of detection (LoD) to standard fluorescent assays while removing the requirement for costly equipment. Furthermore, it remained active after lyophilization, allowing for the possibility of shipment without cold chain, significantly reducing deployment costs. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/606709v1_figSc1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@d66787org.highwire.dtl.DTLVardef@2708eaorg.highwire.dtl.DTLVardef@ba5a86org.highwire.dtl.DTLVardef@8d4f48_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOScheme 1.C_FLOATNO Mechanism of CRISPR-Cas12a, and the signal output produced by enzyme trans-cleavage and the release of LacZ. 1) Initial set-up of inactivated system. 2) DNA isolation and amplification. 3) DNA addition to the biosensor. 4) CRISPR recognition of the DNA target and indiscriminate cleavage of all DNA. 5) LacZ release to the supernatant. 6) Transfer to an X-Gal environment. 7) X-Gal cleavage by LacZ and chromophore oxidation to the intensive blue indigo [illustration created with BioRender.com]. C_FIG

synthetic biology↗

bioRxiv2024

Single-molecule tracking reveals the dynamics of Ipl1 recruitment to the kinetochores and spindles in S. cerevisiae

Aurora kinase B, Ipl1 in Saccharomyces cerevisiae, is the master regulator of cell division required for checkpoint regulation, spindle assembly and disassembly, chromosome segregation, and cytokinesis. Decades of research employed ensemble averaging methods to understand its dynamics and function; however, the dynamic information was lost due to population-based averaging. Here, we use single-molecule imaging and tracking (SMIT) to quantify the recruitment dynamics of Ipl1 at the kinetochores and spindles in live cells. Our data suggest that Ipl1 is recruited to these locations with different dynamics. We have demonstrated how the recruitment dynamics of Ipl1 at the kinetochores during metaphase changes in the presence and absence of tension across the kinetochore, in the absence of protein phosphatase 1 (Glc7), and the absence of its known recruiters (Ctf19 and Bub1). The SMIT of other chromosome passenger complex members suggests its hierarchical assembly at the kinetochore. Hence, SMIT provides a dynamic view of the Ipl1 trafficking at the kinetochores and spindles.

cell biology↗

bioRxiv2024

Early life microbial succession in the gut follows common patterns in humans across the globe

Characterizing the dynamics of microbial community succession in the infant gut microbiome is crucial for understanding child health and development, but no normative model currently exists. Here, we estimate child age using gut microbial taxonomic relative abundances from metagenomes, with high temporal resolution ({+/-}3 months) for the first 1.5 years of life. Using 3,154 samples from 1,827 infants across 12 countries, we trained a random forest model, achieving a root mean square error of 2.61 months. We identified key taxonomic predictors of age, including declines in Bifidobacterium spp. and increases in Faecalibacterium prausnitzii and Lachnospiraceae. Microbial succession patterns are conserved across infants from diverse human populations, suggesting universal developmental trajectories. Functional analysis confirmed trends in key microbial genes involved in feeding transitions and dietary exposures. This model provides a normative benchmark of "microbiome age" for assessing early gut maturation that can be used alongside other measures of child development.

microbiology↗

bioRxiv2024

"Micro-offline gains" convey no benefit for motor skill learning

While practising a new motor skill, resting for a few seconds can improve performance immediately after the rest. This improvement has been interpreted as rapid offline learning1,2 ("micro-offline gains", MOG), supported by neural replay of the trained movement sequence during rest3. Here, we provide evidence that MOG reflect transient performance benefits, partially mediated by motor planning, and not replay-mediated offline learning. In five experiments, participants trained to produce a sequence of finger movements as many times as possible during fixed-duration practice periods. When participants trained during 10-second practice periods, each followed by a 10-second rest period, they produced more correct keypresses during training than participants who trained without taking breaks. However, this benefit vanished within seconds after the end of training, when both groups performed under comparable conditions, revealing similar levels of skill acquisition. This challenges the idea that MOG reflect offline learning, which, if present, should result in sustained performance benefits, compared to training without breaks. Furthermore, sequence-specific replay was not necessary for MOG, given that we observed persistent MOG when participants produced random sequences that never repeated, preventing any effect of (sequence-specific) replay on the performance. Importantly, we observed diminished MOG when participants could not pre-plan the first few movements of an upcoming practice period. We conclude that "micro-offline gains" represent short-lived performance benefits that are partially driven by motor pre-planning, rather than replay-mediated offline learning.

neuroscience↗

bioRxiv2024

DNA walk of specific fused oncogenes exhibit distinct fractal geometric characteristics in nucleotide patterns

Background/ObjectivesThe complex system of cancer has led to an emphasis on understanding the more general causal relationship within the disease. In this context, concepts of symmetry and symmetry-breaking in distinct biological cell features or components have been examined as an approach to cancer investigation. However, there can be possible limitations in directly interpreting the symmetry-based approach from a physical viewpoint due to the lack of understanding of physical laws governing symmetry in complex systems like cancer. MethodsFractal geometry and DNA walk representation were employed to investigate the geometric features i.e., self-similarity and heterogeneity in DNA nucleotide coding sequences of wild-type and mutated oncogenes, tumour-suppressor, and other unclassified genes. The mutation-facilitated self-similar and heterogenous features were quantified by the fractal dimension and lacunarity coefficient measures, respectively. Additionally, the geometrical orderedness and disorderedness in the analyzed sequences were interpreted from the combination of the fractal measures. ResultsThe findings showed distinct fractal geometric features in the case of fusion mutations. It also highlights the possible interpretation of the observed fractal features as geometric analogues concerning explicit observations corresponding to specific cancer types. In addition, the two-dimensional multi-fractal analysis highlighted the presence of a single exponent in the scaling of mutation-mediated gene sequence self-similarity/complexity and heterogeneity. ConclusionsThe approach identified mutation-induced geometric features in gene sequences, demonstrating the potential of DNA walks and fractal analysis in translational research regarding cancer. The findings suggest that investigating fractal parameters can capture unique geometric features in nucleotide sequences, contributing to the understanding of cancers molecular complexity.

bioinformatics↗

bioRxiv2024

Designing a novel Scaffold-Based Multi-Epitope Vaccine to Combat Melioidosis Caused by Burkholderia pseudomallei: An In-silico and Immunoinformatics approach

Burkholderia pseudomallei, the gram-negative bacteria causing melioidosis, is becoming a serious threat to healthcare settings. In recent years, B. pseudomallei has been identified as an emerging and significant etiological agent responsible for localized pyogenic infections primarily observed in India and South Asia. At present, no vaccine against melioidosis is available in the treatment system. This study has undertaken an in-silico reverse vaccinology approach to design a novel multi-epitope vaccine for treating B. pseudomallei-mediated infections. B-cell and T-cell epitopes have been predicted and stitched to develop a multi-epitope vaccine. The predicted vaccine is found to be non-toxic, non-allergic, and immunogenic in nature. Immune simulation results indicate that the designed vaccine can generate an immune response resembling a real-life scenario. The 610 amino-acid long vaccine construct has been codon-optimized and could be cloned in the E. coli K12 system. These findings from this immunoinformatics study offer a foundation for developing a tailored, safe, and potent vaccine targeting B. pseudomallei.

bioinformatics↗