Biology subjects

Sharma, N.

Publications and source records attributed to Sharma, N..

At least 73 records · Page 4Linked to original sources

bioRxiv2023

Spatial organization of collective food distribution in a paper wasp society

In social insect colonies, food transferred through space and time via nestmates carries both nutrition and information. We study the mechanism of spatio-temporal coordination (or the lack thereof) between multiple wasps for them to optimally solve the problem of feeding randomly placed larvae in a social insect colony. We followed each morsel of food brought into semi-natural colonies of the tropical paper wasp Ropalidia marginata, in each of 36 feeding bouts until the food was exhausted. We found that most acts of feeding larvae are performed by wasps that unload food from foragers, but unloading itself is highly skewed among individuals. We also found that larvae closer to the nest center were fed more frequently than those at the periphery, irrespective of their developmental stage. This differential feeding may have fitness consequences as it is known that well-fed larvae become voracious feeders as adults and have a higher likelihood to become reproductives. Using the analogies of the travelling salesman problem and the Hamiltonian path problem, we showed that individuals which disburse food to more larvae within a feeding bout adopted paths that were considerably shorter than expected by chance while the distinction between adopted and random routes was not as pronounced when the number of larvae fed in a bout was fewer. There was no spatial segregation between wasps feeding larvae in parallel, possibly building redundancy and avoiding larval starvation across bouts. Understanding the spatial organization of food transfer may be a key to understanding how insect societies achieve efficient social organization and division of labor. SignificanceThe limited studies on within-nest spatial organization of food distribution have been performed on ants and not primitively eusocial insects like wasps that contain randomly placed yet trackable larvae within the colony. We address the gap in a holistic understanding of spatial organization of food distribution through our study in the social wasp Ropalidia marginata. Through the lens of task partitioning, colony-level larval landscape, and spatial strategies adopted at individual and collective scales, our study presents one of the most detailed account of behavioral and spatio-temporal data mapping sources and sinks of food in a colony chronologically. We found that feeding routes adopted by wasps while feeding randomly placed larvae within a colony may not be a result of random walk but instead the degrees of route optimization based on the food load available to distribute within each feeding bout. We suggest paper wasp colonies to be ideal model systems for spatial studies owing to their observable colony sizes and randomly placed brood. Understanding the mechanism of colony-level problem solving by individuals with limited local information has widespread real-life applications besides a better understanding of social organization in colonies of social insects.

animal behavior and cognition↗

bioRxiv2023

Activity-dependent development of the body's touch receptors

We report a role for activity in the development of the primary sensory neurons that detect touch. Genetic deletion of Piezo2, the principal mechanosensitive ion channel in somatosensory neurons, caused profound changes in the formation of mechanosensory end organ structures and altered somatosensory neuron central targeting. Single cell RNA sequencing of Piezo2 conditional mutants revealed changes in gene expression in the sensory neurons activated by light mechanical forces, whereas other neuronal classes were less affected. To further test the role of activity in mechanosensory end organ development, we genetically deleted the voltage-gated sodium channel Nav1.6 (Scn8a) in somatosensory neurons throughout development and found that Scn8a mutants also have disrupted somatosensory neuron morphologies and altered electrophysiological responses to mechanical stimuli. Together, these findings indicate that mechanically evoked neuronal activity acts early in life to shape the maturation of the mechanosensory end organs that underlie our sense of gentle touch.

neuroscience↗

bioRxiv2023

The minimum intervention principle of optimal control relates the uncontrolled manifold to muscle synergies

The nervous system uses muscle activation patterns to perform successful motor tasks, and motor tasks inevitably satisfy the laws of mechanics. The number of muscles usually exceeds the degrees of freedom of the task such that multiple combinations of muscle activities satisfy mechanical demands. A low-dimensional space usually explains a large variance in the muscle activations, leading to the hypothesis that muscle redundancy is solved by neurally coordinated muscle synergies. In addition to synergies, motor task mechanics also enforce a structure on muscle activity. Muscles satisfy multiple non-negotiable mechanical demands of equilibrium, stability, force, and respect the constraints. The redundancy in the muscle architecture is the degree of freedom available after accounting for the necessary mechanics. In this study, I investigate how task mechanics structure muscle activities by using a biomechanical model of an index finger in contact and published measurements of seven muscle activities during a fingertip force production task. I derive a map from muscle activities to complete task mechanics with the necessary conditions of equilibrium, stability, and force. By invoking the uncontrolled manifold hypothesis, I show that the variability in muscle activities is channeled in the task-irrelevant directions, which is given by the null space of the map from muscle activations to task variables. Furthermore, I show that the principal component that explains maximum variance in muscle activations is oriented along the task-irrelevant direction with the highest projected variance, suggesting that the maximal principal directions correspond to the task-irrelevant subspace rather than the task-relevant directions. This study has consequences for understanding muscular redundancy and synergy, and also provides direct evidence that the simplified biomechanical models satisfy mechanical requirements.

biophysics↗

bioRxiv2023

Deciphering the orthorhombic crystal structure of a novel NEIL1 nanobody with pseudo-merohedral twinning

Nanobodies or VHHs (Variable Heavy domains of Heavy chain) are single domain antibodies that comprise three antigenic complementary determining regions (CDR). Nanobodies are used in numerous scientific applications including, bio-imaging, diagnosis, therapeutics, and macromolecular crystallography. We obtained crystals of a [~]14 kDa nanobody specific for the NEIL1 DNA glycosylase (hereafter called A5) in 0.5 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate pH 5.6, and 1.0 M lithium sulfate monohydrate from the Crystal HT Hampton Research screen that were further optimized. Here, we describe the structure determination and refinement of the A5 crystals to a resolution of 2.1 [A]. The data collected were complicated by the presence of anisotropy and twinning, and while initial space group determination pointed to a higher apparent tetragonal crystal system, the data statistics suggested twinning, placing the crystal in an orthorhombic system. Twinning was confirmed by the Padilla and Yeates test, H-test, and Britton test based on local intensity differences with a twin fraction of 0.4. Molecular replacement produced the best solution in the orthorhombic space group P21212 with four molecules in the asymmetric unit and we were able to model over 96% of the residues in the electron density with a final Rwork and Rfree of 0.1988 and 0.2289 upon refinement. SynopsisThe crystal structure of a specific nanobody against NEIL1 was determined to 2.1 [A]. The structure was ultimately solved in an orthorhombic space group after diffraction data analysis revealed mild anisotropy as well as pseudo-merohedral twinning

biochemistry↗

bioRxiv2023

RAD54L regulates replication fork progression and nascent strand degradation in BRCA1/2-deficient cells

RAD54L is a DNA motor protein with multiple roles in homologous recombination DNA repair (HR). In vitro, RAD54L was shown to also catalyze the reversal and restoration of model replication forks. In cells, however, little is known about how RAD54L may regulate the dynamics of DNA replication. Here, we show that RAD54L restrains the progression of replication forks and functions as a fork remodeler in human cells. Analogous to HLTF, SMARCAL1, and FBH1, and consistent with a role in fork reversal, RAD54L decelerates fork progression in response to replication stress and suppresses the formation of replication-associated ssDNA gaps. Interestingly, loss of RAD54L prevents nascent strand DNA degradation in both BRCA1/2- and 53BP1-deficient cells, suggesting that RAD54L functions in both pathways of RAD51-mediated replication fork reversal. In the HLTF/SMARCAL1 pathway, RAD54L is critical, but its ability to catalyze branch migration is dispensable, indicative of its function downstream of HLTF/SMARCAL1. Conversely, in the FBH1 pathway, branch migration activity of RAD54L is essential, and FBH1 engagement is dependent on its concerted action with RAD54L. Collectively, our results reveal disparate requirements for RAD54L in two distinct RAD51-mediated fork reversal pathways, positing its potential as a future therapeutic target.

cell biology↗

bioRxiv2023

Emergence of resistance to succinate dehydrogenase inhibitor fungicides in Pyrenophora teres f. teres and P. teres f. maculata in Australia

The net blotches are among the most economically significant diseases of barley worldwide. There are two forms of the disease: net-form net-blotch (NFNB, causal agent Pyrenophora teres f. sp. teres [Ptt]) and spot-form net blotch (SFNB, causal agent Pyrenophora teres f. sp. maculata [Ptm]). Alongside varietal choice and cultural practices, fungicides form an important part of the regime for net blotch control. The succinate dehydrogenase inhibitors (SDHIs) are a key class of fungicides used in net blotch management. However, resistance to this group of compounds has emerged in the net blotches in recent years. Here, we describe the first cases of resistance to SDHIs in Australian populations of net blotches. This study was prompted by reports of field failures of SDHI fungicides in controlling NFNB in South Australia and SFNB in Western Australia. Target site mutations in the Sdh complex genes, previously associated with reduced sensitivity in European net blotch populations, were found in Australian isolates, and two mutations which have not been previously observed in P. teres, are also described. The mutations found in Ptt included H134R and S135R in SdhC; and H134Y and D145G in SdhD; the SdhC-H134R mutation was the most frequently observed. In Ptm, the mutations found included H277L in SdhB; S73P, N75S, H134R and S135R in SdhC; and D145G in SdhD; the SdhC-N75S mutation was the most common. These mutations were correlated with reduced in vitro SDHI fungicide sensitivity by microtiter assay. The highest resistance factors to fluxapyroxad and bixafen, the most important SDHI fungicides for net blotch control in Australia, were associated with the SdhC-H134R and SdhC-S135R mutations in Ptt, and with the SdhB-H277L, SdhC-H134R, and SdhC-S135R mutations in Ptm. Modelling of the P. teres Sdh complex showed that the two novel mutations, H277L in SdhB and H134Y in SdhD, result in a highly altered binding mode and lower binding affinity of the SDHI compound compared to the wild-type.

microbiology↗

bioRxiv2023

A DRG genetic toolkit reveals molecular, morphological, and functional diversity of somatosensory neuron subtypes

Mechanical and thermal stimuli acting on the skin are detected by morphologically and physiologically distinct sensory neurons of the dorsal root ganglia (DRG). Achieving a holistic view of how this diverse neuronal population relays sensory information from the skin to the central nervous system (CNS) has been challenging with existing tools. Here, we used transcriptomic datasets of the mouse DRG to guide development and curation of a genetic toolkit to interrogate transcriptionally defined DRG neuron subtypes. Morphological analysis revealed unique cutaneous axon arborization areas and branching patterns of each subtype. Physiological analysis showed that subtypes exhibit distinct thresholds and ranges of responses to mechanical and/or thermal stimuli. The somatosensory neuron toolbox thus enables comprehensive phenotyping of most principal sensory neuron subtypes. Moreover, our findings support a population coding scheme in which the activation thresholds of morphologically and physiologically distinct cutaneous DRG neuron subtypes tile multiple dimensions of stimulus space.

neuroscience↗

bioRxiv2023

Self-loops in Evolutionary Graph Theory: Friends or Foes?

Evolutionary dynamics in spatially structured populations has been studied for a long time. More recently, the focus has been to construct structures that speeds up evolution - so called amplifiers of selection. It has been shown that for a structure to amplify selection, self-loops are necessary when mutants appear predominately in nodes that change often. As a result, for low mutation rates, self-looped amplifiers attain higher steady-state average fitness in the mutation-selection than well-mixed populations. But, what happens when the mutation rate increases such that fixation probabilities alone no longer describe the dynamics? We show that self-loops effects are detrimental outside the low mutation rate regime. In the intermediate and high mutation rate regime, amplifiers of selection attain lower steady-state average fitness than the complete graph and the suppressor of selection. We also provide an estimate of mutation rate beyond which the mutation-selection dynamics on a graph deviates from the weak mutation rate approximation. This involves computing how the average fixation time scales with the population size for several graphs.

evolutionary biology↗

bioRxiv2023

Sustained activation in basal ganglia and cerebellum after repetitive movement in a non-task-specific dystonia

We previously observed sustained fMRI BOLD signal in the basal ganglia in focal hand dystonia patients after a repetitive finger tapping task. Since this was observed in a task-specific dystonia, for which excessive task repetition may play a role in pathogenesis, in the current study we asked if this effect would be observed in a focal dystonia (cervical dystonia [CD]) that is not considered task-specific or thought to result from overuse. We evaluated fMRI BOLD signal time courses before, during, and after the finger tapping task in CD patients. We observed patient/control differences in post-tapping BOLD signal in left putamen and left cerebellum during the non-dominant (left) hand tapping condition, reflecting abnormally sustained BOLD signal in CD. BOLD signals in left putamen and cerebellum were also abnormally elevated in CD during tapping itself and escalated as tapping was repeated. There were no cerebellar differences in the previously studied FHD cohort, either during or after tapping. We conclude that some elements of pathogenesis and/or pathophysiology associated with motor task execution/repetition may not be limited to task-specific dystonias, but there may be regional differences in these effects across dystonias, associated with different types of motor control programs.

neuroscience↗

bioRxiv2023

SiHDA9 interacts with SiHAT3.1 and SiHDA19 to repress dehydration responses through H3K9 deacetylation in foxtail millet

Drought stress affects the growth and productivity of plants, where C4 plants can advantageously perceive and respond to the stress for their survival and reproduction. Epigenetic modifications play a prominent role in conferring drought tolerance in C4 plants; however, the molecular links between histone modifiers and their regulation are unclear. In the present study, we performed a genome-wide H3K9ac enrichment in foxtail millet (Setaria italica) and analyzed their role in regulating the expression of drought-responsive genes. The presence of H3K9ac on these genes were identified through the comparative analysis of dehydration tolerant (cv. IC4) and sensitive (IC41) cultivars of foxtail millet. A histone deacetylase, SiHDA9, showed significant upregulation in the sensitive cultivar during dehydration stress. SiHDA9 overexpression in Arabidopsis thaliana conferred higher sensitivity to dehydration/drought stress than WT plants. We found that SiHDA9 physically interacts with SiHAT3.1 and SiHDA19. This complex is recruited through the SiHAT3.1 recognition sequence on the upstream of drought-responsive genes (SiRAB18, SiRAP2.4, SiP5CS2, SiRD22, SiPIP1;4, and SiLHCB2.3) to decrease H3K9 acetylation levels. The modulations in H3K9ac levels cause repression of gene expression and induce drought-sensitivity in the sensitive cultivar. Overall, the study provides mechanistic insights into SiHDA9-mediated regulation of drought stress response in foxtail millet.

plant biology↗

bioRxiv2023

Role of maternal, fetal and placental histopathology factors in the pathogenesis of retinopathy of prematurity.

PurposeTo investigate if maternal, fetal and placental vascular and/or molecular changes predict the risk for retinopathy of prematurity in preterm infants. MethodologyThe postnatal and antenatal data and placental histopathological changes; H&E staining of placental sections and molecular findings; gene expression analysis by qRT-PCR and protein expression by IHC at the maternal-fetal interface were collected from 20 placental samples and categorized into 3 groups: full-term (n=10), preterm without ROP (n=7) and preterm with ROP (n=6). ResultsThe correlation analysis indicated significant association of increased monocytes (p=0.042), fetal growth retardation (p=0.000), apnoeic spell (p=0.033), ventilation (p=0.009), length in hospital stay (p=0.001) and decreased RBC (p=0.02), Hb (p=0.048), PCV (p=0.010), gestational age (p=0.003), birth weight (p=0.000) with increased risk of ROP. Along with these factors, placental weight(p=0.001), diameter (p=0.019), Tenny-Parker changes (p=0.025), alternating area of small and short hyper mature villi (p=0.033) are also found to be significant determinants of the disease. Gene expression analysis revealed significant increase in hypoxia (HIF-1 gene expression; p=0.007) and non-significant increase in the pro-inflammatory marker IL-6. The protein expression also showed the significantly increased activation of complement pathway (CFH) and NF- KB at maternal-fetal interface. ConclusionsOur preliminary results support the changes in the maternal-fetal factors, placental histopathology and molecular alterations related to hypoxia, inflammation and complement activation at maternal-fetal interface in preterm with ROP placentas. These changes have the potential to predict the risk of the disease but the results are required to be further validated in larger cohort.

pathology↗

bioRxiv2023

A random forest model for predicting exosomal proteins using evolutionary information and motifs

Identification of secretory proteins in body fluids is one of the key challenges in the development of non-invasive diagnostics. It has been shown in the part that a significant number of proteins are secreted by cells via exosomes called exosomal proteins. In this study, an attempt has been made to build a model that can predict exosomal proteins with high precision. All models are trained, tested, and evaluated on a non-redundant dataset comprising 2831 exosomal and 2831 non-exosomal proteins, where no two proteins have more than 40% similarity. Initially, the standard similarity-based method BLAST was used to predict exosomal proteins, which failed due to low-level similarity in the dataset. To overcome this challenge, machine learning based models have been developed using compositional features of proteins and achieved highest AUROC of 0.70. The performance of the ML-based models improved significantly to AUROC of 0.73 when evolutionary information in the form of PSSM profiles was used for building models. Our analysis indicates that exosomal proteins have wide range of motifs. In addition, it was observed that exosomal proteins contain different types of sequence-based motifs, which can be used for predicting exosomal proteins. Finally, a hybrid method has been developed that combines a motif-based approach and an ML-based model for predicting exosomal proteins, achieving a maximum AUROC 0.85 and MCC of 0.56 on an independent dataset. The hybrid model in this study performs better than the presently available methods when assessed on an independent dataset. A web server and a standalone software ExoProPred has been created for the scientific community to provide service, code, and data. (https://webs.iiitd.edu.in/raghava/exopropred/). KeypointsO_LIExosomal proteins or non-classical secretory proteins are secreted by via exosomes C_LIO_LIA method has been developed for predicting exosomal proteins C_LIO_LIModels have been trained, tested, and evaluated on non-redundant dataset C_LIO_LIWide range of sequence motifs have been discovered in exosomal proteins C_LIO_LIA web server and standalone software have been developed C_LI

bioinformatics↗

bioRxiv2023

A method for predicting linear and conformational B-cell epitopes in an antigen from its primary sequence

B-cell is an essential component of the immune system that plays a vital role in providing the immune response against any pathogenic infection by producing antibodies. Existing methods either predict linear or conformational B-cell epitopes in an antigen. In this study, a single method was developed for predicting both types (linear/conformational) of B-cell epitopes. The dataset used in this study contains 3875 B-cell epitopes and 3996 non-B-cell epitopes, where B-cell epitopes consist of both linear and conformational B-cell epitopes. Our primary analysis indicates that certain residues (like Asp, Glu, Lys, Asn) are more prominent in B-cell epitopes. We developed machine-learning based methods using different types of sequence composition and achieved the highest AUC of 0.80 using dipeptide composition. In addition, models were developed on selected features, but no further improvement was observed. Our similarity-based method implemented using BLAST shows a high probability of correct prediction with poor sensitivity. Finally, we came up with a hybrid model that combine alignment free (dipeptide based random forest model) and alignment-based (BLAST based similarity) model. Our hybrid model attained maximum AUC 0.83 with MCC 0.49 on the independent dataset. Our hybrid model performs better than existing methods on an independent dataset used in this study. All models trained and tested on 80% data using cross-validation technique and final model was evaluated on 20% data called independent or validation dataset. A webserver and standalone package named "CLBTope" has been developed for predicting, designing, and scanning B-cell epitopes in an antigen sequence (https://webs.iiitd.edu.in/raghava/clbtope/).

bioinformatics↗

bioRxiv2023

Impact of urbanization on the taxonomic and functional diversity of spider assemblages in Guwahati City, Assam, India

The homogenous nature of the urban environment rapidly alters community dynamics of extant flora and fauna due to short-term spatial and temporal factors. However, such impacts of urbanization are mostly investigated in terms of taxonomic diversity, while its impact on functional diversity remains poorly understood. Whereas taxonomic information is limited to the identity of species, functional traits determine the relationship between species identity and ecosystem functioning. Studies investigating the role of urbanization in altering these ecological parameters have mostly focused on avian communities or plant species, while arthropods such as spiders which are integral components of urban households have largely been overlooked. This study aims to understand the impact of urbanization on both taxonomic diversity and functional diversity of spider assemblages across an urban-semi-urban-forest gradient in Guwahati, a rapidly growing city in northeast India. We surveyed spiders at 13 sites representing four habitat types (urban, urban parks, semi-urban, and forests) using belt transects, and also recorded functional traits relating to key life history processes. Spider species composition differed significantly between various habitats. The taxonomic diversity of spiders was highest in forests and lowest in urban parks. The turnover component was the major contributor to changing the {beta}-diversity of spiders. Reduced diversity in urban regions was likely due to the dominance of a few synanthropic species. Generalised linear mixed-effects model analysis indicated that the habitat types significantly impacted spider abundance. Functional richness was maximum in forests (Fric = 23.43) and minimum in urban habitats (Fric = 12.98), while functional divergence was maximum in urban sites (Fdiv = 0.79). Our study demonstrates that urban land-use change can alter the structure and functioning of the spider community.

ecology↗

bioRxiv2022

Niche partitioning and coexistence of sympatric macaques in a fragmented habitat of the Upper Brahmaputra Valley, northeastern India

How closely related species co-exist, especially under conditions of resource limitation remains an intriguing problem in ecology. Having to share space and resources, such species are expected to have evolved a variety of mechanisms to reduce competition. In this study, we examined the niche partitioning of three congeneric species, northern pig-tailed macaque Macaca leonina, the rhesus macaque Macaca mulatta, and stump-tailed macaque Macaca arctoides, in a tropical lowland rainforest fragment of less than 21 square kilometer, the Hollongapar Gibbon Sanctuary, northeastern India. We conducted behavioural observations on two troops each of the three species over 23 months from March 2008 to January 2010 resulting in 6,471, 11,062 and 16,723 individual scans of pig-tailed, rhesus and stump-tailed macaques respectively. We compared activity budgets and examined niche partitioning among the macaques along space and food axes. The activity budgets of three macaques shows differences in their feeding and foraging behaviours: the stump-tailed were active throughout the day, pig-tailed macaques were most active during mid-day while the rhesus macaques activity peaked after late afternoon. The rhesus macaque utilised the forest edge and surrounding areas whereas the stump-tailed and pig-tailed macaques use forest interiors. Pig-tailed macaques used significantly higher canopy strata, while stump-tailed macaques were predominantly terrestrial while rhesus macaques used the mid-lower canopy. Dietary overlap was highest between rhesus and pig-tailed macaques and lowest between pig-tailed and stump-tailed macaques. Rhesus macaques showed the broadest dietary niche breadth, whereas pig-tailed and stump-tailed macaques exhibited narrower and more specialised diets. Our results demonstrate that fine-scale partitioning of space and food resources facilitates the long-term coexistence of three congeneric macaques within a small and isolated rainforest fragment. These findings provide important insights into primate persistence and conservation in fragmented tropical landscapes.

ecology↗

bioRxiv2022

Intragastric administration of low-dose rotenone post-colitis exacerbates damage to the nigrostriatal dopaminergic system in Parkinson's disease: The pace accelerates even more

BackgroundThe contribution of gastrointestinal (GI) inflammation and local exposure to neurotoxins in the gut offers the most in-depth explanation of Parkinsons disease (PD) etiopathogenesis through abnormal accumulation and spreading of alpha-synuclein (-syn) aggregates from the gut to the brain. ObjectivesThis study was designed to investigate whether dextran sodium sulfate (DSS)-mediated colitis may have lasting effects on dopaminergic pathways in the brain and whether or not colitis exacerbated susceptibility to later exposure to the neurotoxin rotenone. MethodsTo induce chronic colitis, 10 months old C57BL/6 mice were pre-exposed to 3 cycles of 7 days of 1% (w/v) DSS administration in drinking water followed by 14 days of regular drinking water. After colitis-induction, animals received a low dose of intragastric rotenone for the next 8 weeks, followed by testing for Parkinsonian behavior and GI phenotypes of inflammation. At the end of the 8th week after colitis, colon, brain stem, and midbrain tissue were isolated and analyzed for -syn, inflammatory markers, and dopaminergic neuronal loss. Gut microbial composition was assessed by 16S rRNA sequencing analysis. ResultsWe found that local rotenone exposure for 8 weeks did not affect colitis severity and colonic tight junction(TJ) protein expression (ZO-1, Occludin, and Claudin-1). On the other hand, we found that while eight weeks of chronic rotenone administration led to an increase in inflammatory markers, the presence of pre-existing colitis resulted in a considerable change in gut microbiota composition and a decrease in TJs protein expression. In addition, the administration of rotenone in mice post-colitis caused gastrointestinal function impairment and poor behavioral performances. Itworsened rotenone-induced -syn pathology in the colon, which extended upward and resulted in severe dopaminergic neuron loss and significant astroglia activation in the dorsal motor nucleus of the vagus (DMV), locus coeruleus, substantia nigra as well as in striatum. Interestingly, in the case of rotenone alone, we found that -syn induced ChAT+ neuronal death is restricted to the DMV. These findings indicate that long-term rotenone exposure in conjunction with early inflammatory intestinal milieu exacerbates the progression of -syn pathology and aggravates neurodegeneration in the intragastric mouse PD model. ConclusionsThis work provides detailed insight into the involvement of GI inflammation triggered after a neurotoxic insult in the colon and explores their potential to impact central dopaminergic degeneration in PD. This way, we can identify potential therapeutic targets that stop the enteric inflammatory processes involved in progressing PD. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=170 HEIGHT=200 SRC="FIGDIR/small/521569v1_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@e0b5a4org.highwire.dtl.DTLVardef@b556c0org.highwire.dtl.DTLVardef@1526d27org.highwire.dtl.DTLVardef@7c506f_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LILow-dose intragastric rotenone post-colitis aggravates gastrointestinal dysfunction and accelerates the onset of motor impairment. C_LIO_LILow-dose intragastric rotenone did not alter colitis clinical and histological aspects. C_LIO_LILow-dose intragastric rotenone post-colitis exacerbated the progression of -syn pathology from the GI tract to the brain, leading in central dopaminergic neuronal degeneration. C_LI

neuroscience↗

bioRxiv2022

Single-molecule visualization of stalled replication-fork rescue by the Escherichia coli Rep helicase

Genome duplication occurs while the template DNA is bound by numerous DNA-binding proteins. Each of these proteins act as potential roadblocks to the replication fork and can have deleterious effects on cells. In Escherichia coli, these roadblocks are displaced by the accessory helicase Rep, a DNA translocase and helicase that interacts with the replisome. The mechanistic details underlying the coordination with replication and roadblock removal by Rep remain poorly understood. Through real-time fluorescence imaging of the DNA produced by individual E. coli replisomes and the simultaneous visualization of fluorescently-labeled Rep, we show that Rep continually surveils elongating replisomes. We found that this association of Rep with the replisome is stochastic and occurs independently of whether the fork is stalled or not. Further, we visualize the efficient rescue of stalled replication forks by directly imaging individual Rep molecules as they remove a model protein roadblock, dCas9, from the template DNA. Using roadblocks of varying DNA-binding stabilities, we conclude that replication restart is the rate-limiting step of stalled replication rescue.

biochemistry↗

bioRxiv2022

DRG afferents that mediate physiologic and pathologic mechanosensation from the distal colon

The properties of dorsal root ganglia (DRG) neurons that innervate the distal colon are poorly defined, hindering our understanding of their roles in normal physiology and gastrointestinal disease. Here, we report genetically defined subsets of colon innervating DRG neurons with diverse morphologic and physiologic properties. Four colon innervating DRG neuron populations are mechanosensitive and exhibit distinct force thresholds to colon distension. The highest threshold population, selectively labeled using Bmpr1b genetic tools, is necessary and sufficient for behavioral responses to high colon distension, which is partly mediated by the mechanosensory ion channel Piezo2. This HTMR population mediates behavioral over-reactivity to colon distension caused by inflammation in a model of inflammatory bowel disease. Thus, like cutaneous mechanoreceptor populations, colon innervating DRG afferents exhibit distinct anatomical and physiological properties and tile force threshold space, and genetically defined colon innervating HTMRs mediate pathophysiological responses to colon distension revealing a target population for therapeutic intervention.

neuroscience↗