Biology subjects

Sharma, S.

Publications and source records attributed to Sharma, S..

At least 253 records · Page 14Linked to original sources

bioRxiv2023

Neutrophil-derived IL-17 limits protective host responses and promotes tuberculosis pathogenesis

The protective correlates of Mycobacterium tuberculosis (Mtb) infection-elicited host immune responses are incompletely understood. Here, we report pro-pathogenic crosstalk involving Ly6G+granulocytes (Ly6G+Gra), IL-17 and COX2. We show that in the lungs of Mtb-infected wildtype mice, either BCG-vaccinated or not, most intracellular bacilli are Ly6G+Gra-resident four weeks post-infection onwards. In the genetically susceptible IFN{psi} -/- mice, excessive Ly6G+Gra infiltration correlates with severe bacteraemia. Neutralizing IL-17 (anti-IL17mAb) and COX2 inhibition by celecoxib reverse Ly6G+Gra infiltration, associated pathology and death in IFN{psi} -/- mice. Surprisingly, Ly6G+Gra also serves as the major source of IL-17 in the lungs of Mtb-infected WT or IFN{psi} -/- mice. The IL-17-COX2-Ly6G+Gra interplay also operates in WT mice. Inhibiting ROR{psi}t, the key transcription factor for IL-17 production or COX2, reduces the bacterial burden in Ly6G+Gra, leading to reduced bacterial burden and pathology in the lungs of WT mice. In the Mtb-infected WT mice, COX2 inhibition abrogates IL-17 levels in the lung homogenates and significantly enhances BCGs protective efficacy, mainly by targeting the Ly6G+Gra-resident Mtb pool, a phenotype also observed when IL-17 is blocked by ROR{psi}t inhibitor. Furthermore, in pulmonary TB patients, high neutrophil count and IL-17 correlated with adverse treatment outcomes. Together, our results suggest that IL-17 and PGE2 are the negative correlates of protection, and we propose targeting the pro-pathogenic IL-17-COX2-Ly6G+Gra axis for TB prevention and therapy.

immunology↗

bioRxiv2023

The atypical cadherin FAT1 is a novel regulator of STAT1, driving its pro-tumorigenic effect via the STAT1/PDCD4 axis in glioblastoma

FAT1 is an atypical cadherin that has been shown to act both as an oncogene and a tumour suppressor gene (TSG) in different tumor types. We have earlier shown that upregulated FAT1 acts as an oncogene in glial tumors by promoting pro-tumorigenic inflammation and EMT in primary human glioblastoma and in cell lines. One effect was through the suppression of the Tumor Suppressor Gene (TSG), Programmed Cell Death 4 (PDCD4). Here, we have studied how, in glioblastoma, upregulated FAT1 affects downstream events that control PDCD4 expression. In silico analysis of the PDCD4 promoter revealed multiple STAT1 binding sites. We also found a positive correlation in mRNA levels of STAT1 and FAT1 in the Glioblastoma databases, as well as in resected patient derived tumor samples by qPCR. Increased FAT1 as well as STAT1 were associated with poor prognosis in these data bases. In the glioblastoma cell lines LN229 and U87MG, FAT1 knockdown resulted in decreased STAT1 expression. Also, STAT1 knockdown resulted in increased PDCD4 expression, implying that STAT1 may mediate FAT1s role in suppressing PDCD4. Further, ChIP experiments showed that STAT1 protein binds to the PDCD4 promoter and upon FAT1 knockdown, STAT1 binding to the PDCD4 promoter reduces. As for FAT1, STAT1 knockdown also reduces the expression of pro-inflammatory cytokines and EMT markers, also migration and invasion of glioma derived cell lines. This work identifies STAT1 as a novel downstream mediator of FAT1 which mediates its pro-tumorigenic action in suppressing the TSG, PDCD4.

cancer biology↗

bioRxiv2023

When the whole is only the parts: non-holistic object parts predominate face-cell responses to illusory faces.

Humans are inclined to perceive faces in everyday objects with a face-like configuration. This illusion, known as face pareidolia, is often attributed to a specialized network of face cells in primates. We found that face cells in macaque inferotemporal cortex responded selectively to pareidolia images, but this selectivity did not require a holistic, face-like configuration, nor did it encode human faceness ratings. Instead, it was driven mostly by isolated object parts that are perceived as eyes only within a face-like context. These object parts lack usual characteristics of primate eyes, pointing to the role of lower-level features. Our results suggest that face-cell responses are dominated by local, generic features, unlike primate visual perception, which requires holistic information. These findings caution against interpreting neural activity through the lens of human perception. Doing so could impose human perceptual biases, like seeing faces where none exist, onto our understanding of neural activity.

neuroscience↗

bioRxiv2023

High-resolution double vision of the archetypal protein tyrosine phosphatase

Protein tyrosine phosphatase 1B (PTP1B) plays important roles in cellular homeostasis and is a highly validated therapeutic target for multiple human ailments including diabetes, obesity, and breast cancer. However, much remains to be learned about how conformational changes may convey information through the structure of PTP1B to enable allosteric regulation by ligands or functional responses to mutations. High-resolution X-ray crystallography can offer unique windows into protein conformational ensembles, but comparison of even high-resolution structures is often complicated by differences between datasets including non-isomorphism. Here we present the highest-resolution crystal structure of apo wildtype (WT) PTP1B to date, out of [~]350 total PTP1B structures in the PDB. Our structure is in a crystal form that is rare for PTP1B, with two unique copies of the protein that exhibit distinct patterns of conformational heterogeneity, allowing a controlled comparison of local disorder across the two chains within the same asymmetric unit. We interrogate the conformational differences between these chains in our apo structure, and between several recently reported high-resolution ligand-bound structures. We also examine electron density maps in a high-resolution structure of a recently reported activating double mutant, and discover unmodeled alternate conformations in the mutant structure that coincide with regions of enhanced conformational heterogeneity in our new WT structure. Our results validate the notion that these mutations operate by enhancing local dynamics, and suggest a latent susceptibility to such changes in the WT enzyme. Together, our new data and analysis provide a freshly detailed view of the conformational ensemble of PTP1B, and highlight the utility of high-resolution crystallography for elucidating conformational heterogeneity with potential relevance for function.

biophysics↗

bioRxiv2023

Unravelling Genomic Origin of Lumpy Skin Disease Virus in Recent Outbreaks

Lumpy skin disease virus (LSDV) belongs to the genus Capripox virus and family Poxviridae. LSDV was endemic in most of Africa, Middle east and Turkey, but since 2015, several outbreaks have been reported in Asian countries. In this study we used Whole Genome Sequence (WGS) approach to investigate the origin of the outbreak and understand the genomic landscape of the virus. Our study showed that the LSDV strain of 2022 outbreak exhibited many genetic variations, compared to the Reference Neethling strain sequence and the previous field strains from India. A total of 1819 variations were found in 22 genome sequences, which includes 399 extragenic mutations, 153 insertion frameshift mutations, 234 deletion frameshift mutations, 271 Single nucleotide polymorphisms (SNPs) and 762 silent SNPs. 38 genes have more than 2 variations per gene and these genes belong to viral-core protein, viral binding proteins, replication and RNA polymerase proteins. We highlight the importance of several SNPs in various genes which may play an essential role in pathogenesis of LSDV. Phylogenetic analysis performed on all whole genome sequences of LSDV showed two types of variants in India. One group of the variant with fewer mutations was found to lie closer to the LSDV 2019 strain from Ranchi while the other group clustered with previous Russian outbreaks from 2015. Our study highlights the importance of genomic characterization of viral outbreaks to not only monitor the frequency of mutations but also address its role in pathogenesis of LSDV as the outbreak continues.

microbiology↗

bioRxiv2023

Alcohol Responsive Genes in the Neutrophils of Acute-On-Chronic Liver Failure Reveal Modulation of Intracellular Calcium, ROS, and Phagocytosis

Acute-on-chronic liver failure (ACLF) is characterized by rapid depletion of hepatic reserves, innate immunity-driven pathogenesis and high short-term mortality. Elevation of neutrophil counts is associated with mortality in alcoholic-ACLF. In India, one of the most common etiologies in ACLF for both chronic and acute injury is alcohol. We used a combination of clinical transcriptomics and a novel in vitro laboratory model to look at gene signatures unique in alcoholic ACLF patients and study phenotypic changes upon alcohol treatment. CCL20 and IL1{beta} were two of the top overexpressed genes in alcoholic-ACLF which were validated in the alcohol-neutrophil model, using neutrophils isolated from CLD patients (acute-on-chronic model), and healthy individual (acute model). In the alcoholic-neutrophil models, 300 mg/dL dose of ethanol for 24 hours, caused reduced ROS generation, reduced phagocytic ability and dampening of intracellular calcium reserves. We conclude that the effects of alcohol at least partially explain immune dysfunction in ACLF such as dampening of ROS and phagocytosis in neutrophils while retaining inflammatory roles such as expression of CCL20 and IL1{beta}. Systematic curation of previously published alcohol related liver tissue transcriptomic data also confirmed overlapping genes with alcoholic-ACLF circulating neutrophils. Docking of ethanol with CCL20 and IL1{beta} showed spontaneous binding.

cell biology↗

bioRxiv2023

Terminal regions of a protein are a hotspot for low complexity regions (LCRs) and selection

A majority of the protein-coding genes consist of low-complexity regions (LCRs) in eukaryotes. Volatile LCRs are a novel source of adaptive variation, functional diversification, and evolutionary novelty. LCRs contribute to a wide range of neurodegenerative disorders. Conversely, these regions also play a pivotal role in critical cellular functions, such as morphogenesis, signaling, and transcriptional regulation. An interplay of selection and mutation governs the composition and length of LCRs. High %GC and mutations provide length variability because of mechanisms like replication slippage. The selection is nearly neutral for expansion/contraction within the normal range and purifying above a critical length. Because of the complex dynamics between selection and mutation, we need a better understanding of the coexistence and mechanisms of the two. Our findings indicate that site-specific positive selection and LCRs prefer the terminal regions of a gene and co-occur in most of the Tetrapoda clades. Interestingly, positively selected sites (PSS) are significantly favored in LCRs in eight of the twelve clades studied. We also observed a significant favor of PSSs in the polyQ region of MAML2 in five clades. We also found that PSSs in a gene have position-specific roles. Terminal-PSS genes are enriched for adenyl nucleotide binding, while central-PSS genes are involved in glycosaminoglycan binding. Moreover, central-PSS genes mainly participate in defense responses, but terminal-PSS genes are non-specific. LCR-containing genes have a significantly higher %GC and lower {omega} (dN/dS) than genes without repeats across the Tetrapoda clade. A lower {omega} suggests that even though LCRs provide rapid functional diversity, LCR-containing genes face intense purifying selection.

genomics↗

bioRxiv2023

Structure-guided engineering of biased-agonism in the human niacin receptor via single amino acid substitution

The Hydroxycarboxylic acid receptor 2 (HCA2), also known as the niacin receptor or GPR109A, is a prototypical G protein-coupled receptor that plays a central role in the inhibition of lipolytic and atherogenic activities in our body. Interestingly, GPR109A activation also results in vasodilation that is linked to the side-effect of flushing associated with dyslipidemia drugs such as niacin. This receptor continues to be a key target for developing novel pharmacophores and lead compounds as potential therapeutics in dyslipidemia with minimized flushing response, however, the lack of structural insights into agonist-binding and receptor activation has limited the efforts. Here, we present five different cryo-EM structures of the GPR109A-G-protein complexes with the receptor bound to dyslipidemia drugs, niacin or acipimox, non-flushing agonists, MK6892 or GSK256073, and recently approved psoriasis drug, monomethyl fumarate (MMF). These structures allow us to visualize the binding mechanism of agonists with a conserved molecular interaction network, and elucidate the previously lacking molecular basis of receptor activation and transducer-coupling. Importantly, cellular pharmacology experiments, guided by the structural framework determined here, elucidate pathway-selective biased signaling elicited by the non-flushing agonists. Finally, taking lead from the structural insights, we successfully engineered receptor mutants via single amino acid substitutions that either fail to elicit agonist-induced transducer-coupling or exhibits G-protein signaling bias. Taken together, our study provides previously lacking structural framework to understand the agonist-binding and activation of GPR109A, and opens up the possibilities of structure-guided novel drug discovery targeting this therapeutically important receptor.

biochemistry↗

bioRxiv2023

Uncovering Protein Ensembles: Automated Multiconformer Model Building for X-ray Crystallography and Cryo-EM

In their folded state, biomolecules exchange between multiple conformational states that are crucial for their function. Traditional structural biology methods, such as X-ray crystallography and cryogenic electron microscopy (cryo-EM), produce density maps that are ensemble averages, reflecting molecules in various conformations. Yet, most models derived from these maps explicitly represent only a single conformation, overlooking the complexity of biomolecular structures. To accurately reflect the diversity of biomolecular forms, there is a pressing need to shift towards modeling structural ensembles that mirror the experimental data. However, the challenge of distinguishing signal from noise complicates manual efforts to create these models. In response, we introduce the latest enhancements to qFit, an automated computational strategy designed to incorporate protein conformational heterogeneity into models built into density maps. These algorithmic improvements in qFit are substantiated by superior Rfree and geometry metrics across a wide range of proteins. Importantly, unlike more complex multicopy ensemble models, the multiconformer models produced by qFit can be manually modified in most major model building software (e.g. Coot) and fit can be further improved by refinement using standard pipelines (e.g. Phenix, Refmac, Buster). By reducing the barrier of creating multiconformer models, qFit can foster the development of new hypotheses about the relationship between macromolecular conformational dynamics and function.

biophysics↗

bioRxiv2023

A sex-specific homologue of snake waprin is required for embryonic development in the Red Flour Beetle, Tribolium castaneum

1.Waprin, an extracellular secretory protein, is widely known for its antibacterial activity. Through the analysis of sex-specific transcriptomes of adult Tribolium castaneum, we identified a homologue of snake waprin (Tc_WapF) with significantly higher level of its transcripts in females. Developmental- and tissue-specific profiling revealed the widespread expression of Tc_WapF in adult female tissues. Interestingly, Tc_WapF expression is not regulated by the classical sex-determination cascade of T. castaneum, as we fail to get any attenuation in Tc_WapF transcript levels in Tcdsx and Tctra (key players of sex determination cascade of T. castaneum) knockdown females. The eggs laid by Tc_WapF knockdown females never hatched, indicating the involvement of Tc_WapF in the embryonic development in T. castaneum. This is the first report of identification a sex-specific waprin homologue in an insect and its involvement as a novel candidate in the embryonic development. Future investigations on the functional conservation of insect waprins and their mechanistic role in embryonic development can be exploited for improving pest management strategies. Summary statementTribolium castaneum possesses a female-specific homologue of snake Waprin (Tc_WapF) which is essential for its embryonic development. Expression of Tc_WapF is independent of Tribolium sex-determination cascade.

molecular biology↗

bioRxiv2023

Peripheral death by neglect and limited clonal deletion during physiologic B lymphocyte development

Autoreactive B cells generated during B cell development are inactivated by clonal deletion, receptor editing or anergy. Up to 97% of immature B cells appear to die before completing maturation, but the anatomic sites and reasons underlying this massive cell loss are not fully understood. Here, we directly quantitated apoptosis and clonal deletion during physiologic B lymphocyte development using Rosa26INDIA apoptosis indicator mice. Immature B cells displayed low levels of apoptosis in the bone marrow but started dying at high levels in the periphery upon release from bone marrow sinusoids into the blood circulation. Clonal deletion of self-reactive B cells was neither a major contributor to apoptosis in the bone marrow nor the periphery. Instead, most peripheral transitional 1 B cells did not encounter the signals required for positive selection into the mature B cell compartments. This study sheds new light on B cell development and suggests that receptor editing and/or anergy efficiently control most primary autoreactivity in mice. SummaryThe large amount of cell loss predicted during B lymphocyte development is unexplained by clonal deletion of self-reactive cells. Many transitional 1 B cells die in the periphery due to failed selection in the mature B cell compartments.

immunology↗

bioRxiv2023

Heterologous Expression and Characterization of ToxA1 haplotype from India and its interaction with for Spot Blotch Susceptibility in spring wheat

BackgroundToxA, a necrotrophic effector protein, is present in the genome of fungal species like Parastagnospora nodorum, Pyrenophora tritici-repentis and Bipolaris sorokiniana. Tsn1 is the sensitivity gene in the host whose presence indicates more susceptibility to ToxA carrying pathogen, and ToxA-Tsn1 interaction follows an inverse gene-for-gene relationship. Methods and ResultsThe present study involved cloning and expressing the ToxA1 haplotype from B. sorokiniana. It was found that the amplicon exhibited an expected product size of 471 bp. Sequence analysis of the ToxA1 nucleotide sequence revealed the highest identity, 99.79%, with P. tritici-repentis. The protein expression analysis showed peak expression at 16.5kDa. Phylogenetic analysis of the ToxA1 sequence from all the Bipolaris isolates formed an independent clade along with P. tritici-repentis and diverged from P. nodorum. ToxA-Tsn1 interaction was studied in 18 wheat genotypes (11 Tsn1 and 7 tsn1) at both seedling and adult stages, validating the inverse gene-for-gene relationship, as the toxin activity was highest in the K68 genotype (Tsn1) and lowest in WAMI280 (tsn1). ConclusionThe study indicates that the haplotype ToxA1 is prevailing in the Indian population of B. sorokiniana. It would be desirable for wheat breeders to select genotypes with tsn1 locus for making wheat resistant to spot blotch.

plant biology↗

bioRxiv2023

Cryo- EM structure of the mycobacterial 70S ribosome in complex with ribosome hibernation promotion factor RafH, reveals the unique mode of mycobacterial ribosome hibernation

Ribosome hibernation is a key survival strategy bacteria adopt under environmental stress, where a protein, hibernation promotion factor (HPF), transitorily inactivates the ribosome and slows down its overall protein synthesis. The mechanism is well studied in enteric bacteria, which mainly hibernate its ribosome in 100S disome form through a dual domain, long HPF (HPFlong) or a single domain, short HPF (HPFshort) in concert with another ribosome modulation factor. Mycobacteria under hypoxia (low oxygen) stress overexpresses RafH protein regulated under DosR regulon, a critical factor for its survival. The RafH, a dual domain HPF, an orthologue of bacterial HPFlong, hibernates ribosome in 70S monosome form only. Here we report the cryo-EM structure of Mycobacterium smegmatis, a close homologue of M. tuberculosis, 70S ribosome in complex with the RafH factor at an overall 2.8 [A] resolution. The RafH N-terminus domain (NTD) is conserved and binds to the decoding center of the ribosomal small subunit, a similar binding site of HPFlong NTD, but additionally it also interacts with the inter subunit bridge, B2a. Contrary to the HPFlong CTD, the RafH CTD, which is larger, binds to a unique site at the platform binding center of the ribosomal small subunit and sandwiches between bS1 and uS11 ribosomal proteins. The two domain connecting linker regions, which remain mostly disordered in earlier reported HPFlong structures, interacts mainly with the anti-Shine Dalgarno sequence of the 16S rRNA. The helix H54a of 23S rRNA, unique to the mycobacterial ribosome, adopts a different conformation and come close to RafH CTD, suggesting its role in ribosome hibernation. RafH inhibits in-vitro protein synthesis in a concentration dependent manner. Further, the modeling studies provided the structural basis for the incompatibility of mycobacterial ribosomes forming 100S like hibernating ribosomes.

biochemistry↗

bioRxiv2023

Poor biosafety and biosecurity practices and haphazard antibiotics usage in poultry farms in Nepal hindering antimicrobial stewardship

Poultry industry in Nepal has experienced remarkable growth in the last decade, but farm biosafety and biosecurity measures are often overlooked by farmers due to lack of knowledge or to save cost. As a result, farms often suffer from sporadic and regular outbreaks of many zoonotic diseases such as highly pathogenic avian influenza (HPAI), impacting production and creating public health challenges. Poor farm management practices, including overuse of antibiotics for prophylaxis and therapeutics, can complicate the spread of poultry diseases by creating and enhancing antimicrobial resistance (AMR) that is threating to both, poultry, and human health. We assessed biosafety, biosecurity risks and AMR stewardship in sixteen poultry farms located in four districts (Ramechhap, Nuwakot, Sindhupalchowk, and Kavre) surrounding densely populated Kathmandu valley. Risk assessment and AMR stewardship evaluation questionnaire were administered to formulate biosafety and biosecurity compliance matrix (BBCM). Risk assessment checklist assessed facility operations, personnel and standard operating procedures, water supply, cleaning and maintenance, rodent/pest control and farm record keeping. Oral and cloacal samples from the poultry were collected, pooled, and screened for eight poultry pathogens using Polymerase Chain Reaction (PCR) tests. Based on BBCM, we identified one of the farms in Sindhupalchowk (Farm 4) having the most (BBCM score= 67%) and a farm in Kavre (Farm 3) to having the least (BBCM score= 12%) biosafety and biosecurity compliance. Although most of the farms (61.6%) followed general poultry farming practices, only half had clean and well-maintained farms. Personal safety standard procedure compliance (BBCM score = 42.4%) and rodent control (BBCM score = 3.1%) were the biggest gaps. At least one of either bacterial or viral pathogen was detected in all farms. Mycoplasma gallisepticum was the most common disease detected in all but one farm, followed by Mycoplasma synoviae. Although more than half of the farmers considered AMR a threat, over 26% of them used antibiotics as a preventive measure and 81% did not consider withdrawal period for antibiotics prior to processing of their meat products. Additionally, antibiotics classified as Watch and Restrict by the WHO were frequently used by the farmers to treat bacterial infections in their farms. Lack of awareness and inadequate enforcement of regulations have exacerbated the risk of disease transmission in farms and compromised antimicrobial stewardship.

microbiology↗

bioRxiv2023

Dysregulation of Prefrontal Oligodendrocyte Lineage Cells Across Mouse Models of Adversity and Human Major Depressive Disorder

Animal models of adversity have yielded few molecular mechanisms that translate to human stress-related diseases like major depressive disorder (MDD). We congruently analyze publicly available bulk-tissue transcriptomic data from prefrontal cortex (PFC) in multiple mouse models of adversity and in MDD. We apply strategies, to quantify cell-type specific enrichment from bulk-tissue transcriptomics, utilizing reference single cell RNA sequencing datasets. These analyses reveal conserved patterns of oligodendrocyte (OL) dysregulation across animal experiments, including susceptibility to social defeat, acute cocaine withdrawal, chronic unpredictable stress, early life stress, and adolescent social isolation. Using unbiased methodologies, we further identify a dysregulation of layer 6 neurons that associate with deficits in goal-directed behavior after social isolation. Human post-mortem brains with MDD show similar OL transcriptome changes in Brodmann Areas 8/9 in both male and female patients. This work assesses cell type involvement in an unbiased manner from differential expression analyses across animal models of adversity and human MDD and finds a common signature of OL dysfunction in the frontal cortex.

neuroscience↗

bioRxiv2023

SifA SUMOylation governs Salmonella intracellular survival via modulation of lysosomal function

Gastroenteritis causing pathogen Salmonella Typhimurium (S. Tm) during its infection in host cells thrives in a vacuolated compartment, Salmonella Containing Vacuole (SCV), which sequentially acquires host endosomal and lysosomal markers. Long tubular structures, called as Salmonella induced filaments (SIFs), are known to be required for SCVs nutrient acquisition, membrane maintenance and stability. A tightly coordinated interactions involving prominent effector SifA and various host adapters PLEKHM1, PLEKHM2 and Rab GTPases govern SCV integrity and SIF formation. Here, we report for the first time, the functional regulation of SifA is modulated by its SUMOylation at lysine 11. S. Tm expressing lysine 11 mutant SifA (SifAK11R) is defective in intracellular proliferation due to compromised SIF formation and enhanced lysosomal acidification. Furthermore, murine competitive index experiments reveal defective in vivo proliferation and weakened virulence of SifAK11R mutant. Concisely, our results demonstrate that SUMO deficient SifA mutant nearly behaves like a SifA knockout strain which impacts PLEKHM2-M6PR mediated lysosomal acidification pathway. Thus, our results bring forth a novel S. Tm-host crosstalk mechanism involving host mediated effector SUMOylation critical for pathogenicity.

microbiology↗

bioRxiv2023

System analysis of differentially expressed miRNAs in hexaploid wheat display tissue-specific regulatory role during Fe deficiency response

BackgroundIron (Fe) is an essential mineral element, and its deficiency in soil largely affects crop productivity. In plants, the molecular mechanisms underlying the genetic regulation of Fe deficiency responses have yet to be well understood. Specifically, microRNA (miRNA) mediated regulation of Fe deficiency response and its regulatory network is largely elusive. In the current work, we utilized a whole genome transcriptomic approach to identify the Fe deficiency-responsive miRNAs to understand the molecular mechanisms of Fe deficiency response in wheat seedlings. The study also identifies nine novel miRNAs putatively involved in Fe deficiency response. Further, the identified miRNAs showed tissue preferences relating them to differential mechanisms against Fe deficiency. ResultsIn the present study, we performed small RNA-targeted whole genome transcriptome analysis to identify the involvement of sRNAs in Fe deficiency response. The analysis identified 105 differentially expressed miRNAs corresponding to Fe deficiency response, among them, 9 miRNAs were found to be novel in this study. Interestingly, tissue-specific regulation of Fe deficiency response also participates through miRNA-mediated regulation. We identified 17 shoot specific miRNAs and 18 root-specific miRNAs with altered expression. We validated the tissue specificity of these miRNAs by stem-loop quantitative RT-PCR. Further, an attempt was made to predict their targets to speculate their participation in Fe deficiency response. This miRNA target prediction analysis suggested a few major targets of the identified miRNAs, such as multicopper oxidases, E3 ubiquitin ligases, GRAS family, and WRKY transcription factors previously known to play key roles in Fe homeostasis. Our analysis of selected miRNAs also confirmed a temporal regulation of the response. ConclusionThe first information generated here will classify the repository of wheat miRNAs (with few novel miRNAs) for their role in Fe deficiency response. Our work provides insights into miRNA-mediated regulatory pathways during Fe deficiency.

plant biology↗

bioRxiv2023

Out of sight, out of mind: Responses in primate ventral visual cortex track individual fixations during natural vision

During natural vision, primates shift their gaze several times per second with large, ballistic eye movements known as saccades. Open questions remain as to whether visual neurons retain their classical retinotopic response properties during natural vision or whether neurons integrate information across fixations and predict the consequences of impending saccades. Answers are especially wanting for vision in complex scenes relevant to natural behavior. We let 13 monkeys freely view thousands of large natural images, recorded over 883 hours of neuronal responses throughout the ventral visual pathway across 4.7 million fixations, and designed flexible analyses to reveal the spatial, temporal, and feature selectivity of the responses. Ventral visual responses followed each fixation and did not become gaze-invariant as monkeys examined an image over seconds. Computational models revealed that neuronal responses corresponded to eye-centered receptive fields. The results suggest that ventral visual cortex remains predominantly retinotopic during natural vision and does not establish a gaze-independent representation of the world.

neuroscience↗