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Chattopadhyay, D.

Publications and source records attributed to Chattopadhyay, D..

At least 19 recordsLinked to original sources

Increase in sea-level and shelf area positively influenced the development of Cenozoic biodiversity hotspots by modulating turnover rate in marine benthos

Marine biodiversity is unevenly distributed across the oceans, with exceptional concentrations of species richness confined to a few hotspots. Fossil and molecular evidence indicate that marine hotspots have shifted among ocean basins throughout the Cenozoic, but the mechanisms underlying their emergence and persistence have rarely been tested across multiple marine groups. Using standardized fossil occurrence data for molluscs, cnidarians, and foraminifera, we identified marine biodiversity hotspots through the past 66 million years. We then apply a multistep framework linking environmental drivers (sea surface temperature (SST), shelf area, and sea level) to clade-specific macroevolutionary processes (origination, extinction, and immigration) to evaluate the dynamics of these hotspots. Our results reveal contrasting evolutionary dynamics across marine biodiversity hotspots of different marine groups. Benthic groups: Mollusca and Cnidaria exhibit higher evolutionary turnover in hotspots than in non-hotspot regions, whereas planktic foraminifera maintain high diversity through reduced extinction and immigration rates. Increase in the sea level and shelf area positively contribute to the development of hotspot by increasing the origination rate in mollusca and cnidaria. Our study offers an integrative framework for understanding how marine biodiversity hotspots arise through a network of interacting processes: environmental drivers shape macroevolutionary dynamics, which in turn generate clade-specific diversity trajectories; together, these processes determine whether a particular region develops into a biodiversity hotspot.

paleontology↗

β2 adrenergic receptors orchestrate neutrophil demargination and recruitment to the ischemic heart following myocardial infarction.

Neutrophils play a crucial role in instigating inflammation as well as its resolution post-myocardial infarction (MI). Although granulopoiesis in the bone marrow (BM) is the major source of cardiac neutrophils post-MI, infiltration of neutrophils to the heart occurs much quicker than peak granulopoiesis. These observations suggest that sources other than granulopoiesis may supply neutrophils to the heart during the early hours post-MI. Using a combination of flow cytometry, BM ablation of hematopoietic stem cells, confocal microscopy and multiple proteomics analysis, we found that the first wave of neutrophils recruited to the ischemic heart is exclusively sourced from vasculature and not from granulopoiesis in the BM/ spleen. The MI-evoked neutrophilia during the early hours bore all hallmarks of demargination induced by classical demarginating agents such as dexamethasone/ norepinephrine (NE). Various pharmacological and genetic strategies aimed at suppressing NE synthesis or disruption of {beta}-AR signaling reduced both neutrophil demargination as well as recruitment to the heart. Interestingly, however, despite a marked reduction in cardiac neutrophil burden only short-term inhibition of {beta}-ARs improved cardiac remodeling and function. Our findings support a pharmacological strategy to contain the initial onslaught of neutrophils on the ischemic heart using {beta}2-AR blockers to regulate the otherwise runaway inflammatory response.

immunology↗

Cold-responsive MtCBF4-MtJMJ13 positive feedback loop negatively regulates anthocyanin biosynthesis in Medicago truncatula

Legumes, being significant food sources for both humans and animals globally, experience several adverse conditions that considerably affect their crop yield. Medicago sp., an important forage crop, thrives under adverse conditions, such as drought, extreme temperatures (heat and cold), and salinity. Several studies have shed light on the regulatory pathways of cold/chilling stress tolerance in Medicago sp. in recent years. In the present study, we found that a cold-repressed transcription factor, MtCBF4, negatively regulates anthocyanin synthesis by directly repressing the expression of MtLAP1, a critical regulatory gene for anthocyanin synthesis in Medicago truncatula. It leads to the downregulation of anthocyanin biosynthesis genes, and reduced anthocyanin accumulation. Apart from the transcriptional cascade, MtCBF4 exerts its effect through histone H3K27 trimethylation. It directly binds to the promoter of MtJMJ13, an H3K27me3 demethylase, to activate its expression, resulting in decreased H3K27 trimethylation. Furthermore, MtJMJ13 demethylates the gene body of MtCBF4 to positively regulate its expression, forming a positive feedback loop that functions in a cold-responsive manner. MtJMJ13 also demethylates the gene body of MtMYB2, MtKFB1, and MtKFB2 genes, which are negative regulators of anthocyanin biosynthesis. Altogether, we have unveiled a new regulatory loop involving a transcriptional regulator and a histone demethylase, operating together to limit anthocyanin production. This regulatory module is repressed under cold stress, leading to increased anthocyanin production and enhanced cold stress tolerance in M. truncatula.

plant biology↗

ChromPolymerDB: A High-Resolution Database of Single-Cell 3D Chromatin Structures for Functional Genomics

The three-dimensional (3D) organization of chromatin plays a critical role in regulating gene expression and genomic processes like DNA replication, repair, and genome stability. Although these processes occur at the individual-cell level, most chromatin structure data are derived from population-averaged assays, such as Hi-C, obscuring the heterogeneity of single-cell conformations. To address this limitation, we developed a polymer physics-based modelling framework, the Sequential Bayesian Inference Framework (sBIF), that deconvolutes bulk Hi-C data to reconstruct single-cell 3D chromatin conformations. To support a broader use of sBIF, we created ChromPolymerDB, a publicly accessible, high-resolution database of single-cell chromatin structures inferred by sBIF. The database contains [~]108 reconstructed 5 kb-resolution single cell structures, spanning over 60,000 genomic loci across 50 human cell types and experimental conditions. ChromPolymerDB features an interactive web interface with tools for 3D structural analysis and multi-omics integration. Users can explore associations between chromatin conformation and gene expression, epigenetic modifications, and regulatory elements. The platform also supports comparative analyses to identify structural changes across cell types, developmental stages, or disease contexts. ChromPolymerDB offers a unique resource for researchers studying the relationship between genome architecture and gene regulation, and for advancing comparative 3D genomics. ChromPolymerDB is available online at https://chrompolymerdb.bme.uic.edu/. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/678816v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@110c807org.highwire.dtl.DTLVardef@bc713forg.highwire.dtl.DTLVardef@1af0ea9org.highwire.dtl.DTLVardef@1eba638_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

MPK3 mediated phosphorylation of WRKY48 down regulates CIPK6 expression during PstDC3000 challenge in Arabidopsis

WRKY transcription factor (TF) family are one of the key regulators of plant immune responses, functioning as both activators and suppressors depending on the pathogen encountered. Among these, WRKY48, a class IIC TF, functions as a negative regulator of pattern-triggered immunity (PTI) in Arabidopsis thaliana. Our study explicates the regulatory mechanisms underlying the function of WRKY48, revealing its role in repressing the expression of CIPK6, a negative regulator of immune response in Arabidopsis, during Pseudomonas syringae DC3000 (PstDC3000) infection. This suppression is mediated through MPK3-dependent phosphorylation of WRKY48. In vitro phosphorylation assays demonstrated that MPK3 primarily phosphorylates WRKY48 at serine residues S35 and S40. The phosphorylated WRKY48 predominantly localizes to the nucleus, enhancing its DNA-binding affinity and trans-repressive activity at specific W-box motifs in the CIPK6 promoter. Whereas invivo dual luciferase shows that unphosphorylated WRKY48 (S26S35S40 / A26A35A40 ) unable to repress luciferase activity of CIPK6 promoter. The bioinformatics analysis identified two WRKY-binding sites (P1 and P2) on the CIPK6 promoter and electrophoretic mobility shift assays confirms the preferential binding of WRKY48 to the P1 site. Unlike other WRKY TFs (WRKY28 and WRKY8) in the same subgroup, WRKY48 exhibited unique specificity, highlighting the distinct regulatory roles within the WRKY family. Functional studies demonstrated that phosphorylation of WRKY48 enhances its ability to suppress CIPK6 both transcriptionally and translationally, leading to increased reactive oxygen species (ROS) levels and decreased susceptibility to PstDC3000. The reduced expressions of PTI marker genes and ROS-associated genes in wrky48 mutants were associated with enhanced resistance in wrky48 and cipk6 mutants and emphasizes the critical role of WRKY48 in fine-tuning immune responses. Our findings identify a novel MPK3-WRKY48-CIPK6 signaling module that connects calcium-dependent pathways to MAPK signalling to modify plant immunity. HighlightsO_LIWRKY48, a class IIC transcription factor, functions as a negative regulator of pattern-triggered immunity (PTI) in Arabidopsis thaliana during Pseudomonas syringae DC3000 (PstDC3000) infection. C_LIO_LIWRKY48 suppresses the expression of CIPK6, a negative regulator of immune signaling, in response to bacterial infection. C_LIO_LIMAP kinase MPK3 phosphorylates WRKY48 at serine residues S35 and S40, enhancing its nuclear localization and transcriptional repressive activity C_LIO_LIPhosphorylated WRKY48 shows increased binding affinity to W-box motifs in the CIPK6 promoter, especially at the P1 binding site, as confirmed by electrophoretic mobility shift assays (EMSA). C_LIO_LIUnlike WRKY28 and WRKY8, WRKY48 exhibits unique binding specificity, suggesting functional diversification within WRKY subgroup IIC. C_LIO_LISuppression of CIPK6 by phosphorylated WRKY48 leads to: Elevated ROS accumulation, Reduced PTI marker gene expression, Increased susceptibility to PstDC3000 C_LI

molecular biology↗

CBL1/9-CIPK6 complex negatively regulates Respiratory burst oxidase homolog D in Arabidopsis thaliana

Plant innate immune response must be a well-balanced process with positive and negative regulations for the plants to survive. Calcium signalling is essential for pathogen-associated molecular pattern (PAMP)-driven Respiratory burst oxidase homolog D (RbohD)-mediated reactive oxygen species (ROS) burst. We show Calcium-sensors Calcineurin B like protein 1 (CBL1) and CBL9 and their interacting protein kinase CIPK6 negatively regulate RbohD activity and immune response in Arabidopsis thaliana. Arabidopsis mutant cbl1cbl9, like cipk6, exhibited enhanced resistance and ROS production when infected with the bacterial pathogen Pseudomonas syringae pv. tomato (Pst). CBL1 and CBL9 enhanced kinase activity of CIPK6. Plasma membrane localization of CBL1 and CBL9 and CIPK6 kinase activity were associated with the ROS production and immune response. CBL1/9-CIPK6 module interacts with RbohD at the plasma membrane and phosphorylates its N-terminal cytoplasmic domain at a non-conserved (Ser33) and a conserve (Ser39) Serine residue. While Ser39 phosphorylation increased RbohD activity, Ser33 phosphorylation drastically reduced it and superseded the effect of Ser39 phosphorylation. Replacement of Ser33 with alanine or aspartic acid made RbohD a super-active or low-active enzyme, respectively. Our study reports a direct mechanism of negative regulation of ROS production and plant immune response by a Calcium-signalling module in Arabidopsis. Overall, this study provides a novel insight into how calcium signaling integrates with immune regulation to prevent excessive ROS accumulation, ensuring a balanced plant immune response. One Sentence SummaryInactivation of RbohD by CBL1/CBL9-CIPK6 complex negatively regulates the plant immunity against Pst DC3000 infection in Arabidopsis.

plant biology↗

A mechanistic study on the tolerance of PAM distal end mismatch by SpCas9

CRISPR-Cas9 is the newest technology available for targeted genome editing. It is very efficient and cheap compared to other genome editing techniques. However, its therapeutic application is limited due to its off-target activity. To have a better understanding of this off-target effect, we concentrated our efforts on its mismatch-prone PAM distal end. Current off-target prediction algorithms use RNA-DNA complementation derived energy as a major factor in predicting off-target effect. RNA-DNA complementation derived energy drives Cas9 conformational change, which in turn drives its functional activity. In the case of lower RNA-DNA complementarity, a partial conformational change occurs resulting in a slower reaction rate and partial activity. However, extensive mismatches are often tolerated despite lower complementation derived energy available from RNA: DNA duplex formation. Thus, the off-target activity of Cas9 depends directly on the nature of mismatches which in turn result in deviation of the active site of the enzyme due to structural instability in the duplex strand. In order to test the hypothesis, we have designed an array of mismatched target sites and performed in vitro and cell line-based experiments to assess the effects of PAM distal mismatches in Cas9 activity. For further mechanistic validation, Molecular dynamics simulation was performed and it revealed that certain mismatch mutations induced pronounced conformational instability within the RNA-DNA duplex, leading to elevated root mean square deviation (RMSD) values. We found that, target sites having mismatches in the 18th to 16th position upstream of the PAM showed no to little activity.

genomics↗

An associative transcriptomics study on rice bean (Vigna umbellata) provides new insights into genetic basis and candidate genes governing flowering, maturity and seed weight

Rice bean is an underrated legume with significant potential to support food and nutritional security worldwide, being a rich source of proteins, minerals, and essential fatty acids. Therefore, we considered three pivotal production traits of rice bean; flowering, maturity and seed weight, to identify associated candidate genes. One-hundred diverse genotypes out of 1800 evaluated rice bean accessions from the Indian National Genebank were considered for phenotypic data collection and genotyping by transcriptome sequencing approach. Association analysis involving various GWAS models was conducted to identify significant marker-trait associations. The results revealed association of 82 markers on 48 transcripts for flowering, 26 markers on 22 transcripts for maturity and 22 markers on 21 transcripts for seed weight. The annotation of associated transcripts unraveled the functional genes related to the considered traits. Among the significant candidate genes identified, HSC80, P-II PsbX, phospholipid-transporting-ATPase-9, pectin-acetylesterase-8 and E3-ubiquitin-protein-ligase-RHG1A were found associated with flowering. Further, associations of WRKY1 and DEAD-box-RH27 with seed weight, PIF3 and pentatricopeptide-repeat-containing-gene with maturity & seed weight and aldo-keto-reductase with flowering & maturity have been revealed. The present investigation provides insights into the genetic mechanisms governing economically-essential traits like flowering, maturity and seed weight that can be potentially utilized for rice bean improvement. HighlightsThe present investigation is the first associative transcriptomics approach implemented on Vigna umbellata. Based on the marker-trait association analysis, candidate genes for flowering, maturity and seed weight traits are reported.

bioinformatics↗

Transgenic Mouse Models Establish a Protective Role of Type 1 IFN Response in SARS-CoV-2 infection-related Immunopathology

Type 1 interferon (IFN-I) response is the first line of host defense against invading viruses. In the absence of definite mouse models, the role of IFN-I in SARS-CoV-2 infections remained to be perplexing. Here, we developed two mouse models, one with constitutively high IFN-I response (hACE2; Irgm1-/-) and the other with dampened IFN-I response (hACE2; Ifnar1-/-) to comprehend the role of IFN-I response during SARS-CoV-2 invasion. We found that hACE2; Irgm1-/- mice were resistant to lethal SARS-CoV-2 infection with substantially reduced cytokine storm and immunopathology. In striking contrast, a severe SARS-CoV-2 infection along with immune cells infiltration, inflammatory response, and enhanced pathology was observed in the lungs of hACE2; Ifnar1-/- mice. Additionally, hACE2; Ifnar1-/- mice were highly susceptible to SARS-CoV-2 neuroinvasion in the brain accompanied by immune cell infiltration, microglia/astrocytes activation, cytokine response, and demyelination of neurons. The hACE2; Irgm1-/- Ifnar1-/- double knockout mice or hACE2; Irgm1-/- mice treated with STING or RIPK2 pharmacological inhibitors displayed loss of the protective phenotypes observed in hACE2; Irgm1-/- mice suggesting that heightened IFN-I response accounts for the observed immunity. Taken together, we explicitly demonstrate that IFN-I protects from lethal SARS-CoV-2 infection, and Irgm1 (IRGM) could be an excellent therapeutic target. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/520843v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@a3aad4org.highwire.dtl.DTLVardef@12452fcorg.highwire.dtl.DTLVardef@1c43dc0org.highwire.dtl.DTLVardef@b2167d_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

MicroRNA397 regulates tolerance to drought and fungal infection by regulating lignin deposition in chickpea root

Plants deposit lignin in the secondary cell wall as a common response to drought and pathogen attacks. Cell wall localized multicopper oxidase family enzymes LACCASES (LACs) catalyze the formation of monolignol radicals and facilitate lignin formation. We show an upregulation of the expression of several LAC genes and a downregulation of microRNA397 (CamiR397) in response to natural drought in chickpea roots. CamiR397 was found to target LAC4 and LAC17L out of twenty annotated LACs in chickpea. CamiR397 and its target genes are expressed in root. Overexpression of CamiR397 reduced expression of LAC4 and LAC17L and lignin deposition in chickpea root xylem causing reduction in xylem diameter. Downregulation of CamiR397 activity by expressing a short tandem target mimic (STTM397) construct increased root lignin deposition in chickpea. CamiR397-overexpressing (miR397OX) and STTM397 chickpea lines showed sensitivity and tolerance, respectively, to drought. Infection with a fungal pathogen Macrophomina phaseolina, responsible for dry root rot disease in chickpea, induced local lignin deposition and LAC gene expression. CamiR397-overexpressing and STTM397 chickpea lines showed more sensitivity and tolerance, respectively, to dry root rot. Our results demonstrated the regulatory role of CamiR397 in root lignification during drought and dry root rot in an agriculturally important crop chickpea.

plant biology↗

Controls of spatial grain size and environmental variables on observed beta diversity of molluscan assemblage at a regional scale

Beta diversity, which quantifies the compositional variation among communities, is one of the fundamental partitions of biodiversity and is associated with abiotic and biotic drivers. Unveiling these drivers is essential for understanding various ecological processes in past and recent faunal communities. Although the quantification of measures of beta diversity has improved over the years, the potential dependence of beta diversity on methodological choices are relatively understudied. Here, we investigate the effect of the variable scale of sampling on different measures of beta diversity at a regional scale. The west coast of India bordering the eastern margin of the Arabian sea, presents a coastal stretch of approximately 6100km from 8-21{degrees}N. We used marine bivalve distribution data, consisting of live occurrence data from literature reports and abundance data from death assemblages collected from localities representing latitude bins. We tested if the observed variation in beta diversity is explained by variable sampling scales due to differences in bin sizes and unequal coastline length. We developed a null model to generate a beta diversity pattern with an increase in spatial scale of sampling by increasing the spatial grain size along the 14 latitude bins progressively. Our null model demonstrates that for the both live and dead dataset, the total beta diversity measured by Bray-Curtis, Whittaker and Sorenson indices decreases with increasing sampling scale. The species replacement (turnover) evaluated by Simpson index decreases and the species loss (nestedness) measured by Sorenson index increases with increasing sampling scale. A comparison between the simulated and observed beta diversity distribution using K-S test demonstrated that the observed pattern of beta diversity is significantly different from the pattern generated from the null model in both live and death assemblages. This implies that sampling alone does not generate the spatial variation in beta diversity in this region. The results show that environmental parameters such as salinity, productivity, and cyclones play a significant role in shaping the regional beta diversity along the west coast. Our study provides an approach for evaluating the effect of variable sampling scale on comparing regional beta diversity. It also highlights the importance of spatial standardization while inferring about processes driving spatial diversity changes.

paleontology↗

Development of an Agrobacterium-delivered codon-optimized CRISPR/Cas9 system for chickpea genome editing

Chickpea is considered recalcitrant to in vitro tissue culture. The Clustered, Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9 (CRISPR/Cas9) based genome editing in chickpea can remove the bottleneck of limited genetic variation in this cash crop rich in nutrients and protein. However, the generation of stable mutant lines using CRISPR/Cas9 requires efficient and highly reproducible transformation approaches. We modified a binary vector pPZP200 by introducing a codon-optimized Cas9 gene for chickpea and the promoters of Medicago truncatula U6 snRNA for expressing guide RNA targeted to the Phytoene Desaturase (PDS) gene. The dissected single cotyledons with half embryo of chickpea were used as explants for genetic transformation. A single gRNA was found sufficient to achieve high efficiency (42%) editing with the generation of PDS mutants with albino phenotypes. A simple, rapid, highly reproducible, stable transformation and CRISPR/Cas9-based genome editing system for chickpea was established. For the first time, this study aimed to demonstrate this systems applicability by performing a gene knockout of the chickpea phytoene desaturase gene (CaPDS) in stable shoots using an improved chickpea transformation protocol.

plant biology↗

Biochemical analysis of anthocyanin and proanthocyanidin and their regulation in determining chickpea flower and seed coat colours

Flower and seed coat colour are important agronomic traits in chickpea (Cicer arietinum L.). Cultivated chickpeas are of two types namely, desi (dark seeded, purple flower) and kabuli (light colour seeded, white flower). There has been limited information about the molecular mechanism underlying the colour variation of flower and seed coats in desi and kabuli chickpea. We profiled the anthocyanin and proanthocyanidin (PA) contents in chickpea flowers and seed coats. Tissue-specific silencing of two genes encoding a basic helix-loop-helix (CabHLH) protein and a tonoplast-localized multidrug and toxic compound extrusion (CaMATE1) transporter in a desi genotype resulted in the reduction in expressions of anthocyanin and PA biosynthetic genes and anthocyanin and PA contents in the flower and seed coat and produced flowers and seeds with kabuli characteristics. Transcriptional regulation of a subset of anthocyanin and PA biosynthetic genes by a natural CabHLH variant and transport assay of a natural CaMATE1 variant explained the association of these alleles with the kabuli phenotype. We carried out a detailed molecular characterization of these genes, and provided evidences that kabuli chickpea flower and seed colour phenotype can be derived by manipulation of single genes in a desi chickpea background. HighlightIn this study, we have defined the molecular link between flower and seed color in chickpea and identified CaMATE1 and CabHLH as the regulators of both the traits.

plant biology↗

Community structure and sample size affect estimates of predation intensity and prey selection: A model-based validation

Predation estimates inferred from the preserved records of predation traces are essential in evaluating the evolutionary effect of ecological interactions. It is, however, crucial to establish how sampling intensity and community composition of an assemblage influence the reliability of these measures. Using a resampling technique, we evaluated the effect of sampling intensity and a communitys evenness on the inferred predation estimates. We theoretically simulated model communities representing different levels of evenness, predation intensity, and predatory behavior (selective, non-selective). We calculated the total predation intensity and the number of prey species for each community. We then resampled each community without replacement and noted variations in the inferred measure from the accurate estimate as the sampling intensity increased. Our results demonstrate that the evenness of a community does not influence the inferred predation intensity for non-selective predation. However, communities with highly selective predation are sensitive to evenness and sampling intensity; inferred predation intensity of these assemblages can substantially differ from the actual value. The inferred number of prey species is also influenced by the communitys original evenness, predation selectivity, and predation intensity. When predation is selective, sampling intensity heavily influences communities with low evenness and low predation intensity; inferred predation intensity is underrepresented in smaller sample sizes. For communities of low evenness and predation intensity where rare species are attacked preferentially, the inferred prey richness differs significantly at a small sample size. We proposed a post-facto standardization method for comparing predation estimates of discrete communities that differ in the sample size. We validated its utility using the published predation data of the Plio-Pleistocene molluscan fossil assemblage. The present approach attempts to provide critical insight into the reliability of predation estimates and may help in comparing predation patterns across time and space. Several factors, including preservation bias, might impact the final predation signature of an assemblage. It warrants a future research direction to develop a comprehensive framework of post-hoc standardization of assemblages with differing predation styles and preservation history.

paleontology↗

Genome duplication and transposon mediated gene alteration shapes the pathogenicity of Rhizoctonia solani AG1-IA

Rhizoctonia solani AG1-IA is a polyphagous basidiomycete fungal pathogen that causes sheath blight disease in rice. In a high-quality genome assembly-based analysis, we report a recent whole genome duplication in R. solani AG1-IA. Duplicated syntenic gene blocks showed presence of district clusters of transposable elements (TEs), which introduced disruption in the continuity of synteny and caused alterations in gene structures. Genome duplication followed by TE-mediated gene structure alterations caused neofunctionalization of genes associated with pathogenicity, as experimentally shown by variation in expression patterns and their involvement during plant colonization. High throughput genome sequencing of forty-two rice field isolates of R. solani AG1-IA from different agro-climatic zones of India profiled the population genetic structure of the Indian isolates and classified those into three distinct groups and a subgroup of admixture, emphasizing exchange of genetic material under field conditions. Genetic diversity analysis of this population predicted the regions that are that are targets for diversifying and purifying selections. Experimental evidence showed that the genes undergoing diversifying and purifying selections were essential for pathogenicity. Together, our data and the analysis revealed profound impact of genome duplication and the transposable elements on genomic diversity and evolution that shaped the pathogenicity of R. solani AG1- IA.

evolutionary biology↗

The extracellular RNA pool within Zea mays apoplast: composition and differential expression during Ustilago maydis infection

The existence of an extracellular pool of RNA (exRNA) has been documented in both animal and plant cells in a number of instances. These exRNA species play important role in host response against different environmental stimuli. The mechanism of their function however remains largely unknown. In this study we report the composition of the exRNA pool within the leaf apoplast of Z. mays under normal growth condition. We could detect RNA transcripts originating from both the genic as well as the intergenic regions of the nuclear, mitochondrial and chloroplast genomes of maize in our exRNA sequencing data. Our data showed increased abundance of about 75% of the exRNA transcripts during infection with a basidiomycete smut fungi, Ustilago maydis. Functional classification of the differentially abundant exRNA transcripts within U. maydis SG200 WT infected maize apoplast with respect to uninfected apoplast revealed significant enrichment of the exRNA transcripts corresponding to the ribosome biogenesis pathway. Data related to the effect of two extracellular T2 type ribonucleases, Nuc1 and Nuc2 from U. maydis on the composition of exRNA pool of maize is also presented.

plant biology↗

The response of Oligo-Miocene bivalve fauna of the Kutch Basin (western India) to regional changes in tectonics and climate

Tectonic changes has influenced the evolution of the marine community by changing the land and seaway configuration through time. Two such tectonic events during Oligo-Miocene times -- the closure of the Tethyan seaway due to development of the Gomphotherium-Landbridge leading to separation of the Arabian Sea from proto-Mediterranean Sea ([~]19 Ma) and significant uplift of the Tibetan plateu marking the initiation of the monsoon ([~]16 Ma) -- represent a classic case of tectonic shift influencing the regional environment of the Indian subcontinent. We investigated the taxonomic and body size related response of the shallow marine fauna to this regional change using bivalves from 11 time-constrained shellbeds of the Kutch Basin (western India) from three formations -- Maniyara Fort (Chattian), Khari Nadi (Aquitanian) and Chhasra (Burdigalian-Langian) representing a time span of [~]9 Ma (24.4 - 15 Ma). Our collection of over 2000 individuals represents a total of 15 families and 61 morphospecies. The fossils are predominantly calcitic in nature and families of aragonitic composition are often preserved as molds indicating a potential negative effect of diagenesis. The taphonomic nature, however, does not vary substantially across shellbeds and hence, less likely produced a temporal pattern. The five most abundant species, Ostrea latimarginata, Ostrea angulata, Talochlamys articulata, Anomia primaeva and Placuna lamellata occur in all the formations. The species composition of the Maniyara Fort formation is substantially different from those of the younger formations implying the possible effect of biogeographic separation. Moreover, the absence of proto-Mediterranean taxa in Oligocene shellbeds support a limited faunal exchange as early as [~]24.4Ma (Chattian) ago. We observed a monotonic increase in the overall rarefied species richness and a decrease in evenness from the Maniyara Fort to the Chhasra Formation. However, shellbed analyses show a dominantly conservative behavior of diversity and body size without a strong directional trend through time. Although it is difficult to rule out the negative influence of taphonomy on the diversity of the studied fauna, Oligo-Miocene marine bivalve fauna of the Kutch Basin demonstrate little or no influence of the Tethyan closure and Himalayan upliftment.

paleontology↗

MICROMORPHY OFFERS EFFECTIVE DEFENCE AGAINST PREDATION: INSIGHTS FROM THE COST-BENEFIT ANALYSES OF MICRO GASTROPOD PREDATION RECORD

Predation, an important driver of natural selection, is studied in the fossil record using quantifiable traces like drill holes produced by gastropods and repair scars produced after durophagous attacks. Despite the abundance of such records in molluscan prey, predation records of micromolluscs (<5mm) remained unexplored. Using a Miocene assemblage of microgastropods from the Quilon Limestone, India, we established the predatory-prey dynamics with the help of cost-benefit analyses. The overall predation intensity is low (DF = 0.06, RF= 0.04) and does not depend on the relative abundance of prey groups suggesting a non-random prey selection regardless of the encounter frequency. The predation is selective in terms of taxonomy, ornamentation, and size of the prey. The smallest size class has the lowest DF and RF supporting a negative size refugia. Higher IDF in larger size class and ornamented groups implies morphological defense resulting in higher failure. Microgastropods show a lower predation intensity than their regular-sized counterparts in a global comparison of coeval records. Results of the cost-benefit analyses explain this difference; the net energy gain from predatory drilling is found to increase monotonically with increasing prey size making the small prey less beneficial. Because the predators try to maximize net energy gain from a predatory attack, the microgastropod prey characterized by relatively low net energy yield is not preferred in the presence of larger prey. Micromorphy, therefore, appears a viable strategy for the prey group to be adopted as an evolutionary response against predation, especially in resource-limited conditions that fail to support large body size.

paleontology↗