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Das, A.

Publications and source records attributed to Das, A..

At least 145 records · Page 8Linked to original sources

Molecular basis for dual functions in pilus assembly modulated by the lid of a pilus-specific sortase

The biphasic assembly of Gram-positive pili begins with the covalent polymerization of distinct pilins catalyzed by a pilus-specific sortase, followed by the cell wall anchoring of the resulting polymers mediated by the housekeeping sortase. In Actinomyces oris, the pilus-specific sortase SrtC2 not only polymerizes FimA pilins to assemble type 2 fimbriae with CafA at the tip, but it can also act as the anchoring sortase, linking both FimA polymers and SrtC1-catalyzed FimP polymers (type 1 fimbriae) to peptidoglycan when the housekeeping sortase SrtA is inactive. To date, the structure-function determinants governing the unique substrate specificity and dual enzymatic activity of SrtC2 have not been illuminated. Here, we present the crystal structure of SrtC2 solved to 2.10-[A] resolution. SrtC2 harbors a canonical sortase fold and a lid typical for class C sortases and additional features specific to SrtC2. Structural, biochemical, and mutational analyses of SrtC2 reveal that the extended lid of SrtC2 modulates its dual activity. Specifically, we demonstrate that the polymerizing activity of SrtC2 is still maintained by alanine-substitution, partial deletion, and replacement of the SrtC2 lid with the SrtC1 lid. Strikingly, pilus incorporation of CafA is significantly reduced by these mutations, leading to compromised polymicrobial interactions mediated by CafA. In a srtA mutant, the partial deletion of the SrtC2 lid reduces surface anchoring of FimP polymers, and the lid-swapping mutation enhances this process, while both mutations diminish surface anchoring of FimA pili. Evidently, the extended lid of SrtC2 enables the enzyme the cell wall-anchoring activity in a substrate-selective fashion.

microbiology↗

The N-terminal region of DNMT3A combines multiple chromatin reading motifs to guide recruitment.

DNA methyltransferase 3A (DNMT3A) plays a critical role in establishing and maintaining DNA methylation patterns. However, the mechanisms underlying DNMT3A recruitment to and function within different chromatin environments remain unclear. Using a combination of biochemical and structural approaches we find that DNMT3A interacts using multiple interfaces with chromatin; directly binding generic nucleosome features as well as site-specific post-translational histone modifications. The N-terminal region, unique to the DNMT3A1 isoform, is essential for these interactions and stabilises H3K36me2-nucleosome recruitment. Intriguingly, in the same region critical for nucleosome binding we also map a ubiquitylation-dependent recruitment motif (UDR). The UDR binds specifically to ubiquitylated H2AK119, explaining the previously observed recruitment to Polycomb-occupied heterochromatin. A cryo-EM structure of DNMT3A1-DNMT3L with a modified nucleosome reveals that the UDR interacts with the nucleosome surface including the acidic patch. Previously unexplained disease-associated mutations are present in the UDR and ablate nucleosome interactions. This leads to an increased understanding of how DNMT3A1 recruitment occurs in the genome and highlights the importance of multivalent binding of DNMT3A to histone modifications and the nucleosome.

biochemistry↗

Cas13d-mediated isoform-specific RNA knockdown with a unified computational and experimental toolbox

Alternative splicing is an essential mechanism for diversifying proteins, in which mature RNA isoforms produce proteins with potentially distinct functions. Two major challenges in characterizing the cellular function of isoforms are the lack of experimental methods to specifically and efficiently modulate isoform expression and computational tools for complex experimental design. To address these gaps, we developed and methodically tested a strategy which pairs the RNA-targeting CRISPR/Cas13d system with guide RNAs that span exon-exon junctions in the mature RNA. We performed a high-throughput essentiality screen, quantitative RT-PCR assays, and PacBio long read sequencing to affirm our ability to specifically target and robustly knockdown individual RNA isoforms. In parallel, we provide computational tools for experimental design and screen analysis. Considering all possible splice junctions annotated in GENCODE for multi-isoform genes and our gRNA efficacy predictions, we estimate that our junction-centric strategy can uniquely target up to 89% of human RNA isoforms, including 50,066 protein-coding and 11,415 lncRNA isoforms. Importantly, this specificity spans all splicing and transcriptional events, including exon skipping and inclusion, alternative 5 and 3 splice sites, and alternative starts and ends.

genomics↗

Assessing variation in Citrus limon "Assam lemon": morphological, seed availability pattern, and biochemical diversity across different districts of Assam

The Assam lemon is a highly valued Citrus cultivar known for its unique aroma, flavor, and seedless fruit characteristic. This study aimed to investigate for the first time the morphological, seeding pattern, and biochemical, variations within 133 populations of Assam lemon cultivar growing across 22 districts of Assam, India, and including control population, with the objective to offer comprehensive understanding that could facilitate the improvement of breeding programs and further improvement of this important cultivar. Using the dendrogram-based UPGMA algorithm, morphological and seeding pattern data were analyzed at both district and population levels. The resulting dendrograms revealed two major clusters, where all the populations of Upper Assam districts were in the same cluster with the original stock (control population). However, populations from Tinsukia and Dhemaji districts displayed more close similarities with the control population in comparison to other populations of Upper Assam districts. Another interesting observation was regarding flowering patterns, while some populations displayed both bisexual and unisexual flowers with less concentration of unisexual flowers, others had bisexual and unisexual flowers of almost equal concentration. Unisexual flowers contained only the male reproductive organs with 40 anthers, while bisexual flowers had 36 anthers. Seeding patterns were examined across the districts, and it was found that populations from Tinsukia, Dhemaji, Lakhimpur, Dibrugarh, Jorhat, and the control population exhibited seedless characteristic while populations from other selected districts displayed a combination of seedless and seeded traits. Interestingly, Golaghat district appears as the linking district and showed availability of both seeded and seedless Assam lemon fruit, connecting the regions of Upper, Central, Lower and North Assam and Barak valley. Biochemical analysis showed significant variations across districts, however, the populations from Dhemaji, Tinsukia, Lakhimpur, Dibrugarh, and Jorhat districts displayed similarity with the control population. The study also investigated variability in soil nutrient content revealing substantial variation among the populations studied, potentially influencing observed morphological variations. This comprehensive investigation provides valuable insights into the morphological, seeding pattern, and biochemical diversity within the Assam lemon cultivar. These findings can be instrumental in breeding programs to enhance this Citrus cultivar, particularly in producing high-quality seedless fruits to meet consumer demands.

plant biology↗

Genome and transcriptome mining revealed evolutionary insights and tissue-specific expression patterns of Cytochrome P450 superfamily in Aquilaria sinensis

The Cytochrome P450 (CYPs) enzyme superfamily has evolved and expanded in plants to play a significant role in the biosynthesis of valuable secondary metabolites. In Aquilaria plant, the process of wounding and fungal infection results in the accumulation of distinct aromatic metabolites which contribute to the formation of resinous agarwood. The members of CYPs in plants genomes have diversified to catalyze a wide array of fragrant metabolites. Therefore, this study aimed to identify and provide insights into the evolution and expansion of the CYP superfamily members in Aquilaria sinensis and elucidate their tissue-specific functional role through mapping and expression analyses. In total, 179 AsCYPs were identified and subsequently classified into 8 clans and 42 families which were found to be dispersed in the 8 chromosomes. Duplication analysis highlights slow segmental events as a major force, coupled with negative selection pressure, behind the expansion of the AsCYPs. We observed their participation in the biosynthesis of various secondary metabolites, particularly sesquiterpenoids. Expression analysis showed variation in the expression pattern of the genes in different tissues, revealing that the diversification of the AsCYP superfamily occurred to carry out tissue-specific functional role. Additionally, molecular docking of a sesquiterpene oxidase which is specifically expressed in wounded wood, indicated its potential to generate sesquiterpenoids derivatives in agarwood. This study sheds light on the evolution and expansion of the AsCYPs in the genome of A. sinensis and highlights their crucial role in the biosynthesis of various secondary metabolites found in different parts of the plant. Further functional exploration may pave the way for advancements in the field of Aquilaria-based fragrance development and natural product synthesis.

genomics↗

ChromaFold predicts the 3D contact map from single-cell chromatin accessibility

The identification of cell-type-specific 3D chromatin interactions between regulatory elements can help to decipher gene regulation and to interpret the function of disease-associated non-coding variants. However, current chromosome conformation capture (3C) technologies are unable to resolve interactions at this resolution when only small numbers of cells are available as input. We therefore present ChromaFold, a deep learning model that predicts 3D contact maps and regulatory interactions from single-cell ATAC sequencing (scATAC-seq) data alone. ChromaFold uses pseudobulk chromatin accessibility, co-accessibility profiles across metacells, and predicted CTCF motif tracks as input features and employs a lightweight architecture to enable training on standard GPUs. Once trained on paired scATAC-seq and Hi-C data in human cell lines and tissues, ChromaFold can accurately predict both the 3D contact map and peak-level interactions across diverse human and mouse test cell types. In benchmarking against a recent deep learning method that uses bulk ATAC-seq, DNA sequence, and CTCF ChIP-seq to make cell-type-specific predictions, ChromaFold yields superior prediction performance when including CTCF ChIP-seq data as an input and comparable performance without. Finally, fine-tuning ChromaFold on paired scATAC-seq and Hi-C in a complex tissue enables deconvolution of chromatin interactions across cell subpopulations. ChromaFold thus achieves state-of-the-art prediction of 3D contact maps and regulatory interactions using scATAC-seq alone as input data, enabling accurate inference of cell-type-specific interactions in settings where 3C-based assays are infeasible.

bioinformatics↗

Disease-associated gut microbiome and metabolome changes in chronic low back pain patients with bone marrow lesions

Chronic low back pain (LBP) is the leading cause of global disability. Vertebral bone marrow lesions (BMLs), one etiological factor for chronic LBP, are MRI signal changes in the vertebral bone marrow that extend from the disc endplate. The adipogenesis of bone marrow mesenchymal stem cells (BM-MSCs) could explain fatty replacement (FR) in normal bone marrow. FR is the most common type of BMLs. Here we show how the gut microbiome and serum metabolome change and how they interact in LBP patients with or without FR. The serum metabolome of chronic LBP patients with FR is characterized by decreased levels of branched-chain amino acids (BCAAs), which correlate with a gut microbiome that has important capability to regulate BCAA degradation pathway. Ruminococcus gnavus, Roseburia hominis and Lachnospiraceae bacterium 8 1 57FAA are identified as the main species driving the association between biosynthesis of BCAAs and BM-MSCs metabolism in LBP with FR individuals. In vitro work demonstrates that BCAAs can induce the adipogenesis of BM-MSCs by activating the SIRT4 pathway. Our findings provide a deep insight into understanding the role of the disturbed gut ecosystem in FR and LBP.

cell biology↗

An ancient respiratory enzyme metabolically modulates Fusobacterium nucleatum virulence

A prominent oral commensal and opportunistic pathogen, Fusobacterium nucleatum can traverse to extra-oral sites such as placenta and colon, promoting adverse pregnancy outcomes and colorectal cancer, respectively. How this anaerobe sustains many metabolically changing environments enabling its virulence potential remains unclear. Informed by our genome-wide transposon mutagenesis, we report here that the highly conserved Rnf complex, encoded by the rnfCDGEAB gene cluster, is key to fusobacterial metabolic adaptation and virulence. Genetic disruption of the Rnf complex via non-polar, in-frame deletion of rnfC ({Delta}rnfC) abrogates polymicrobial interaction (or coaggregation) associated with adhesin RadD and biofilm formation. The defect in coaggregation is not due to reduced cell surface of RadD, but rather an increased level of extracellular lysine, which binds RadD and inhibits coaggregation. Indeed, removal of extracellular lysine via washing {Delta}rnfC cells restores coaggregation, while addition of lysine inhibits this process. These phenotypes mirror that of a mutant ({Delta}kamA) that fails to metabolize extracellular lysine. Strikingly, the {Delta}rnfC mutant is defective in ATP production, cell growth, cell morphology, and expression of the enzyme MegL that produces hydrogen sulfide from cysteine. Targeted metabolic profiling demonstrated that catabolism of many amino acids, including histidine and lysine, is altered in {Delta}rnfC cells, thereby reducing production of ATP and metabolites including H2S and butyrate. Most importantly, we show that the {Delta}rnfC mutant is severely attenuated in a mouse model of preterm birth. The indispensable function of Rnf complex in fusobacterial pathogenesis via modulation of bacterial metabolism makes it an attractive target for developing therapeutic intervention. IMPORTANCEAlthough viewed as an oral commensal, the Gram-negative F. nucleatum is an opportunistic pathogen that can spread to extra-oral sites such as placenta and colon, promoting adverse pregnancy outcomes and colorectal cancer, respectively. How this anaerobe sustains various metabolically changing environments enabling its virulence potential remains unclear. We demonstrate here that the highly conserved Rnf complex is key to fusobacterial metabolic adaptation and virulence. Genetic disruption of this Rnf complex causes global defects in polymicrobial interaction, biofilm formation, cell growth and morphology, H2S production, and ATP synthesis. Targeted metabolomic profiling demonstrates that the loss of this respiratory enzyme significantly diminishes catabolism of numerous amino acids, which negatively impacts fusobacterial virulence as tested in a preterm birth model in mice.

microbiology↗

Centromere-specifying nucleosomes persist in aging mouse oocytes in the absence of nascent assembly

SUMMARYCentromeres direct genetic inheritance but are not themselves genetically encoded. Instead, centromeres are defined epigenetically by the presence of a histone H3 variant, CENP-A1. In cultured somatic cells, an established paradigm of cell cycle-coupled propagation maintains centromere identity: CENP-A is partitioned between sisters during replication and replenished by new assembly, which is restricted to G1. The mammalian female germline challenges this model because of the cell cycle arrest between pre-meiotic S-phase and the subsequent G1, which can last for the entire reproductive lifespan (months to decades). New CENP-A chromatin assembly maintains centromeres during prophase I in worm and starfish oocyte2,3, suggesting that a similar process may be required for centromere inheritance in mammals. However, we show that centromere chromatin is maintained long-term independent of new assembly during the extended prophase I arrest in mouse oocytes. Conditional knockout of Mis18, an essential component of the assembly machinery, in the female germline at the time of birth has almost no impact on centromeric CENP-A nucleosome abundance nor any detectable detriment to fertility.

cell biology↗

Comparing FRET pairs that report on intersubunit rotation in bacterial ribosomes

Mediated by elongation factor G (EF-G), ribosome translocation along mRNA is accompanied by rotational movement between ribosomal subunits. Here, we reassess whether the intersubunit rotation requires GTP hydrolysis by EF-G or can occur spontaneously. To that end, we employ two independent FRET assays, which are based on labeling either ribosomal proteins (bS6 and bL9) or rRNAs (h44 of 16S and H101 of 23S rRNA). Both FRET pairs reveal three FRET states, corresponding to the non-rotated, rotated and semi-rotated conformations of the ribosome. Both FRET assays show that in the absence of EF-G, pre-translocation ribosomes containing deacylated P-site tRNA undergo spontaneous intersubunit rotations between non-rotated and rotated conformations. While the two FRET pairs exhibit largely similar behavior, they substantially differ in the fraction of ribosomes showing spontaneous fluctuations. Nevertheless, instead of being an invariable intrinsic property of each FRET pair, the fraction of spontaneously fluctuating molecules changes in both FRET assays depending on experimental conditions. Our results underscore importance of using multiple FRET pairs in studies of ribosome dynamics and highlight the role of thermally-driven large-scale ribosome rearrangements in translation.

biochemistry↗

Genome-wide analysis of Respiratory burst oxidase homolog (Rboh) genes in Aquilaria species and its association with agarwood formation

Respiratory burst oxidase homolog (Rboh), generate reactive oxygen species (ROS) to maintain normal growth and pathogen induced defence responses in plants. In Aquilaria plants, wounding and fungal invasion results in the biosynthesis of secondary metabolites as a defence response which with due course develop into agarwood. During pathogen invasion, Aquilaria tree accumulate ROS species through the action of Rboh enzymes. Although in agarwood formation role of Rboh gene family has been implicated, an comprehensives study on Rboh gene family and information of its role during agarwood formation in missing. In this study, seven Rboh genes were identified from the genomes of two Aquilaria species viz., Aquilaria agallocha and Aquilaria sinensis and phylogenetically classified into five groups. Stress response, hormone regulation, and development related regulatory elements were identified in the promoter regions. The protein sequences comprised of four conserved domains, an EF-hand domain, and a transmembrane region which they probably utilise for MAPK signaling, plant-pathogen interaction and plant hormone signal transduction pathways. Expression analyses revealed that among the seven members, AaRbohA and AaRhobC were involved in generation of ROS species, and also probably play role in agarwood formation. These findings provide valuable information regarding the Rboh members of A. agallocha which can be further used for functional analyses for in-depth understanding of ROS mediated signalling and regulation of agarwood formation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/539809v1_figu1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@169f501org.highwire.dtl.DTLVardef@1541667org.highwire.dtl.DTLVardef@18ad549org.highwire.dtl.DTLVardef@1b8b7b2_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

Mouse Homolog of Human IRF8G388S Mutation Provides Novel Insight into Osteoclastogenesis and Tooth Root Resorption

Previously, we reported a novel mutation in the Interferon Regulatory Factor 8 (IRF8) gene associated with multiple idiopathic cervical root resorption (MICRR), an aggressive form of tooth root resorption mediated by increased osteoclast activity. The IRF8 G388S variant in the highly conserved C-terminal motif is predicted to alter the protein structure, likely impairing IRF8 function. To investigate the molecular basis of MICRR and IRF8 function, we generated Irf8 knock-in (KI) mice using CRISPR/Cas9 modeling the human IRF8G388S mutation. The heterozygous (Het) and homozygous (Homo) Irf8 KI mice showed no gross morphological defects, and the development of hematopoietic cells was unaffected and similar to that in wild-type (WT) mice. The Irf8 KI Het and Homo mice showed no difference in macrophage gene signatures important for antimicrobial defenses and inflammatory cytokine production. Consistent with the phenotype observed in MICRR patients, Irf8 KI Het and Homo mice demonstrated significantly increased osteoclast formation and resorption activity in vivo and in vitro when compared to WT mice. The oral ligature inserted Irf8 KI Het and Homo mice displayed increased osteoclast-mediated alveolar bone loss and tooth root resorption compared to WT mice. The increased osteoclastogenesis noted in KI mice is due to the inability of mutant Irf8 G388S isoform to negatively inhibit NFATc1-dependent transcriptional activation and downstream osteoclast specific transcripts. This translational study delineates the IRF8 domain important for osteoclast function and provides novel insights into the IRF8 mutation associated with MICRR. Irf8G388S mutation mainly affects osteoclastogenesis while sparing immune cell development and function. The Irf8 KI mice serve as a novel translational model for studying the etiopathology of MICRR and developing targeted therapies for MICRR and other skeletal disorders mediated by increased osteoclast activity.

genetics↗

Alpha and SSVEP power outperforms Gamma power in capturing Attentional Modulation in Human EEG

The effect of visual attention has been extensively studied using various techniques such as macaque neurophysiology that yields spikes and local field potential (LFP), and human electro/magneto encephalogram (EEG/MEG). Attention typically suppresses power at low frequencies such as alpha band (8-12 Hz) and increases power in gamma band (>30 Hz) in brain signals. In addition, EEG studies often use flickering stimuli that produce a specific measure called steady-state visually evoked potential (SSVEP), whose power also increases with attention. However, effectiveness of these various neural measures in capturing attentional modulation is unknown since the stimuli and task paradigms vary widely across these studies. In a recent macaque neurophysiology study with flickering stimuli, we found that the effect of attention was more salient in the gamma band and beyond of the LFP, compared to alpha or SSVEP. To compare this with human EEG, we designed an orientation change detection task where we presented both static and counterphasing stimuli of matched difficulty levels to male (N=15) and female (N=11) subjects, allowing us to compare attentional modulation of various measures under similar conditions. We report two main results. First, attentional modulation was comparable for SSVEP and alpha. Second, non-foveal stimuli produced weak gamma despite various stimulus optimizations and showed a negligible effect of attention although full-screen gratings showed robust gamma activity. Our results are useful for brain-machine-interfacing studies where suitable features depending on recording modality are used for decoding attention, and also provide clues about the spatial scales of neural mechanisms underlying attention. Significance StatementVarious neural measures such as alpha and gamma band power or SSVEP power capture signatures of visual attention. A systematic comparison of their effectiveness in capturing attentional modulation is important for understanding different neural computations underlying attention and for developing brain-machine-interfaces (BMIs) that can decode the focus of attention. Since stimulus configuration and task paradigms vary widely across visual attention studies, we recorded all the relevant neural signals during an attention task under similar stimulus and behavioral conditions in human EEG. In contrast to invasive recordings in which gamma outperforms other measures, our results show that in human EEG, attentional modulation of alpha and SSVEP are comparable, and non-foveal stimuli produce weak gamma which is not well modulated by attention.

neuroscience↗

Vitamin D signaling orchestrates skeletal muscle metabolic flexibility by regulating its fuel choice.

Vitamin D deficiency is associated with skeletal muscle pathologies. However, the role of vitamin D signaling in maintenance of muscle function is not well understood. Mice lacking vitamin D receptor (VDR) exhibit severe muscle wasting after weaning and this is associated with accumulation of muscle glycogen and energy deprivation. Here we show that the skeletal muscles of vdr-/- mice exhibit upregulation of fatty acid oxidation pathway and PPAR pathway and are predisposed to utilize fatty acids as the energy source even in a carbohydrate-enriched diet. As a result, fat-enriched diets could alleviate energy deprivation and atrophy of vdr-/- skeletal muscles. However, the complete restoration of muscle mass and systemic metabolism of vdr-/- mice depended on the quality of diets. Despite increasing muscle energy levels, a lard-based high-fat diet (HFD) disrupted glucose homeostasis by specifically inhibiting the insulin synthesis in pancreatic islets. Surprisingly, milk-based high-fat diets (MBD) could restore both muscle mass and pancreatic insulin response. This study reveals a micronutrient-macronutrient interaction network that connects vitamin D signaling with muscle fuel selection and pancreatic insulin response to enable energy homeostasis under different metabolic landscapes.

physiology↗

State-dependent modulation of dependencies in a laminar cortical circuit

Spatial attention is a quintessential example of adaptive information processing in the brain and is critical for recognizing behaviorally relevant objects in a cluttered environment. Object recognition is mediated by neural encoding along the ventral visual hierarchy. How the deployment of spatial attention aids these hierarchical computations is unclear. Prior studies point to two distinct mechanisms: an improvement in the efficacy of information directed from one encoding stage to another1-5, and/or a suppression of shared information within encoding stages6,7. To test these proposals, it is crucial to estimate the attentional modulation of unique information flow across and shared information within the encoding stages of the visual hierarchy. We investigated this in the multi-stage laminar network of visual area V4, an area strongly modulated by attention8-10. Using network-based dependency estimation from multivariate data, we quantified the modulation of inter-layer information flow during a change detection task and found that deployment of attention indeed strengthened unique dependencies between the input and superficial layers. Using the partial information decomposition framework11,12, we estimated the modulation of shared dependencies and found that they are reduced specifically in the putative excitatory subpopulations within a layer. Surprisingly, we found a strengthening of unique dependencies within the laminar populations, a finding not previously predicted. Crucially, these modulation patterns were also observed during successful behavioral outcomes (hits) that are thought to be mediated by endogenous brain state fluctuations13-15, and not by experimentally imposed attentive states. Finally, phases of endogenous fluctuations that were optimal for hits were associated with reduced neural excitability. A reduction in neural excitability, potentially mediated by diminished shared inputs, suggests a novel mechanism for enhancing unique information transmission during optimal states. By decomposing the modulation of multivariate information, and combined with prior theoretical work16, our results suggest common computations of optimal sensory states that are attained by either task demands or endogenous fluctuations.

neuroscience↗

Whole genome sequencing of Red Chittagong Cattle (RCC) cattle and insight into genetic variants in candidate genes for disease resistance

Detection of genome-wide genetic variation is one of the primary goals in bovine genomics. Genomes of several cattle breeds have been sequenced so far to understand the genetic variation associated with important phenotypes. Red Chittagong Cattle (RCC) is a locally adopted and disease-resistant indicine cattle breed in Bangladesh. In this study, we describe the first genome sequence of the RCC breed and in silico analyses of identified functional variants. Deep sequencing of a RCC bull genome on the NanoBall sequencing platform generated approximately 110 Gb paired-end data, resulting in 31X of genome coverage. Quality filtering retained 360,711,803 paired-end reads. Of the filtered reads, 99.8% were mapped to the bovine reference genome (ARSUCD1.2). A total of 17. 8 million Single nucleotide variants (SNVs) and 2.1 insertions and deletions (INDELs) were identified in the RCC genome. Ts/Tv ratio was computed and found to be 2.21. In total, 332 4621 variants were novel compared with dbSNP data (NCBI dbSNP bovine build 150). Functional annotation identified 54961 SNVs exonic regions, 63.75% of which were synonymous, whereas 30.42% were non-synonymous changes. The percentage of coding INDELs was 0.25% (Frameshift deletion 0.19% and Frameshift insertion 0.06%). We identified 120 variants in 26 candidates for five diseases-foot and mouth disease (FMD), Mastitis, Parasite, para-tuberculosis, and tick. Of the 120 variants, 50 were non-synonymous / frameshift (NS/FS), while 70 were synonymous/non-frameshift (SS/NFS). The identified catalog of genomic variants in RCC may establish a paradigm for cattle research in Bangladesh by filling the void and providing a database for genome-wide variation for future functional studies in RCC.

genomics↗

Reconstruction of 3-dimensional tissue organization at the single-cell resolution

Recent advances in spatial transcriptomics (ST) have allowed for the mapping of tissue heterogeneity, but this technique lacks the resolution to investigate gene expression patterns, cell-cell communications and tissue organization at the single-cell resolution. ST data contains a mixed transcriptome from multiple heterogeneous cells, and current methods predict two-dimensional (2D) coordinates for individual cells within a predetermined space, making it difficult to reconstruct and study three-dimensional (3D) tissue organization. Here we present a new computational method called scHolography that uses deep learning to map single-cell transcriptome data to 3D space. Unlike existing methods, which generate a projection between transcriptome data and 2D spatial coordinates, scHolography uses neural networks to create a high-dimensional transcriptome-to-space map that preserves the distance information between cells, allowing for the construction of a cell-cell proximity matrix beyond the 2D ST scaffold. Furthermore, the neighboring cell profile of a given cell type can be extracted to study spatial cell heterogeneity. We apply scHolography to human skin, human skin cancer and mouse brain datasets, providing new insights into gene expression patterns, cell-cell interactions and spatial microenvironment. Together, scHolography offers a computational solution for digitizing transcriptome and spatial information into high-dimensional data for neural network-based mapping and the reconstruction of 3D tissue organization at the single-cell resolution.

bioinformatics↗

Anti-Biofilm Potential of Nanonized Eugenol against Pseudomonas aeruginosa

This study dealt with nanonization of eugenol, a major phytochemical present in basil leaf, which has pharmacological potential as an anti-bacterial agent. Eugenol nanoparticle (ENP) was synthesized by simple ultrasonic cavitation method through emulsification of hydrophobic eugenol into hydrophilic gelatin. Thus, the nanonization process made the water-insoluble eugenol to water-soluble nano-eugenol, making the nano-form bioavailable. The average size of the ENPs was 20-30 nm. Entrapment efficiency of eugenol within gelatin cap was about 80% of the eugenol, that was used as precursor in the nanonization reaction. In vitro release of eugenol from gelatin cap was slow and sustained over a period of five days. The ENP had higher anti-biofilm potency than eugenol for both formation and eradication of biofilm, formed by clinically relevant pathogen Pseudomonas aeruginosa. Minimal biofilm inhibitory concentration and minimal biofilm eradication concentration of ENPs were 2.0 and 4.0 mM respectively. In addition, the measurement of P. aeruginosa biofilm biomass, biofilm pellicle formation, biofilm thickness, amount of biofilm-forming extra-polymeric substance, cell surface hydrophobicity, cell swarming and twitching efficiencies, cellular morphology and biofilm formation in catheter demonstrated that the anti-biofilm efficacy of nano-eugenol was 30-40% higher than that of bulk eugenol. Thus, ENP can be used as a potential drug against pneumonia, a chronic infection in lung caused by P. aeruginosa, which is difficult to treat with antibiotics, due to natural intrinsic resistance of biofilm-formed cells to most antibiotics. The overall actions of ENP have been presented in the figure 1. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=146 SRC="FIGDIR/small/521144v1_fig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@12445e2org.highwire.dtl.DTLVardef@6813aforg.highwire.dtl.DTLVardef@e4779borg.highwire.dtl.DTLVardef@1688a9a_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFigure 1:C_FLOATNO Graphical abstract showing overall anti-biofilm action of ENP that is capable to inhibit each and every step of biofilm formation. ENP also carries the potential to destroy EPS and kill the biofilm residing cells by membrane disruption. Bacterial colonization has been found to be prevented significantly on ENP-coated catheter. C_FIG HighlightsO_LINano-formulation of eugenol, an important phytochemical, by ultrasonic cavitation method, which was simple, time-saving, low-cost and eco-friendly. C_LIO_LINanonization made water-insoluble eugenol into water-soluble form with enhanced therapeutic efficacy. C_LIO_LIThe eugenol nanoparticle (ENP) could inhibit formation of biofilm as well as facilitate eradication of pre-formed biofilm of P. aeruginosa. C_LIO_LIBiofilm formation was found to be prevented significantly on ENP-coated catheter. C_LIO_LINano-eugenol may be used as a potential drug against bacterial diseases, caused by pseudomonal biofilm, which are difficult to treat by antibiotics. C_LIO_LINano-formulated eugenol may also be used as an effective anti-fouling agent for biomedical devices like contact lens, pace-maker, materials for organ transplantation etc. to prevent bacterial colonization. C_LI

microbiology↗