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Biology subjects

Mandal, M.

Publications and source records attributed to Mandal, M..

At least 19 recordsLinked to original sources

Non-covalent reversibly photoconvertible fluorescent tags for wash-free protein labeling

Reversibly photoswitchable fluorophores are widely used in advanced bioimaging but their design remains demanding. Here, we introduce a new series spanning the whole visible range, which results from combining a large set of fluorogens with the FAST protein scaffold. We first demonstrate that these well-established labeling fluorescent protein tags turn into negative reversible photoswitchers upon decreasing the fluorogen concentration and increasing light intensity. We then show that using not anymore one but two fluorogens adds new responses to illumination. Thus, we obtain positive reversible photoswitchers, that increase their brightness under illumination. We also generate a palette of non-covalent reversibly photoconvertible fluorescent proteins changing their fluorescence color upon illumination, a reversible behavior that still remains absent in regular fluorescent proteins. This light-induced color change opens the possibility to discriminate six spectrally similar FAST variants in live cells upon demonstrating the superiority of using multiple spectral channels for exploiting the time dependence of the fluorescence response to illumination.

biophysics↗

Photoejection turns non-covalent fluorescent tags into negative reversible photoswitchers

Reversibly photoswitchable fluorophores have enabled a broad range of applications in advanced fluorescence bioimaging. Here, we introduce RSpFAST, a new class of reversibly photoswitchable fluorescent labels that combine a biomolecular host (pFAST protein tag) with a reversibly photoisomerizable guest (fluorogen), allowing fluorescence brightness to be modulated through illumination and molecular complexation. We combine thermokinetic, photochemical, and structural investigations to obtain a comprehensive mechanistic and kinetic understanding of RSpFAST. Building on this theoretical framework, we demonstrate in both live and fixed cells that RSpFAST exhibits an unprecedented dual behavior: a stable and wash-free fluorescent labeling tag turns into a negative reversible photoswitcher by lowering the fluorogen concentration and increasing light intensity. In this photoejection-driven kinetic regime, RSpFAST is shown to be an efficient marker for dynamic contrast and super-resolution microscopy.

biochemistry↗

Synergy unleashed: Leishmania donovani GP63 paralogues cooperatively function to drive parasite infectivity at various pathogenic stages and regulate host survival mechanisms

Highly plastic genome of Leishmania is thought to underlie its remarkable ability to adapt to diverse host microenvironments, yet how this plasticity translates into dermal versus visceral persistence remains unclear. GP63, a zinc metalloprotease, is a well-established determinant of promastigote infectivity, particularly in cutaneous leishmaniasis. Despite this, its role in amastigote stage and in visceral disease caused by Leishmania donovani remains undefined. Here, using an integrated approach combining phylogenetics, CRISPR-mediated genome editing, and biochemical analyses, we demonstrate that GP63 paralogues in L. donovani have undergone independent evolutionary diversification to support visceral infection. While GP63-paralogues encoded on chromosome 10, previously implicated in cutaneous manifestation caused by L. major, were found severely truncated and dispensable in L. donovani, two distinct GP63-paralogues encoded on chromosome 28 and 31 were found essential to establish visceral infection. LdGP63_31 facilitates promastigote attachment to macrophages by promoting lipid raft engagement and complement inactivation, thereby enabling host entry and subsequent amastigote differentiation. LdGP63_28 is essential for intracellular amastigote survival by suppressing host inflammatory pyroptosis. Structural and enzymatic analyses revealed preferential host localization and substrate specificities, possibly resulting from distinct amino acid substitution within conserved motifs of these proteases, indicating independent evolutionary adaptations. Importantly, loss of the LdGP63_28 more severely impaired amastigote reinfection than loss of its counterpart LdGP63_31. Together, these findings reveal coordinated functional specialization of GP63-paralogues ensuring visceral adaptation.

microbiology↗

Effects of CwlM, a peptidoglycan synthesis regulator, on beta-lactam resistance and host-pathogen interactions

BackgroundThe emergence and spread of multidrug-resistant (MDR) strains of Mycobacterium tuberculosis (Mtb) urge the development of novel drugs and efficient therapeutic programs. A recent study aiming to uncover differential beta-lactam susceptibility phenotypes in clinical strains of Mtb found that the M237V substitution in cwlM (Rv3915) was associated with increased susceptibility to amoxicillin. Considering that Mycobacterium smegmatis (Msm) is a widely used surrogate model for Mtb, we constructed a cwlM knockdown mutant in Msm using CRISPR interference (CRISPRi) to elucidate the role of CwlM in beta-lactam susceptibility and intracellular survival. ResultsQuantitative RT-PCR assays confirmed the successful repression of cwlM, while the phenotyping assays confirmed the essentiality of CwlM-related processes for mycobacterial viability. Collectively, the antibiotic susceptibility assays suggested that CwlMSMEG may promote beta-lactam resistance, particularly to meropenem and cefotaxime. Moreover, CwlMSMEG was found to support M. smegmatis intracellular survival within THP-1-derived macrophages. To address conflicting reports regarding its predicted peptidoglycan (PG) hydrolase activity, we purified recombinant CwlMTB. The Micrococcus luteus-derived PG-based zymogram indicated that CwlMTB lacks PG-hydrolytic activity, suggesting it might act as a regulator of PG biosynthesis instead. ConclusionsOur findings indicate that CwlM contributes to beta-lactam resistance and intracellular survival, regardless of lacking detectable PG-hydrolytic activity. Overall, CwlM was found to be essential and highly vulnerable, highlighting its potential as a therapeutic target that warrants further investigation.

microbiology↗

Jk DNA GAGA MOTIFS ARE REQUIRED FOR LOCAL NUCLEOSOME REMODELING AND Vk-Jk RECOMBINATION

Immunoreceptor gene recombination requires complementary 12 bp and 23 bp recombination signal sequences (RSSs). In addition, the RSSs that assemble the RAG proteins, recombination centers, must be accessible yet flanked by a 5 nucleosome decorated with H3K4me3. In Drosophila, DNA GAGA motifs play an important role in nucleosome positioning. Herein, we report that 5 to each functional Jk RSS is a DNA GAGA motif conserved across mammalian species. In mice, the GAGA motif 5 to Jk1 regulated local RSS accessibility and 5 nucleosome placement. Furthermore, it was required for Vk-Jk1 recombination. Murine Jk3 is nonfunctional, having mutations in both RSS and GAGA motifs. Restoring both GAGA and RSS motifs rescued Vk-Jk3 recombination. In contrast, restoring the RSS alone did not. Genome-wide, strong cryptic 23 RSSs were preferentially bound to nucleosomes. Furthermore, evolutionary selection against cRSS only occurred in the A Compartment of B lymphocytes, not embryonic stem cells. These data indicate that in developing B cells, nucleosome positioning both enables and restricts recombination to Jk. Furthermore, our data suggest an expanded definition of recombination center-associated RSSs to include a 5 GAGA sequence that dictates the local epigenetic state required for gene recombination. SummaryRecombination center assembly requires a specific epigenetic topology at recombination signal sequences. Herein, we report that conserved GAGA motifs 5 to each Jk segment are required for establishing this epigenetic topology and subsequent local gene recombination.

cell biology↗

The impact of fold-dilution and diluent volume on the estimation of colony forming units in a bacterial culture

Considering the non-uniform distribution of bacteria in a liquid culture, accurate enumeration of bacteria by serial dilution is important yet challenging in microbiological research. The deviation of estimated population size from the actual population size is anticipated in view of the sampling error arising at dilution, which is known to increase at each successive dilution; and the sampling error associated with the sample volume, where it is inversely proportional. In the dilution process of such population following a Poisson distribution, the relation of sampling error with the sequentially diluted suspensions is yet to be empirically demonstrated. Also, as a given-fold dilution can be achieved by passaging of either a higher or a lower sample volume, the sampling error associated in this case with the volume being passaged also remains to be evaluated. In view of that, the current experimental study was undertaken to further understand bacterial distribution and the underlying sampling error in dimensions previously not demonstrated. We demonstrated that sampling error in the enumeration process is independent of the bacterial cell densities of the diluted suspensions, which was on contrary to the theoretical assumptions. Moreover, sampling error is also not dependent on the number of passages in the dilution process. Importantly, we also demonstrated that passaging either a higher or lower sample volumes during serial dilution yielded similar enumeration, which was exceptional with regards to the statistical fluctuations inherent to a Poisson distribution.

microbiology↗

Tissue-independent nature of plant susceptibility: a comparative pathogenicity study of the systemic phytopathogen Ralstonia pseudosolanacearum in eggplant and tomato seedlings through root and leaf

Ralstonia pseudosolanacearum causes a lethal bacterial wilt disease in many plant species, posing significant economic challenges. Although tomato has been a primary model host for investigating the pathogenicity and systemic infection of this bacterium, this manuscript presents a comparative pathogenicity study between two closely related solanaceous hosts, tomato and eggplant, revealing differential host responses to the same pathogen, specifically through leaves and roots. Interestingly, eggplant seedlings exhibited a significantly higher susceptibility to cotyledon leaf inoculation than tomato seedlings. In the case of tomato, a few seedlings escaped wilting (called escapees), which was usual at a high pathogen load, unlike the case of eggplant seedlings where escapees could not be observed even at a 100-fold lower pathogen concentration. The greater susceptibility of eggplant was further demonstrated by performing both single- and double-leaf inoculations in the seedlings. Surprisingly, root inoculations resulted in a significantly lower mortality for eggplant than for tomato seedlings. The contrasting susceptibility between the two hosts regarding root and leaf regions indicates the tissue-dependent nature of susceptibility. The study underscores the value of employing multiple host species to uncover new insights into pathogen behaviour and host-pathogen interactions.

pathology↗

Morphology of softening and translucency in the stems of tomato and eggplant seedlings due to infection by Ralstonia pseudosolanacearum F1C1

Ralstonia pseudosolanacearum F1C1 is a soil-borne phytopathogenic bacterium with a broad host range that infects several economically important crops. This study primarily focuses on the infection of this phytopathogen in two such important crop seedlings: tomato and eggplant. The observations of the study reveal a complex set of symptoms that include drooping and blackening of the seedling stem, as well as blackening, chlorosis, and curling of cotyledon leaves. Notably, the symptom of stem softening and translucency is seen primarily in the water-submerged stem regions of both root- and leaf-inoculated seedlings. While the wild-type R. pseudosolanacearum F1C1 strain and its weakly virulent mutant phcA::{Omega} exhibited this phenotype in both tomato and eggplant seedlings, the virulence-deficient hrpB::{Omega} mutant did so only in a few eggplant seedlings but not in tomato seedlings. By investigating these unique pathological phenotypes in the infected seedlings, this study uncovers a unique symptom previously not reported in seedling inoculation experiments. The work also touches upon the distinct escape mechanisms exhibited by seedlings, revealing how some of its host plants might resist wilting despite infection, offering new avenues for future research. These findings contribute to the understanding of R. pseudosolanacearum pathogenesis, shedding light on its virulence and host response mechanisms.

plant biology↗

BRWD1 establishes epigenetic states for germinal center initiation, maintenance, and function

Germinal center (GC) B cells segregate into three subsets that compartmentalize the antagonistic molecular programs of selection, proliferation, and somatic hypermutation. In bone marrow, the epigenetic reader BRWD1 orchestrates and insulates the sequential stages of cell proliferation and Igk recombination. We hypothesized BRWD1 might play similar insulative roles in the periphery. In Brwd1-/- follicular B cells, GC initiation and class switch recombination following immunization were inhibited. In contrast, in Brwd1-/- GC B cells there was admixing of chromatin accessibility across GC subsets and transcriptional dysregulation including induction of inflammatory pathways. This global molecular GC dysregulation was associated with specific defects in proliferation, affinity maturation, and tolerance. These data suggest that GC subset identity is required for some but not all GC-attributed functions. Furthermore, these data demonstrate a central role for BRWD1 in orchestrating epigenetic transitions at multiple steps along B cell developmental and activation pathways.

immunology↗

A divide and conquer approach (DACA) to predict high fidelity structure of large multidomain protein BRWD1

Therapeutic importance in inhibiting Bromodomain and WD Repeat Domain containing BRWD1 against numerous human pathophysiological processes including cancers prompts prediction of a workable structure of this large protein. Here, a novel divide and conquer strategy was adopted to utilize smaller overlapping sequence-fragments of BRWD1 to further utilize their predicted structures as derived templates for prediction of complete BRWD1 structure in absence of its desired homologues in the template database. The novelty of this methodology stemmed from the requirement of templates of high sequence similarity in any comparative model based predictors whereas, the own fragments of the same target protein, BRWD1 could successfully fulfill this criteria. Additionally, the outputs of different high performing predictors including AlphaFold and RoseTTAFold were systematically integrated under the premise of Inductive Reasoning. The resultant structures were validated using existing validation parameters. Finally, a new validation paradigm was adopted to screen the best structure from the result presenting in-silico studies of known interactions of BRWD1 with various small molecules like, BD inhibitors, modified histone tails, DNA motifs and interacting proteins. The algorithm proposed in this work also paved the way for prediction of authentic structures of large size proteins.

bioinformatics↗

BRWD1 orchestrates chromatin topology by converting static to dynamic cohesin complexes

Lymphocyte development consists of sequential and mutually exclusive cell states of proliferative selection and antigen receptor gene recombination1. Transitions between each state require large, coordinated changes in epigenetic landscapes and transcriptional programs2,3. How this occurs remains unclear. Herein, we demonstrate that in small pre-B cells, the lineage and stagespecific epigenetic reader Bromodomain and WD Repeating Containing Protein 1 (BRWD1)2,4 reorders three-dimensional chromatin topology to affect transition between proliferative and gene recombination molecular programs. BRWD1 regulated the switch between poised and active enhancers interacting with promoters and coordinated this with Igk locus contraction. BRWD1 did so by converting chromatin-bound static cohesin to dynamic complexes competent to mediate long-range looping. Remarkably, ATP depletion recapitulated cohesin distributions observed in Brwd1-/- cells. Therefore, in small pre-B cells, cohesin conversion is the main energetic mechanism dictating where dynamic looping occurs in the genome. Our findings provide a new mechanism of cohesin regulation and reveal how cohesin function can be dictated by lineage contextual mechanisms to facilitate specific cell fate transitions.

immunology↗

STAT3 signaling in B cells controls germinal center zone organization and recycling

Germinal centers (GCs), sites of antibody affinity maturation, are organized into dark (DZ) and light (LZ) zones. Here, we uncovered a B cell intrinsic role for STAT3 in GC DZ and LZ organization. Altered zonal organization of STAT3-deficient GCs dampened GC output of long-lived plasma cells (LL-PCs) but increased memory B cells (MBCs). Tfh-GC B cell interaction drive STAT3 tyrosine 705 and serine 727 phosphorylation in LZ B cells, facilitating their recycling into the DZ. An inducible system confirmed STAT3 is not involved in initiating or maintaining the GC but sustains GC zonal organization by regulating GC B cell recycling. RNAseq and ChIPseq analysis identified genes regulated by STAT3 that are critical for LZ cell recycling and transiting through the DZ proliferation and differentiation phases of the DZ. Thus, STAT3 signaling in B cells controls GC zone organization and recycling, and GC egress of LL-PCs, but negatively regulates MBC output. SummaryFike et al. describe a previously unrecognized mechanism by which B cell intrinsic STAT3 signaling controls the germinal center (GC) dark and light zone organization, GC B cell recycling, and GC output of long-lived plasma cells but negatively regulates memory B cells.

immunology↗

Micro-colony observation: A rapid and simple approach to count bacterial colony forming units

For enumerating viable bacteria, traditional dilution plating to count colony forming units (CFU) has always been the preferred method in microbiology owing to its simplicity, albeit laborious and time-consuming. Similar CFU counts can be obtained by quantifying growing micro-colonies in conjunction with the perks of a microscope. Here, we employed a simple method of five microliter spotting of differently diluted bacterial culture multiple times on a single Petri dish followed by finding out CFU by counting micro-colonies using a phase-contrast microscope. In this method, the CFU of an Escherichia coli culture can be estimated within a four-hour period. Further, within a ten-hour period, CFU in a culture of Ralstonia solanacearum, a bacterium with a generation time of around 2 h, can be estimated. The CFU number determined by micro-colonies observed is comparable with that obtained by the dilution plating method. Micro-colonies number observed in the early hours of growth (2 h in case of E. coli and 8 h in case of R. solanacearum) were found to remain consistent at later hours, though there was a noticeable increase in the size of the colonies. It suggested that micro-colonies observed in the early hours indeed represent the bacterial number in the culture. Practical applications to this counting method were employed in studying the rifampicin-resistant mutation rate as well as performing the fluctuation test in E. coli. The method described here results in a 90% reduction of labour, time and resources. Thus, the method is likely to be adopted by many microbiologists in their routine laboratory research.

microbiology↗

Making Common Fund data more Findable: Catalyzing a Data Ecosystem

The Common Fund Data Ecosystem (CFDE) has created a flexible system of data federation that enables users to discover datasets from across the U.S. National Institutes of Health Common Fund without requiring that data owners move, reformat, or rehost those data. The CFDEs federation system is centered on a catalog that ingests metadata from individual Common Fund Programs Data Coordination Centers (DCCs) into a uniform metadata model that can then be indexed and searched from a centralized portal. This uniform Crosscut Metadata Model (C2M2) supports the wide variety of data types and metadata terms used by the individual DCCs and is designed to enable easy expansion to accommodate new data types. We describe its use to ingest and index data from ten DCCs.

bioinformatics↗

CureSCi Metadata Catalog - Making sickle cell studies findable

ObjectivesTo adopt the FAIR principles (Findable, Accessible, Interoperable, Reusable) to enhance data sharing, the Cure Sickle Cell Initiative (CureSCi) MetaData Catalog (MDC) was developed to make Sickle Cell Disease (SCD) study datasets more Findable by curating study metadata and making them available through an open-access web portal. MethodsStudy metadata, including study protocol, data collection forms, and data dictionaries, describe information about study patient-level data. We curated key metadata of 16 SCD studies in a three-tiered conceptual framework of category, subcategory, and data element using ontologies and controlled vocabularies to organize the study variables. We developed the CureSCi MDC by indexing study metadata to enable effective browse and search capabilities at three levels: study, Patient-Reported Outcome (PRO) Measures, and data element levels. ResultsThe CureSCi MDC offers several browse and search tools to discover studies by study level, PRO Measures, and data elements. The "Browse Studies," "Browse Studies by PRO Measures," and "Browse Studies by Data Elements" tools allow users to identify studies through pre-defined conceptual categories. "Search by Keyword" and "Search Data Element by Concept Category" can be used separately or in combination to provide more granularity to refine the search results. This resource helps investigators find information about specific data elements across studies using public browsing/search tools, before going through data request procedures to access controlled datasets. The MDC makes SCD studies more Findable through browsing/searching study information, PRO Measures, and data elements, aiding in the reuse of existing SCD data.

bioinformatics↗

Decellularized micro-scaffolds as stem cell carriers for regeneration of cartilage defects

Cartilage regeneration remains a great challenge in orthopedic treatment owing to their avascular in nature and lack of self-healing ability. Various clinical treatment options are widely used including osteochondral graft transplantation, micro-fracture, blood clot formation and tissue debridement to recover the damaged cartilage. In this circumstance, cartilage defect recovery via tissue engineered functional micro tissue delivery is becoming an emerging trend in musculoskeletal therapeutics. In this study, functional micro-scaffolds (MS) were generated from Capra ear cartilage, and were separated into size-wise groups. The scaffolds were decellularized via NaOH treatment. The cell adhesion study indicated that Capra adipose tissue derived mesenchymal stem cells (ADMSCs) adhesion is more in ~100 m MSs in comparison to 150-300 m MSs. It may be assumed that the cells are compatible to grow on fibrous surface area (100 m) in comparison to dense surface (150-300 m). Further, 100 m MSs were transformed into functional micro tissues (FMTs) in presence of high density ADMSCs in a hanging droplet culture system. The FMTs was transferred to F127 block polymer hydrogel for 3D culture. After 21 d cultures, the FMT clusters were evaluated for quantitative gene expression. To assess the in vivo cartilage defect regeneration potential, FMTs were delivered to rabbit auricular cartilage defect for 15, 30 and 60 d studies. The H&E-stained histological analysis showed that the cartilage defect is almost healed in 60 d study in comparison to 15 and 30 d study.

bioengineering↗

Proton egress pathway during the S1 to S2 transition of the Oxygen Evolving Complex ofPhotosystem II

Photosystem II uses water as the ultimate electron source of the photosynthetic electron transfer chain. Water is oxidized to dioxygen at the Oxygen Evolving Complex (OEC), a Mn4CaO5 inorganic core embedded in the lumenal side of PSII. Water-filled channels are thought to bring in substrate water molecules to the OEC, remove the substrate protons to the lumen, and may transport the product oxygen. Three water-filled channels, denoted large, narrow, and broad, that extend from the OEC towards the aqueous surface more than 15 [A] away are seen. However, the actual mechanisms of water supply to the OEC, the removal of protons to the lumen and diffusion of oxygen away from the OEC have yet to be established. Here, we combine Molecular Dynamics (MD), Multi Conformation Continuum Electrostatics (MCCE) and Network Analysis to compare and contrast the three potential proton transfer paths during the S1 to S2 transition of the OEC. Hydrogen bond network analysis shows that the three channels are highly interconnected with similar energetics for hydronium as calculated for all paths near the OEC. The channels diverge as they approach the lumen, with the water chain in the broad channel better interconnected that in the narrow and large channels, where disruptions in the network are observed at about 10 [A] from the OEC. In addition, the barrier for hydronium translocation is lower in the broad channel, suggesting that a proton from the OEC could access the paths near the OEC, and likely exit to the lumen via the broad channel, passing through PsbO.

biophysics↗

The Chinese chestnut genome: a reference for species restoration

Forest tree species are increasingly subject to severe mortalities from exotic pests, diseases, and invasive organisms, accelerated by climate change. Forest health issues are threatening multiple species and ecosystem sustainability globally. While sources of resistance may be available in related species, or among surviving trees, introgression of resistance genes into threatened tree species in reasonable time frames requires genome-wide breeding tools. Asian species of chestnut (Castanea spp.) are being employed as donors of disease resistance genes to restore native chestnut species in North America and Europe. To aid in the restoration of threatened chestnut species, we present the assembly of a reference genome with chromosome-scale sequences for Chinese chestnut (C. mollissima), the disease-resistance donor for American chestnut restoration. We also demonstrate the value of the genome as a platform for research and species restoration, including new insights into the evolution of blight resistance in Asian chestnut species, the locations in the genome of ecologically important signatures of selection differentiating American chestnut from Chinese chestnut, the identification of candidate genes for disease resistance, and preliminary comparisons of genome organization with related species.

genomics↗