XPA tumor variant leads to defects in NER that sensitize cells to cisplatin.

Nucleotide excision repair (NER) reduces efficacy of treatment with platinum (Pt)-based chemotherapy by removing Pt lesions from DNA. Previous study has identified that missense mutation or loss of the NER genes Excision Repair Cross Complementation Group 1 and 2 (ERCC1 and ERCC2) leads to improved patient outcomes after treatment with Pt-based chemotherapies. Although most NER gene alterations found in patient tumors are missense mutations, the impact of mutations in the remaining nearly 20 NER genes is unknown. Towards this goal, we previously developed a machine learning strategy to predict genetic variants in an essential NER protein, Xeroderma Pigmentosum Complementation Group A (XPA), that disrupt repair. In this study, we report in-depth analyses of a subset of the predicted variants, including in vitro analyses of purified recombinant protein and cell-based assays to test Pt agent sensitivity in cells and determine mechanisms of NER dysfunction. The most NER deficient variant Y148D had reduced protein stability, weaker DNA binding, disrupted recruitment to damage, and degradation. Our findings demonstrate that tumor mutations in XPA impact cell survival after cisplatin treatment and provide valuable mechanistic insights to improve variant effect prediction. Broadly, these findings suggest XPA tumor variants should be considered when predicting chemotherapy response.

Depletion of lamins B1 and B2 promotes chromatin mobility and induces differential gene expression by a mesoscale-motion-dependent mechanism.

BACKGROUND: B-type lamins are critical nuclear envelope proteins that interact with the three-dimensional genomic architecture. However, identifying the direct roles of B-lamins on dynamic genome organization has been challenging as their joint depletion severely impacts cell viability. To overcome this, we engineered mammalian cells to rapidly and completely degrade endogenous B-type lamins using Auxin-inducible degron technology. RESULTS: Using live-cell Dual Partial Wave Spectroscopic (Dual-PWS) microscopy, Stochastic Optical Reconstruction Microscopy (STORM), in situ Hi-C, CRISPR-Sirius, and fluorescence in situ hybridization (FISH), we demonstrate that lamin B1 and lamin B2 are critical structural components of the nuclear periphery that create a repressive compartment for peripheral-associated genes. Lamin B1 and lamin B2 depletion minimally alters higher-order chromatin folding but disrupts cell morphology, significantly increases chromatin mobility, redistributes both constitutive and facultative heterochromatin, and induces differential gene expression both within and near lamin-associated domain (LAD) boundaries. Critically, we demonstrate that chromatin territories expand as upregulated genes within LADs radially shift inwards. Our results indicate that the mechanism of action of B-type lamins comes from their role in constraining chromatin motion and spatial positioning of gene-specific loci, heterochromatin, and chromatin domains. CONCLUSIONS: Our findings suggest that, while B-type lamin degradation does not significantly change genome topology, it has major implications for three-dimensional chromatin conformation at the single-cell level both at the lamina-associated periphery and the non-LAD-associated nuclear interior with concomitant genome-wide transcriptional changes. This raises intriguing questions about the individual and overlapping roles of lamin B1 and lamin B2 in cellular function and disease.

Mismatch repair protein MLH1 suppresses replicative stress in BRCA2-deficient breast tumors.

Loss of BRCA2 (breast cancer 2) is lethal for normal cells. Yet it remains poorly understood how, in BRCA2 mutation carriers, cells undergoing loss of heterozygosity overcome the lethality and undergo tissue-specific neoplastic transformation. Here, we identified mismatch repair gene mutL homolog 1 (MLH1) as a genetic interactor of BRCA2 whose overexpression supports the viability of Brca2-null cells. Mechanistically, we showed that MLH1 interacts with Flap endonuclease 1 (FEN1) and competes to process the RNA flaps of Okazaki fragments. Together, they restrained the DNA2 nuclease activity on the reversed forks of lagging strands, leading to replication fork (RF) stability in BRCA2-deficient cells. In these cells, MLH1 also attenuated R-loops, allowing the progression of stable RFs, which suppressed genomic instability and supported cell viability. We demonstrated the significance of their genetic interaction by the lethality of Brca2-mutant mice and inhibition of Brca2-deficient tumor growth in mice by Mlh1 loss. Furthermore, we described estrogen as inducing MLH1 expression through estrogen receptor α (ERα), which might explain why the majority of BRCA2 mutation carriers develop ER-positive breast cancer. Taken together, our findings reveal a role of MLH1 in relieving replicative stress and show how it may contribute to the establishment of BRCA2-deficient breast tumors.

An encyclopedia of enhancer-gene regulatory interactions in the human genome.

Identifying transcriptional enhancers and their target genes is essential for understanding gene regulation and the impact of human genetic variation on disease1-6. Here we create and evaluate a resource of >13 million enhancer-gene regulatory interactions across 352 cell types and tissues, by integrating predictive models, measurements of chromatin state and 3D contacts, and largescale genetic perturbations generated by the ENCODE Consortium7. We first create a systematic benchmarking pipeline to compare predictive models, assembling a dataset of 10,411 elementgene pairs measured in CRISPR perturbation experiments, >30,000 fine-mapped eQTLs, and 569 fine-mapped GWAS variants linked to a likely causal gene. Using this framework, we develop a new predictive model, ENCODE-rE2G, that achieves state-of-the-art performance across multiple prediction tasks, demonstrating a strategy involving iterative perturbations and supervised machine learning to build increasingly accurate predictive models of enhancer regulation. Using the ENCODE-rE2G model, we build an encyclopedia of enhancer-gene regulatory interactions in the human genome, which reveals global properties of enhancer networks, identifies differences in the functions of genes that have more or less complex regulatory landscapes, and improves analyses to link noncoding variants to target genes and cell types for common, complex diseases. By interpreting the model, we find evidence that, beyond enhancer activity and 3D enhancer-promoter contacts, additional features guide enhancerpromoter communication including promoter class and enhancer-enhancer synergy. Altogether, these genome-wide maps of enhancer-gene regulatory interactions, benchmarking software, predictive models, and insights about enhancer function provide a valuable resource for future studies of gene regulation and human genetics.

A rapid, low-cost, and highly sensitive SARS-CoV-2 diagnostic based on whole-genome sequencing.

Early detection of SARS-CoV-2 infection is key to managing the current global pandemic, as evidence shows the virus is most contagious on or before symptom onset. Here, we introduce a low-cost, high-throughput method for diagnosing and studying SARS-CoV-2 infection. Dubbed Pathogen-Oriented Low-Cost Assembly & Re-Sequencing (POLAR), this method amplifies the entirety of the SARS-CoV-2 genome. This contrasts with typical RT-PCR-based diagnostic tests, which amplify only a few loci. To achieve this goal, we combine a SARS-CoV-2 enrichment method developed by the ARTIC Network (https://artic.network/) with short-read DNA sequencing and de novo genome assembly. Using this method, we can reliably (>95% accuracy) detect SARS-CoV-2 at a concentration of 84 genome equivalents per milliliter (GE/mL). The vast majority of diagnostic methods meeting our analytical criteria that are currently authorized for use by the United States Food and Drug Administration with the Coronavirus Disease 2019 (COVID-19) Emergency Use Authorization require higher concentrations of the virus to achieve this degree of sensitivity and specificity. In addition, we can reliably assemble the SARS-CoV-2 genome in the sample, often with no gaps and perfect accuracy given sufficient viral load. The genotypic data in these genome assemblies enable the more effective analysis of disease spread than is possible with an ordinary binary diagnostic. These data can also help identify vaccine and drug targets. Finally, we show that the diagnoses obtained using POLAR of positive and negative clinical nasal mid-turbinate swab samples 100% match those obtained in a clinical diagnostic lab using the Center for Disease Control's 2019-Novel Coronavirus test. Using POLAR, a single person can manually process 192 samples over an 8-hour experiment at the cost of ~$36 per patient (as of December 7th, 2022), enabling a 24-hour turnaround with sequencing and data analysis time. We anticipate that further testing and refinement will allow greater sensitivity using this approach.

Characterization of BRCA2 R3052Q variant in mice supports its functional impact as a low-risk variant.

Pathogenic variants in BRCA2 are known to significantly increase the lifetime risk of developing breast and ovarian cancers. Sequencing-based genetic testing has resulted in the identification of thousands of BRCA2 variants that are considered to be variants of uncertain significance (VUS) because the disease risk associated with them is unknown. One such variant is p.Arg3052Gln, which has conflicting interpretations of pathogenicity in the ClinVar variant database. Arginine at position 3052 in BRCA2 plays an important role in stabilizing its C-terminal DNA binding domain. We have generated a knock-in mouse model expressing this variant to examine its role on growth and survival in vivo. Homozygous as well as hemizygous mutant mice are viable, fertile and exhibit no overt phenotype. While we did not observe any hematopoietic defects in adults, we did observe a marked reduction in the in vitro proliferative ability of fetal liver cells that were also hypersensitive to PARP inhibitor, olaparib. In vitro studies performed on embryonic and adult fibroblasts derived from the mutant mice showed significant reduction in radiation induced RAD51 foci formation as well as increased genomic instability after mitomycin C treatment. We observed mis-localization of a fraction of R3052Q BRCA2 protein to the cytoplasm which may explain the observed in vitro phenotypes. Our findings suggest that BRCA2 R3052Q should be considered as a hypomorphic variant.

Interferon restores replication fork stability and cell viability in BRCA-defective cells via ISG15.

DNA replication and repair defects or genotoxic treatments trigger interferon (IFN)-mediated inflammatory responses. However, whether and how IFN signaling in turn impacts the DNA replication process has remained elusive. Here we show that basal levels of the IFN-stimulated gene 15, ISG15, and its conjugation (ISGylation) are essential to protect nascent DNA from degradation. Moreover, IFNß treatment restores replication fork stability in BRCA1/2-deficient cells, which strictly depends on topoisomerase-1, and rescues lethality of BRCA2-deficient mouse embryonic stem cells. Although IFNß activates hundreds of genes, these effects are specifically mediated by ISG15 and ISGylation, as their inactivation suppresses the impact of IFNß on DNA replication. ISG15 depletion significantly reduces cell proliferation rates in human BRCA1-mutated triple-negative, whereas its upregulation results in increased resistance to the chemotherapeutic drug cisplatin in mouse BRCA2-deficient breast cancer cells, respectively. Accordingly, cells carrying BRCA1/2 defects consistently show increased ISG15 levels, which we propose as an in-built mechanism of drug resistance linked to BRCAness.

Depletion of lamins B1 and B2 alters chromatin mobility and induces differential gene expression by a mesoscale-motion dependent mechanism.

BACKGROUND: B-type lamins are critical nuclear envelope proteins that interact with the 3D genomic architecture. However, identifying the direct roles of B-lamins on dynamic genome organization has been challenging as their joint depletion severely impacts cell viability. To overcome this, we engineered mammalian cells to rapidly and completely degrade endogenous B-type lamins using Auxin-inducible degron (AID) technology. RESULTS: Paired with a suite of novel technologies, live-cell Dual Partial Wave Spectroscopic (Dual-PWS) microscopy, in situ Hi-C, and CRISPR-Sirius, we demonstrate that lamin B1 and lamin B2 depletion transforms chromatin mobility, heterochromatin positioning, gene expression, and loci-positioning with minimal disruption to mesoscale chromatin folding. Using the AID system, we show that the disruption of B-lamins alters gene expression both within and outside lamin associated domains, with distinct mechanistic patterns depending on their localization. Critically, we demonstrate that chromatin dynamics, positioning of constitutive and facultative heterochromatic markers, and chromosome positioning near the nuclear periphery are significantly altered, indicating that the mechanism of action of B-type lamins is derived from their role in maintaining chromatin dynamics and spatial positioning. CONCLUSIONS: Our findings suggest that the mechanistic role of B-type lamins is stabilization of heterochromatin and chromosomal positioning along the nuclear periphery. We conclude that degrading lamin B1 and lamin B2 has several functional consequences related to both structural disease and cancer.

The ENCODE Uniform Analysis Pipelines.

The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the Homo sapiens and Mus musculus genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and available via the ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL; https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environments via Cromwell. Access to the pipelines and data via the cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses.

Time-dependent plastic behavior of bacteria leading to rupture.

A study of the mechanical response of bacteria is essential in designing an antibacterial surface for implants and food packaging applications. This research evaluated the mechanical response of Escherichia coli under different loading conditions. Indentation and prolonged creep tests were performed to understand their viscoelastic-plastic response. The results indicate that varying loading rates from 1 µm/s to 5 µm/s show an increase in modulus of 182% and 90%, calculated in the loading and unloading cycles, respectively, and a decrease in adhesion force by 42%. However, on varying loads from 5 nN to 25 nN, nominal change is observed in both modulus and adhesion force. The rupture curve at 100 nN load shows elastic and a small plastic deformation accompanied by a sharp peak indicating the cell wall rupture. The rupture force at the peak was found to be 34.38 ± 5.15 nN, irrespective of the loading rate, making it a failure criterion for bacteria rupture. The creep response of bacteria increases (for 6 s) and then remains constant (for 15 s) with time, indicating that a standard linear solid (SLS) model applies to this behavior. This work attempts to evaluate the mechanical properties of E. coli bacteria focusing on its rupture by contact killing mechanism.

Chromatin alternates between A and B compartments at kilobase scale for subgenic organization.

Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally studied at a finer scale, but the impact of looping on proximal interactions remains enigmatic. Here, we critically examine nuclear compartments and CTCF loop-proximal interactions using a combination of in situ Hi-C at unparalleled depth, algorithm development, and biophysical modeling. Producing a large Hi-C map with 33 billion contacts in conjunction with an algorithm for performing principal component analysis on sparse, super massive matrices (POSSUMM), we resolve compartments to 500 bp. Our results demonstrate that essentially all active promoters and distal enhancers localize in the A compartment, even when flanking sequences do not. Furthermore, we find that the TSS and TTS of paused genes are often segregated into separate compartments. We then identify diffuse interactions that radiate from CTCF loop anchors, which correlate with strong enhancer-promoter interactions and proximal transcription. We also find that these diffuse interactions depend on CTCF's RNA binding domains. In this work, we demonstrate features of fine-scale chromatin organization consistent with a revised model in which compartments are more precise than commonly thought while CTCF loops are more protracted.

The ENCODE Uniform Analysis Pipelines.

The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create a comprehensive catalog of functional elements in the human genome. The current database comprises more than 19000 functional genomics experiments across more than 1000 cell lines and tissues using a wide array of experimental techniques to study the chromatin structure, regulatory and transcriptional landscape of the Homo sapiens and Mus musculus genomes. All experimental data, metadata, and associated computational analyses created by the ENCODE consortium are submitted to the Data Coordination Center (DCC) for validation, tracking, storage, and distribution to community resources and the scientific community. The ENCODE project has engineered and distributed uniform processing pipelines in order to promote data provenance and reproducibility as well as allow interoperability between genomic resources and other consortia. All data files, reference genome versions, software versions, and parameters used by the pipelines are captured and available via the ENCODE Portal. The pipeline code, developed using Docker and Workflow Description Language (WDL; https://openwdl.org/) is publicly available in GitHub, with images available on Dockerhub (https://hub.docker.com), enabling access to a diverse range of biomedical researchers. ENCODE pipelines maintained and used by the DCC can be installed to run on personal computers, local HPC clusters, or in cloud computing environments via Cromwell. Access to the pipelines and data via the cloud allows small labs the ability to use the data or software without access to institutional compute clusters. Standardization of the computational methodologies for analysis and quality control leads to comparable results from different ENCODE collections - a prerequisite for successful integrative analyses.

A lab-on-chip solution for the detection and suppression of COVID-19 severity.

At present, the conventional method for detecting COVID-19 infection is reverse transcription-polymerase chain reaction (RT-PCR) performed on nasopharyngeal and pharyngeal swabs. In addition, other detection techniques such as isothermal nucleic acid amplification, enzyme-linked immunosorbent assay (ELISA) have also been proposed and are being used. However, these techniques are limited to central hospitals and pathologies. Point-of-care solutions may play an important role in rapid and timely detection by an individual at their doorstep. In addition, the disease adversely affects the functioning of various constituents of human blood. For example, it reduces the platelets count, increases production of proinflammatory cytokine which results in cytokine storm, and increases level of various plasma proteins with the severity of the disease. Therefore, monitoring and transfusion of blood plasma and platelets may play an essential role in detection and suppression of severity of COVID-19 infection. In this regard, we propose evolution of our existing microdevice for the detection and suppression of severity of COVID-19 infection. We propose modification of our microdevice in the following ways (i) as a platelet-rich plasma separation unit, (ii) as an on-chip device to study inter-cellular properties of platelets, and (iii) for on-chip detection of infection by separating plasma. The integration of these microdevices with lateral flow assays, flow-virometry reader (FVR), direct serological biosensor assay along with proprietary technology based on plasmonic, place these microdevices in an advantageous position. Moreover, coupling of the microdevices with machine leaning application for rapid detection of the severity of COVID-19 and platelets related disorders makes these microdevices as a complete unit for point-of-care application.

Mithplatins: Mithramycin SA-Pt(II) Complex Conjugates for the Treatment of Platinum-Resistant Ovarian Cancers.

DNA coordinating platinum (Pt) containing compounds cisplatin and carboplatin have been used for the treatment of ovarian cancer therapy for four decades. However, recurrent Pt-resistant cancers are a major cause of mortality. To combat Pt-resistant ovarian cancers, we designed and synthesized a conjugate of an anticancer drug mithramycin with a reactive Pt(II) bearing moiety, which we termed mithplatin. The conjugates displayed both the Mg2+ -dependent noncovalent DNA binding characteristic of mithramycin and the covalent crosslinking to DNA of the Pt. The conjugate was three times as potent as cisplatin against ovarian cancer cells. The DNA lesions caused by the conjugate led to the generation of DNA double-strand breaks, as also observed with cisplatin. Nevertheless, the conjugate was highly active against both Pt-sensitive and Pt-resistant ovarian cancer cells. This study paves the way to developing mithplatins to combat Pt-resistant ovarian cancers.

Clinical and Etiological Profiles of Patients With Pancytopenia in a Tertiary Care Hospital.

Background Pancytopenia is more of a manifestation of a spectrum of underlying diseases affecting the bone marrow. Specific treatment relies solely on early diagnosis and identification of the accurate etiology. We aimed to generate data on the clinical and etiological profiles of patients diagnosed with pancytopenia. Materials and methods Fifty patients more than 13 years of age with pancytopenia who reported to a tertiary care hospital were included in the study. Thorough clinical examination, hematological investigation, and bone marrow biopsies were performed, and relevant data were recorded and analyzed statistically. Results Pancytopenia was most common in the age group of 25-34 years, with a male preponderance. The most common presenting complaints were fatigue and fever, with pallor present in all patients, followed by splenomegaly and hepatomegaly in a few patients. Aplastic anemia is the most common cause of pancytopenia, followed by megaloblastic anemia and leukemia. Conclusion While fatigue and fever are the most usual symptoms of pancytopenia, clinical pallor, hepatomegaly, and splenomegaly may be evident. Among the several etiologies, aplastic anemia is one of the most common causes of pancytopenia.

Organic carbon dynamics in the continental shelf waters of the eastern Arabian Sea.

The seasonal and spatial distribution of total organic carbon (TOC) is presented for the coastal waters of the eastern Arabian Sea, which experiences seasonal suboxia during the late southwest monsoon (SWM). This study reveals that high TOC was observed off Kochi as compared to Goa and Mangalore transects, and may be attributed to stronger upwelling along the Kerala coast. This is also supported by the excess carbon due to upwelling during the late SWM that varied from 37 µM (Goa), 39 µM (Mangalore), to 51 µM (Kochi). Our seasonal data from 2014 to 2020 at the Goa transect indicates that high TOC is seen during late SWM to fall inter monsoon (FIM) and between the late northeast monsoon (NEM) to the early spring inter monsoon (SIM). The high TOC concentrations and C/N ratios observed during the FIM are a combination of high primary production, the buildup of remnant organic matter from the previous season (due to prevailing low oxygen conditions), accumulation of refractory organic carbon, and release from diatoms (especially Chaetoceros sp.). Inter-annual variations indicate that phytoplankton blooms resulted in higher TOC concentrations, especially during the year 2020. Based on a comparison with an Elnino-Southern Oscillation (ENSO) year (2015), we can infer that the partitioning of carbon may increase from particulate to dissolved phase in future warming scenarios.

Case Report: Pharyngeal Diphtheria in a Pregnant Woman from South India.

Diphtheria is a vaccine-preventable disease and is caused by toxigenic strains of Corynebacterium diphtheriae. Several case reports have been published in the recent years, and this resurgence of cases has occurred mainly in adolescent and adult populations. Also, several research articles have reported waning immunity against diphtheria in adults who have completed childhood immunization. Thus, it is an important need to conduct larger sero-surveillance studies to understand the cause of rising diphtheria cases. Here, we report a case of a 23-year-old pregnant women of 8 weeks' gestation who presented to the outpatient department with fever, severe throat pain, odynophagia, dysphagia, neck pain, and neck swelling of 3 days' duration. On clinical examination, a gray, leathery membrane was noted on the soft palate. An Albert's stain from the membrane revealed organisms resembling Corynebacterium diphtheriae. Appropriate treatment was initiated immediately, and follow-up examination at 2 weeks from date of discharge was uneventful. The gray membrane had completely resolved. Contact tracing was done and the appropriate antimicrobial agent was administered. This case study indicates the importance of timely clinical and microbiological diagnosis and reinforces the previously reported resurgence of diphtheria infection.

Diagnostic Performance of the PalmScan VF2000 Virtual Reality Visual Field Analyzer for Identification and Classification of Glaucoma.

PURPOSE: To evaluate the diagnostic test properties of the Palm Scan VF2000Ⓡ Virtual Reality Visual Field Analyzer for diagnosis and classification of the severity of glaucoma. METHODS: This study was a prospective cross-sectional analysis of 166 eyes from 97 participants. All of them were examined by the HumphreyⓇ Field Analyzer (used as the gold standard) and the Palm Scan VF 2000Ⓡ Virtual Reality Visual Field Analyzer on the same day by the same examiner. We estimated the kappa statistic (including 95% confidence interval [CI]) as a measure of agreement between these two methods. The diagnostic test properties were assessed using sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). RESULTS: The sensitivity, specificity, PPV, and NPV for the Virtual Reality Visual Field Analyzer for the classification of individuals as glaucoma/non-glaucoma was 100%. The general agreement for the classification of glaucoma between these two instruments was 0.63 (95% CI: 0.56-0.78). The agreement for mild glaucoma was 0.76 (95% CI: 0.61-0.92), for moderate glaucoma was 0.37 (0.14-0.60), and for severe glaucoma was 0.70 (95% CI: 0.55-0.85). About 28% of moderate glaucoma cases were misclassified as mild and 17% were misclassified as severe by the virtual reality visual field analyzer. Furthermore, 20% of severe cases were misclassified as moderate by this instrument. CONCLUSION: The instrument is 100% sensitive and specific in detection of glaucoma. However, among patients with glaucoma, there is a relatively high proportion of misclassification of severity of glaucoma. Thus, although useful for screening of glaucoma, it cannot replace the HumphreyⓇ Field Analyzer for the clinical management in its current form.

Carbonaceous aerosols and their light absorption properties over the Bay of Bengal during continental outflow.

The marine atmosphere of the Bay of Bengal (BoB) is prone to get impacted by anthropogenic aerosols from the Indo-Gangetic Plain (IGP) and Southeast Asia (SEA), particularly during the northeast monsoon (NEM). In this study, we quantify and characterize carbonaceous aerosols and their absorption properties collected in two cruise campaigns onboard ORV Sindhu Sadhana during the continental outflow period over the BoB. Aerosol samples were classified based on the air mass back trajectory analyses, wherein samples were impacted by the continental air parcel (CAP), marine air parcel (MAP), and mix of both (CAP + MAP). Significant variability in the PM10 mass concentration (in µg m-3) is found with a maximum value for MAP samples (75.5 ± 36.4) followed by CAP + MAP (58.5 ± 27.3) and CAP (58.5 ± 27.3). The OC/EC ratio (>2) and diagnostic tracers i.e. nss-K+/EC (0.2-0.96) and nss-K+/OC (0.11-1.32) along with the absorption angstrom exponent (AAE: 4.31-6.02) and MODIS (Moderate Resolution Imaging Spectroradiometer) derived fire counts suggest the dominance of biomass burning emission sources. A positive correlation between OC and EC (i.e. r = 0.86, 0.70, and 0.42 for CAP, MAP, and CAP + MAP, respectively) further confirmed the similar emission sources of carbonaceous species. Similarly, a significant correlation between estimated secondary organic carbon (SOC) and water-soluble organic carbon (WSOC; r = 0.99, 0.96, and 0.97 for CAP, MAP, and CAP + MAP, respectively) indicate their similar chemical nature as well as dominant contribution of SOC to WSOC. The absorption coefficient (babs-365) and mass absorption efficiency (MAEBrC-365) of the soluble fraction were estimated at 365 nm wherein, babs-365 showed a linear relationship with WSOC and nss-K+, signifying the contribution of water soluble brown carbon from biomass burning emissions. The estimated MAEBrC-365 (0.30-0.93 m2 g-1), during this study, was consistent with the earlier observations over the BoB, particularly during the continental outflow season.

Microbial consortia adaptation to substrate changes in anaerobic digestion.

Renewable natural gas (RNG) produced from anaerobic digestion (AD) of agricultural residues is emerging a serious biofuel alternative. Complex nature of lignocellulosic biomass residues coupled with complex biochemical transformations involving a large spectrum of microbial communities make anaerobic digestion of biomass difficult to understand and control. The present work aims at studying adaptation of microbial consortia in AD to substrates changes and correlating these to biogas generation. The double edged study deals with (a) using a common starting culture inoculum on different fractions of pretreated lignocellulosic biomass (LBM) fractions; and (b) using different starter inocula for gas generation from simple glucose substrate. Taxonomic analysis using 16S amplicon sequencing is shown to highlight changes in microbial community structure and predominance, majorly in hydrolytic bacterial populations. Observed variations in the rate of digestion with different starter inocula could be related to differences in microbial community structure and relative abundance. Results with different treated biomass fractions as substrates indicated that AD performance could be related to abundance of substrate-specific microbial communities. The work is a step to a deeper understanding of AD processes that may lead to better control and operation of AD for super-scale production of RNG from biomass feedstocks.