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"Gupta, Anjali"
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Genome-wide analysis of major intrinsic proteins in the tree plant Populus trichocarpa: Characterization of XIP subfamily of aquaporins from evolutionary perspective
by
Sankararamakrishnan, Ramasubbu
,
Gupta, Anjali Bansal
in
Agriculture
,
Amino Acid Sequence
,
Analysis
2009
Background
Members of major intrinsic proteins (MIPs) include water-conducting aquaporins and glycerol-transporting aquaglyceroporins. MIPs play important role in plant-water relations. The model plants
Arabidopsis thaliana
, rice and maize contain more than 30 MIPs and based on phylogenetic analysis they can be divided into at least four subfamilies.
Populus trichocarpa
is a model tree species and provides an opportunity to investigate several tree-specific traits. In this study, we have investigated
Populus
MIPs (PtMIPs) and compared them with their counterparts in
Arabidopsis
, rice and maize.
Results
Fifty five full-length MIPs have been identified in
Populus
genome. Phylogenetic analysis reveals that
Populus
has a fifth uncharacterized subfamily (XIPs). Three-dimensional models of all 55 PtMIPs were constructed using homology modeling technique. Aromatic/arginine (ar/R) selectivity filters, characteristics of loops responsible for solute selectivity (loop C) and gating (loop D) and group conservation of small and weakly polar interfacial residues have been analyzed. Majority of the non-XIP PtMIPs are similar to those in
Arabidopsis
, rice and maize. Additional XIPs were identified from database search and 35 XIP sequences from dicots, fungi, moss and protozoa were analyzed. Ar/R selectivity filters of dicots XIPs are more hydrophobic compared to fungi and moss XIPs and hence they are likely to transport hydrophobic solutes. Loop C is longer in one of the subgroups of dicot XIPs and most probably has a significant role in solute selectivity. Loop D in dicot XIPs has higher number of basic residues. Intron loss is observed on two occasions: once between two subfamilies of eudicots and monocot and in the second instance, when dicot and moss XIPs diverged from fungi. Expression analysis of
Populus
MIPs indicates that
Populus
XIPs don't show any tissue-specific transcript abundance.
Conclusion
Due to whole genome duplication,
Populus
has the largest number of MIPs identified in any single species. Non-XIP MIPs are similar in all four plant species considered in this study. Small and weakly polar residues at the helix-helix interface are group conserved presumably to maintain the hourglass fold of MIP channels. Substitutions in ar/R selectivity filter, insertion/deletion in loop C, increasing basic nature of loop D and loss of introns are some of the events occurred during the evolution of dicot XIPs.
Journal Article
Nanomembranes-Affiliated Water Remediation: Chronology, Properties, Classification, Challenges and Future Prospects
2023
Water contamination has become a global crisis, affecting millions of people worldwide and causing diseases and illnesses, including cholera, typhoid, and hepatitis A. Conventional water remediation methods have several challenges, including their inability to remove emerging contaminants and their high cost and environmental impact. Nanomembranes offer a promising solution to these challenges. Nanomembranes are thin, selectively permeable membranes that can remove contaminants from water based on size, charge, and other properties. They offer several advantages over conventional methods, including their ability to remove evolving pollutants, low functioning price, and reduced ecological influence. However, there are numerous limitations linked with the applications of nanomembranes in water remediation, including fouling and scaling, cost-effectiveness, and potential environmental impact. Researchers are working to reduce the cost of nanomembranes through the development of more cost-effective manufacturing methods and the use of alternative materials such as graphene. Additionally, there are concerns about the release of nanomaterials into the environment during the manufacturing and disposal of the membranes, and further research is needed to understand their potential impact. Despite these challenges, nanomembranes offer a promising solution for the global water crisis and could have a significant impact on public health and the environment. The current article delivers an overview on the exploitation of various engineered nanoscale substances, encompassing the carbonaceous nanomaterials, metallic, metal oxide and metal–organic frameworks, polymeric nano-adsorbents and nanomembranes, for water remediation. The article emphasizes the mechanisms involved in adsorption and nanomembrane filtration. Additionally, the authors aim to deliver an all-inclusive review on the chronology, technical execution, challenges, restrictions, reusability, and future prospects of these nanomaterials.
Journal Article
Factors influencing meiotic recombination revealed by whole-genome sequencing of single sperm
2019
During meiosis, homologous chromosomes undergo doublestrand breaks in DNA that can cross over, shuffling genetic material. However, not every double-strand break resolves in a crossover event. Hinch et al. wanted to determine the rules governing DNA recombination. They developed a method to sequence individual mouse sperm and applied it to mice carrying two different alleles of a protein involved in mammalian crossovers. A high-resolution genetic map revealed the relationships between the distribution of crossovers, proteins involved in recombination, and specific factors determining whether a double-strand break becomes a crossover. Science , this issue p. eaau8861 A high-resolution map from single-cell sequencing identifies factors responsible for crossover resolution in individual murine sperm cells. Recombination is critical to meiosis and evolution, yet many aspects of the physical exchange of DNA via crossovers remain poorly understood. We report an approach for single-cell whole-genome DNA sequencing by which we sequenced 217 individual hybrid mouse sperm, providing a kilobase-resolution genome-wide map of crossovers. Combining this map with molecular assays measuring stages of recombination, we identified factors that affect crossover probability, including PRDM9 binding on the non-initiating template homolog and telomere proximity. These factors also influence the time for sites of recombination-initiating DNA double-strand breaks to find and engage their homologs, with rapidly engaging sites more likely to form crossovers. We show that chromatin environment on the template homolog affects positioning of crossover breakpoints. Our results also offer insights into recombination in the pseudoautosomal region.
Journal Article
Microbial surfactants
by
Gupta, Anjali
,
Tripathy, Divya
in
Chemistry
,
Environmental
,
Environmental science, engineering & technology
2024
This book will incorporate the latest research, developments, and advancements in the field, as well as providing a more comprehensive and in-depth analysis of the subject matter. Additionally, incorporating unique perspectives, innovative approaches, and interactive elements (such as case studies, illustrations) will make the book stand out and provide a better learning experience for readers. The objective of the proposed book is to create a comprehensive, high-quality resource that provides valuable information and insights to researchers, professionals, and students in the field of microbial surfactants.
Persistence of symptoms and quality of life at 35 days after hospitalization for COVID-19 infection
2020
Characterizing the prevalence and persistence of symptoms associated with COVID-19 infection following hospitalization and their impact is essential to planning post-acute community-based clinical services. This study seeks to identify persistent COVID-19 symptoms in patients 35 days post-hospitalization and their impact on quality of life, health, physical, mental, and psychosocial function.
This prospective cohort study used the PROMIS® Instruments to identify symptoms and quality of life parameters in consecutively enrolled patients between March 22 and April 16, 2020, in New Jersey. The 183 patients (median age 57 years; 61.5% male, 54.1% white) reported persistent symptoms at 35 days, including fatigue (55.0%), dyspnea (45.3%), muscular pain (51%), associated with a lower odds rating general health (41.5%, OR 0.093 [95% CI: 0.026, 0.329], p = 0.0002), quality of life (39.8%; OR 0.116 [95% CI: 0.038, 0.364], p = 0.0002), physical health (38.7%, OR 0.055 [95% CI: 0.016, 0.193], p <0.0001), mental health (43.7%, OR 0.093 [95% CI: 0.021, 0.418], p = 0.0019) and social active role (38.7%, OR 0.095 [95% CI: 0.031, 0.291], p<0.0001), as very good/excellent, particularly adults aged 65 to 75 years (OR 8·666 [95% CI: 2·216, 33·884], p = 0·0019).
COVID-19 symptoms commonly persist to 35 days, impacting quality of life, health, physical and mental function. Early post-acute evaluation of symptoms and their impact on function is necessary to plan community-based services.
Journal Article
Unsuspected Malaria Infection in a Case with Pancytopenia
2025
Globally, an estimated 300-500 million clinical episodes of malaria occur annually, primarily due to P. falciparum and P. vivax infections.1 P. vivax remains the second most significant cause of malaria, notable for its potential to relapse due to the reactivation of dormant hypnozoites in hepatocytes.2 Common hematological abnormalities associated with malaria include anemia, thrombocytopenia, leukopenia, leukocytosis, neutropenia, neutrophilia, monocytosis, and, less frequently, disseminated intravascular coagulation.3 Examination of peripheral blood smear remains the gold standard for diagnosing malaria. Awoke N, Arota A. Awoke N, Arota A. Profiles of hematological parameters in Plasmodium falciparum and Plasmodium vivax malaria patients attending Tercha General Hospital, Dawuro Zone, South Ethiopia. Plasmodium vivax mimicking morphologic features of Plasmodium falciparum.
Journal Article
Altering the Binding Properties of PRDM9 Partially Restores Fertility across the Species Boundary
by
Cebrian-Serrano, Alberto
,
Preece, Chris
,
Davies, Benjamin
in
Animals
,
Binding
,
Chromosome Pairing
2021
Abstract
Sterility or subfertility of male hybrid offspring is commonly observed. This phenomenon contributes to reproductive barriers between the parental populations, an early step in the process of speciation. One frequent cause of such infertility is a failure of proper chromosome pairing during male meiosis. In subspecies of the house mouse, the likelihood of successful chromosome synapsis is improved by the binding of the histone methyltransferase PRDM9 to both chromosome homologs at matching positions. Using genetic manipulation, we altered PRDM9 binding to occur more often at matched sites, and find that chromosome pairing defects can be rescued, not only in an intersubspecific cross, but also between distinct species. Using different engineered variants, we demonstrate a quantitative link between the degree of matched homolog binding, chromosome synapsis, and rescue of fertility in hybrids between Mus musculus and Mus spretus. The resulting partial restoration of fertility reveals additional mechanisms at play that act to lock-in the reproductive isolation between these two species.
Journal Article
Thermal and chemical properties of the eROSITA bubbles from Suzaku observations
by
Gupta, Anjali
,
Krongold, Yair
,
Das, Sanskriti
in
Bubbles
,
Chemical properties
,
Emission measurements
2023
The X-ray bright bubbles at the Galactic Centre provide an opportunity to understand the effects of feedback on galaxy evolution. The shells of the eROSITA bubbles show enhanced X-ray emission over the sky background. Previously, these shells were assumed to have a single temperature component and to trace the shock-heated lower-temperature halo gas. Using Suzaku observations, we show that the X-ray emission of the shells is more complex and best described by a two-temperature thermal model: one component close to the Galaxy’s virial temperature and the other at supervirial temperatures. Furthermore, we demonstrate that temperatures of the virial and supervirial components are similar in the shells and in the ambient medium, although the emission measures are significantly higher in the shells. This leads us to conclude that the eROSITA bubble shells are X-ray bright because they trace denser gas, not because they are hotter. Given that the pre- and postshock temperatures are similar and the compression ratio of the shock is high, we rule out that the bubble shells trace adiabatic shocks, in contrast to what was assumed in previous studies. We also observe non-solar Ne/O and Mg/O ratios in the shells, favouring stellar feedback models for the formation of the bubbles and settling a long-standing debate on their origin.The eROSITA bubbles and their surrounding regions are best described by the same two-temperature model, implying that the shells are bright because they are denser, not hotter. Also reported are non-solar Mg/O and Ne/O ratios, which support the stellar-feedback origin of the bubbles.
Journal Article
From facial expressions to algorithms: a narrative review of animal pain recognition technologies
by
Gupta, Anjali
,
Chiavaccini, Ludovica
,
Chiavaccini, Guido
in
Algorithms
,
Animal welfare
,
AnimalFACS
2024
Facial expressions are essential for communication and emotional expression across species. Despite the improvements brought by tools like the Horse Grimace Scale (HGS) in pain recognition in horses, their reliance on human identification of characteristic traits presents drawbacks such as subjectivity, training requirements, costs, and potential bias. Despite these challenges, the development of facial expression pain scales for animals has been making strides. To address these limitations, Automated Pain Recognition (APR) powered by Artificial Intelligence (AI) offers a promising advancement. Notably, computer vision and machine learning have revolutionized our approach to identifying and addressing pain in non-verbal patients, including animals, with profound implications for both veterinary medicine and animal welfare. By leveraging the capabilities of AI algorithms, we can construct sophisticated models capable of analyzing diverse data inputs, encompassing not only facial expressions but also body language, vocalizations, and physiological signals, to provide precise and objective evaluations of an animal's pain levels. While the advancement of APR holds great promise for improving animal welfare by enabling better pain management, it also brings forth the need to overcome data limitations, ensure ethical practices, and develop robust ground truth measures. This narrative review aimed to provide a comprehensive overview, tracing the journey from the initial application of facial expression recognition for the development of pain scales in animals to the recent application, evolution, and limitations of APR, thereby contributing to understanding this rapidly evolving field.
Journal Article
Socioeconomic disparities in immunotherapy use among advanced-stage non-small cell lung cancer patients: analysis of the National Cancer Database
2023
Socioeconomic and racial disparities exist in access to care among patients with non-small cell lung cancer (NSCLC) in the United States. Immunotherapy is a widely established treatment modality for patients with advanced-stage NSCLC (aNSCLC). We examined associations of area-level socioeconomic status with receipt of immunotherapy for aNSCLC patients by race/ethnicity and cancer facility type (academic and non-academic). We used the National Cancer Database (2015–2016), and included patients aged 40–89 years who were diagnosed with stage III-IV NSCLC. Area-level income was defined as the median household income in the patient’s zip code, and area-level education was defined as the proportion of adults aged ≥ 25 years in the patient’s zip code without a high school degree. We calculated adjusted odds ratios (aOR) with 95% confidence intervals (95% CI) using multi-level multivariable logistic regression. Among 100,298 aNSCLC patients, lower area-level education and income were associated with lower odds of immunotherapy treatment (education: aOR 0.71; 95% CI 0.65, 0.76 and income: aOR 0.71; 95% CI 0.66, 0.77). These associations persisted for NH-White patients. However, among NH-Black patients, we only observed an association with lower education (aOR 0.74; 95% CI 0.57, 0.97). Across all cancer facility types, lower education and income were associated with lower immunotherapy receipt among NH-White patients. However, among NH-Black patients, this association only persisted with education for patients treated at non-academic facilities (aOR 0.70; 95% CI 0.49, 0.99). In conclusion, aNSCLC patients residing in areas of lower educational and economic wealth were less likely to receive immunotherapy.
Journal Article