Biology subjects

Basu, P.

Publications and source records attributed to Basu, P..

28 records · Page 2Linked to original sources

bioRxiv2021

How effective are frogs in regulating crop pest population in a natural multi-trophic system??

Potential of frogs as important natural pest control agents has been highlighted earlier. But the effectiveness of frogs in regulating the pest load in intensive agricultural landscape in a multi-trophic system is not clear. We performed controlled field experiment in paddy field with a varying density (observed in high and low agricultural intensity (AI) areas) of a commonly found frog species and compared the pest and pest predator build-up. The consumption rate of the model amphibian was studied using enclosure experiment. The consequent trophic cascade effect of frogs on both crop pest and other arthropod pest predator was analyzed using mathematical population growth models. Although frogs consumed pests, they could not reduce crop pest abundance. although a lesser frog density found in high AI areas significantly affected the pest predator abundance. Based on the functional response result, mathematical growth models demonstrated that with a constant harvesting factor (Hollings Type II) frogs will always have a negative impact on the beneficial natural enemy population due to intraguild predation thereby limiting its potential as a pest regulator. Our study challenges the notion of frogs as an effective pest control agent and argues that increasing habitat diversity might improve overall biological pest suppression.

ecology↗

bioRxiv2020

RNA binding of Hfq monomers promotes RelA-mediated hexamerization in a limiting Hfq environment

The RNA chaperone Hfq acting as a hexamer, is a known mediator of post-transcriptional regulation expediting basepairing between small RNAs (sRNAs) and their target mRNAs. However, the intricate details associated with Hfq-RNA biogenesis are still unclear. Previously, we reported that the stringent response regulator, RelA is a functional partner of Hfq that facilitates Hfq-mediated sRNA-mRNA regulation in vivo and induces Hfq hexamerization in vitro. Here, for the first time we show that RelA-mediated Hfq hexamerization requires an initial binding of RNA, preferably sRNA to Hfq monomers. By interacting with a Shine-Dalgarno-like sequence (GGAG) in the sRNA, RelA stabilizes the initially unstable complex of RNA bound-Hfq monomer, enabling the attachment of more Hfq subunits to form a functional hexamer. Overall, our study showing that RNA binding to Hfq monomers is at the heart of RelA-mediated Hfq hexamerization, challenges the previous concept that only Hfq hexamers can bind RNA.

microbiology↗

bioRxiv2020

Structural and molecular dynamics of Mycobacterium tuberculosis malic enzyme, a potential anti-TB drug target

Tuberculosis (TB) is the most lethal bacterial infectious disease worldwide. It is notoriously difficult to treat, requiring a cocktail of antibiotics administered over many months. The dense, waxy outer membrane of the TB-causing agent, Mycobacterium tuberculosis (Mtb), acts as a formidable barrier against uptake of antibiotics. Subsequently, enzymes involved in maintaining the integrity of the Mtb cell wall are promising drug targets. Recently, we demonstrated that Mtb lacking malic enzyme (MEZ) has altered cell wall lipid composition and attenuated uptake by macrophages. These results suggest that MEZ provides the required reducing power for lipid biosynthesis. Here, we present the X-ray crystal structure of MEZ to 3.6 [A] resolution and compare it with known structures of prokaryotic and eukaryotic malic enzymes. We use biochemical assays to determine its oligomeric state and to evaluate the effects of pH and allosteric regulators on its kinetics and thermal stability. To assess the interactions between MEZ and its substrate malate and cofactors, Mn2+ and NAD(P)+, we ran a series of molecular dynamics (MD) simulations. First, the MD analysis corroborates our empirical observations that MEZ is unusually disordered, which persists even with the addition of substrate and cofactors. Second, the MD simulations reveal that MEZ subunits alternate between open and closed states and that MEZ can stably bind its NAD(P)+ cofactor in multiple conformations, including an inactive, compact NAD+ form. Together the structure of MEZ and insights from its dynamics can be harnessed to inform the design of MEZ inhibitors that target Mtb.

biochemistry↗

bioRxiv2020

Molecular conservation and Differential mutation on ORF3a gene in Indian SARS-CoV2 genomes

A global emergency due to the COVID-19 pandemic demands various studies related to genes and genomes of the SARS-CoV2. Among other important proteins, the role of accessory proteins are of immense importance in replication, regulation of infections of the coronavirus in the hosts. The largest accessory proteins in the SARS-CoV2 genome is ORF3a which modulates the host response to the virus infection and consequently it plays an important role in pathogenesis. In this study, an attempt is made to decipher the conservation of nucleotides, dimers, codons and amino acids in the ORF3a genes across thirty two genomes of Indian patients. ORF3a gene possesses single and double point mutations in Indian SARS-CoV2 genomes suggesting the change of SARS-CoV2s virulence property in Indian patients. We find that the parental origin of the ORF3a gene over the genomes of SARS-CoV2 and Pangolin-CoV is same from the phylogenetic analysis based on conservations of nucleotides and so on. This study highlights the accumulation of mutation on ORF3a in Indian SARS-CoV2 genomes which may provide the designing therapeutic approach against SARS-CoV2.

genomics↗

bioRxiv2019

An assessment of land use land cover change in Central Highland of Deccan Peninsula and Semi-Arid tracts of India

Human consumption and management of land, i.e., how people transmit to a landscape as a source of livelihood, shelter, recreation, or industry, are powerful forces shaping patterns and dynamics in human-occupied landscapes. Understanding and managing landscape change, therefore, requires a thorough knowledge of the developmental processes the area is undergoing, causing the change in the land use pattern over time. In this study land use/cover dynamics of the Central Highland of Deccan Peninsula and Semi-Arid zone of Gujarat Rajputana bio-geographic regions of India was assessed using a combination of hybrid classification, markov analysis approach within the time frame of 2000-2013. In this time frame, major changes have been identified in dense forest, open forest, cropland, fallow land and in the barren landforms. The landscape has witnessed a substantial increase in built-up areas from 31317 sq. km. in 2000 to 52338 sq. km in 2013. The scrubland has largely declined from 35713.06 sq. km in 2000 to 23003.88 sq.km in 2013; it might have resulted from the transition of scrubland to the fallow land which was predicted as more than 70% in the first phase and more than 30% in the later phase. The area under dense forest constantly decreased in the studied time (84027 sq. km to 71225.37 sq. km). The Markov analysis estimated a probability of changing of open forest types to fallow land (36% in 2000-2006 and 20% in 2006-2013). As the environmental damage is irreversible due to industrialization, therefore a sound strategy needs to be implemented for sustainable use of natural resources that can go hand in hand.

ecology↗

bioRxiv2019

A mixed nitrogen diet and compartmentalized utilization for Mycobacterium tuberculosis replicating in host cells: results of a systems-based analysis

Nitrogen metabolism of Mycobacterium tuberculosis (Mtb) is crucial for the survival and virulence of this pathogen inside host macrophages but little is known about the nitrogen sources acquired from the host or their route of assimilation. Here we performed a systems-based analysis of nitrogen metabolism in intracellullar Mtb and developed 15N-Flux Spectral Ratio Analysis (FSRA) to probe the metabolic cross-talk between the host cell and Mtb. We demonstrate that intracellular Mtb acquires nitrogen from multiple amino acids in the macrophage including glutamate, glutamine, aspartate, alanine, glycine and valine, with glutamine being the predominant nitrogen donor. Each nitrogen source is uniquely assimilated into specific intracellular pools indicating compartmentalised metabolism. This was not observed for in vitro-grown Mtb indicating that there is a switch in nitrogen metabolism when the pathogen enters the intracellular environment. These results provide clues about the potential metabolic targets for development of innovative anti-tuberculosis therapies.

microbiology↗

bioRxiv2018

The variations of human miRNAs and Ising like base pairing models

miRNAs are small about 22-base pair long, RNA molecules are of extreme biological importance. Like other longer RNA molecules, messages in miRNAs are encoded by the permutations of only four nucleotide bases represented by A, U, C and G. However, just like words in any language, not all combination of these alphabets make a meaningful word. In fact, we find that the distributions of nucleotides bases in human miRNAs show significant deviation from randomness. First, a miRNA sequence containing four bases are mapped into a binary string with three kinds of classifications according to their chemical properties. Then, we propose a simple nearest neighbor model (Ising model) to understand the statistical variations in human miRNAs.

bioinformatics↗

bioRxiv2018

Making honey bees lie: experimental dissociation of flight experience and dance communication.

Honey bees use their dance to communicate flight distance and direction of a food source to their nest mates in the hive. How bees transpose flight information to generate a corresponding walking (dance) behavior is still unknown. We now present a detailed study of the changes in dance duration of individual bees after shifting feeder distance. Our experiments indicated that most bees needed two or more foraging trips to the new position before showing an updated dance duration. In addition, only a few bees significantly changed dance duration immediately, whereas most bees first produced intermediary durations. Double shift experiments showed that under certain conditions bees do not update dance duration but continued to perform dance duration for the previously visited feeder position. We propose that generation of dance information involves two memory contents one for newly acquired and one for previously stored distance information.\n\nOne Sentence SummaryGeneration of dance information is temporally separated from immediate flight experience and involves two different memory contents.

animal behavior and cognition↗

bioRxiv2017

Distribution of Purines and Pyrimidines over miRNAs of Human, Gorilla and Chimpanzee

Meaningful words in English need vowels to break up the sounds that consonants make. The Nature has encoded her messages in RNA molecules using only four alphabets A, U, C and G in which the nine member double-ring bases (adenine (A) and Guanine (G)) are purines, while the six member single-ring bases (cytosine (C) and uracil (U)) are pyrimidines. Four bases A, U, C and G of RNA sequences are divided into three kinds of classifications according to their chemical properties. One of the three classifications, the purine-pyrimidine class is important. In understanding the distribution (organization) of purines and pyrimidines over some of the non-coding regions of RNA, all miRNAs from three species of Family Hominidae (namely human, gorilla and chimpanzee) are considered. The distribution of purines and pyrimidines over miRNA shows deviation from randomness. Based on the quantitative metrics (fractal dimension, Hurst exponent, Hamming distance, distance pattern of purine-pyrimidine, purine-pyrimidine frequency distribution and Shannon entropy) five different clusters have been made. It is identified that there exists only one miRNA in human hsa-miR-6124 which is purely made of purine bases only.\n\nAMS Subject Classification: 92B05 & 92B15

bioinformatics↗

bioRxiv2017

Sugar intake elicits a small-scale search behavior in flies and honey bees that involves capabilities found in large-scale navigation

Social insects, particularly bees and ants, show exceptional large-scale navigational skills to find and carry back food to their nests. Honey bees further evolved a symbolic communication to direct nest mates to attractive food sources. Till now it is unclear how these capabilities evolved. Sixty years ago, Vincent Dethier demonstrated that a small-scale sugar-elicited search behavior identified in flies shows remarkable similarities with honey bee dance behavior. Those findings suggested that both behaviors are based on common mechanisms and are likely evolutionary related. We now present for the first time a detailed comparison of the sugar-elicited search behavior in Drosophila melanogaster and Apis mellifera. In both species, intake of sugar elicits a complex of searching responses. The most obvious response was an increase in turning frequency, but more importantly we found that flies and honey bees returned to the location of the sugar drop. They even returned to the food location when we prevented them from using visual and chemosensory cues indicating that this small scale local search involves path integration mechanisms. Finally, we show that visual landmarks presented in the vicinity of the sugar drop affected the search trajectory and in honey bees the sugar intake induced learning of landmarks. Together, our experiments indicate that the sugar-elicited local search exhibits two major behavioral capabilities of large-scale navigation, path integration and landmark orientation.\n\nSignificance StatementTo search for food social insects evolved sophisticated strategies of spatial orientation and large-scale navigation. We now show that even a small-scale local search behavior in solitary flies and social honey bees involves path integration and landmark learning two major mechanisms of large-scale navigation. We propose that in the future sugar-elicited local search can be used to identify neural circuits involved in navigation, path integration, and landmark learning.

animal behavior and cognition↗