Biology subjects

Patel, Z.

Publications and source records attributed to Patel, Z..

4 recordsLinked to original sources

bioRxiv2024

Deciduous forests hold conservation value for birds within South Andaman Island, India

Greater diversity of habitats on islands is often correlated with higher species richness (including endemic and threatened taxa), implying the need to understand species-habitat associations. Such habitat associations would also point towards the role of abiotic filtering and competition in structuring species communities, necessitating the examination of the role of species traits and phylogenetic relationships in intra-island community organisation, an aspect poorly examined in literature. We investigated the composition and structuring of forest bird communities in closely co-occurring evergreen and deciduous forests within South Andaman Island (Indian Ocean), wherein the importance of deciduous forests for birds is undervalued. We sampled 27 transects over two years and compared bird species composition and diversity across the two habitats. We examined species-specific associations with habitat (forest) type, basal area, and distance from human settlements, and tested if these responses were explained by species functional traits and tested for phylogenetic niche conservatism after factoring the effects of environmental predictors. Bird species compositions were markedly distinct across the two habitat types, with deciduous forests having greater taxonomic, but not functional or phylogenetic, diversity of forest birds. The distribution of forest birds, including several endemic and threatened species within the island was largely explained by habitat type (with 39% of the bird species analysed showing higher occurrence probabilities in deciduous forests), followed by distance from human settlements and basal area. We did not find evidence of species traits or phylogenetic relationships mediating these habitat preferences, perhaps due to a relatively impoverished species pool, as is typical on islands. Nevertheless, our results underscore the value of deciduous forests in harbouring high islandic species diversity, and being the preferred habitat of several endemic and threatened bird species. Given the historic focus on evergreen forests and the increasing anthropogenic pressure on the forests of the Andamans, we highlight the critical need to include the rapidly diminishing deciduous forests in existing conservation plans.

ecology↗

bioRxiv2024

The Molecular Determinants of a Universal Prion Acceptor

In prion diseases, the species barrier limits the transmission of prions from one species to another. However, cross-species prion transmission is remarkably efficient in bank voles, and this phenomenon can be recapitulated in mice by expression of the bank vole prion protein (BVPrP). The molecular determinants of BVPrPs ability to function as a universal or near-universal acceptor for prions remain incompletely defined. Building on our finding that cultured cells expressing BVPrP can replicate both mouse and hamster prion strains, we conducted a systematic analysis to identify key residues in BVPrP that permit cross-species prion replication. Consistent with previous findings, we demonstrate that residues N155 and N170 of BVPrP, which are absent in mouse PrP but present in hamster PrP, are critical for cross-species prion replication. Additionally, BVPrP residues V112, I139, and M205, which are absent in hamster PrP but present in mouse PrP, are also required to enable replication of both mouse and hamster prions. Unexpectedly, we found that residues E227 and S230 near the C-terminus of BVPrP severely restrict the accumulation of prions following cross-species prion challenge, suggesting that they may have evolved to counteract the inherent propensity of BVPrP to misfold. PrP variants with an enhanced ability to replicate both mouse and hamster prions displayed accelerated spontaneous aggregation kinetics in vitro. These findings suggest that BVPrPs unusual properties are governed by a key set of amino acids and that the enhanced misfolding propensity of BVPrP may enable cross-species prion replication.

neuroscience↗

bioRxiv2023

Mycobacterium tuberculosis employs atypical and different classes of B12 switches to control separate operons

Vitamin B12 (B12), an essential cofactor in all domains of life, is produced de novo by only a small subset of prokaryotes, but B12-sensing riboswitches are some of the most widely distributed riboswitches in bacteria. Mycobacterium tuberculosis, the causative agent of the ongoing tuberculosis pandemic, encodes two distinct vitamin B12 riboswitches. One controls the expression of metE, encoding a B12-independent methionine synthase, while the other is located upstream of ppe2, a PE/PPE family gene whose function is still unresolved. Here, we analyse ligand sensing, secondary structure architecture, and gene expression control mechanisms of these two riboswitches. Our results provide the first evidence of direct ligand binding by metE and ppe2 riboswitches and show that the two switches exhibit different preferences for natural isoforms of B12, use distinct regulatory and structural elements, and act as translational OFF switches. Based on our results, we propose that the ppe2 switch represents a new Class IIc of B12-sensing riboswitches. Moreover, we have identified small translated open reading frames (uORFs) upstream of both metE and ppe2, which modulate the expression of the respective downstream genes in opposite directions. Translation of the metE riboswitch uORF suppresses MetE expression, while translation of the uORF in the ppe2 switch is essential for PPE2 expression via the synthesis of a uORF-PPE2 fusion protein. In summary, our findings reveal an unexpected diversity and complexity of B12-dependent cis-regulation in M. tuberculosis, with potential implications for host-pathogen interactions.

molecular biology↗

bioRxiv2022

Term-seq reveals an abundance of conditional, Rho-dependent termination in Mycobacterium tuberculosis.

Little is known about the decisions behind transcription elongation versus termination in the human pathogen Mycobacterium tuberculosis. By applying Term-seq to M. tuberculosis we found that the majority of transcription termination is premature and associated with translated regions, i.e. within previously annotated or newly identified open reading frames. Computational predictions and Term-seq analysis upon depletion of termination factor Rho suggests that Rho-dependent transcription termination dominates all TTS including those associated with regulatory 5 leaders. Moreover, our results suggest that tightly coupled translation, in the form of overlapping stop and start codons, may suppress Rho-dependent termination. This study provides detailed insights into novel M. tuberculosis cis-regulatory elements, where Rho-dependent, conditional termination of transcription and translational coupling together play major roles in gene expression control. Our findings contribute to a deeper understanding of the fundamental regulatory mechanisms that enable M. tuberculosis adaptation to the host environment offering novel potential points of intervention.

microbiology↗