Biology subjects

Akhtar, S.

Publications and source records attributed to Akhtar, S..

6 recordsLinked to original sources

bioRxiv2023

Assessing variation in Citrus limon "Assam lemon": morphological, seed availability pattern, and biochemical diversity across different districts of Assam

The Assam lemon is a highly valued Citrus cultivar known for its unique aroma, flavor, and seedless fruit characteristic. This study aimed to investigate for the first time the morphological, seeding pattern, and biochemical, variations within 133 populations of Assam lemon cultivar growing across 22 districts of Assam, India, and including control population, with the objective to offer comprehensive understanding that could facilitate the improvement of breeding programs and further improvement of this important cultivar. Using the dendrogram-based UPGMA algorithm, morphological and seeding pattern data were analyzed at both district and population levels. The resulting dendrograms revealed two major clusters, where all the populations of Upper Assam districts were in the same cluster with the original stock (control population). However, populations from Tinsukia and Dhemaji districts displayed more close similarities with the control population in comparison to other populations of Upper Assam districts. Another interesting observation was regarding flowering patterns, while some populations displayed both bisexual and unisexual flowers with less concentration of unisexual flowers, others had bisexual and unisexual flowers of almost equal concentration. Unisexual flowers contained only the male reproductive organs with 40 anthers, while bisexual flowers had 36 anthers. Seeding patterns were examined across the districts, and it was found that populations from Tinsukia, Dhemaji, Lakhimpur, Dibrugarh, Jorhat, and the control population exhibited seedless characteristic while populations from other selected districts displayed a combination of seedless and seeded traits. Interestingly, Golaghat district appears as the linking district and showed availability of both seeded and seedless Assam lemon fruit, connecting the regions of Upper, Central, Lower and North Assam and Barak valley. Biochemical analysis showed significant variations across districts, however, the populations from Dhemaji, Tinsukia, Lakhimpur, Dibrugarh, and Jorhat districts displayed similarity with the control population. The study also investigated variability in soil nutrient content revealing substantial variation among the populations studied, potentially influencing observed morphological variations. This comprehensive investigation provides valuable insights into the morphological, seeding pattern, and biochemical diversity within the Assam lemon cultivar. These findings can be instrumental in breeding programs to enhance this Citrus cultivar, particularly in producing high-quality seedless fruits to meet consumer demands.

plant biology↗

bioRxiv2023

Genome and transcriptome mining revealed evolutionary insights and tissue-specific expression patterns of Cytochrome P450 superfamily in Aquilaria sinensis

The Cytochrome P450 (CYPs) enzyme superfamily has evolved and expanded in plants to play a significant role in the biosynthesis of valuable secondary metabolites. In Aquilaria plant, the process of wounding and fungal infection results in the accumulation of distinct aromatic metabolites which contribute to the formation of resinous agarwood. The members of CYPs in plants genomes have diversified to catalyze a wide array of fragrant metabolites. Therefore, this study aimed to identify and provide insights into the evolution and expansion of the CYP superfamily members in Aquilaria sinensis and elucidate their tissue-specific functional role through mapping and expression analyses. In total, 179 AsCYPs were identified and subsequently classified into 8 clans and 42 families which were found to be dispersed in the 8 chromosomes. Duplication analysis highlights slow segmental events as a major force, coupled with negative selection pressure, behind the expansion of the AsCYPs. We observed their participation in the biosynthesis of various secondary metabolites, particularly sesquiterpenoids. Expression analysis showed variation in the expression pattern of the genes in different tissues, revealing that the diversification of the AsCYP superfamily occurred to carry out tissue-specific functional role. Additionally, molecular docking of a sesquiterpene oxidase which is specifically expressed in wounded wood, indicated its potential to generate sesquiterpenoids derivatives in agarwood. This study sheds light on the evolution and expansion of the AsCYPs in the genome of A. sinensis and highlights their crucial role in the biosynthesis of various secondary metabolites found in different parts of the plant. Further functional exploration may pave the way for advancements in the field of Aquilaria-based fragrance development and natural product synthesis.

genomics↗

bioRxiv2023

Genome-wide analysis of Respiratory burst oxidase homolog (Rboh) genes in Aquilaria species and its association with agarwood formation

Respiratory burst oxidase homolog (Rboh), generate reactive oxygen species (ROS) to maintain normal growth and pathogen induced defence responses in plants. In Aquilaria plants, wounding and fungal invasion results in the biosynthesis of secondary metabolites as a defence response which with due course develop into agarwood. During pathogen invasion, Aquilaria tree accumulate ROS species through the action of Rboh enzymes. Although in agarwood formation role of Rboh gene family has been implicated, an comprehensives study on Rboh gene family and information of its role during agarwood formation in missing. In this study, seven Rboh genes were identified from the genomes of two Aquilaria species viz., Aquilaria agallocha and Aquilaria sinensis and phylogenetically classified into five groups. Stress response, hormone regulation, and development related regulatory elements were identified in the promoter regions. The protein sequences comprised of four conserved domains, an EF-hand domain, and a transmembrane region which they probably utilise for MAPK signaling, plant-pathogen interaction and plant hormone signal transduction pathways. Expression analyses revealed that among the seven members, AaRbohA and AaRhobC were involved in generation of ROS species, and also probably play role in agarwood formation. These findings provide valuable information regarding the Rboh members of A. agallocha which can be further used for functional analyses for in-depth understanding of ROS mediated signalling and regulation of agarwood formation. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/539809v1_figu1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@169f501org.highwire.dtl.DTLVardef@1541667org.highwire.dtl.DTLVardef@18ad549org.highwire.dtl.DTLVardef@1b8b7b2_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

Genome-wide investigation of Cytochrome P450 superfamily of Aquilaria agallocha: association with terpenoids and phenylpropanoids biosynthesis

P450 superfamily (CYPs) has been known as contributors to the metabolites diversity and their promiscuous nature has led to the flexibility in substrate specificity and functional diversity. Current study was designed to investigate CYPs in the genome of an agarwood producing plant species named Aquilaria agallocha. Agarwood, the resinous fragrant wood with numerous phytochemicals, produced when an Aquilaria plant respond to wound and microbial infection. These chemicals are of great interest to industries ascribing it a high economic value. However, the pathways for the biosynthesis of these metabolites have not been studied in context of Aquilaria CYPs. We identified 136 A. agallocha CYP proteins from the genome, characterized and classified them into 8 clans and 38 families. Functional analysis unveiled their participation in terpenoids, phenolics, flavonoids and other valuable metabolites biosynthesis. Conserved motifs were detected and evolutionary analysis revealed duplicated and orthologous pairs. Potential members for the biosynthesis of sesquiterpenoids and phenylpropanoids reported in Aquilaria and agarwood were elucidated and validated through expression profiles in stress induced callus tissues and infected Aquilaria tress. This study provides a strong foundation for biochemical characterization of Aquilaria CYPs which will aid heterologous production of valuable phytochemicals and untangle molecular mechanism of agarwood formation.

plant biology↗

bioRxiv2018

A Critical Appraisal of Predatory Journals in Pathology

Predatory or pseudo journals have recently come into focus due to their massive internet expansion and extensive spam email soliciting. Recent studies explored this urging problem in several biomedical disciplines. In the present study, we identified 69 potential predatory (pseudo) pathology journals that were contrasted to 89 legitimate pathology journals obtained from the major bibliographic databases. All potential predatory journals in pathology shared at least one of the features proposed by previous studies (e.g. a poor web-site integrity, submissions via email, unclear or ambiguous peer-review process, missing names of the editorial board members, missing or pending the journal ISSN). Twenty-one (30%) of the potential predatory pathology journals had misleading titles mimicking those of legitimate journals. Only one of the identified journals was listed in the Directory of Open Access journals whereas none (0%) was indexed in PubMed/MEDLINE or Web of Science, listed in the Committee on Publication Ethics nor have they had a legitimate impact factor in the Journal Citation Reports.

scientific communication and education↗

bioRxiv2017

The role of N-terminal modification of MeCP2 in the pathophysiology of Rett syndrome

Methyl CpG-binding protein 2 (MeCP2), the mutated protein in Rett syndrome (RTT), is a crucial chromatin-modifying and gene-regulatory protein that has two main isoforms (MeCP2_E1 and MeCP2_ E2) due to the alternative splicing and switching between translation start codons in exons one and two. Functionally, these two isoforms appear to be virtually identical; however, evidence suggests that only MeCP2_E1 is relevant to RTT, including a single RTT missense mutation in exon 1, p.Ala2Val. Here, we show that N-terminal co- and post- translational modifications differ for MeCP2_E1, MeCP2_E1-p.Ala2Val and MeCP2_E2, which result in different protein degradation rates in vitro. We report partial N-methionine excision (NME) for MeCP2_E2, whereas NME for MeCP2_E1 is complete. Surprisingly, we also observed evidence of excision of multiple alanine residues from the N-terminal polyalanine stretch. Regarding MeCP2_E1-Ala2Val, we also observed only partial NME and N-acetylation (NA) of either methionine or valine. The localization of MeCP2_E1 and co-localization with chromatin appear to be unaffected by the p.Ala2Val mutation. However, a higher proteasomal degradation rate was observed for MeCP2_E1-Ala2Val compared with that for wild type (WT) MeCP2_E1. Thus, the etiopathology of p.Ala2Val is likely due to a reduced bio-availability of MeCP2 because of the faster degradation rate of the unmodified defective protein. MeCP2_E1 is thought to have a much higher translational efficiency than MeCP2_E2. Our data suggest that this increased efficiency may be balanced by a higher degradation rate. The higher turnover rate of the MeCP2_E1 protein suggests that it may play a more dynamic role in cells than MeCP2_E2.\n\nSignificance statementThe Rett syndrome protein, MeCP2, undergoes a number of modifications before becoming functionally active in the bodys cells. Here, we report the presence of N-terminal modifications in both MeCP2 isoforms, MeCP2_E1 and MeCP2_E2, and that the only reported Rett missense mutation in exon 1, p.Ala2Val, disrupts these modifications, decreasing the longevity of the protein. Interestingly, p.Ala2Val mutations have been reported in many other disease genes, such as DKCX, ECHS1, IRF6, SMN1, and TNNI3, and the etiopathological mechanism(s) have never been explained. Thus, this work is important not only for the understanding of the pathophysiology of Rett syndrome but also for a deeper understanding of the effects of genetic mutations at the N-terminal end of genes in general.

genetics↗