Biology subjects

Gazara, R. K.

Publications and source records attributed to Gazara, R. K..

7 recordsLinked to original sources

bioRxiv2022

Gut Microbiome Prediction: From Current Human Evidence to Future Possibilities

The gut microbiome is an indispensable component of the human body. Alteration in the gut microbiota composition leads to various diseases such as obesity, Type 2 Diabetes, Inflammatory Bowel Syndrome, and depression. Microbiome-based precision tests offer a futuristic strategy for wellness and longevity. However, this approach is limited by the lack of definition of a healthy microbiome in different populations and accurate disease prediction. In this study, we aimed to capture the healthy gut microbiome for different populations using the xNARA Gut Profile Test kit and in-house built proprietary algorithm and reference databases. We found that gut microbiome of different populations from India, UAE, and Singapore varied significantly, indicating a distinct geographic gut microbiome signature and Gut Health Index. The gut microbial diversity as measured by the Shannon index revealed UAE had significantly greater alpha diversity than India and Singapore. Prevotella copri (19.27%), Faecalibacterium prausnitzii (4.08%) and Levilactobacillus brevis (4.0%) were the predominant species in the Indian gut. Faecalibacterium prausnitzii (8.54%), Blautia obeum (8.10%), and Phocaeicola vulgatus (4.6%) were primarily present in Singapore participants whereas Prevotella copri (14.92%), Blautia obeum (6.09%) and Roseburia intestinalis (5.81%) were present in UAE participants. Beta diversity indicated the gut microbiota of Indian-origin participants in Singapore and UAE clustered with the indigenous inhabitants of Singapore and UAE. This highlights that geographic location has a profound effect on shaping the gut microbiome architecture than ethnicity. Regional diet and lifestyle could be crucial factors responsible for shaping the gut microbiome. The prediction accuracy of the xNARA Gut algorithm ranged from 66.66-100% when matched with the blood reports. Participants agreed with the xNARA disease risk outcomes for metabolic conditions (60%-100%), gastrofitness (62.5%-100%), mental health (50%-100%), skin conditions (50%-100%) and physical fitness (50%-100%). These observations imply the promising role of gut-based personalized diet and probiotic recommendations for lifestyle and wellness management.

microbiology↗

bioRxiv2022

Stepwise origin and evolution of a transcriptional activator and repressor system integrating nutrient signaling in plants

Plants possess a unique transcriptional regulatory system in which two related MYB-related transcription factors (TFs) coordinate gene expression according to phosphate (Pi) and nitrogen (N) availability. The Phosphorus Starvation Response (PSR) type TFs are transcriptional activators integrating the cellular Pi sensing machinery and gene regulation majorly under Pi starvation. The Hypersensitivity To Low Pi-Elicited Primary Root Shortening (HRS) type TFs are transcriptional repressors integrating the Pi and N availability signals through different feedback loops. They are highly connected through multiple signaling loops to finetune the transcriptional responses according to nutrient availability. Molecular functions of these TFs are fairly uncovered in model systems; however, how plants evolved this activator-repressor system is currently unknown. In this study, using sensitive evolutionary analysis, we identified a stepwise origin of the PSR-HRS regulatory system in plants. The PSR TFs were originated before the split of Prasinodermophyta and Chlorophyta. The HRS TFs were originated later in the Streptrophycean algae. We also identified the asymmetric expansion of this TF repertoire in land plants majorly shaped by genome duplication and triplication events. The phylogenetic reconstruction coupled with motif analysis revealed that the origin of the specific accessory motifs is a major contributing factor in the functional divergence which led to the evolution of different sub-families preceding the angiosperm radiation. The spatiotemporal gene expression analysis in different developmental stages and nutrient availability conditions in angiosperms identified a critical role of expression divergence in shaping the functions of these TF families which is essential for adaptive plasticity of plants.

plant biology↗

bioRxiv2021

Characterization of cellular, biochemical and genomic features of the diazotrophic plant growth-promoting bacterium Azospirillum sp. UENF-412522, a novel member of the Azospirillum genus

Given their remarkable beneficial effects on plant growth, several Azospirillum isolates currently integrate the formulations of various commercial inoculants. Our research group isolated a new strain, Azospirillum sp. UENF-412522, from passion fruit rhizoplane. This isolate uses carbon sources that are partially distinct from closely-related Azospirillum isolates. Scanning electron microscopy analysis and population counts demonstrate the ability of Azospirillum sp. UENF-412522 to colonize the surface of passion fruit roots. In vitro assays demonstrate the ability of Azospirillum sp. UENF-412522 to fix atmospheric nitrogen, to solubilize phosphate and to produce indole-acetic acid. Passion fruit plantlets inoculated with Azospirillum sp. UENF-41255 showed increased shoot and root fresh matter, as well as root dry matter, further highlighting its biotechnological potential for agriculture. We sequenced the genome of Azospirillum sp. UENF-412522 to investigate the genetic basis of its plant-growth promotion properties. We identified the key nif genes for nitrogen fixation, the complete PQQ operon for phosphate solubilization, the acdS gene that alleviates ethylene effects on plant growth, and the napCAB operon, which produces nitrite under anoxic conditions. We also found several genes conferring resistance to common soil antibiotics, which are critical for Azospirillum sp. UENF-412522 survival in the rhizosphere. Finally, we also assessed the Azospirillum pangenome and highlighted key genes involved in plant growth promotion. A phylogenetic reconstruction of the genus was also conducted. Our results support Azospirillum sp. UENF-412522 as a good candidate for bioinoculant formulations focused on plant growth promotion in sustainable systems.

microbiology↗

bioRxiv2019

Systematic analysis of 1,298 RNA-Seq samples and construction of a comprehensive soybean (Glycine max) expression atlas

Soybean (Glycine max [L.] Merr.) is a major crop in animal feed and human nutrition, mainly for its rich protein and oil contents. The remarkable rise in soybean transcriptome studies over the past five years generated an enormous amount of RNA-seq data, encompassing various tissues, developmental conditions, and genotypes. In this study, we have collected data from 1,298 publicly available soybean transcriptome samples, processed the raw sequencing reads, and mapped them to the soybean reference genome in a systematic fashion. We found that 94% of the annotated genes (52,737/56,044) had detectable expression in at least one sample. Unsupervised clustering revealed three major groups, comprising samples from aerial, underground, and seed/seed-related parts. We found 452 genes with uniform and constant expression levels, supporting their roles as housekeeping genes. On the other hand, 1,349 genes showed heavily biased expression patterns towards particular tissues. A transcript-level analysis revealed that 95% (70,963/74,490) of the known transcripts overlap with those reported here, whereas 3,256 assembled transcripts represent potentially novel splicing isoforms. The dataset compiled here constitute a new resource for the community, which can be downloaded or accessed through a user-friendly web interface at http://venanciogroup.uenf.br/resources/. This comprehensive transcriptome atlas will likely accelerate research on soybean genetics and genomics.

plant biology↗

bioRxiv2018

Transcriptional landscape of soybean (Glycine max) embryonic axes during germination in the presence of paclobutrazol, a gibberellin biosynthesis inhibitor

Gibberellins (GA) are key positive regulators of seed germination. Although the GA effects on seed germination have been studied in a number of species, little is known about the transcriptional reprogramming modulated by GA during this phase in species other than Arabidopsis thaliana. Here we report the transcriptome analysis of soybean embryonic axes during germination in the presence of paclobutrazol (PBZ), a GA biosynthesis inhibitor. We found a number of differentially expressed cell wall metabolism genes, supporting their roles in cell expansion during germination. Several genes involved in the biosynthesis and signaling of other phytohormones were also modulated, indicating an intensive hormonal crosstalk at the embryonic axis. We have also found 26 photosynthesis genes that are up-regulated by PBZ at 24 hours of imbibition (HAI) and down-regulated at 36 HAI, which led us to suggest that this is part of a strategy to implement an autotrophic growth program in the absence of GA-driven mobilization of reserves. Finally, 30 transcription factors (mostly from the MYB, bHLH and bZIP families) that are down-regulated by PBZ and are likely downstream GA targets that will drive transcriptional changes during germination.

plant biology↗

bioRxiv2017

Expansion and diversification of the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1) in land plants

Gibberellic acid (gibberellins, GA) controls key developmental processes in the life-cycle of land plants. By interacting with the GIBBERELLIN INSENSITIVE DWARF1 (GID1) receptor, GA regulates the expression of a wide range of genes through different pathways. Here we report the systematic identification and classification of GID1s in 52 plants genomes, encompassing from bryophytes and lycophytes, to several monocots and eudicots. We investigated the evolutionary relationship of GID1s using a comparative genomics framework and found strong support a previously proposed phylogenetic classification of this family in land plants. We identified lineage-specific expansions of particular subfamilies (i.e. GID1ac and GID1b) in different eudicot lineages (e.g. GID1b in legumes). Further, we found both, shared and divergent structural features between GID1ac and GID1b subgroups in eudicots, which provide mechanistic insights on their functions. Gene expression data from several species show that at least one GID1 gene is expressed in every sampled tissue, with a strong bias of GID1b expression towards underground tissues and dry legume seeds (typically with low GA levels). Taken together, our results support that GID1ac retained canonical GA signaling roles, whereas GID1b specialized in conditions of low GA concentrations. We propose that this functional specialization occurred initially at the gene expression level and was later fine-tuned by specific mutations that conferred greater GA affinity to GID1b, including a Phe residue in the GA-binding pocket. Finally, we discuss the importance of our findings to understand the diversification of GA perception mechanisms in land plants.

plant biology↗

bioRxiv2017

De novo transcriptome sequencing and comparative analysis of midgut tissues of four non-model insects pertaining to Hemiptera, Coleoptera, Diptera and Lepidoptera

Despite the great morphological diversity of insects, there is a regularity in their digestive functions, which is apparently related to their physiology. In the present work we report the de novo midgut transcriptomes of four non-model insects from four distinct orders: Spodoptera frugiperda (Lepidoptera), Musca domestica (Diptera), Tenebrio molitor (Coleoptera) and Dysdercus peruvianus (Hemiptera). We employed a computational strategy to merge assemblies obtained with two different algorithms, which substantially increased the quality of the final transcriptomes. Unigenes were annotated and analyzed using the eggNOG database, which allowed us to assign some level of functional and evolutionary information to 79.7% to 93.1% of the transcriptomes. We found interesting transcriptional patterns, such as: i) the intense use of lysozymes in digestive functions of M. domestica larvae, which are streamlined and adapted to feed on bacteria; ii) the up-regulation of orthologous UDP-glycosyl transferase and cytochrome P450 genes in the whole midguts different species, supporting the presence of an ancient defense frontline to counter xenobiotics; iii) evidence supporting roles for juvenile hormone binding proteins in the midgut physiology, probably as a way to activate genes that help fight anti-nutritional substances (e.g. protease inhibitors). The results presented here shed light on the digestive and structural properties of the digestive systems of these distantly related species. Furthermore, the produced datasets will also be useful for scientists studying these insects.

genomics↗