51 research outputs found
Enhancers in proboscis monkey: a primer
No full textEnhancers are indispensable elements in various developmental stages, orchestrating numerous biological processes via the elevation of gene expression with the aid of transcription factors. Enhancer variations have been linked to various onset of genetic diseases, highlighting their equal importance as the coding regions in the genome. Despite the first enhancer, SV40 been discovered four decades ago, the progress in enhancer identification and characterization is still in its infancy. As more genome sequences are made available, especially from that of the non-human primates, we can finally study the enhancer landscape of these primates that differs evolutionarily from that of human. One interesting genome to investigate is that of the proboscis monkey as it is deemed as one of the most ancient primates alive to date with unique morphological and dietary characteristicsit is also one of the IUCN endangered species with the strong demands for immediate conservation. In this review, we provide some justifications and considerations of selecting the proboscis monkey as a model for enhancer landscape discovery. It is hoped that more conservation research and protective measures can come in time to prevent this species from extinction
Phylogenetic and expression of Atp-Binding cassette transporter genes in Rasbora Sarawakensis
No full textThe ATP-Binding Cassette transporters (ABC transporters) function in various physiological activity, allowing vertebrate to thrive even in polluted environment. The objective of this study is to discover ABC genes in Rasbora sarawakensis, a species endemic to Borneo and to understand the respective genes regulation. In this research, nine gene partial transcripts were isolated via RT-PCR and cloning approaches. Our study showed that most gene transcripts identified share high identities with conserved motif distributions across family. Further phylogenetic analysis revealed a clear divergence into three major functional clades (A2, E1, F1D2B4, B8, C2, G2). Expression profiles in six tissues (i.e., brain, eye, gill, intestine, muscle, and skin) revealed divergence that shed light on tissue-specific gene functional specialization, with highlight on B4, B8, and E1 which are expressed in all six organs. The brain and eye were also found to express all ABC genes selected in this study. In conclusion, nucleotide profiles of these genes are comparable to the phylogenetic analysis and expression patterns across family. This study implies that an alternative vertebrate model organism can possibly complement the current zebrafish researches
A micro review on the role of recently emerged Artificial Intelligence (AI) tools and algorithms in microbiome-gut-brain-axis associated disease therapy via psychobiotics
No full textThe microbiome-gut-brain axis involves the bidirectional connection between the gastrointestinal tract, gut microbiome, and central nervous system, and it is pivotal for mental well-being. Imbalances in the gut microbiome (dysbiosis) can disrupt neurotransmitter synthesis, leading to neurodegenerative diseases. Recent researches highlight psychobiotics as effective treatments for mental health conditions like depression. With advancements in artificial intelligence (AI) and large datasets, psychobiotic research has accelerated. AI tools are increasingly used for the prediction, identification, and diagnosis of gut microbiome compositions, enabling faster and more accurate discovery of therapeutic candidates. This review explores the role of AI in enhancing microbiome-gut-brain-axis-related disease therapies through psychobiotics and discusses future directions for this rapidly evolving research field
Genomic Landscape of Sago Palm (Metroxylon sagu Rottb.)
No full textThe sago palm (Metroxylon sagu Rottboll) is a halophytic tree and the ultimate solution to two major global issues: food security and the rapid loss of saline free agricultural lands. This palm can produce high amount of starch, besides being resistant to saline and almost disease free. Unfortunately, this valuable palm is currently underappreciated by the scientific community and the genomic landscape of this palm remained scarce to date. The
aim of this study is to sequence and characterise the sago palm chloroplast genome, document the organellar genome copy number changes across various developmental stages, organs, localities and phenotypes as well as sequence the entire nuclear genome of sago palm. The sago palm chloroplast and nuclear genome sizes determined in this study are 157,300 bp and 616,599,600 bp respectively, yielded via next generation sequencing technologies. The organellar genome copy number investigation employing the combinatorial approach of both qPCR and long-PCR assays had unearthed that the mature
leaf is generally most enriched with unimpeded plastome and mitogenome among other organs. The Plawei Manit growth stage was discovered to have the highest unimpeded organellar genomes copy numbers (over 180,000) among the five major growth stages. The trunking phenotype was proven to be superior to that of the spiny and non-trunking phenotypes in terms of organellar genomes copy numbers (over 188,000). Interestingly, the organellar genome copy numbers across four main Sarawak localities in Malaysia are indifferent statistically. This study serves as a groundwork for preliminary sago palm genomic landscape to support future haplotype and genome wide association studies
Isolation and cloning of ABCE1 gene in Rasbora sarawakensis
No full textThe ABCE1 gene is one of the members of ABCE/ABCF subfamily in the ATP-binding cassette (ABC) transporter superfamily. The loss-of-function mutation of ABCE1 gene is a proven potential human cancer therapy for prostate, esophageal, oral and lung adenocarcinoma. The current zebrafish ecotoxicological studies may not be applicable domestically. The aim of this research is to isolate and clone ABCE1 gene from Rasbora sarawakensis. To examine this, total RNA was isolated from this fish using TRIzol and reverse transcribed. A pair of degenerative primers (forward primer: 5'-GCCAAYTCCTTCAARCTGCA-3'; reverse primer: j'-ACAGCAGATGAAGTCNGACA-3') were designed for RT-PCR amplification of this gene based on conserved sequences from multiple alignment of six selected freshwater fishes. The size of the gene amplified is around 580 bp in length which is close to its expected size (600 bp). Sequencing result and BLASTn analysis revealed that this gene from R. sarawakensis have high similarity of 94% to that of Danio rerio with E-value of
0.0. pGEM®-T Easy Vector was utilized as biological delivery vehicle for this gene in cloning, and cloning had yielded 30 white and 11 blue colonies with transformation efficiency of 2.02 x 105 transformantslJ.lg. Not! restriction enzyme digestion was done to prove plasmid propagation of the insert DNA. 100% homology was obtained after BLASTp pairwise alignment between ORFs of R. sarawakensis and D. rerio. Phylogenetic analysis revealed great resemblance between this gene from these two fishes in the maximum likelihood tree. The e results may suggest divergent evolutionary relationship between these two fish species which is beneficial to future establishment of this fish as a model in domestic ecotoxicological studies
Identification and Characterization of Liver-Specific Enhancer Elements in Chromosome 18 of the Nasalis larvatus Genome
No full textEnhancers play major roles in the regulation of gene expression at various developmental stages and biological processes temporally and spatially. Albeit the first enhancer was discovered for more than four decades ago, the identification of enhancers is still at its infancy as there is no single universal enhancer mark revealed to date. With the booming emergence of genome sequences of various non-human primates, the study of enhancer landscape across these primates had been made possible recently. Therefore, this study aimed to identify, isolate and characterize enhancers from the genome of one of the most ancient colobine primate, the proboscis monkey (Nasalis larvatus). A total of 13 liver-specific enhancers were identified using three different in silico approaches and they were inserted into expression plasmids before tested further for their activities in HepG2 and A549 cell lines. Two of the strong enhancers and one weak enhancer were subjected to deletion analysis and activity determination subsequently in both cell lines. This study has discovered several clusters of adjacently located transcription factor binding sites that influence enhancer activities and tissue specificities greatly. The results from this research will drive future investigations on the enhancer landscape of the proboscis monkey and comparison of the landscape across different primates.
Keywords: Enhancer, identification, proboscis monkey, in silico, expressio
Linking microbiome to cancer: A mini-review on contemporary advances
No full textThe intricate relationship between the human microbiome and cancer has garnered significant interest in recent years, transforming our understanding of how microbial communities influence health and disease. The microbiome, particularly in the gut, is known to interact with host immune responses, metabolic processes, and inflammation pathways, all of which play roles in cancer development and progression. This mini-review presents current advances linking microbial dysbiosis to cancer, focusing on the mechanisms through which specific microbial populations contribute to oncogenesis, as well as their impact on tumor microenvironments, immune modulation, and treatment responses. Additionally, we explore how microbial profiling and manipulation strategies, such as probiotics, prebiotics, and fecal microbiota transplantation, are emerging as promising adjuncts in cancer prevention and therapy. Understanding the dynamic interactions between microbes and cancer cells may provide innovative perspectives on cancer treatment, opening avenues for microbiome-targeted therapies and personalized medicine
Organellar genome copy number variations and integrity across different organs, growth stages, phenotypes and main localities of sago palm (Metroxylon sagu Rottboll) in Sarawak, Malaysia
No full textThe sago palm (Metroxylon sagu Rottboll) is one valuable food crop that has both high economic and nature value with promising potential to curb future global hunger issues. The organellar genomes, namely mitogenome and plastome, are indispensable in various development processes of plants, orchestrating the survivability and adaptability of the host and fulfilling its physiological needs. The long-PCR and qPCR approaches were used in couple to reveal the organellar genome copy number variations across different organs, growth stages, phenotypes and main localities in Sarawak, Malaysia. In this study, the mature leaf achieved among the highest unimpeded plastome and mitogenome copy number among other organs such as young root, mature root, young shoot, aged leaf and pneumatophore. The Plawei Manit stage scored the highest in terms of unimpeded mitogenome and plastome copy number across other four growth stages. The non-trunking and spiny phenotypes inspected have lower organellar genome copy numbers than the trunking phenotype. All three phenotypes sampled from four different localities in Sarawak, Malaysia showed no significant difference. This study serves as a steppingstone in unravelling the organellar genome copy number variations of sago palm and this knowledge is essential for future genotyping studies
Analysis of Seven Human Respiratory Coronavirus (CoV) S Proteins from a Bioinformatics Approach
No full textThe coronavirus disease 2019 (COVID-19) has caused a huge pandemic repercussion across the globe and it is mainly contributed by the human severe acute respiratory syndrome coronavirus (SARS-CoV-2). There are seven human respiratory coronaviruses identified to date, namely HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1, MERS-CoV, SARS-CoV and SARS-CoV-2. A recently published bioinformatic human CoV comparison only covered four human CoV. Therefore, in this study, a bioinformatics approach-based analyses route was taken to dissect the S proteins of all the available (seven) human respiratory coronaviruses publicly available in the GenBank database. The antigenic epitope amount is postulated to be the most accurate bioindicator among all in determining the severity of a particular human respiratory coronavirus. Other powerful bioinformatic indicators are global similarity index, maximum likelihood phylogenetic analysis as well as domain analysis. The data generated in this study can be channelled to the vaccine and antiviral drug development to combat the current and future spread of the human respiratory coronaviruses
Salt Tolerance Research in Sago Palm (Metroxylon sagu Rottb.): Past, Present and Future Perspective
No full textThe sago palm (Metroxylon sagu Rottb.) is one of the underdogs in the food crop planting industries for its potential which is extremely vast but the community appreciating it is scarce. Its capabilities to thrive well in undesirable environmental conditions, salt tolerance and high starch yield are one of the many advantages it possesses over other food crops like wheat, corn and rice. One important factor to look into for crop plantation is none other than its salt tolerance. The salt tolerance researches on this unique palm have commenced since 1977 and the pace of research was unbelievably slow in progression. Nevertheless, it was not until recently that this palm was being placed in the limelight once more. In this review, we are focusing on salt tolerance research and further detailed on the past, present and future of this research line. It is anticipated that consolidation of talents and resources can come in time and in tandem for the utilization of this cash palm to end world hunger
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