Journal of Genetic Engineering and Biotechnology最新文献

Background

The Arabidopsis “Redox Responsive Transcription Factor1” (RRTF1) promoter is transiently activated by salt stress in roots over 6 h period, followed by an adaptation phase during which its activity returns to baseline levels, even if the salt stress is prolonged. This enables the short-term production of genes that, while initially advantageous to the plant, will have long-term detrimental effects if expressed at high levels indefinitely.

Results

In this paper, we demonstrate that the RRTF1 promoter salt adaption response is a dominant feature of the promoter, that cannot be overwritten by a strong enhancer. While maintaining the transient activation profile of the RRTF1 promoter, linking it to the 35S enhancer results in a significant boost of salt stress induction in roots.

Conclusion

The RRTF1 promoter’s enhanced and still adaptable activity could become a useful tool in plant biotechnology.

Background

The common mudskipper (Periophthalmus kalolo Lesson, 1831) belongs to a group of fish species that exhibit amphibious lifestyles during specific daily periods. However, identifying this species poses a challenge due to its morphological similarities with other mudskipper species. These similarities have occasionally caused misidentifications of mudskippers. In Indonesia, previous studies have examined the genetic variation of common mudskippers, but these investigations have been limited to a few specific areas, particularly along the southern coast of Java. As a result, the available data remain fragmented, and no comprehensive genetic population analysis of common mudskippers on the southern coast of Java has been conducted. Therefore, our study aimed to establish DNA barcodes of COI mtDNA and explore the genetic variation and relationship among these common mudskipper populations from the southern coast of Java. We collected nine specimens from two populations, Cilacap Mangrove Forest and Kondang Bandung Beach, and supplemented our dataset with 38 previously collected COI sequences of common mudskippers from three different populations from the southern coast of Java (Pasir Mendit Beach, Bogowonto Lagoon, and Baros Beach).

Results

The study revealed that 47 common mudskippers from five different populations are separated into three genetically distinct clades (A, B, and C). These clades display genetic divergences ranging from 0.97% to 1.91%. Each clade exhibits high levels of haplotype diversity but relatively low nucleotide diversity, suggesting a previous bottleneck in population followed by a fast expansion. However, the phylogeny, haplotype network, and principal coordinate analysis indicate overlapping populations with no geographic separation within these clades. This suggests the potential occurrence of gene flow among these populations, which might have been facilitated by past geological events.

Conclusions

These results enhance our understanding of common mudskipper biodiversity in Indonesia. Further studies involving common mudskipper populations from various geographical sites in Indonesia are required to further enrich our understanding of the variation and evolution of this species.

Background

Genome association studies have shown that gene-gene interactions or epistasis play a crucial role in identifying the etiology, prognosis, and treatment response of many complex diseases beyond their main effects. Skeletal dysplasias are a heterogeneous group of congenital bone and cartilage disorders with a genetic and gen-gen interaction etiology. The current classification of skeletal dysplasias distinguishes 461 diseases in 42 groups, and the incidence of all skeletal dysplasias is more than 1 in every 5000 newborns. The objective is to present the case of a patient with four variants that generates gen-gen interactions in the skeletal dysplasia.

Case presentation

A 1-year-old male patient was diagnosed with skeletal dysplasia based on prenatal ultrasound showing micromelia and pyelocalyceal dilation. Postnatal physical examination revealed body disproportion and involvement of other organs and systems.

Materials and Methods

A sequencing study and deletions/duplications analysis were performed for 358 candidate genes associated with skeletal dysplasia.

The GeneMANIA interface was used to evaluate the expression network of genes associated with each other for the gen-gen interaction.

Results

Four pathogenic variants were obtained two heterozygous variants with pathogenic significance in SLC26A, one heterozygous pathogenic variant in CLCN7 and another heterozygous pathogenic variant in CEP120.

The GeneMANIA interface reveals 77.64% physical interactions, 8.01% co-expression, 5.37% prediction, 3.63% co-localization, 2.87% genetic interactions, 1.88% route of action, and 0.60% shared protein domains.

Discussion and Conclusions

These results suggest that the interaction between these genes affects the activity of the inorganic anion exchanger, leading to disorganization of collagen fibers, early mineralization, and decreased assembly of fibronectin in the bone extracellular matrix. Identifying gene-gene interactions is a fundamental step in understanding proper cell function and thus understanding the pathophysiology of many complex human diseases, improving diagnosis, and the possibilities of new personalized therapies.

Background

Frequent drought events due to climate change have become a major threat to maize (Zea mays L.) production and food security in Africa. Genetic engineering is one of the ways of improving drought tolerance through gene introgression to reduce the impact of drought stress in maize production. This study aimed to evaluate the efficacy of Event MON 87460 (CspB; DroughtGard®) gene in more than 120 conventional drought-tolerant maize hybrids in Kenya, South Africa, and Uganda for 3–6 years under managed drought-stress and optimal conditions and establish any additional yield contribution or yield penalties of the gene in traited hybrids relative to their non-traited isohybrids. Germplasm used in the study were either MON 87460 traited un-adapted (2008–2010), adapted traited DroughtTEGO® (2011–2013) or a mix of both under confined field trials.

Results

Results showed significant yield differences (p < 0.001) among MON 87460 traited and non-traited hybrids across well-watered and managed drought-stress treatments. The gene had positive and significant effect on yield by 36–62% in three hybrids (CML312/CML445; WMA8101/CML445; and CML312/S0125Z) relative to non-traited hybrids under drought, and without significant yield penalty under optimum-moisture conditions in Lutzville, South Africa. Five traited hybrids (WMA2003/WMB4401; CML442/WMB4401; CML489/WMB4401; CML511/CML445; and CML395/WMB4401) had 7–13% significantly higher yield than the non-traited isohybrids out of 34 adapted DroughtTEGO® hybrids with same background genetics in the three countries for ≥ 3 years. The positive effect of MON 87460 was mostly observed under high drought-stress relative to low, moderate, or severe stress levels.

Conclusion

This study showed that MON 87460 transgenic drought tolerant maize hybrids could effectively tolerate drought and shield farmers against severe yield loss due to drought stress. The study signified that development and adoption of transgenic drought tolerant maize hybrids can cushion against farm yield losses due to drought stress as part of an integrated approach in adaptation to climate change effects.

Background

Kidney renal clear cell carcinoma (KIRC), with low survival rate, is the most frequent subtype of renal cell carcinoma. Recently, more and more studies indicate that cuproptosis-related genes (CRGs) and long non-coding RNAs (lncRNAs) play a vital role in the occurrence and development of many types of cancers. However, the roles of cuproptosis-related lncRNAs (CRlncRNAs) in the KIRC was uncertain.

Results

In our study, CRlncRNAs were obtained by coexpression between differentially expressed and prognostic CRGs and differentially expressed and prognostic lncRNAs, and an 8-CRlncRNAs (AC007743.1, AC022915.1, AP005136.4, APCDD1L-DT, HAGLR, LINC02027, MANCR and SMARCA5-AS1) risk model was established according to least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression. This risk model could differentiate immune cell infiltration, immune function and gene mutation.

Conclusions

This 8-CRlncRNAs risk model may be promising for the clinical prediction of prognoses, tumor immune, immunotherapy response and chemotherapeutic response in KIRC patients.

Background

Spondyloepimetaphyseal dysplasias (SEMD) are a large group of skeletal disorders represented by abnormalities of vertebrae in addition to epiphyseal and metaphyseal areas of bones. Several genes have been identified underlying different forms. ACAN gene mutations were found to cause Aggrecan-related bone disorders (spondyloepimetaphyseal dysplasias,spondyloepiphyseal dysplasias, familial osteochondritis dissecans and short stature syndromes). This study aims to find the disease causing variant in Egyptian patient with SEMD using whole exome sequencing.

Methods

Whole-exome sequencing was performed for an Egyptian male patient who presented with short stature, clinical and radiological features suggestive of unclassified SEMD.

Results

The study identified a novel de novo heterozygous ACAN gene variant (c.7378G>A; p.Gly2460Arg) in G3 domain. Mutations in ACAN gene have been more commonly associated with short stature than SEMD. The phenotype of our patient was intermediate in severity between spondyloepiphyseal dysplasia presentation; Kimberley type(SEDK) and Spondyloepimetaphyseal dysplasias Aggrecan (SEMDAG)

Conclusions

Whole exome sequencing revealed a novel de novo ACAN gene variant in patient with SEDK. The clinical and skeletal phenotype of our patient was much severe than those reported originally and showed more metaphyseal involvement. To the best of our knowledge, two previous studies reported a heterozygous variant in ACAN with spondyloepiphyseal dysplasia presentation; Kimberley type.

Background

As the world settles down from the COVID-19 pandemic, many countries are faced with an unexpected outbreak of monkeypox infection. Monkeypox is a zoonotic disease caused by monkeypox virus (MPXV), which is an enveloped, double stranded DNA virus belonging to the Poxviridae family. Presently, we construct and analyze the phylo-geo-network and the corresponding haplogroups. Presently, we performed the haplogroup analysis with their defining mutations and phylogenetic lineage study along with geographical distributions with the aim to understand the evolutionary path of the MPXV across the world.

Results

Information about 719 full length genomes of MPXV were collected from GISAID repository and the sequences extracted from NCBI. The alignment of 719 MPXV genomes and their subsequent analysis revealed a total of 1530 segregating sites of which 330 were parsimony informative (PI) sites. The variations had a positive value of Tajima’s D statistic indicating some mutations being prevalent and hence balancing selection. A total of 39 haplogroups were observed in the phylo-geo-network and their defining mutations along with the evolutionary path has been discussed. The phylo-geo-network revealed the nodal haplogroup is represented by GISAID ID 13889450, haplogroup A1, an isolate from Germany, having a total of 296 identical sequences in the study incident across 22 countries. The localized evolution is highlighted by country specific sequences and haplogroups. USA had a total of 58 genomes and 13 haplogroups as compared to Peru (89 genomes, 7 haplogroups) and Germany (26 genomes, 6 haplogroups).

Conclusions

The evolution of MPXV can be happening in a localized manner and hence accumulation of variations in the MPXV genomes needs to be monitored in order to be prepared for any possible threats.

Background

The hepatocellular carcinoma (HCC) incident rate is gradually increasing yearly despite all the research and efforts taken by scientific communities and governing bodies. Approximately $90\%$ of all liver cancer cases belong to HCC. Usually, HCC patients approach the treatment in the late stages of this malignancy which becomes the primary cause of high mortality rate. The knowledge about molecular pathogenesis of HCC is limited and needs more attention from researchers to identify the driver genes and miRNAs, which causes to translate this information into clinical practice. Therefore, the key regulators identification of miRNA-mRNA regulatory network is essential to identify HCC-associated genes.

Methodology

We extracted microRNA (miRNA) and messenger RNA (mRNA) expression datasets of normal and tumor HCC patient samples from UCSC Xena followed by identifying differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs). Univariate and multivariate cox-proportional hazard models were utilized to identify DEMs having significant association with overall survival (OS). Kaplan-Meier (KM) plotter was used to validate the presence of prognostic DEMs. A risk-score model was used to evaluate the effectiveness of KM-plotter validated DEMs combination on risk of samples. Target DEGs of prognostic miRNAs were identified via sources such as miRTargetLink and miRWalk followed by their validation in an external microarray cohort and enrichment analysis.

Results

562 DEGs and 388 DEMs were identified followed by seven prognostic miRNAs (i.e., miR-19a, miR-19b, miR-30d-5p, miR-424-5p, miR-3677-5p, miR-3913-5p, miR-7705) post univariate, multivariate, risk-score model evaluation and KM-plotter analyses. ANLN, MRO, CPEB3 were their targets and were also validated in GSE84005 dataset.

Conclusions

The findings of this study decipher that most significant miRNAs and their identified target genes have association with apoptosis, inflammation, cell cycle regulation and cancer-related pathways, which appear to contribute to HCC pathogenesis and therefore, the discovery of new targets.

Background

Bacterial community found in biodynamic preparations (BD500–BD507) can help improve soil health, plant development, yield, and quality. The current work describes a metagenomic investigation of these preparations to identify the bacterial communities along with the functional diversity present within them.

Results

Metagenome sequencing was performed using the Illumina MiSeq platform, which employs next-generation sequencing (NGS) technology, to provide an understanding of the bacterial communities and their functional diversity in BD preparations. NGS data of BD preparations revealed that maximum operational taxonomic units (OTUs) of the phylum Proteobacteria were present in BD506 (23429) followed by BD505 (22712) and BD501 (21591), respectively. Moreover, unclassified phylum (16657) and genus (16657) were also highest in BD506. Maximum alpha diversity was reported in BD501 (1095 OTU) and minimum in BD507 (257 OTU). Further, the OTUs for five major metabolic functional groups viz carbohydrate metabolism, xenobiotic degradation, membrane transport functions, energy metabolism, and enzyme activities were abundant in BD506 and BD501.

Conclusion

The bacterial communities in BD506 and BD501 are found to be unique and rare; they belong to functional categories that are involved in enzyme activity, membrane transport, xenobiotic degradation, and carbohydrate metabolism. These preparations might therefore be thought to be more effective. The investigation also found a highly varied population of bacteria, which could explain why BD preparations work well in the field. In view of this, the BD preparations may be utilized for unexploited bacterial communities for sustainable agriculture production.

Background

Xanthomonas oryzae pv. oryzae is a plant pathogen responsible for causing one of the most severe bacterial diseases in rice, known as bacterial leaf blight that poses a major threat to global rice production. Even though several experimental compounds and chemical agents have been tested against X. oryzae pv. oryzae, still no approved drug is available. In this study, a subtractive genomic approach was used to identify potential therapeutic targets and repurposible drug candidates that could control of bacterial leaf blight in rice plants.

Results

The entire proteome of the pathogen underwent an extensive filtering process which involved removal of the paralogous proteins, rice homologs, non-essential proteins. Out of the 4382 proteins present in Xoo proteome, five hub proteins such as dnaA, dnaN, recJ, ruvA, and recR were identified for the druggability analysis. This analysis led to the identification of dnaN-encoded Beta sliding clamp protein as a potential therapeutic target and one experimental drug named [(5R)-5-(2,3-dibromo-5-ethoxy-4hydroxybenzyl)-4-oxo-2-thioxo-1,3-thiazolidin-3-yl]acetic acid that can be repurposed against it. Molecular docking and 100 ns long molecular dynamics simulation suggested that the drug can form stable complexes with the target protein over time.

Conclusion

Findings from our study indicated that the proposed drug showed potential effectiveness against bacterial leaf blight in rice caused by X. oryzae pv. oryzae. It is essential to keep in consideration that the procedure for developing novel drugs can be challenging and complicated. Even the most promising results from in silico studies should be validated through further in vitro and in vivo investigation before approval.