The human angiotensin converting enzyme 2 (ACE2) gene encodes a type I transmembrane protein, which is homologous to angiotensin I-converting enzyme (ACE) and belongs to the angiotensin-converting enzyme family of dipeptidyl carboxypeptidases. As highlighted by the COVID-19 pandemic, ACE2 is not only crucial for the renin-angiotensin-aldosterone system (RAAS), but also displays great affinity with the SARS-CoV-2 spike protein, representing the major receptor of the virus. Given the significance of ACE2 in COVID-19, especially among cancer patients, the present study aims to explore the transcriptional landscape of ACE2 in human cancer and non-cancerous cell lines through the design and implementation of a custom targeted long-read sequencing approach. Bioinformatics analysis of the massive parallel sequencing data led to the identification of novel ACE2 mRNA splice variants (ACE2 sv.7-sv.12) that demonstrate previously uncharacterized exon-skipping events as well as 5' and/or 3' alternative splice sites. Demultiplexing of the sequencing data elucidated the differential expression profile of the identified splice variants in multiple human cell types, whereas in silico analysis suggests that some of the novel splice variants could produce truncated ACE2 isoforms with altered functionalities, potentially influencing their interaction with the SARS-CoV-2 spike protein. In summary, our study sheds light on the complex alternative splicing landscape of the ACE2 gene in cancer cell lines, revealing novel splice variants that could have significant implications for SARS-CoV-2 susceptibility in cancer patients. These findings contribute to the increased understanding of ACE2's role in COVID-19 and highlight the importance of considering alternative splicing as a key factor in viral pathogenesis. Undoubtably, further research is needed to explore the functional roles of these variants and their potential as therapeutic targets in the ongoing fight against COVID-19.

Ex vivo lung perfusion (EVLP) is a critical strategy to rehabilitate marginal donor lungs, thereby increasing lung transplantation (LTx) rates. Ischemia-reperfusion (I/R) injury inevitably occurs during LTx. Exploring the common mechanisms between EVLP and I/R may unveil new treatment targets to enhance LTx outcomes.

Transposable elements (TEs) are prevalent in the genomes of orthopteran insects, contributing significantly to their genome evolution and diversity. In light of the existing gap in our understanding of TEs transcript dynamics in orthopteran insects, we recognize the critical need to undertake comprehensive analyses in this area. Therefore, we have decided to delve into the characterization of TE transcripts, their abundance profiles, and the formation of chimeric transcripts using RNA-seq data and genome assemblies. The transcript analysis of TEs across various species revealed significant differences in TE abundance and expression patterns. In particular, Schistocerca americana exhibited twice the number of transcripts within the genus Schistocerca compared to the average of other species, while Gryllus bimaculatus displayed the lowest number of transcripts. Despite this, all Schistocerca species shared similar fractions of TE transcripts at the clade level, with DNA transposons (45%) being the most abundant, followed by LINE (19%) and LTR elements (18%). Interestingly, Acrida cinerea displayed different TE abundance patterns compared to Schistocerca species, particularly with an increased proportion of LTR transcripts, accounting for 31% of the total transcripts. Further analysis revealed tissue-specific transcriptional activity of TE clades, with notable differences between male and female specimens. In Gryllus bimaculatus, TEs were highly transcribed across ovaries and gut tissues in females compared to male testes and gut. Conversely, Gastrimargus marmoratus displayed higher TE transcription in male tissues compared to females, indicating species-specific expression patterns. A similar pattern has been observed in Acrida cinerea, except in female gonads, where 4618 TEs were transcribed compared to 3757 in male gonads. Despite these variations, no correlation was found between genome size and TE transcript abundance. Additionally, highly conserved TEs were involved in the formation of chimeric transcripts, indicating potential regulatory roles in gene expression. The expression quantification analysis of chimeric TEs and genes revealed tissue-specific expression patterns, and TEs do not control the overall expression of all genes except some, suggesting regulatory roles of TEs in gene expression. Overall, our study underscores tissue-specific variations in TE expression and transcript abundance among different species. Additionally, our findings suggest the involvement of highly conserved TEs in the formation of chimeric transcripts across different species.

Long non-coding RNAs (lncRNAs) are long RNA transcripts with length > 200 nucleotides that do not encode proteins. They play a crucial role in regulating HIV-1 infection, yet their involvement in myeloid cells remains underexplored. Myeloid cells are susceptible to HIV infection and contribute substantially to the latent HIV reservoir. Therefore, disruption of latency within these reservoirs is crucial for achieving a definite cure. In this study, we aimed to ascertain the role of MALAT1 lncRNA in reversal of HIV-1 latency. Latently HIV-infected cell line, U1 was treated with SAHA, followed by qRT-PCR assays to confirm HIV-1 reactivation, and MALAT1 expression was assessed. The in vitro experiments revealed a significant increase in MALAT1 expression following latency reactivation and HIV-1 infection, while its knockdown using siRNA resulted in suppression of HIV transcription, which implies that MALAT1 play a significant role in facilitating the reversal of HIV-1 latency by promoting HIV transcription. Clinical samples were analysed to measure MALAT1 and pro-inflammatory cytokines expression. The elevated MALAT1 expression in treatment-naïve subjects compared to treated subjects and HIV-negative controls suggests its association with HIV replication. Moreover, correlation analysis revealed a positive association between MALAT1 expression and pro-inflammatory cytokines, TNF-α and IP-10. To conclude, MALAT1 lncRNA emerged as a crucial facilitator of HIV-1 latency reversal in latently infected monocytes by inducing the expression of pro-inflammatory factors. These findings highlight that MALAT1 could potentially be explored as the therapeutic intervention to reactivate latent cells in monocytes.

Mesenchymal stem cells (MSCs) have demonstrated promising therapeutic potential in the treatment of type 1 diabetes mellitus (T1DM); however, the underlying mechanism remains unclear. The primary pathological mechanism of T1DM involves activated T cells infiltrating the pancreas, leading to islet inflammation and the destruction of β-cells. However, the question of whether exosomes derived from MSCs can suppress the migration of T cells to the pancreas in the context of T1DM remains unresolved. In this study, we observed that miR-25 was highly expressed in MSCs exosomes and associated with signaling pathways related to cell migration. In vitro assay, we synthesized a miR-25 mimic and transiently transfected it into activated T cells, which revealed that miR-25 can effectively reduce the expression of CXCR3. Additionally, according to the in vivo T1DM mouse model, we found that there was a significant increase in miR-25 levels in T1DM mice treated with MSCs and the number of T cells decreased. Overall, our findings suggest that MSCs exosomes containing miR-25 can impede the infiltration of activated T cells into the pancreas in T1DM by repressing CXCR3 expression in these cells.

CALML6 is an inflammation-related gene, and its expression may be associated with cancer. Here we evaluated the role of CALML6 expression in papillary thyroid carcinoma (PTC).

Transaminases, enzymes known for their amino group transfer capabilities, encompass four distinct subfamilies: D-alanine transaminase (DATA), L-selective Branched chain aminotransferase (BCAT), and 4-amino-4-deoxychorismate lyase (ADCL) and R-selective aminotransferase (RATA). RATA enzymes are particularly valuable in biocatalysis for synthesizing chiral amines and resolving racemic mixtures, yet their identification in sequence databases is challenging due to the lack of robust motif-based screening methods. Constructing a sequence dataset of transaminases, and categorizing them to various subfamilies, the conserved motifs are screened over the experimentally known ones, and the novel motifs are explored. Phylogenetic clustering of these subfamilies and structural localization of the identified motifs on the Alphafold-predicted protein models of the representative sequences validate their functional importance. For the ADCL, BCAT, DATA, and RATA datasets, we identified 5, 7, 10, and 2 novel motifs, with 3, 5, 7, and 2 motifs localized on secondary structures, confirming their structural importance. Furthermore, the analysis revealed 1, 3, 2, and 1 unique residue patterns of 293-KxxxR-297; 336-KxxxxY-341, 379-ExxxxNxF-386, and 453-ExFxxGT-459; 187-HxxRL-191, and 284-DxRWxxCDIK-293; and 191-HxxRL-195, integrating of which in the known computational tools would improve their accuracy. The conserved residue pattern or motif-based computational approach for robustly screening the transaminases holds promise for unveiling the novel RATA enzymes, facilitating their exploitation in biocatalytic applications.

The intima-media thickness (IMT) of the carotid artery, an indicator of subclinical atherosclerosis, varies in close association with various factors such as diabetes and immune response. The extent of changes in IMT varies among individuals owing to both genetic and epigenetic factors. In this study, we aimed to identify single nucleotide polymorphisms (SNPs) and DNA methylation patterns that affect carotid IMT in monozygotic (MZ) twins.

Rheumatoid arthritis (RA) is a systemic autoimmune disease characterized by chronic inflammation and joint destruction, with emerging evidence implicating gut microbiota dysbiosis in its pathogenesis. The current study explores the role of ferroptosis, a form of regulated cell death driven by iron-dependent lipid peroxidation, in modulating gut microbiota and metabolic dysregulation through the enzyme peptidyl arginine deiminase 4 (PAD4) in collagen-induced arthritis (CIA) mouse model. Our findings demonstrate that ferroptosis exacerbates RA-related inflammatory responses and joint damage by upregulating PAD4 expression, which, in turn, influences the gut microbial composition and associated metabolite profiles. Erastin, a known ferroptosis agonist, significantly increased the relative abundance of pro-inflammatory bacteria such as Proteobacteria while reducing beneficial taxa like Firmicutes and Bacteroidetes. This microbial shift was associated with heightened oxidative stress and an imbalance in key metabolites, such as lysophosphatidyl ethanolamine 14:0 (LysoPE 14:0), further exacerbated by ferroptosis. Co-treatment with GSK484, a PAD4 inhibitor, reversed these effects, restoring microbial homeostasis and reducing joint inflammation. This study suggests that ferroptosis-mediated PAD4 activity contributes to RA pathogenesis by disrupting the gut-joint axis, providing novel insights into potential therapeutic targets for RA. Our results highlight the intricate interplay between immune-mediated cell death, gut microbiota, and systemic inflammation, emphasizing the importance of ferroptosis as a therapeutic target in mitigating RA progression.

Increasing morbidity and mortality in CRC is a potential threat to human health. The major challenges for better treatment outcomes are the heterogeneity of CRC cases, complicated molecular pathway cross-talks, the influence of gut dysbiosis in CRC, and the lack of multimodal target-specific drug delivery. The overexpression of many receptors in CRC cells may pave the path for targeting them with multiple ligands. The design of a more target-specific drug-delivery device with multiple ligand-functionalized, green-synthesized silver nanoparticles is highly promising and may also deliver other approved chemotherapeutic agents. This review presents the various aspects of colorectal cancer and over-expressed receptors that can be targeted with appropriate ligands to enhance the specific drug delivery potency of green synthesised silver nanoparticles. This review aims to broaden further research into this multi-ligand functionalised, safer and effective silver nano drug delivery system.

Diploid mammalian genome has paired alleles for each gene; typically allowing for equal expression of the two alleles within the cell/tissue. However, genetic regulatory elements and epigenetic modifications can disrupt this equality, leading to preferential expression of one allele. Examining high-confidence allele-specific expression (ASE) is vital for understanding genetic variations and their impact on major diseases like cancers and diabetes. ASE analysis not only aids in disease prognosis and diagnosis but also helps identify regulatory mechanisms operating within the genome. While advances in sequencing technologies have greatly improved our understanding of ASE, challenges remain in estimating it accurately. In this article, we reviewed methods for detecting ASE using both bulk RNASeq and single-cell RNASeq data to provide deeper insights beyond the mere prediction of ASE genes. Fundamentally, ASE detection methods are data-driven and can be classified according to type of data used. Some methods utilize both, DNA genotyping information and RNASeq while others rely solely on RNASeq data. This article offers a comparative analysis of these methods and compilation of repositories providing valuable insights.

Staphylococcus aureus (S. aureus) is one of the notorious bacteria responsible for community and hospital infections. It can attach to the indwelling medical devices to form biofilms, which increases resistance to antibiotics and causes frequent chronic or persistent infections. This study attempted to determine the contribution and mechanism between the efflux pump norB gene and biofilm development in S. aureus. The expression levels of norB gene were detected by quantitative real-time polymerase chain reaction (qRT-PCR). The norB gene knockout strain USA300 ΔnorB was constructed by homologous recombination technology. Crystal violet staining was utilized to detect the biofilm formation ability. Differentially expressed genes between norB knockout strains and wild-type strains were screened by RNA-Seq technology and verified by qRT-PCR. In comparison to strains with weak biofilm development capacity, higher expression levels of the norB gene were detected in S. aureus strains that showed strong biofilm forming capabilities. The expression levels of norB were significantly up-regulated in biofilm bacteria in comparison to planktonic bacteria. The knockout of norB gene reduced the biofilm formation ability in S. aureus. The deletion of norB gene up-regulated the expression of genes related to biofilm formation including agrD, sdrC, sdrD, agrB, agrC, fnbB, nuc, lytS, lrgA, sdrE, agrA and saeS, and down-regulated the expression of genes related to biofilm formation including clfA, icaR, sarA and rot. In conclusion, the efflux pump norB gene serves as a crucial role in the production of biofilm, thus rendering it a promising avenue for biofilm suppression.

5,10-Methylenetetrahydrofolate reductase (MTHFR, MIM #607093) is a key enzyme in the folate cycle that catalyzes the conversion of 5,10-methylenetetrahydrofolate (5,10-MTHF) to 5-methyltetrahydrofolate (5-methylTHF), a critical step for the remethylation of homocysteine to methionine. Methylenetetrahydrofolate reductase deficiency is an autosomal recessive disease and the most common congenital defect in folate metabolism. A deficiency in MTHFR results in elevated serum homocysteine levels. In this study, we evaluated a patient diagnosed with epilepsy and elevated homocysteine levels, who carried compound heterozygous variants c.781-6G>A and c.1316T>C in the MTHFR gene. We primarily focused on the unreported non-canonical splicing variants c.781-6G>A in this patient and identified several complex splicing variant patterns. The c.1316T>C variant results in a substitution of leucine at position 439 with proline and this variant has been previously reported and is considered pathogenic. Our study mainly utilized RNA-seq and TA cloning to reveal the complex splicing patterns exhibited by this non-canonical splicing variant. Additionally, this finding was confirmed through in vitro experiments. This provided deeper insights into the underlying reasons for the patient's disease manifestation. Furthermore, despite apparently normal circulating folate and vitamin B12, we found two family members to exhibit mildly elevated homocysteine levels. While these individuals did not present overt clinical symptoms, the potential harm associated with high homocysteine levels should not be overlooked. This study not only provides additional genetic evidence for the clinical diagnosis of the patient but also broadens our understanding of the clinical manifestations of MTHFR deficiency.

Lactate is recognized as a principal energy substrate for male germ cells. Lactate dehydrogenases (LDHs) catalyze the reversible conversion between pyruvate and lactate, which are required for male fertility. Among them, lactate dehydrogenase A-like 6B (Ldhal6b) has been identified as a testis-specific LDH gene. However, its precise roles in spermatogenesis remain to be elucidated. In this study, we used a Ldhal6b knockout mouse model to assess its impact on spermatogenesis. Our findings reveal that Ldhal6b knockout mice exhibit normal development and no significant alterations in male fertility. Further, LDHAL6B is localized to mitochondria and closely associated with germ granules. Nevertheless, its depletion does not result in significant abnormalities in mitochondria, germ granules or impact piRNA biogenesis. We also observed alterations in the abundance of proteins related to mitochondrial metabolism in sperm from Ldhal6b knockout mice, align with its specific localization to mitochondria. Overall, our results indicate that Ldhal6b is dispensable for both mouse development and spermatogenesis under normal laboratory conditions.

Extracellular signal-regulated kinase 5 (ERK5), a mitogen-activated protein kinase (MAPK) family member, plays an important role in various biological processes, such as proliferation, apoptosis, differentiation, survival, and cell regulation. However, studies on the effects of ERK5 on porcine preimplantation embryos are limited. In this study, to determine the function of ERK5 during porcine embryo development, ERK5 function was inhibited by adding the ERK5 inhibitor JWG-071. The ERK5 mRNA and protein expression levels tended to decrease from the 4-cell stage compared to the 1-cell and 2-cell stages, suggesting that ERK5 is the maternal gene. During embryonic development in pigs, adding 5 μM of JWG-071 significantly reduced the phosphorylation of ERK5 and the blastocyst development rate (control: 53.44 ± 8.38 %; treatment: 26.65 ± 3.40 %). Additionally, ERK5 inhibition increased the expression of UPR-related proteins, glucose-regulated protein (GRP78), and C/EBP homologous protein (CHOP) by inducing ER stress. Compared to the control group, the expression of the autophagy-related proteins LC3 and ATG7 was significantly increased in the ERK5 inhibition group, indicating that the inhibition of ERK5 induced autophagy. In addition, ERK5 inhibition increased the expression of BAX, a pro-apoptotic gene, resulting in apoptosis. In conclusion, the results show that ERK5 inhibition during porcine embryonic development induces autophagy and apoptosis by increasing ER stress, resulting in a negative effect on embryonic development in pigs.

Mitochondrial DNA has been widely utilized as a valuable tool for studying the evolutionary and demographic history both within and between different livestock speciesover the past three decades. Evaluation of the evolutionary history, population structure and genetic diversity is imperative for their productivity, ecosystem services, and breeding and conservation strategies for effective management. The present study included complete mitogenome of 78 cattle, out of which 33 samples belonged to 6 Bos indicus breeds of India. Mitogenome diversity of zebu cattle within population (π- nucleotide, haplotype diversity) was estimated using DnaSP v6 software and between populations (F ratio, AMOVA analysis) was estimated using Arlequin 3.5.2.2. Ladakhi breed showed maximum (π = 0.00645) while Gir (π = 0.00042) and Tharparkar (π = 0.00053) showed minimum diversity. The diversity between the breeds of Indian cattle was 16.34 %. There were 13 and 14 haplotypes in each of I and I halogroups respectively suggesting that the divergence of Bos indicus haplotypes likely occurred within the Indian subcontinent. The Bos indicus and Bos taurus cattle lineages separated approximately 0.75 million years ago. The divergence pattern observed in zebu cattle highlighted the probability of a distinct ancestor and supported notion of independent divergence of Bos indicus.

Cervical cancer remains a significant health burden worldwide, emphasizing the need for early detection and intervention. DNA replication is perturbed in cancer cells, and the minichromosome maintenance protein 10 plays an important role in origin firing. By analyzing the MCM10 mRNA expression in healthy controls, precancerous lesions, and cervical cancer using qRT-PCR, we can infer if it can be considered a biomarker. We collected cervical smear samples from patients and performed MCM10 expression analysis to set up thresholds for risk stratification. We also investigated the HPV status among the patient samples with precancerous lesions and cervical cancer and found 70 % of them to be positive. Our results demonstrated a significant upregulation of MCM10 mRNA expression in tumor samples (n = 40, 7.83 ± 1.2) and precancerous lesions (n = 54, 5.69 ± 1.4) compared to normal (n = 50, 4.27 ± 0.80) with a R value of 0.59, confirming its role in the progression and development of cervical cancer. In conclusion, this study emphasizes the potential role of MCM10 as a biomarker. Our study would improve early detection rates, and we propose MCM10-based community screening for risk stratification, prevention, and prognosis.

The fat mass and obesity associated (FTO) gene, previously identified as a pivotal genetic locus associated with adiposity, has recently been linked to various cancers. In this study, we established an FTO knockout (KO) cell line in porcine iliac artery endothelial cells (PIECs) utilizing CRISPR/Cas9 technology to systematically investigate the gene's function and effect through transcriptomic and metabolomic analysis. Our results revealed significant gene expression and metabolic profiles differences between the FTO KO and wild-type (WT) cells. Furthermore, enrichment analysis highlighted the involvement of differentially expressed genes in metabolic processes, cellular components, and molecular functions, as well as in complement and coagulation cascades, mineral absorption, glutathione metabolism, insulin signaling, fluid shear stress, and atherosclerosis pathways. The metabolomic profiling revealed clear distinctions between the FTO KO and WT cells, indicating profound modifications in cellular metabolism. Correlation analysis of transcriptomic and metabolomic data revealed a significant association between six metabolites and twenty genes, with melatonin showing specific correlations with the expression of several genes, indicating a complex regulatory network between gene expression and metabolic changes. This study provides a foundation for further research on the FTO gene's role in cellular processes and molecular mechanisms underlying physiological and pathological conditions.

A certain percentage of Duchenne muscular dystrophy (DMD) patients remain genetically undiagnosed after routine genetic testing. Accurate genetic diagnosis is crucial for determining eligibility for mutation-specific therapies and providing relatives with reliable genetic and reproductive counselling. In this study, we utilized RNA sequencing to achieve precise genetic diagnoses in three DMD patients. We identified a deep intronic variant, NC_000023.11:g. 32644691A>C (NM_004006.3:c.1149+273T>G), responsible for creating a novel exon in one patient. An abnormal splicing event was also observed in the second patient. Additionally, RNA sequencing of the pathological muscle samples revealed differentially expressed genes. Based on these findings, we proposed a comprehensive, stepwise diagnostic procedure for DMD. Our study suggests that RNA sequencing can be instrumental in diagnosing disease-causing intronic variants, and the proposed procedure aims to enhance the clarity and accuracy of genetic diagnoses in DMD.

Walnut (Juglans regia L.) is a high-value tree species planted worldwide, but the incomplete less developed genetic transformation system limits its gene function analysis. In this study, virus-induced gene silencing (VIGS) mediated by tobacco rattle virus (TRV) technology was applied to walnut seedlings to degrade the transcript of target gene. Different infiltration methods were used to explore the effects of infection mode, Agrobacterium cell density, silencing fragment length, and walnut cultivars. The results showed that spray infiltration of seedlings resulted in a photobleaching phenotype of the whole plant. Leaf injection was a more effective way of infiltration. The optimal combination was the Agrobacterium cell density at OD = 1.1 with target fragment = 255 bp for the treatment of walnut early-fruiting cultivar 'Xiangling.' This combination can reach up to 48 % of gene silencing efficiency. Based on this optimized VIGS system, silencing a walnut chlorophyll synthesis-related gene, JrPOR (Protochlorophyllide reductase), to further validate the system's effect. The results showed that the expression of JrPOR was significantly repressed, and the chlorophyll level of the silenced plants was significantly decreased compared with the control. The above results indicate that the walnut TRV-VIGS system has been successfully established and can be used for reverse genetic studies, providing an option for verifying gene function in walnut.

Euphorbia fauriei, a perennial plant endemic to South Korea, exhibits both morphological characteristics and intricate genetic identities akin to E. pekinensis. This study aimed to provide clarity on the taxonomic status of E. faurirei and E. pekinensis through a comprehensive chloroplast (cp) genome analysis. Additionally, we sequenced the Acalypha australis chloroplast genome as an outgroup for the construction of a phylogenetic tree with other Euphorbia species. The three chloroplast genomes, ranging from 162,834 bp to 168,832 bp, displayed typical quadripartite structures. The Euphorbia genomes contained 111 unique genes, whereas the A. australis genome contained two additional protein-coding genes (PCGs), rpl32 and rps16. Comparative analysis unveiled the loss of rpl32 and rps16 as synapomorphic characteristics in Euphorbia, whereas the loss of infA occurred across Euphorbiaceae. High collinearity and sequence similarity were observed among Euphorbia species, accompanied by significant inversion regions in the E. pekinensis chloroplast genomes from China and Japan, indicating regional genetic variability. Nucleotide substitution analysis revealed that the ndh group exhibited the highest K/K values (0.224), whereas the atp, psa, psb and rps groups had the lowest. Phylogenomic analysis utilizing whole genomes, PCGs, and intron and intergenic regions consistently demonstrated that E. pekinensis from South Korea clusters closely with E. fauriei. These findings challenge the current taxonomic distinction between E. pekinensis and E. fauriei in Korea, suggesting that while they exhibit distinct characteristics, E. fauriei should be considered a closely related subspecies rather than the same species as E. pekinensis. This study emphasizes the need for population studies to clarify the taxonomic relationships between E. pekinensis and E. fauriei.