Polymorphism Patterns Research Articles

The role of cardiac magnetic resonance in sports cardiology: results from a large cohort of athletes.

Cardiac magnetic resonance (CMR) provides information on morpho-functional abnormalities and myocardial tissue characterisation. Appropriate indications for CMR in athletes are uncertain. To analyse the CMR performed at our Institute to evaluate variables associated with pathologic findings in a large cohort of athletes presenting with different clinical conditions. All the CMR performed at our Institute in athletes aged > 14years were recruited. CMR indications were investigated. CMR was categorised as "positive" or "negative" based on the presence of morphological and/or functional abnormalities and/or the presence of late gadolinium enhancement (excluding the right ventricular insertion point), fat infiltration, or oedema. Variables associated with "positive" CMR were explored. A total of 503 CMR were included in the analysis. "Negative" and "positive" CMR were 61% and 39%, respectively. Uncommon ventricular arrhythmias (VAs) were the most frequent indications for CMR, but the proportion of positive results was low (37%), and only polymorphic ventricular patterns were associated with positive CMR (p = 0.006). T-wave inversion at 12-lead ECG, particularly on lateral and inferolateral leads, was associated with positive CMR in 34% of athletes (p = 0.05). Echocardiography abnormalities resulted in a large proportion (58%) of positive CMR, mostly cardiomyopathies. CMR is more efficient in identifying a pathologic cardiac substrate in athletes in case of VAs (i.e., polymorphic beats), abnormal ECG repolarisation (negative T-waves in inferolateral leads), and borderline echocardiographic findings (LV hypertrophy, mildly depressed LV function). On the other hand, CMR is associated with a large proportion of negative results. Therefore, a careful clinical selection is needed to indicate CMR in athletes appropriately.

Development of SCAR Markers for Genetic Authentication of Metarhizium acridum.

In this study, molecular typing using Randomly Amplified Polymorphic DNA (RAPD-PCR) was conducted on 16 original isolates of Metarhizium acridum obtained from locusts (Schistocerca piceifrons ssp. piceifrons.) in Mexico (MX). The analysis included reference strains of the genus Metarhizium sourced from various geographical regions. The isolates were identified by phenotypic (macro and micromorphology) and genotypic methods (RAPD-PCR and Amplified Fragment Length Polymorphisms (AFLP), through a multidimensional analysis of principal coordinates (PCoA) and a minimum spanning network (MST). Subsequently, Sequences-Characterized Amplified Region (SCAR) markers were developed for the molecular detection of M. acridum, these markers were chosen from polymorphic patterns obtained with 14 primers via RAPD-PCR. Phenotypic and genotypic characterization identified the MX isolates as M. acridum. Of all the polymorphic patterns obtained, only OPA04 and OPA05 were chosen, which presented species-specific bands for M. acridum, and further utilized to create SCAR markers through cloning and sequencing of the specific bands. The specificity of these two markers was confirmed via Southern hybridization. The SCAR markers (Ma-160OPA-05 and Ma-151OPA-04) exhibit remarkable sensitivity, detecting down to less than 0.1 ng, as well as high specificity, as evidenced by their inability to cross-amplify or generate amplification with DNAs from other strains of Metarhizium (as Metarhizium anisopliae) or different genera of entomopathogenic fungi (Cordyceps fumosorosea and Akanthomyces lecanii). These SCAR markers yield readily detectable results, showcasing high reproducibility. They serve as a valuable tool, especially in field applications.

Association Analysis of MMP-13 (rs2252070) Gene Polymorphism and the Susceptibility to Chronic Periodontitis.

Chronic periodontitis is a multifactorial inflammatory condition influenced by genetic factors. Matrix metalloproteinase(MMP)-13, serving as a crucial enzyme involved in extracellular matrix remodeling, is associated with the degradation of periodontal tissues. Therefore, this study assesses the genetic link between the MMP-13 (rs2252070) genetic variation and chronic periodontitis in a Southern Indian demographic. The study was conducted at Saveetha Dental Collegein Chennai, India. It involved a total of 100 subjects,50 individualsaffected with periodontitis (classified as stage II and above, American Association of Periodontology 2018 criteria) and 50 individuals who were periodontally healthy or were diagnosed as having mild gingivitis. We isolated DNAfrom the blood samples obtained from the participants. Specific primers that flank the BsrI region of the MMP-13 receptor gene were used in the process of DNA amplification. Subsequently, a restriction fragment length analysis using the BsrI enzyme was carried out for genotyping of the amplicon. Based on the restriction fragment length polymorphism pattern, we obtained certain genotypes. These were further recorded and followed by statistical analysis. We conducted a chi-square test to draw a comparison in terms of their genotype and allele frequencies. We calculated the odds ratio, along with 95% confidence intervals. The frequency of genotypes and distribution of MMP-13 polymorphism did not exhibit a statistically significant difference at χ2 degrees of freedom (P = 0.913). We inferred from our study that there was no significant difference between the groups concerning homozygous and heterozygous mutant genotypes (AA vs. AG + GG), with a P-value of 0.6871. The observed frequencies of GG (47% vs. 43%) and AG+AA (41% vs. 42%) genotypes did not indicate a significant difference between the groups. Similarly, there was no noteworthydistinction between the A allele (62% vs. 65%) and G allele (38% vs. 35%) in the case and control groups. Thefindings of the study reveal that there is no correlation between MMP-13 (rs2252070)gene polymorphism and periodontitis.

Characterization of genetic diversity in Curcuma longa L. cultivars using Start Codon Targeted (SCoT) markers

Curcuma longa L. (Family- Zingiberaceae), commonly called turmeric, is one of the most important commercial spices. Being a center of turmeric's diversity, India boasts of more than fifty cultivars with variable agronomic characters and curcumin content. However, the quest for calibrating their genetic variability remains debatable as popular molecular marker-based studies have yielded inconsistent results. A promising PCR-based approach, known as the Start Codon Targeted (SCoT)-PCR system has been established to be more efficient than random DNA marker systems because this technique can generate more information on genetic polymorphism patterns. Hence, the present study proposes to use Start Codon Targeted (SCoT) markers to assess inter-cultivar genetic diversity of turmeric. We report an orthogonal L16 (45) design-based approach to investigate the influence of five crucial factors (dNTPs, Taq DNA polymerase, primer, template DNA and annealing temperature of primer) on the efficiency of the polymerase chain reaction (PCR) for development of an optimized Start Codon Targeted (SCoT) amplification protocol using twenty-seven different cultivars of C. longa. The optimized PCR protocol yields best results with a 20 uL reaction mixture, containing 10×PCR Buffer (with 15 mM MgCl2), 2.5 mM dNTPs, 10 mM SCoT primer, Taq polymerase (2 U), template DNA (50 ng), which was verified by using twenty-five SCoT primers. This standardized rapid protocol of SCoT-PCR reported here was employed to examine genetic diversity among twenty-seven Indian cultivars of turmeric, revealing high range of polymorphism ranging from 81.25 % to 100 %. Unweighted pair group method of arithmetic averages (UPGMA) cluster analysis of the SCoT marker data segregated the twenty-seven cultivars into two main clusters. The first cluster comprised of nine cultivars (36 % of the cultivars) which was further divided into three sub-clusters and the second one consisted of eighteen cultivars (64 %) which further divided into four sub-clusters. From the results of this study, it can be inferred that the employment of SCoT markers can be an effective tool for analysing genetic variability, phylogenetic relationships and develop a rich genetic resource management system for C. longa cultivars.

Genetic Association of ICAM-1 (rs5498) Gene Polymorphism With Susceptibility to Stage II Grade B Periodontitis: A Case-Control Study in South Indian Population.

In the contemporary perspective, periodontitis is considered a complex issue triggered and perpetuated by bacteriabut strongly influenced by the way the body reacts to bacterial plaque. Recent research has indicated that variations in genes might have an impact on the development of periodontitis. This study was conducted to explore a probable link between the genetic variations in intercellular adhesion molecule-1 (ICAM-1) represented by rs5498 and the occurrence of periodontitis. Methods: A total of 100 participants, 50 with periodontitis and 50 with periodontally healthy or mild gingivitis, were recruited for this study. Whole blood drawn from the participants was used to obtain genomic DNA. The ICAM-1 gene polymorphism (rs5498) was determined using polymerase chain reaction (PCR) amplification and digestion. The ICAM-1 gene's flanking primers were used to amp up the DNA. For statistical analysis, the genotype that was analyzed using the pattern of restriction fragment length polymorphism was recorded. The Chi-square test compared genotype and allele frequency distributions between both groups. The odds ratio with 95% confidence intervals with each individual allele or genotype was used to compute the risk. Statistical significance was established in all tests when the p-value was less than 0.05. There was no discernible difference between the genotype frequencies of patients and controls χ2df (P = 0.6065). The findings demonstrated that no significant difference was present between the two groups for homozygous or heterozygous mutant genotypes (AA vs. AG+GG; P = 0.6854). There was no discernible difference in the detected frequencies of the A allele (58% vs. 61%), G allele (42% vs. 39%), TT (16% vs. 24%), AG (40% vs. 36%), and TT genotypes in the studied groups. According to the results of the current investigation, the ICAM-1 (rs5498) gene polymorphism is not associated with periodontitis in the population investigated.

Contrasting segregation patterns among endogenous retroviruses across the koala population

Koalas (Phascolarctos cinereus) have experienced a history of retroviral epidemics leaving their trace as heritable endogenous retroviruses (ERVs) in their genomes. A recently identified ERV lineage, named phaCin-β, shows a pattern of recent, possibly current, activity with high insertional polymorphism in the population. Here, we investigate geographic patterns of three focal ERV lineages of increasing estimated ages, from the koala retrovirus (KoRV) to phaCin-β and to phaCin-β-like, using the whole-genome sequencing of 430 koalas from the Koala Genome Survey. Thousands of ERV loci were found across the population, with contrasting patterns of polymorphism. Northern individuals had thousands of KoRV integrations and hundreds of phaCin-β ERVs. In contrast, southern individuals had higher phaCin-β frequencies, possibly reflecting more recent activity and a founder effect. Overall, our findings suggest high ERV burden in koalas, reflecting historic retrovirus-host interactions. Importantly, the ERV catalogue supplies improved markers for conservation genetics in this endangered species.

Contrasting PRRSV temporal lineage patterns at the individual farm, production system, and regional levels in Ohio and neighboring states from 2017 to 2021

Porcine reproductive and respiratory virus (PRRSV), one of the most significant viruses in the swine industry, has been challenging to control due to its high mutation and recombination rates and complexity. This retrospective study aimed to describe and compare the distribution of PRRSV lineages obtained at the individual farm, production system, and regional levels. PRRSV-2 (type 2) sequences (n = 482) identified between 2017 – 2021 were provided by a regional state laboratory (Ohio Department of Agriculture, Animal Disease Diagnostic Center (ODA-ADDL)) collected from swine farms in Ohio and neighboring states, including Indiana, Michigan, Pennsylvania, and West Virginia. Additional sequences (n = 138) were provided by one collaborating swine production system. The MUSCLE algorithm on Geneious Prime® was used to align the ORF5 region of PRRSV-2 sequences along with PRRSV live attenuated vaccine strains (n = 6) and lineage anchors (n = 169). Sequenced PRRSV-2 were assigned to the most identical lineage anchors/vaccine strains. Among all sequences (n = 620), 29.8% (185/620) were ≥ 98.0% identity with the vaccine strains, where 93.5% (173/185) and 6.5% (12/185) were identical with the L5 Ingelvac PRRS® MLV and L8 Fostera® PRRS vaccine strains, respectively, and excluded from the analysis. At the regional level across five years, the top five most identified lineages included L1A, L5, L1H, L1C, and L8. Among non-vaccine sequences with production system known, L1A sequences were mostly identified (64.3% – 100.0%) in five systems, followed by L1H (0.0% - 28.6%), L1C (0.0% – 10.5%), L5 (0.0% – 14.4%), L8 (0.0% – 1.3%), and L1F (0.0% – 0.5%). Furthermore, among non-vaccine sequences with the premise identification available (n = 262), the majority of sequences from five individual farms were either classified into L1A or L5. L1A and L5 sequences coexisted in three farms, while samples submitted by one farm contained L1A, L1H, and L5 sequences. Additionally, the lineage classification results of non-vaccine sequences were associated with their restriction fragment length polymorphism (RFLP) patterns (Fisher’s exact test, p < 0.05). Overall, our results show that individual farm and production system-level PRRSV-2 lineage patterns do not necessarily correspond to regional-level patterns, highlighting the influence of individual farms and systems in shaping PRRSV occurrence within those levels, and highlighting the crucial goal of within-farm and system monitoring and early detection for accurate knowledge on PRRSV-2 lineage occurrence and emergence.

Association between interleukin-6-174G/C gene polymorphism and asthma severity: exploring the role of total serum IgE, blood eosinophils, and FeNO as markers of type 2 inflammation

BackgroundWhile a connection has been established between serum interleukin-6 (IL-6) levels and the IL-6 gene (− 174G/C) polymorphism in allergic diseases such as asthma, its specific association with severe asthma remains unexplored. This study examined the relationship between the IL-6 (− 174G/C) gene polymorphism and mild and severe asthma, focusing on its influence on type 2 inflammation.MethodsOur study comprised 98 patients with mild asthma and 116 with severe asthma. Additionally, we recruited 121 healthy participants to serve as controls for comparative analyses. The IL-6 gene (− 174G/C) polymorphism was assessed utilizing the polymerase chain reaction-restriction fragment length polymorphism (PCR–RFLP) method.ResultsIn our study, the risk of mild asthma exhibited a significant fourfold increase in individuals with the GG genotype pattern compared to healthy controls, yielding an odds ratio (OR) of 4.4 (p < 0.001). Conversely, we found no significant correlation between the IL-6 − 174G/C gene polymorphism and severe asthma when compared to the healthy control group. However, a noteworthy pattern emerged when we compared subgroups of mild and severe asthma. The risk of severe asthma increased fivefold in individuals with the GC polymorphism pattern, with an OR of 4.99 (p < 0.001), while the likelihood of mild asthma showed a similar fourfold increase with the GG polymorphism pattern, OR = 4.4 (p < 0.001). Consequently, we observed a significantly higher frequency of the C allele in patients with severe asthma, whereas the G allele was more prevalent in individuals with mild asthma (p = 0.05). Additionally, the correlation between markers of type 2 inflammation and the dominant model of the IL-6 gene -174G/C polymorphism (CC + CG vs GG) revealed a significant increase in total serum immunoglobulin E (IgE), Blood Eosinophil Counts (BEC), and Fractional Exhaled Nitric Oxide (FeNO) levels in asthmatic patients with the CC + CG gene pattern compared to those with GG, with p-values of 0.04, 0.03, and 0.04, respectively. Furthermore, after adjusting for other risk factors, the likelihood of developing severe asthma increased from fourfold to eightfold, with an OR of 8.12 (p = 0.01) with (CC + CG) gene pattern. Other predictors for severe asthma included older age and childhood-onset disease (OR = 1.13 and 19.19, p < 0.001). Allergic rhinitis (AR) and nasal polyps (NP) also demonstrated a substantial association with an increased risk of severe asthma, with odds ratios of 5 and 32.29 (p = 0.01 and < 0.001), respectively. Additionally, elevated Body Mass Index (BMI), BEC, and FeNO were linked to severe asthma, with ORs of 1.11, 1.00, and 1.04, respectively (p = 0.04, 0.05, and 0.001).ConclusionThis study illuminated the intricate relationship between the IL-6 gene polymorphism, type 2 inflammation markers, and diverse risk factors in shaping asthma severity. As a significant association between the GG polymorphism of the IL-6 gene (− 174G/C) and mild asthma was found, while possessing at least one C allele, whether in a homozygous (CC) or heterozygous (CG) combination, independently predicts the likelihood of severe asthma.

In-silico Functional and Structural Annotation of Rheumatoid arthritis linked Gene and Protein

Background: Rheumatoid arthritis (RA) is an autoimmune disease marked by chronic inflammation and immune system dysregulation. The Ankyrin repeat domain 55 (ANKRD55) gene, located on chromosome 5q11.2, has been associated with RA susceptibility. Understanding the gene and protein characteristics could illuminate pathways involved in RA and aid in the development of targeted therapies. Objective: To conduct a detailed analysis of the ANKRD55 gene and protein, focusing on its structure, expression profile, functional domains, and polymorphisms, thereby establishing its role in RA and potential as a therapeutic target. Methods: Using bioinformatics tools, we analyzed ANKRD55's genomic localization (NCBI), peptide sequences (Uniprot), physicochemical properties (Protparam Server), signal peptides (SignalP v4.1), transmembrane helices (TMHMM), and glycosylation sites (NetNGlyc 1.0). Polymorphism and methylation patterns were examined using PolyPhen and MethyCancer, respectively. Splice variants were identified, and protein-protein interaction networks were assessed (STRING database). Protein domains were characterized, including the prediction of RhoGAP domains. Structural modeling was conducted to identify potential drug-binding pockets with the DoGSite Scorer server. Results: ANKRD55's expression was predominantly observed in the testis (RPKM 1.8) and to a lesser extent in lymph nodes (0.8), appendix (0.6), and brain (0.2). It encodes a 614-amino-acid protein with a molecular weight of approximately 68.4 kDa and a pI of 6.72. Six splice variants were identified, enriching the understanding of its potential isoform diversity. No significant N-glycosylation sites were predicted, and methylation analysis suggested a nuclear localization without DNA methylation sites. Structural analysis revealed drug-binding pockets with volumes ranging from 233.35 to 5389.58 A^3, with drug scores between 0.78 and 0.82. Conclusion: The study concludes that while several factors contribute to student satisfaction in public sector medical colleges, infrastructure and facilities, along with quality instructional materials and clinical exposure, are key drivers. Enhancing these areas could lead to a more positive educational experience for students.

Development of Gene-Based InDel Markers on Putative Drought Stress-Responsive Genes and Genetic Diversity of Durian (Durio zibethinus).

Insertion-deletion (InDel) markers are co-dominant, relatively abundant and practical for agarose gel genotyping. InDel polymorphism usually affects gene functions. Nucleotide sequences of durian (Durio zibethinus) are available, but InDel makers have not been well established. This study aimed to develop drought-related gene-based InDel markers for durian through bioinformatic analysis of RNA-Seq datasets. The polymorphism of the markers was verified in 24 durian genotypes local to Thailand. Bioinformatic analysis indicated 496 InDel loci having lengths more than 9bp. To evaluate these InDel markers, 15 InDel loci were selected. Nine markers were successfully amplified a clear polymorphic band pattern on 2% agarose gel. The polymorphic information content (PIC) of these nine markers ranged from 0.1103 to 0.5808. The genetic distance between the 24 genotypes ranged from 0.222 to 0.889. The phylogeny based on the nine InDel loci distinguished the 24 genotypes and divided samples into four groups. This set of gene-based InDel markers on putative drought-responsive genes will be useful for genetic studies.

Occurrence and risk‐related features of Bacillus cereus in fluid milk

This work assessed the prevalence and risk‐related phenotypes of Bacillus cereus in milk products. Bacillus was the most dominant genus of 113 collected strains from 41 milk samples, and B. cereus (19.27%) was the most abundant species showing a high genetic diversity with seven random amplified polymorphic DNA patterns. Most B. cereus isolates were strong biofilm formers with good motility, extracellular polymeric substance‐producing ability, high proteolytic and lipolytic activities. Antibiotic resistance analysis suggested the majority B. cereus strains were resistant to oxacillin (90.48%), tetracycline (95.24%), and penicillin G sodium (47.62%). Results revealed the genotypic diversity of B. cereus, and their potential risk in dairy industry.

Research Note: Possible influence of thermal selection on patterns of HSP70 and HSP90 gene polymorphisms in Thai indigenous and local chicken breeds and red junglefowls

The thermal stress caused by global climate change adversely affects the welfare, productivity, and reproductive performance of farm animals, including chickens, and causes substantial economic losses. However, the understanding of the genetic basis of the indigenous chicken adaptation to high ambient temperatures is limited. Hence, to reveal the genetic basis of thermal stress adaptation in chickens, this study investigated polymorphisms in the heat shock protein 70 (HSP70) and HSP90 genes, known mechanisms of cellular defense against thermal stress in indigenous and local chicken breeds and red junglefowls in Thailand. The result revealed seven alleles of the HSP70 gene. One allele exhibited a missense mutation, where an amino acid changed from Asn to His in the substrate-binding and peptide-binding domains, which is exclusive to the Lao Pa Koi chicken breed. Twenty new alleles with silent mutations in the HSP90 gene highlighted its greater complexity. Despite this diversity, distinct population structures were not found for either HSP70 or HSP90, which suggests incomplete impact on the domestication process and selection. The low genetic diversity, shown by the sharing of alleles between red junglefowls and Thai indigenous and local chicken breeds, aligns with the hypothesis that these alleles have undergone selection in tropical regions, such as Thailand. Selection signature analysis suggests the purifying selection of HSP70 for thermotolerance. This study provides valuable insights for enhancing the conservation of genetic resources with thermotolerant traits, which are essential for developing breeding programs to increase poultry production in the context of global climate change.

Dermoscopy for the Differentiation of Subacute Cutaneous Lupus Erythematosus from Other Erythematous Desquamative Dermatoses-Psoriasis, Nummular Eczema, Mycosis Fungoides and Pityriasis Rosea.

Subacute cutaneous lupus erythematosus (SCLE) is a condition that might pose a diagnostic challenge. The aim of this study was to assess the usefulness of videodermoscopy in the differentiation of SCLE from other erythematous-desquamative dermatoses. Consecutive patients with SCLE (n = 27), psoriasis (n = 36), nummular eczema (n = 30), mycosis fungoides (n = 26), and pityriasis rosea (n = 20) referred to our Department of Dermatology were recruited for this study. A representative lesion was visualized using a Canfield D200EVO Videodermatoscope (Canfield Scientific GmbH, Bielefeld, Germany) and evaluated for the following parameters: vessels (morphology and distribution), scales (color and distribution), follicular findings, colors and morphologies, and presence of specific clues. SCLE was predominantly characterized by a polymorphous vascular pattern (92.6%) of unspecific distribution (92.6%) over a pink-red background (74.1%). Gray-brown dots were present in 10 (37.0%) cases, and pigmentation was noted in 15 (55.6%) patients, including peripheral pigmentation in 7 (25.9%) patients. Videodermoscopic evaluation showed significant differences between SCLE and psoriasis, which was characterized by regularly distributed dotted vessels. Although some common dermoscopic features with MF were noted, the presence of yellow structureless areas and red dots/globules favored the diagnosis of MF. In conclusion, a polymorphic vascular pattern, especially in association with gray-brown dots and/or peripheral pigmentation, is a valuable clue for the differentiation of SCLE from other erythematous-desquamative dermatoses.

Stochastic processes and changes in evolutionary rate are associated with diversification in a lineage of tropical hard pines (Pinus)

The study of the patterns of polymorphism and molecular evolution among closely related species is key to understanding the evolutionary forces involved in the diversification of lineages. This point is a big challenge in species with slow evolutionary rates, long life cycles, and ancient, shared polymorphisms such as conifers. Under the premise of divergence in a stepwise migration process, we expect clinal geographical patterns of purifying selection efficiency, and genetic structure related to latitude or longitude. If migration is accompanied by changes in the environment, we could further expect a role of positive selection in driving species divergence. Here, we infer patterns of polymorphism, efficiency of purifying selection, and molecular evolution using a dataset of 161 nuclear genes (∼71 Kb) in a lineage of hard pines from North America, the Caribbean, Mexico, and Central America presumed to have migrated from North America toward lower latitudes with tropical conditions. Under the premise of differences in selective pressures, we also look for possible signals of positive selection. To test our hypothesis, first we estimated different indices to infer patterns of polymorphism and efficiency of purifying selection (Ka, Ks, Ka/Ks, dN, dS, dN/dS, and dxy) and compared these metrics across five clades. Also, we investigated possible clinal patterns in these indices and morphological traits (needle length and cone length). Then we inferred genetic structure and environmental differences among species to test for possible signals of positive selection using phylogenetic methods in specific clades. We found differences among clades using Ka, Ks, and Ka/Ks with a relaxation of purifying selection, especially in the Elliotti and Patula clades. We also found environmental differences related to geographic distance, and among clades suggesting differences in selective pressures. The indices Ks, dxy, and needle length had relationships with geography but not ovulate cone length. Finally, we found that most analyzed genes are under purifying selection, but there was an exception of faster evolutionary rate in some pine species, suggesting the possible action of positive selection in divergence. Our study indicated that stochastic processes have played a key role in the diversification of the group, with a possible input of positive selection in pines from Mexico and Central America.

Phytotoxicity and genotoxicity study of reactive red 141 dye on mung bean (Vigna radiata (L.) Wilczek) seedlings.

Reactive Red (RR) 141 dye is widely used in various industrial applications, but its environmental impact remains a growing concern. In this study, the phytotoxic and genotoxic effects of RR 141 dye on mung bean seedlings (Vigna radiata (L.) Wilczek) were investigated, serving as a model for potential harm to plant systems. Short-term (14 days) and long-term (60 days) experiments in paddy soil pot culture exposed mung bean seedlings to RR 141 dye. The dye delayed germination and hindered growth, significantly reducing germination percentage and seedling vigor index (SVI) at concentrations of 50 and 100ml/L. In short-term exposure, plumule and radical lengths dose-dependently decreased, while long-term exposure affected plant length and grain weight, leaving pod-related parameters unaffected. To evaluate genotoxicity, high annealing temperature-random amplified polymorphic DNA (HAT-RAPD) analysis was employed with five RAPD primers having 58-75% GC content. It detected polymorphic band patterns, generating 116 bands (433 to 2857bp) in plant leaves exposed to the dye. Polymorphisms indicated the appearance/disappearance of DNA bands in both concentrations, with decreased genomic template stability (GTS) values suggesting DNA damage and mutation. These findings demonstrate that RR 141 dye has a significant impact on genomic template stability (GTS) and exhibits phytotoxic and genotoxic responses in mung bean seedlings. This research underscores the potential of RR 141 dye to act as a harmful agent within plant model systems, highlighting the need for further assessment of its environmental implications.

Sustainable Use of Gum Acacia as a Biopolymeric Additive in Ultra‐High Performance Concrete

The main objective of this research is to analyze whether biopolymer (gum acacia) can be used as an admixture for ultra‐high performance concrete (UHPC) and to elucidate the strength, durability, microstructure, and transport properties of biopolymer (gum acacia) incorporated UHPC mixes in combination with the shrinkage reducing agent (SRA). The mechanical, thermal, and durability aspects of UHPC were studied at different ages and curing conditions by adding gum acacia in combination with the SRA. After 28 days under hybrid curing, the compressive strength increased by 22.19% and the flexural strength increased by 41.59% for 1% biopolymer addition. The highest strength and durability were obtained using the hybrid curing procedure using superplasticizer and gum acacia biopolymer at a water‐binder ratio of 0.35. With an improved microstructure, the results revealed improved hydration and durability as revealed through the scanning electron microscopic (SEM) images. The SEM photographs of the concrete showed more polymorphic patterns and crystals overall relative to the UHPC with SRA, while exhibiting little to no microfractures. Through adjustment of the biopolymer proportion and adoption of a suitable curing method, this research presents a new strategy for addressing the negative impact produced by the usage of SRA in UHPC.

The association of ACE gene polymorphism and serum ACE levels with diabetic nephropathy-a cross-sectional study

Diabetic nephropathy (DN) is the microvascular complication of type-2 diabetes that leads to end-stage renal disease. The angiotensin-converting enzyme gene that is a part of the renin-angiotensin-aldosterone system is considered one of the candidate genes responsible for the genetic predisposition of DN. To compare serum angiotensin converting enzyme (ACE) levels, the pattern of ACE gene polymorphism in patients with type-2 diabetes with or without nephropathy, to find the association between ACE gene polymorphism and various stages of DN, the association between serum ACE levels and various stages of DN. We enrolled 108 patients diagnosed with type-2 diabetes and 108 DN patients. Serum levels were estimated by ELISA and gene polymorphism was performed with gene sequencing. It was found that the serum ACE levels were higher in DN patients than in type-2 diabetics although the p-value was not significant. There was no significant association between serum ACE levels and various stages of nephropathy. The wild (GG genotype) distribution was more predominant in type-2 diabetic patients than in DN patients. There was a significant difference in the frequency of genotype with various stages of nephropathy and estimated glomerular filtration rate which was statistically significant (p = 0.0018). In summary, the study did not find a significant association between serum ACE levels and DN, nor did it observe a substantial impact of ACE gene polymorphism on serum ACE levels in DN patients. The findings also indicated that the ACE gene polymorphism might not have a direct influence on albuminuria stages. However, the wild-type genotype showed a trend toward protection against albuminuria development, while the carrier patients had a higher prevalence of severe albuminuria. Further research with larger sample sizes and longitudinal studies may provide deeper insights into the role of serum ACE levels and ACE gene polymorphism in the development and progression of DN.

Phylogenetic and population genetic analyses of Thrips tabaci Lindeman (Thysanoptera: Thripidae) on Allium host in India.

Onion thrips (Thrips tabaci) is a complex of cryptic species with subtle morphological differences and distinct genetic backgrounds; thus, species identification using traditional methods remains challenging. The existence of different haplotypes and genotypes within a species can significantly influence various aspects of its biology, including host preference, reproductive capacity, resistance to pesticides, and vector competence for plant viruses. Understanding the genetic diversity and population structure of cryptic species within T. tabaci will not only aid in the development of more effective control strategies tailored to specific genetic variants but also in monitoring population dynamics, tracking invasive species, and implementing quarantine measures to prevent the spread of economically damaging thrips biotypes. This study aims to explore intraspecies genetic diversity and molecular evolutionary relationships of the mitochondrial cytochrome oxidase gene subunit I (mtCOI) in T. tabaci populations from India. To capture diversity within the Indian T. tabaci populations, amplicon sequencing was performed for the thrips mtCOI gene from eight diverse localities in India. A total of 48 sequences retrieved for the mtCOI gene from the NCBI Nucleotide database were analysed. Multiple insertions and deletions were detected at various genomic positions across the populations from different localities, with the highest variation observed in the 300-400 genome position range. Molecular diversity analyses identified 30 haplotypes within the population, with certain subpopulations exhibiting higher gene flow. Analysis of single nucleotide polymorphism patterns within the mtCOI gene across diverse Indian locales revealed significant intrapopulation genetic heterogeneity and its potential repercussions on gene functionality. Elevated F statistics (Fst) values in the northern-western subpopulations suggested high genetic variability, particularly evident in haplotype networks originating mainly from the northern region, notably Delhi. While most populations displayed stable and ancient evolutionary histories, thrips populations from northern, western, and north-eastern regions indicated rapid growth.

High-Quality Genome Assemblies Reveal Evolutionary Dynamics of Repetitive DNA and Structural Rearrangements in the Drosophila virilis Subgroup.

High-quality genome assemblies across a range of nontraditional model organisms can accelerate the discovery of novel aspects of genome evolution. The Drosophila virilis group has several attributes that distinguish it from more highly studied species in the Drosophila genus, such as an unusual abundance of repetitive elements and extensive karyotype evolution, in addition to being an attractive model for speciation genetics. Here, we used long-read sequencing to assemble five genomes of three virilis group species and characterized sequence and structural divergence and repetitive DNA evolution. We find that our contiguous genome assemblies allow characterization of chromosomal arrangements with ease and can facilitate analysis of inversion breakpoints. We also leverage a small panel of resequenced strains to explore the genomic pattern of divergence and polymorphism in this species and show that known demographic histories largely predicts the extent of genome-wide segregating polymorphism. We further find that a neo-X chromosome in Drosophila americana displays X-like levels of nucleotide diversity. We also found that unusual repetitive elements were responsible for much of the divergence in genome composition among species. Helitron-derived tandem repeats tripled in abundance on the Y chromosome in D. americana compared to Drosophila novamexicana, accounting for most of the difference in repeat content between these sister species. Repeats with characteristics of both transposable elements and satellite DNAs expanded by 3-fold, mostly in euchromatin, in both D. americana and D. novamexicana compared to D. virilis. Our results represent a major advance in our understanding of genome biology in this emerging model clade.

No Evidence that Selection on Synonymous Codon Usage Affects Patterns of Protein Evolution in Bacteria.

Bias in synonymous codon usage has been reported across all kingdoms of life. Evidence suggests that codon usage bias is often driven by selective pressures, typically for translational efficiency. These selective pressures have been shown to depress the rate at which synonymous sites evolve. We hypothesize that selection on synonymous codon use could also slow the rate of protein evolution if a non-synonymous mutation changes the codon from being preferred to unpreferred. We test this hypothesis by looking at patterns of protein evolution using polymorphism and substitution data in two bacterial species, Escherichia coli and Streptococcus pneumoniae. We find no evidence that non-synonymous mutations that change a codon from being unpreferred to preferred are more common than the opposite. Overall, selection on codon bias seems to have little influence over non-synonymous polymorphism or substitution patterns.