Expanding the repertoire of pyrrolidyl PNA analogues for DNA/RNA hybridization selectivity: aminoethylpyrrolidinone PNA (aepone-PNA)

New PNA analogues derived from aminoethylpyrrolidin- 5-one backbone show stabilization of aepone-PNA:DNA hybrids and destabilization of the corresponding RNA hybrids compared to unmodified PNA

PNA C-C<SUP>+</SUP> i-motif: superior stability of PNA TC<SUB>8</SUB> tetraplexes compared to DNA TC<SUB>8</SUB> tetraplexes at low pH

Study of self-assembly of PNA TC8 monitored by UV thermal transition at 295 nm indicates formation of a C-C+ tetraplex (i-motif) in acidic pH, with higher stability than the analogous dTC8

Anti-Depressant Activity of Zizyphus xylopyrus

The present study was undertaken to investigate the effect of ethanolic extract (ext.), ethyl acetate (EA) fractions and precipitate fraction (ppt.) of total ethanolic extract of Zizyphus xylopyrus on depression in rats. In the present study, the antidepressant effect of Zizyphus xylopyrus was examined using two behavioral models, the forced swimming test (FST) in rats and tail suspension test (TST) in rats.Ethanolic extract when administered at an acute dose of 50 mg/kg of body weight (P&lt;0.01) reduced the immobility time by 10 and 15 seconds as compared to the immobility time of control in both the screening models. Similarly EA reduced latter by 30 and 35 secs. The ppt. fraction showed the best activity, reducing the immobility time by 50 and 60 secs. in both the tests. These results showed that after standard i.e. Imipramine HCl (30 mg/kg), the ppt. fraction is potent amongst all the studied drugsThe present study clearly demonstrated that Zizyphus xylopyrus exerts an antidepressant effect in these two behavioral models. It may be due to present of flavonoids.Keywords: Zizyphus xylopyrus, Flavanoides, forced swimming test, tail suspension test

Anti-Depressant Activity of Zizyphus xylopyrus

The present study was undertaken to investigate the effect of ethanolic extract (ext.), ethyl acetate (EA) fractions and precipitate fraction (ppt.) of total ethanolic extract of Zizyphus xylopyrus on depression in rats. In the present study, the antidepressant effect of Zizyphus xylopyrus was examined using two behavioral models, the forced swimming test (FST) in rats and tail suspension test (TST) in rats.Ethanolic extract when administered at an acute dose of 50 mg/kg of body weight (P&lt;0.01) reduced the immobility time by 10 and 15 seconds as compared to the immobility time of control in both the screening models. Similarly EA reduced latter by 30 and 35 secs. The ppt. fraction showed the best activity, reducing the immobility time by 50 and 60 secs. in both the tests. These results showed that after standard i.e. Imipramine HCl (30 mg/kg), the ppt. fraction is potent amongst all the studied drugsThe present study clearly demonstrated that Zizyphus xylopyrus exerts an antidepressant effect in these two behavioral models. It may be due to present of flavonoids.Keywords: Zizyphus xylopyrus, Flavanoides, forced swimming test, tail suspension test

Functionally relevant microsatellites in sugarcane unigenes

<p>Abstract</p> <p>Background</p> <p>Unigene sequences constitute a rich source of functionally relevant microsatellites. The present study was undertaken to mine the microsatellites in the available unigene sequences of sugarcane for understanding their constitution in the expressed genic component of its complex polyploid/aneuploid genome, assessing their functional significance <it>in silico</it>, determining the extent of allelic diversity at the microsatellite loci and for evaluating their utility in large-scale genotyping applications in sugarcane.</p> <p>Results</p> <p>The average frequency of perfect microsatellite was 1/10.9 kb, while it was 1/44.3 kb for the long and hypervariable class I repeats. GC-rich trinucleotides coding for alanine and the GA-rich dinucleotides were the most abundant microsatellite classes. Out of 15,594 unigenes mined in the study, 767 contained microsatellite repeats and for 672 of these putative functions were determined <it>in silico</it>. The microsatellite repeats were found in the functional domains of proteins encoded by 364 unigenes. Its significance was assessed by establishing the structure-function relationship for the beta-amylase and protein kinase encoding unigenes having repeats in the catalytic domains. A total of 726 allelic variants (7.42 alleles per locus) with different repeat lengths were captured precisely for a set of 47 fluorescent dye labeled primers in 36 sugarcane genotypes and five cereal species using the automated fragment analysis system, which suggested the utility of designed primers for rapid, large-scale and high-throughput genotyping applications in sugarcane. Pair-wise similarity ranging from 0.33 to 0.84 with an average of 0.40 revealed a broad genetic base of the Indian varieties in respect of functionally relevant regions of the large and complex sugarcane genome.</p> <p>Conclusion</p> <p>Microsatellite repeats were present in 4.92% of sugarcane unigenes, for most (87.6%) of which functions were determined <it>in silico</it>. High level of allelic diversity in repeats including those present in the functional domains of proteins encoded by the unigenes demonstrated their use in assay of useful variation in the genic component of complex polyploid sugarcane genome.</p

Cloning and functional validation of early inducible Magnaporthe oryzae responsive CYP76M7 promoter from rice

Cloning and functional characterization of plant pathogen inducible promoters is of great significance for their use in the effective management of plant diseases. The rice gene CYP76M7 was up regulated at 24, 48, and 72 hours post inoculation (hpi) with two isolates of Magnaporthe oryzae Mo-ei-11 and Mo-ni-25. In this study, the promoter of CYP76M7 gene was cloned from rice cultivar HR-12, characterized and functionally validated. The Transcription Start Site of CYP76M7 was mapped at 45 bases upstream of the initiation codon. To functionally validate the promoter, 5′ deletion analysis of the promoter sequences was performed and the deletion fragments fused with the β-glucuronidase (GUS) reporter gene were used for generating stable transgenic Arabidopsis plants as well as for transient expression in rice. The spatial and temporal expression pattern of GUS in transgenic Arabidopsis plants and also in transiently expressed rice leaves revealed that the promoter of CYP76M7 gene was induced by M. oryzae. The induction of CYP76M7 promoter was observed at 24 hpi with M. oryzae. We report that, sequences spanning -222 bp to -520 bp, with the cluster of three W-boxes, two ASF1 motifs and a single GT-1 element may contribute to the M. oryzae inducible nature of CYP76M7 promoter. The promoter characterized in this study would be an ideal candidate for the overexpression of defense genes in rice for developing durable blast resistance rice lines

Chronic renal insufficiency among Asian Indians with type 2 diabetes: I. Role of RAAS gene polymorphisms

BACKGROUND: Renal failure in diabetes is mediated by multiple pathways. Experimental and clinical evidences suggest that renin-angiotensin-aldosterone system (RAAS) has a crucial role in diabetic kidney disease. A relationship between the RAAS genotypes and chronic renal insufficiency (CRI) among type 2 diabetes subjects has therefore been speculated. We investigated the contribution of selected RAAS gene polymorphisms to CRI among type 2 diabetic Asian Indian subjects. METHODS: Twelve single nucleotide polymorphisms (SNPs) from six genes namely-renin (REN), angiotensinogen (ATG), angiotensin converting enzyme I (ACE), angiotensin II type 1 receptor (AT1) and aldosterone synthase (CYP11B2) gene from the RAAS pathway and one from chymase pathway were genotyped using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method and tested for their association with diabetic CRI using a case-control approach. Successive cases presenting to study centres with type 2 diabetes of ≥2 years duration and moderate CRI diagnosed by serum creatinine ≥3 mg/dl after exclusion of non-diabetic causes of CRI (n = 196) were compared with diabetes subjects with no evidence of renal disease (n = 225). Logistic regression analysis was carried out to correlate various clinical parameters with genotypes, and to study pair wise interactions between SNPs of different genes. RESULTS: Of the 12 SNPs genotyped, Glu53Stop in AGT and A>T (-777) in AT1 genes, were monomorphic and not included for further analysis. We observed a highly significant association of Met235Thr SNP in angiotensinogen gene with CRI (O.R. 2.68, 95%CI: 2.01–3.57 for Thr allele, O.R. 2.94, 95%CI: 1.88–4.59 for Thr/Thr genotype and O.R. 2.68, 95%CI: 1.97–3.64 for ACC haplotype). A significant allelic and genotypic association of T>C (-344) SNP in aldosterone synthase gene (O.R. 1.57, 95%CI: 1.16–2.14 and O.R. 1.81, 95%CI: 1.21–2.71 respectively), and genotypic association of GA genotype of G>A (-1903) in chymase gene (O.R. 2.06, 95%CI: 1.34–3.17) were also observed. CONCLUSION: SNPs Met235Thr in angiotensinogen, T>C (-344) in aldosterone synthase, and G>A (-1903) in chymase genes are significantly associated with diabetic chronic renal insufficiency in Indian patients and warrant replication in larger sample sets. Use of such markers for prediction of susceptibility to diabetes specific renal disease in the ethnically Indian population appears promising

Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]

<p>Abstract</p> <p>Background</p> <p>Pigeonpea [<it>Cajanus cajan </it>(L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping.</p> <p>Results</p> <p>In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped <it>in silico </it>identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population.</p> <p>Conclusion</p> <p>We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing. From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the genus <it>Cajanus</it>. A comprehensive set of genic-SSR markers was developed as an important genomic resource for diversity analysis and genetic mapping in pigeonpea.</p

Yoga Practice Is Beneficial for Maintaining Healthy Lifestyle and Endurance Under Restrictions and Stress Imposed by Lockdown During COVID-19 Pandemic

Uncertainty about Coronavirus disease 2019 (COVID-19) and resulting lockdown caused widespread panic, stress, and anxiety. Yoga is a known practice that reduces stress and anxiety and may enhance immunity. This study aimed to (1) investigate that including Yoga in daily routine is beneficial for physical and mental health, and (2) to evaluate lifestyle of Yoga practitioners that may be instrumental in coping with stress associated with lockdown. This is a pan-India cross-sectional survey study, which was conducted during the lockdown. A self-rated scale, COVID Health Assessment Scale (CHAS), was designed by 11 experts in 3 Delphi rounds (Content valid ratio = 0.85) to evaluate the physical health, mental health, lifestyle, and coping skills of the individuals. The survey was made available digitally using Google forms and collected 23,760 CHAS responses. There were 23,290 valid responses (98%). After the study's inclusion and exclusion criteria of yogic practices, the respondents were categorized into the Yoga (n = 9,840) and Non-Yoga (n = 3,377) groups, who actively practiced Yoga during the lockdown in India. The statistical analyses were performed running logistic and multinomial regression and calculating odds ratio estimation using R software version 4.0.0. The non-Yoga group was more likely to use substances and unhealthy food and less likely to have good quality sleep. Yoga practitioners reported good physical ability and endurance. Yoga group also showed less anxiety, stress, fear, and having better coping strategies than the non-Yoga group. The Yoga group displayed striking and superior ability to cope with stress and anxiety associated with lockdown and COVID-19. In the Yoga group, participants performing meditation reportedly had relatively better mental health. Yoga may lead to risk reduction of COVID-19 by decreasing stress and improving immunity if specific yoga protocols are implemented through a global public health initiative

Genome-Wide Distribution and Organization of Microsatellites in Plants: An Insight into Marker Development in Brachypodium

Plant genomes are complex and contain large amounts of repetitive DNA including microsatellites that are distributed across entire genomes. Whole genome sequences of several monocot and dicot plants that are available in the public domain provide an opportunity to study the origin, distribution and evolution of microsatellites, and also facilitate the development of new molecular markers. In the present investigation, a genome-wide analysis of microsatellite distribution in monocots (Brachypodium, sorghum and rice) and dicots (Arabidopsis, Medicago and Populus) was performed. A total of 797,863 simple sequence repeats (SSRs) were identified in the whole genome sequences of six plant species. Characterization of these SSRs revealed that mono-nucleotide repeats were the most abundant repeats, and that the frequency of repeats decreased with increase in motif length both in monocots and dicots. However, the frequency of SSRs was higher in dicots than in monocots both for nuclear and chloroplast genomes. Interestingly, GC-rich repeats were the dominant repeats only in monocots, with the majority of them being present in the coding region. These coding GC-rich repeats were found to be involved in different biological processes, predominantly binding activities. In addition, a set of 22,879 SSR markers that were validated by e-PCR were developed and mapped on different chromosomes in Brachypodium for the first time, with a frequency of 101 SSR markers per Mb. Experimental validation of 55 markers showed successful amplification of 80% SSR markers in 16 Brachypodium accessions. An online database ‘BraMi’ (Brachypodium microsatellite markers) of these genome-wide SSR markers was developed and made available in the public domain. The observed differential patterns of SSR marker distribution would be useful for studying microsatellite evolution in a monocot–dicot system. SSR markers developed in this study would be helpful for genomic studies in Brachypodium and related grass species, especially for the map based cloning of the candidate gene(s)