A silver staining procedure for nucleic acids in polyacrylamide gels without fixation and pretreatment

Genetic diversity in Sickleweed (Falcaria vulgaris) and using stepwise regression to identify marker associated with traits

One of the well-known medicinal plants in the Falcaria genus is Sickleweed. Falcaria species exhibit a high degree of genetic variability, posing challenges in the examination of genetic diversity due to the significant potential for hybridization and introgression among them. Utilizing morphological traits and molecular markers may prove to be a valuable approach in evaluating and harnessing germplasm, considering the current obstacles faced in breeding this medicinal herb. In 2021, fifteen Sickleweed populations were cultivated in pots under field conditions, employing a randomized complete block design with three replications. This aimed to assess genetic diversity and conduct marker-trait association analyses utilizing morpho-physiological characteristics and SSR markers. The Sickleweed populations displayed considerable genetic diversity across all traits. Through cluster analysis of traits and the utilization of the UPGMA method based on the Gower distance matrix, the population was classified into three distinct clusters. Upon examining all genotypes, 52 polymorphic bands were detected, with an average of 8.68 bands per primer. The average expected heterozygosity across all loci was 0.864, while the average PIC was 0.855. Molecular data analysis employing the Jaccard similarity index and UPGMA method revealed the division of Sickleweed populations into two major groups. Furthermore, the results of molecular variance analysis indicated that variation within the population exceeded that between populations. Thirty-two SSR fragments were found to be significantly associated with genomic regions controlling the studied traits, determined through the application of stepwise regression. Selection based on molecular markers offers a rapid method for breeding programs, with the genetic information obtained from these markers playing a crucial role. Therefore, alongside traits, selecting superior genotypes and populations of high value in breeding programs becomes feasible. The findings highlight that certain markers are linked to multiple traits, emphasizing the critical importance of this characteristic in plant breeding for the simultaneous improvement of numerous traits. The study's insights regarding markers hold potential for application in Sickleweed breeding programs.

Sex-specific signalling of individual personality by a mutual plumage ornament in a passerine

Abstract

The significance of colour signals in species with strong sexual dimorphism and/or elaborated visual ornaments is rather well-understood. Less attention has, however, been devoted to study colour signals in species with weak or no apparent sexual dimorphism. In such species, an interesting possibility arises as both sexes can bear the same colour ornament(s) (i.e. sexes are mutually ornamented), but their signalling value might differ in males and females. We aimed to explore this possibility by investigating the phenotypic correlates of the black bib, a melanin-based plumage ornament, in the Eurasian tree sparrow (Passer montanus). More specifically, we studied the sex-dependent relationships between bib size and three aspects of individuals’ phenotype: body condition (i.e. size-corrected body mass), physiology (i.e. cellular innate immunity/inflammation status, expressed through total leucocyte counts, and chronic physiological stress, expressed through the ratio of heterophils to lymphocytes) and individual personality (i.e. activity in a novel environment). We found that bib size was not associated with body condition and cellular innate immunity/inflammation status, but was positively related to physiological stress levels independent of sex. Furthermore, bib size was negatively associated with activity in males but positively in females. Our findings bring important correlative evidence that mutual ornamental traits may have sex-specific signalling value.

Significance statement

The signalling role of elaborated colourful ornaments, that are usually possessed only by males in sexually dimorphic species, is well-established. The function of various colour traits which are borne by both sexes (i.e. mutual ornaments), however, is less obvious. Do they have a signalling value in both sexes? If yes, do they signal the same information in males and females? Or, most intriguingly, can they convey different information in the two sexes? To test these alternatives, we studied the signalling value of the black bib, a melanin-based mutual plumage ornament, in Eurasian tree sparrows (Passer montanus). Apart from being correlated with chronic stress in both sexes, bib size was positively related to activity in females but negatively in males. Our results suggest that the information content of the same colour trait in males and females can be different in mutually ornamented species.

Molecular mapping of a novel lesion mimic gene (lm4) associated with enhanced resistance to stripe rust in bread wheat

BACKGROUND

Lesion mimics (LMs) are disease-like symptoms that occur randomly on plant green leaves in the absence of pathogens. A previous study showed that LMs are related to enhanced resistance to a broad spectrum of diverse pathogen races and programmed cell death (PCD). Stripe rust is a globally epidemic fungal disease that can substantially reduce the quality and yield of crops. The development of resistant cultivars is an economical and environmentally friendly way to enhance the adaptability and yield stability of crops instead of the use of fungicide applications.

RESULTS

In this study, a novel LM gene affording Pst resistance was identified and mapped with molecular markers developed for marker-assisted selection (MAS)-based wheat breeding. In this study, a novel LM gene named lm4, which is closely linked (8.06 cM) to SSR markers Xgwm210 and Xgwm455, was identified by using a Yanzhan 1/Neixiang 188 RIL population. The genetic distance of lm4 was then narrowed such that it was flanked by SSR markers with 0.51 cM and 0.77 cM intervals. Two SSR markers, lm4_01_cib and lm4_02_cib, were developed based on the content in the Chinese Spring genome database and wheat 660 K SNP results; these markers can be used to conduct MAS of LMs in wheat. The results also showed that lm4 significantly improved the resistance of stripe rust in wheat.

CONCLUSIONS

Therefore, lm4 is associated with stripe rust resistance, which may provide theoretical support for future crop disease-resistance breeding and for understanding the plant apoptosis mechanism.

The associations between dietary patterns and bone health, according to the TGF-β1 T869→C polymorphism, in postmenopausal Iranian women

BACKGROUND/OBJECTIVE

Recent studies have shown that dietary variants and genetic variants play a decisive role in the risk of developing osteoporosis. Therefore, the objective of the present study was to examine associations between dietary pattern and bone health, according to the TGF-β1 T869→C polymorphism, in postmenopausal Iranian women.

MATERIALS AND METHODS

In this study, 264 postmenopausal women aged from 46 to 78 years were examined. Body composition was measured by a body composition analyzer and physical activity by the short-form physical activity questionnaire. Bone mineral density was measured by the DEXA method. Dietary patterns were determined using factor analysis on 27 foods groups, employing a valid, reliable 147-item semi-quantitative food frequency questionnaire. The dietary patterns were analyzed by the factor analysis method. Blood samples were taken for measuring blood parameters. DNA samples from participants were genotyped using the RFLP-PCR method.

RESULTS

Three dietary patterns were identified, namely: mediterranean diet, traditional diet, and unhealthy diet-one of which was associated with bone health. Postmenopausal women following a Mediterranean diet had lower weight and central obesity (0.05 > P). Higher adherence to a Mediterranean pattern was positively associated with Z-score L2_L4 lumbar spine (0.05 > P). TGF-β1 T869→C genotypes, after adjustment, were not directly correlated with bone mineral density and body composition (0.05 < P). Moreover, these findings demonstrated that in participants adhering to a Traditional dietary pattern, the C allele carrier group (TC and CC genotypes) had a lower L2_L4 Z-score (P = 0.05).

CONCLUSION

It seems that the mediterranean diet can be a beneficial dietary pattern in the prevention of osteoporosis and obesity in postmenopausal women. Furthermore (probably in the C allele carrier group), lower vitamin D intake, coupled with adherence to a traditional dietary pattern, reduces the deposition of TGF-beta and increases the risk of lumbar spine osteoporosis.

A Fast Silver Staining Protocol Enabling Simple and Efficient Detection of SSR Markers using a Non-denaturing Polyacrylamide Gel

Simple Sequence Repeat (SSR) is one of the most effective markers used in plant and animal genetic research and molecular breeding programs. Silver staining is a widely used method for the detection of SSR markers in a polyacrylamide gel. However, conventional protocols for silver staining are technically demanding and time-consuming. Like many other biological laboratory techniques, silver staining protocols have been steadily optimized to improve detection efficiency. Here, we report a simplified silver staining method that significantly reduces reagent costs and enhances the detection resolution and picture clarity. The new method requires two major steps (impregnation and development) and three reagents (silver nitrate, sodium hydroxide, and formaldehyde), and only 7 min of processing for a non-denaturing polyacrylamide gel. Compared to previously reported protocols, this new method is easier, quicker and uses fewer chemical reagents for SSR detection. Therefore, this simple, low-cost, and effective silver staining protocol will benefit genetic mapping and marker-assisted breeding by a quick generation of SSR marker data.

Molecular Characterization of Mx1 Gene in Native Indian Breeds of Chicken

The genetic polymorphism of Mx1 gene was explored in Indian chicken breeds. PCR-RFLP analysis in 102 bp fragment of partial intron 13 and partial exon 14 of Mx1 gene revealed two genotypes viz. RS and SS with two alleles viz. R and S both in Naked Neck and Tellicherry breeds of chicken. The homozygous genotype RR was not identified. When deduced amino acid sequences were compared, the asparagine amino acid was found to be substituted in "R" allele for serine in "S" allele. PCR-SSCP analysis of 284 bp fragment in 5'-UTR and partial promoter region revealed three genotypes viz. CC, CG, and CH with three different alleles viz. C, G, and H in Naked Neck breed of chicken and five genotypes viz. DI, JK, KK, KL, and KM with six different alleles viz. D, I, J, K, L, and M in Tellicherry breed of chicken. The homozygous genotypes viz. GG and HH in Naked Neck and DD, II, JJ, LL, and MM in Tellicherry chicken was not identified. The nucleotide substitution rate estimated to be in the range of 0.004-0.011. The identified genetic variation can be helpful for better insight to disease resistance property of the Mx1 gene.

Analysis of NSP4 Gene and Its Association with Genotyping of Rotavirus Group A in Stool Samples

Background

Non-structural protein 4 (NSP4) is a critical protein for rotavirus (RV) replication and assembly. This protein has multiple domains and motifs that predispose its function and activity. NSP4 has a sequence divergence in human and animal RVs. Recently, 14 genotypes (E1-E14) of NSP4 have been identified, and E1 and E2 have been shown to be the most common genotypes in human.

Methods

The gene and protein sequence of NSP4 in RV-positive samples were inspected with the aim of NSP4 genotyping and variation analysis in viroporin and other domains. P and G typings of RV samples were carried out by WHO primers using a semi-multiplex PCR method. Non-typeable RV samples were amplified by conserved primers and sequenced.

Results

In viroporin and enterotoxin, conserved sequence was detected, and amino acids substitution with the same biochemical properties was found.

Conclusion

Association of NSP4 genotype with P or G genotyping G1/G9 correlates with E1 genogroups. In electrophoretyping of RV, E2 genotype had a short pattern when compared to E1.

Simple and efficient way to detect small polymorphic bands in plants

There are many ways to detect polymorphism. In this study we use the microsatellite markers to detect the polymorphism for the salt tolerance. This method has been successfully conducted in Oryza sativa and Brassica juncea. The results are reproducible. In contrast to previous methods, our method is simple and quite accurate for detecting the polymorphic bands. In this study instead of using agarose gel and ethidium bromide staining, we used non-denaturing polyacrylamide gel and a low-cost improved method for silver staining when we compare it to 11 other methods for their ability to detect simple sequence repeat polymorphisms as small as 50 bp in denaturing polyacrylamide gels. All methods detected the same alleles and banding pattern. However, important differences in sensitivity, contrast, time consumption and background were observed.

Arg25Pro (c.915G>C) polymorphism of transforming growth factor β1 gene suggests an association with increased risk for Hashimoto's thyroiditis

BACKGROUND

The etiopathogenesis of Hashimoto's thyroiditis (HT) - has not been clearly elucidated although the role of chronic inflammation, endothelial dysfunction, and imbalance between pro- and anti-inflammatory cytokines has been established. Transforming growth factor β1 (TGFβ1) is required to maintain immune homeostasis, and is implicated in lymphocyte infiltration, production of autoantibodies and thyrocyte destruction seen in patients with HT.

AIM

The aim of the present study was to investigate the possible association of Leu10Pro (c.869T>C) and Arg25Pro (c.915G>C) single nucleotide polymorphisms (SNPs) of TGFβ1 gene with the occurrence of HT.

METHODS

We analyzed the genotype and allele frequencies of polymorphisms at codon 10 and 25 in 178 patients who had been diagnosed as having HT and 197 healthy controls using PCR-restriction fragment length polymorphism (RFLP).

RESULTS

There was no notable risk for HT afflicted by Leu10Pro (c.869T>C) polymorphism of TGFβ1 gene. However, there was a significant increase of Arg25Pro (c.915G>C) C allele frequency in patients with HT compared with healthy controls (p=0.003, OR=1.87, 95% CI=1.23-2.84). Moreover, heterozygous (CG) subjects had a 2.53-fold increased risk for developing HT with respect to wild (GG) homozygotes (p<0.001, 95% CI=1.57-4.05). TSH levels in CG heterozygous patients were increased in comparison with wild homozygotes (p=0.006).

CONCLUSION

This study indicates that the Arg25Pro (c.915G>C) polymorphism of TGFβ1 gene may be related to increased risk for HT.

Association of HPV with genetic and epigenetic alterations in colorectal adenocarcinoma from Indian population

Several studies from developing countries have shown human papillomavirus to be associated with colorectal cancers, but the molecular characteristics of such cancers are poorly known. We studied the various genetic variations like microsatellite instability (MSI), oncogenic mutations and epigenetic deregulations like CpG island methylation in HPV associated and nonassociated colorectal cancer patients from Indian population. HPV DNA was detected by PCR using My09/My11 and Gp5+/Gp6+ consensus primers and typed using HPV16 and HPV18 specific primers. MSI was detected using BAT 25 and BAT 26 markers, and mutation of KRAS, TP53 and BRAF V600E were detected by direct sequencing. Methyl specific polymerase chain reaction (MSP) was used to determine promoter methylation of the classical CIMP panel markers (P16, hMLH1, MINT1, MINT2 and MINT31) and other tumour-related genes (DAPK, RASSF1, BRCA1 and GSTP1). HPV DNA was detected in 34/93 (36.5 %) colorectal tumour tissues, HPV 18 being the predominant high-risk type. MSI was detected in 7.5 % cases; KRAS codon 12, 13, BRAF V600E and TP53 mutations were detected in 36.5, 3.2 and 37.6 % of the cases, respectively. CIMP-high was observed in 44.08 % cases. HPV presence was not associated with age, stage or grade of tumours, MSI or mutations in KRAS, TP53 or BRAF genes. Higher methylation frequencies of all genes/loci under study except RASSF1, as well as significantly higher CIMP-high characteristics were observed in HPV positive tumours as compared to negative cases. HPV in association with genetic and epigenetic features might be a potent risk factor for colorectal cancer in Indian population.

Contribution of Mouse Embryonic Stem Cells and Induced Pluripotent Stem Cells to Chimeras through Injection and Coculture of Embryos

Blastocyst injection and morula aggregation are commonly used to evaluate stem cell pluripotency based on chimeric contribution of the stem cells. To assess the protocols for generating chimeras from stem cells, 8-cell mouse embryos were either injected or cocultured with mouse embryonic stem cells and induced pluripotent stem cells, respectively. Although a significantly higher chimera rate resulted from blastocyst injection, the highest germline contribution resulted from injection of 8-cell embryos with embryonic stem cells. The fully agouti colored chimeras were generated from both injection and coculture of 8-cell embryos with embryonic stem cells. Additionally, microsatellite DNA screening showed that the fully agouti colored chimeras were fully embryonic stem cell derived mice. Unlike embryonic stem cells, the mouse chimeras were only generated from injection of 8-cell embryos with induced pluripotent stem cells and none of these showed germline transmission. The results indicated that injection of 8-cell embryos is the most efficient method for assessing stem cell pluripotency and generating induced pluripotent stem cell chimeras, embryonic stem cell chimeras with germline transmission, and fully mouse embryonic stem cell derived mice.

A comparison of silver staining protocols for detecting DNA in polyester-backed polyacrylamide gel

Eight silver-staining protocols were applied to detect DNA in polyester-backed gels to select the optimal. Results showed important differences in staining quality and that four methods were well-suited for TGGE gels due to high sensitivity and low background, including the Bassam et al. methods, the manufacturer method and our improved method.