G-ACP: a machine learning approach to the prediction of therapeutic peptides for gastric cancer

Conventional Gastrointestinal (GI) cancer treatments are quite expensive and have major hazards. Nowadays, a different strategy places more emphasis on creating tiny biologically active peptides that do not cause severe poisoning. Anticancer peptides (ACPs) are found through experimental screening, which is time-dependent and frequently fraught with difficulties. Gastric ACPs are emerging as a promising GI cancer treatment in the current day. It is crucial to identify novel gastric ACPs to have an improved knowledge of their functioning processes and treatment of gastric cancer. As a result of the post-genomic era's massive production of peptide sequences, rapid and effective ACPs using a computational method are essential. Several adaptive statistical techniques for distinguishing ACPs and non-ACPs have recently been developed. A variety of adapted statistically significant methods have been developed to differentiate between ACPs and non-ACPs. Despite significant progress, there is no specific model for the prediction of gastric ACPs because the specific model will predict a particular type of peptide more accurately and quickly. To overcome this, an initiative is taken for the creation of a reliable framework for the accurate identification of gastric ACPs. The current technique in particular contains four possible features along with one hybrid feature encoding mechanisms which are the target-class motif previously indicated by Amino Acid Composition, Dipeptide Composition, Tripeptide Composition (TPC), Pseudo Amino Acid Composition (PAAC), and their Hybrid. Machine Learning algorithms make high-performance and accurate prediction tools. Moreover, highly variable and ideal deep feature selection is done using an ANOVA-based F score for feature pruning. Experiments on a range of algorithms are carried out to identify the optimal operating strategy due to the diverse nature of learning. Following analysis of the empirical results, Naïve Bayes with TPC and Hybrid feature space outperforms other methods with 0.99 accuracy score on the testing dataset. To find the model generalization an external validation is carried out. In external datasets, the Extra Trees with PAAC features outperforms with the accuracy of 0.94. The comparison study shows that our suggested model will predict gastric ACPs more accurately and will be useful in drug development and gastric cancer. The predictive model can be freely accessed at https://github.com/humeraazad10/G-ACP.git.Communicated by Ramaswamy H. Sarma.

High Genetic Diversity in the Himalayan Common Bean (Phaseolus vulgaris) Germplasm with Divergence from Its Center of Origin in the Mesoamerica and Andes

The common bean is found in the Himalayan region of Pakistan with substantial morphological variability. Genetic diversity within any crop species is a precursor for genetic improvement; however, little is known about common bean genetic diversity in this region. We explored the genetic diversity in the common bean from the Himalayan region (Khyber Pakhtunkhwa, Gilgit-Baltistan, Kashmir) of Pakistan. Microsatellite genotyping was carried out for 147 samples with 40 simple sequence repeat (SSR) markers. The results revealed a clear divergence of the Pakistani population from the primary gene pool (with FST values of 0.2 with Andes and 0.27 with Mesoamerica). However, within the Himalayan germplasm, no clear evidence of spatial structure was observed (with the maximum FST values of only 0.025), probably due to the dispersal of seeds by human activity within the region. This was further elucidated by the discriminant analyses of principal components. Considering the diversity parameters, high genotypic diversity was observed for the indigenous lines (0.990), comparable to the primary gene pool (0.976 for Mesoamerica and 0.976 for Andes populations). A high genotypic diversity was observed within the Himalayan population (ranging from 0.500 for Upper Dir to 0.952 for Mansehra). Gene diversity across loci varied between 0.28 for Chitral to 0.38 for Kurram. Our results suggested a divergent and independent evolution of the Himalayan population, which might have led to the diversification of the common bean germplasm in the region postintroduction into the region. The diversity observed could also be exploited in future breeding programs for the development and introduction of climate-resilient varieties.

The comparative transcriptome analysis of two green super rice genotypes with varying tolerance to salt stress

BACKGROUND

Salinity is one of the main abiotic factors that restrict plant growth, physiology, and crop productivity is salt stress. About 33% of the total irrigated land suffers from severe salinity because of intensive underground water extraction and irrigation with brackish water. Thus, it is important to understand the genetic mechanism and identify the novel genes involved in salt tolerance for the development of climate-resilient rice cultivars.

METHODS AND RESULTS

In this study, two rice genotypes with varying tolerance to salt stress were used to investigate the differential expressed genes and molecular pathways to adapt under saline soil by comparative RNA sequencing at 42 days of the seedling stage. Salt-susceptible (S3) and -tolerant (S13) genotypes revealed 3982 and 3463 differentially expressed genes in S3 and S13 genotypes. The up-regulated genes in both genotypes were substantially enriched in different metabolic processes and binding activities. Biosynthesis of secondary metabolites, phenylpropanoid biosynthesis, and plant signal transduction mechanisms were highly enriched. Salt-susceptible and -tolerant genotypes shared the same salt adaptability mechanism with no significant quantitative differences at the transcriptome level. Moreover, bHLH, ERF, NAC, WRKY, and MYB transcription factors were substantially up-regulated under salt stress. 391 out of 1806 identified novel genes involved in signal transduction mechanisms. Expression profiling of six novel genes further validated the findings from RNA-seq data.

CONCLUSION

These findings suggest that the differentially expressed genes and molecular mechanisms involved in salt stress adaptation are conserved in both salt-susceptible and salt-tolerant rice genotypes. Further molecular characterization of novel genes will help to understand the genetic mechanism underlying salt tolerance in rice.

Bacopa monnieri: A promising herbal approach for neurodegenerative disease treatment supported by in silico and in vitro research

Neurodegenerative disorders, caused by progressive neuron loss, are a global health issue. Among the various factors implicated in their pathogenesis, dysregulation of acetylcholinesterase activity has been recognized as a key contributor. Acetylcholinesterase breaks down the neurotransmitter acetylcholine, important for neural transmission. Evaluating phyto-compounds from Bacopa monnieri Linn. through in vitro and in silico analysis may expand their role as alternative therapeutic agents by modulating the function of acetylcholinesterase and complementing existing treatments. To accomplish this objective, chemical structures of phyto-compounds were retrieved from PubChem database and subjected to in silico and in vitro approaches. Virtual screening was performed through molecular docking and molecular dynamic simulation resulting in four top hit compounds including quercetin, apigenin, wogonin, and bacopaside X (novel lead compound for acetylcholinesterase inhibitor) with least binding score. Further, dose dependent acetylcholinesterase inhibition biochemical assay depicted that bacopaside X, apigenin, quercetin, and wogonin exhibited strong potential against acetylcholinesterase with IC50 values of 12.78 μM, 13.83 μM, 12.73 μM and 15.48 μM respectively, in comparison with the donepezil (IC50: 0.0204 μM). The in silico and in vitro research suggests that B. monnieri phyto-compounds have the potential to modulate molecular targets associated with neurodegenerative diseases and have a role in neuroprotection.

Synergistic neuroprotection by phytocompounds of Bacopa monnieri in scopolamine-induced Alzheimer's disease mice model

BACKGROUND

Millions of people around the globe are affected by Alzheimer's disease (AD). This crippling condition has no treatment despite intensive studies. Some phytocompounds have been shown to protect against Alzheimer's in recent studies.

METHODS

Thus, this work aimed to examine Bacopa monnieri phytocompounds' synergistic effects on neurodegeneration, antioxidant activity, and cognition in the scopolamine-induced AD mice model. The toxicity study of two phytocompounds: quercetin and bacopaside X revealed an LD50 of more than 2000 mg/kg since no deaths occurred.

RESULTS

The neuroprotection experiment consists of 6 groups i.e., control (saline), scopolamine (1 mg/kg), donepezil (5 mg/kg), Q (25 mg/kg), BX (20 mg/kg), and Q + BX (25 mg/kg + 20 mg/kg). Visual behavioral assessment using the Morris water maze showed that animals in the diseased model group (scopolamine) moved more slowly toward the platform and exhibited greater thigmotaxis behavior than the treatment and control groups. Likewise, the concentration of biochemical NO, GSH, and MDA improved in treatment groups concerning the diseased group. mRNA levels of different marker genes including ChAT, IL-1α, IL-1 β, TNF α, tau, and β secretase (BACE1) improved in treatment groups with respect to the disease group.

CONCLUSION

Both bacopaside X and quercetin synergistically have shown promising results in neuroprotection. Therefore, it is suggested that Q and BX may work synergistically due to their antioxidant and neuroprotective property.

Potential of nanotechnology to replace cancer stem cells

Stem cells, which were initially identified in the 1900s, are distinct cells with the potential to replenish themselves as well as differentiate into specialised cells with certain forms and functions. Cancer stem cells play a significant role in the growth and recurrence of the tumours and, similar to normal stem cells, are capable of proliferating and differentiating. Traditional cancer treatments are ineffective against cancer stem cells, which leads to tumour regrowth. Cancer stem cells are thought to emerge as a result of epithelial-to-mesenchymal transition pathways. Brain, prostate, pancreatic, blood, ovarian, lung, liver, melanomas, AML, and breast cancer stem cells are among the most prevalent cancer forms. This review aims to comprehend the possibility of using specific forms of nanotechnology to replace cancer stem cells. In terms of nanotechnology, magnetic nanoparticles can deliver medications, especially to the target region without harming healthy cells, and they are biocompatible. In order to kill glioma cancer stem cells, the gold nanoparticles bond with DNA and function as radio sensitizers. In contrast, liposomes can circulate and traverse biological membranes and exhibit high therapeutic efficacy, precise targeting, and better drug release. Similar to carbon nanotubes, grapheme, and grapheme oxide, these substances can be delivered specifically when utilized in photothermal therapy. Recent treatments including signaling pathways and indicators targeted by nanoparticles are being researched. Future research in nanotechnology aims to develop more effective and targeted medicinal approaches. The results of the current investigation also showed that this technology's utilization will improve medical therapy and treatment.

Screening and validation of salt-stress responsive cg-SSR markers in wheat (Triticum aestivum L.) germplasm of Pakistan

BACKGROUND

Soil salinity has been affecting wheat production worldwide over past few decades. Evaluation of wheat genotypes for salinity tolerance at germination and vegetative growth level is crucial. Marker assisted selection is a technique used extensively for choosing salt-tolerant genotypes from breeding populations to introduce novel genes.

METHODS AND MATERIALS

The current study's main goal was to discover salt-stress resistant genes; genetic divergence and genome-wide connection by using recently designed candidate gene-based simple-sequence-repeat markers (cg-SSRs). The phenotypic connection of morphological features during the germination growth stage i.e., germination period, root length/weight and shoot length/weight, and vegetative growth stages i.e., root length/weight and shoot length/weight were tested in a group of 50 wheat genotypes. Significant difference was observed in germination rate, root length and weight among control and saline treatments.

CONCLUSION

Total 30 SSR markers were utilized to test salinity resistance genes in wheat genotypes. Three (10%) of which were monomorphic, one (3.34%) showed no result, and the other 26 (86%) were polymorphic. Using 30 polymorphic markers discovered total 37 alleles. The polymorphic information content (PIC), quantifies each SSR locus capacity to discriminate between wheat, varied from 0.00 to 0.38 with an average of 0.19. Association analysis revealed that 26 primers were associated with morphological features, 03 with root length and the remaining 23 with germination. Utilizing morphological data, stress tolerance index (STI) was designed concluding that Auqab-2000, Margala-99 and Ufaq showed better resistance against salinity among other wheat genotypes. Cluster analysis demonstrated that wheat genotypes have vast genetic variability.

CRISPR/Cas9 editing of wheat Ppd-1 gene homoeologs alters spike architecture and grain morphometric traits

Mutations in Photoperiod-1 (Ppd-1) gene are known to modify flowering time and yield in wheat. We cloned TaPpd-1 from wheat and found high similarity among the three homoeologs of TaPpd-1. To clarify the characteristics of TaPpd-1 homoeologs in different photoperiod conditions for inflorescence architecture and yield, we used CRISPR/Cas9 system to generate Tappd-1 mutant plants by simultaneous modification of the three homoeologs of wheat Ppd-1. Tappd-1 mutant plants showed no off-target mutations. Four T₀-edited lines under short-day length and three lines under long-day length conditions with the mutation frequency of 25% and 21%, respectively. These putative transgenic plants of all the lines were self-fertilized and generated T₁ and T₂ progenies and were evaluated by phenotypic and expression analysis. Results demonstrated that simultaneously edited TaPpd-1- A1, B1, and D1 homoeologs gene copies in T2_SDL-8-4, T2_SDL-4-5, T2_SDL-3-9, and T2_{_}LDL-10-9 showed similar spike inflorescence, flowering time, and significantly increase in 1000-grain weight, grain area, grain width, grain length, plant height, and spikelets per spike due to mutation in both alleles of Ppd-B1 and Ppd-D1 homoeologs but only spike length was decreased in T2_SDL-8-4, T2_SDL-4-5, and T2_{_}LDL-13-3 mutant lines due to mutation in both alleles of Ppd-A1 homoeolog under both conditions. Our results indicate that all TaPpd1 gene homoeologs influence wheat spike development by affecting both late flowering and earlier flowering but single mutant TaPpd-A1 homoeolog affect lowest as compared to the combination with double mutants of TaPpd-B1 and TaPpd-D1, TaPpd-A1 and TaPpd-B1, and TaPpd-A1 and TaPpd-D1 homoeologs for yield enhancement. Our findings further raised the idea that the relative expression of the various genomic copies of TaPpd-1 homoeologs may have an impact on the spike inflorescence architecture and grain morphometric features in wheat cultivars.

Temporal Comparative Transcriptome Analysis on Wheat Response to Acute Cd Toxicity at the Seedling Stage

Cadmium (Cd) is a non-essential and toxic metal that accumulates in plant's tissues and diminishes plant growth and productivity. In the present study, differential root transcriptomic analysis was carried out to identify Cd stress-responsive gene networks and functional annotation under Cd stress in wheat seedlings. For this purpose, the Yannong 0428 wheat cultivar was incubated with 40 µm/L of CdCl₂·2.5H₂O for 6 h at three different seedling growth days. After the quality screening, using the Illumina Hiseq 2000 platform, more than 2482 million clean reads were retrieved. Following this, 84.8% to 89.3% of the clean reads at three time points under normal conditions and 86.5% to 89.1% of the reads from the Cd stress condition were mapped onto the wheat reference genome. In contrast, at three separate seedling growth days, the data analysis revealed a total of 6221 differentially expressed genes (DEGs), including 1543 (24.8%) up-regulated genes and 4678 (75.8%) down-regulated genes. In total, 120 DEGs were co-expressed throughout all the growth days, whereas 1096, 1088, and 2265 DEGs were found to be selectively up-/down-regulated at 7d, 14d, and 30d, respectively. However, the clustering of DEGs, through utilizing the Kyoto Encyclopedia of Genes and Genomes (KEGG), revealed that the DEGs in the metabolic category were frequently annotated for phenylpropanoid biosynthesis. In comparison, a considerable number of DEGs were linked to protein processing in the endoplasmic reticulum under the process of genetic information processing. Similarly, in categories in organismal systems and cellular processes, DEGs were found in plant hormone signal transduction pathways, and DEGs were identified in the plant-pathogen interaction pathway, respectively. However, DEGs in "endocytosis pathways" were enriched in environmental information processing. In addition, in-depth annotations of roughly specific heavy metal stress-response genes and pathways were also mined, and the expression patterns of eight DEGs were studied using quantitative real-time PCR. The results were congruent with the findings of RNA sequencing regarding transcript abundance in the studied wheat cultivar.

Anxiety, depression and stress among internally displaced persons and host community in an armed conflict region: A comparative study

This study compares the psychological profile of Internally Displaced Persons (IDPs) and individuals living in host communities in the war-affected setting. We conducted a cross-sectional survey from October-November 2019. Subjects were recruited from six IDPs camps and the surrounding host communities within the metropolis of Maiduguri, Nigeria by convenience sampling. Data were collected using the Hausa version of Depression Anxiety Stress Scale-21, and analysed by logistic regression using adjusted odds ratio (AOR) at 95% Confidence Interval (CI). A total of 562 subjects were recruited. Living in IDP camp was the most significantly predictor of depression, anxiety, and stress. The common predictors were living in an IDP camp, and marital status (separated). Aged 18-29years was a protective factor compared to those ≥50years. Living in IDP camps, separated from partners, lack of education and pre-conflict employment were significant predictors of depression, anxiety and stress.

In silico-prediction of chloroquine as a multi-targeted drug against CDKN2A signaling network associated with cutaneous malignant melanoma

Melanoma is one of the most common skin infections, has triggered significant morbidity and mortality across the globe. Previous studies have reported that mutations in CDKN2A signalling network is associated with cutaneous malignant melanoma. In the present study, initially, the BioGrid database was utilized, and then hierarchical clustering was performed to identify the CDKN2A signature pathways. In addition, a GO Enrichment analysis was investigated using DAVID (n=187 genes) toolkit. Subsequently, the cBioPortal cancer genomic platform was exploited using alteration ranked frequency to determine the role of the CDKN2A signaling network in 363 samples of cutaneous malignant melanoma patients and we find that CDKN2A and its close interactors PTEN and HUWE1 show highest mutations. Further, we systematically employed molecular docking approach via MOE to target PTEN, CDKN2A and HUWE1 with chloroquine which is naturally occurring in medicinal plant Nigella sativa (NS) and observed virtuous interactions between all receptors and ligand molecules with a binding energy of -11.379, -10.324 and -9.06 Kcal/mol, respectively. The outcomes obtained stipulate a vigorous research resource for using chloroquine as a multitargeted anticancer drug. This novel evidence should help the development of effective therapeutic compounds for the treatment of cancer. Our results reveal that chloroquine is a relevant and novel potential therapeutic drug for the treatment of melanoma.

Probiotic Yeast Saccharomyces: Back to Nature to Improve Human Health

Saccharomyces cerevisiae var. boulardii is best known for its treatment efficacy against different gastrointestinal diseases. This probiotic yeast can significantly protect the normal microbiota of the human gut and inhibit the pathogenicity of different diarrheal infections. Several clinical investigations have declared S. cerevisiae var. boulardii a biotherapeutic agent due to its antibacterial, antiviral, anti-carcinogenic, antioxidant, anti-inflammatory and immune-modulatory properties. Oral or intramuscular administration of S. cerevisiae var. boulardii can remarkably induce health-promoting effects in the host body. Different intrinsic and extrinsic factors are responsible for its efficacy against acute and chronic gut-associated diseases. This review will discuss the clinical and beneficial effects of S. cerevisiae var. boulardii in the treatment and prevention of different metabolic diseases and highlight some of its health-promising properties. This review article will provide fundamental insights for new avenues in the fields of biotherapeutics, antimicrobial resistance and one health.

Impact of Pre-Anthesis Drought Stress on Physiology, Yield-Related Traits, and Drought-Responsive Genes in Green Super Rice

Optimum soil water availability is vital for maximum yield production in rice which is challenged by increasing spells of drought. The reproductive stage drought is among the main limiting factors leading to the drastic reduction in grain yield. The objective of this study was to investigate the molecular and morphophysiological responses of pre-anthesis stage drought stress in green super rice. The study assessed the performance of 26 rice lines under irrigated and drought conditions. Irrigated treatment was allowed to grow normally, while drought stress was imposed for 30 days at the pre-anthesis stage. Three important physiological traits including pollen fertility percentage (PFP), cell membrane stability (CMS), and normalized difference vegetative index (NDVI) were recorded at anthesis stage during the last week of drought stress. Agronomic traits of economic importance including grain yield were recorded at maturity stage. The analysis of variance demonstrated significant variation among the genotypes for most of the studied traits. Correlation and principal component analyses demonstrated highly significant associations of particular agronomic traits with grain yield, and genetic diversity among genotypes, respectively. Our study demonstrated a higher drought tolerance potential of GSR lines compared with local cultivars, mainly by higher pollen viability, plant biomass, CMS, and harvest index under drought. In addition, the molecular basis of drought tolerance in GSR lines was related to upregulation of certain drought-responsive genes including OsSADRI, OsDSM1, OsDT11, but not the DREB genes. Our study identified novel drought-responsive genes (LOC_Os11g36190, LOC_Os12g04500, LOC_Os12g26290, and LOC_Os02g11960) that could be further characterized using reverse genetics to be utilized in molecular breeding for drought tolerance.

Genome-wide characterization and expression analysis of pseudo-response regulator gene family in wheat

Pseudo-response regulator (PRR) gene family members play a significant role in plant circadian clocks, flowering time inflorescence architecture development during transition from vegetative growth phase to reproductive phase. In current study, we analyzed the expression profiling, phylogenetic relationship, and molecular characterization of PRR gene family members of common wheat by using IWGSC Ref seq v1.1 wheat genome database with a coverage rate of 90%. By using bioinformatic approach total 20 candidate gene sequences were identified and divided into six groups and four clades. It was found that mostly genes have same number of exons and introns showed similar features because they originated through duplication events during evolution processes. Although all the proteins have conserved PRR domains, but some are distinct in their sequences suggesting functional divergence. By comparative synteny analysis it was revealed that Group 1, 2, 3 and 11-D of group 4 have duplication events while group 5 and TaPRR9-B,10-D showed conservation with previously identified PRR members from rice. While expression variation of six groups from each analysis matches with each other. Five groups highly expressed in leaf, spike, and roots in pattern like leaf > spike > root at all three stages booting, heading and anthesis of spike development. This suggests that TaPRR genes play important roles in different photoperiod signaling pathways in different organs at different stages of spike development and flowering via unknown pathway. These findings will also provide comprehensive knowledge about future investigations on wheat PRR family members involved in complex network of circadian system for plant development.

Molecular Identification and Characterization of Bacillus sp. NIGAB-1 for Phenol Degradation Under Saline Conditions

Background

Phenol is an aromatic pollutant in industrial wastes that in combination with salts is highly toxic for all forms of life. Phenol elimination is the foremost challenge to meet the goal of pollutant-free environment.

Objective

The present study was carried out to isolate phenol degrading bacteria which can degrade phenol under saline conditions and to identify the isolated strains using 16S rRNA gene sequence analysis.

Material and Methods

Sediment samples were collected from Rawal Lake, Islamabad, Pakistan and enriched in mineral salt medium (MSM) containing phenol (150 mg.L^-1). Isolated strains were identified on the basis of 16S rRNA gene sequence analysis. Growth of strains were tested at different pH, NaCl concentrations and temperature using Tryptic Soy Agar (TSA). Tolerance to phenol (0-750 mg.L^-1) was checked at 5% NaCl and phenol degrading experiment was performed at 4% NaCl, pH 7 and 30 oC. In both, phenol tolerance and degradation study, phenol was used a sole source of carbon and energy.

Results

Thirteen bacterial strains were isolated after enrichment among which, NIGAB-1 was found capable of degrading phenol in saline conditions. This strain was identified as Bacillus sp. NIGAB-1 on the basis of 16S rRNA gene sequence analysis and the closest match was Bacillus marisflavi with 99.71% sequence identity. The Bacillus sp. NIGAB-1 exhibited best growth at 30 oC at pH 7 with 10% NaCl. The optimum phenol concentration for growth was recorded as 300 mg.L^-1. This strain degraded 300 mg.L-1 of phenol at 4% NaCl in 120 hours with the average degradation rate of 2.63 mg.L^-1.h.

Conclusion

These findings suggest that this strain could be efficient in phenol degradation at adverse environmental conditions and helpful in remediation of phenol where the salt concentration is high.

What are farmers really planting? Measuring the presence and effectiveness of Bt cotton in Pakistan

Genetically modified, insect-resistant Bacillus thuringiensis (Bt) cotton is cultivated extensively in Pakistan. Past studies, however, have raised concerns about the prevalence of Bt cotton varieties possessing weak or nonperforming insect-resistance traits conferred by the cry gene. We examine this issue using data drawn from a representative sample of cotton-growing households that were surveyed in six agroclimatic zones spanning 28 districts in Pakistan in 2013, as well as measurements of Cry protein levels in cotton tissue samples collected from the sampled households’ main fields. The resultant dataset combines information from 593 sampled households with corresponding plant tissue diagnostics from 70 days after sowing, as well as information from 589 sampled households with corresponding diagnostics from 120 days after sowing. Our analysis indicates that 11 percent of farmers believed they were cultivating Bt cotton when, in fact, the Cry toxin was not present in the tested tissue at 70 days after sowing (i.e., a Type I error). The analysis further indicates that 5 percent of farmers believed they were cultivating non-Bt cotton when, in fact, the Cry toxin was present in the tested tissue (i.e., a Type II error). In addition, 17 percent of all sampled farmers were uncertain whether or not they were cultivating Bt cotton. Overall, 33 percent of farmers either did not know or were mistaken in their beliefs about the presence of the cry gene in the cotton they cultivated. Results also indicate that toxic protein levels in the plant tissue samples occurred below threshold levels for lethality in a significant percentage of cases, although these measurements may also be affected by factors related to tissue sample collection, handling, storage, and testing procedures. Nonetheless, results strongly suggest wide variability both in farmers’ beliefs and in gene expression. Such variability has implications for policy and regulation in Pakistan’s transgenic cotton seed market.

WSA206, a paralog of duplicated MPF2-like MADS-box family is recruited in fertility function in Withania

Best known for their implication in calyx inflation, MPF2-like genes pertinent to the STMADS11 clade of the MADS-box family exert their functions in leaf development, flowering time, inflorescence architecture and floral reversion to just name but a few. However, our knowledge about their involvement in fertility function remained obscure. Therefore the major thrust of this study was to probe the recruitment of WSA206 (MPF2-like) protein in fertility function. The WSA206 functions were revealed by knocking down and overexpressing this protein in Withania somnifera. The WSA206 promoter functions were defined by stable integration in Arabidopsis using GUS tag. The interactions of WSA206 were investigated by screening Arabidopsis Oligo-dT yeast library and YFP-split analysis. WSA206 knockdown plants revealed fewer flowers, abortion in seed set, reduction in pollen number and deformed non-viable pollen in comparison with wild type counterparts. Overexpression of WSA206 in Withania generated more berries/seeds and healthier viable pollen grains. Remarkably, along with fertility control, the impairment in calyx inflation in knockdown Withania plants and extraordinary growth of sepals in overexpression lines is observed. Thus, fertility and calyx inflation are tightly coupled traits under the control of WSA206. Coding sequence revealed SNP mutations from arginine to lysine as well as a leucine-rich motif duplication at the C-terminus, a characteristic feature of pollen specific and fertility function proteins. The protein-protein interaction spectrum of WSA206 comprises 40% of those MADS and non-MADS-box proteins implicated in floral/anther expression and embryogenesis. Predominant WSA206 promoter:GUS expression accrued in the anthers/pollen may be attributed to of the presence of GAAATTGTTA pollen specific proximal motifs along with several other anther specific homotypic cis-clusters. MPF2-like protein WSA206 through interactions with MADS-box and non-MADS-domain proteins confers male fertility in Withania regulated by anther/pollen specific promoter motif GAAATTGTTA.

WITHDRAWN: Physiological and biochemical characterization of tomato transgenic lines overexpressing Arabidopsis thaliana cold responsive-element binding factor 3 (AtCBF3) gene under chilling stress

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WsMAGO2, a duplicated MAGO NASHI protein with fertility attributes interacts with MPF2-like MADS-box proteins

WsMAGO2 a duplicated protein in Withania through interactions with MPF2-like proteins affects male fertility by producing fewer flowers and aborted non-viable pollens/seeds regulated by anther-specific GAATTTGTGA motif. The MAGO NASHIs are highly conserved genes that encode proteins known to be involved in RNA physiology and many other developmental processes including germ cell differentiation in animals. However, their structural and functional implications in plants as fertility function proteins remained fragmented. MAGO (shorter name of MAGO NASHI) proteins form heterodimers with MPF2-like MADS-box proteins which are recruited in calyx identity and male fertility in Solanaceous plants. Four MAGO genes namely WsMAGO1 and WsMAGO2 and TaMAGO1 and TaMAGO2 were isolated from Withania somnifera and Tubocapsicum anomalum, respectively. These genes have duplicated probably due to whole genome duplication event. Dysfunction of WsMAGO2 through double-stranded RNAi in Withania revealed suppression of RNA transcripts, non-viable pollens, fewer flowers and aborted non-viable seeds in the developing berry suggesting a role of this protein in many traits particularly male fertility. WsMAGO2 flaunted stronger yeast 2-hybrid interactions with MPF2-like proteins WSA206, WSB206 and TAB201 than other MAGO counterparts. The native transcripts of WsMAGO2 culminated in stamens and seed-bearing berries though other MAGO orthologs also exhibited expression albeit at lower level. Coding sequences of the two orthologs are highly conserved, but they differ substantially in their upstream promoter regions. Remarkably, WsMAGO2 promoter is enriched with many anther-specific cis-motifs common in fertility function genes promoters. Among them, disruption of GAATTTGTGA abolished YFP/GUS gene expression in anthers alluding towards its involvement in regulating expression of MAGO in anther. Our findings support a possible recruitment of WsMAGO2 in fertility trait in Withania. These genes have practical application in hybrid production through cytoplasmic male sterility maintenance for enhancement in crops yield.

Dealing naturally with stumbling blocks on highways and byways of TRAIL induced signaling

In-depth analysis of how TRAIL signals through death receptors to induce apoptosis in cancer cells using high throughput technologies has added new layers of knowledge. However, the wealth of information has also highlighted the fact that TRAIL induced apoptosis may be impaired as evidenced by experimental findings obtained from TRAIL resistant cancer cell lines. Overwhelmingly, increasing understanding of TRAIL mediated apoptosis has helped in identifying synthetic and natural compounds which can restore TRAIL induced apoptosis via functionalization of either extrinsic or intrinsic pathways. Increasingly it is being realized that biologically active phytochemicals modulate TRAIL induced apoptosis, as evidenced by cell-based studies. In this review we have attempted to provide an overview of how different phytonutrients have shown efficacy in restoring apoptosis in TRAIL resistant cancer cells. We partition this review into how the TRAIL mediated signaling landscape has broadened over the years and how TRAIL induced signaling machinery crosstalks with autophagic protein networks. Subsequently, we provide a generalized view of considerable biological activity of coumarins against a wide range of cancer cell lines and how coumarins (psoralidin and esculetin) isolated from natural sources have improved TRAIL induced apoptosis in resistant cancer cells. We summarize recent updates on piperlongumine, phenethyl isothiocyanate and luteolin induced activation of TRAIL mediated apoptosis. The data obtained from pre-clinical studies will be helpful in translation of information from benchtop to the bedside.

Functional evolution of cis-regulatory modules of STMADS11 superclade MADS-box genes

Evolution of phenotypic morphologies is closely associated with modular organization of cis-regulatory elements underlying expression divergence. The MADS-box gene family is the subject of extensive studies that try to unscramble the structural complexity of flowering plants. This study is envisaged to explore the potential of CRMs in highly constrained non-coding elements of STMADS11superclade MADS-box genes in expression divergence. Phylogenetic reconstruction differentiated the STMADS11 genes into SVP-like, ZMM19-like, MPF1-like and MPF2-like clades. Differential gene expression in vegetative and floral organs was evident within the clades as well as at inter-clade level. The genomic DNA search for clusters of short motifs and sequence conservation of the -2 kb promoter region of particularly, MPF2-like clade permitted to establish three well defined CRMs where transcription factors bind, being CRM1 the activator, CRM2 the repressor, and CRM3 the enhancer element. Similar clusters were also mapped in the large 1st introns in the coding region. Within these CRMs many transcription factor-binding sites, particularly the hotspots for MADS-domain TF binding elements--CArG-boxes, directing sepal specific expression in Arabidopsis--were accrued in the CRM1 of MPF2-like promoters. Site-directed mutagenesis and motif swapping through reporter assays allude towards their implication as functionally active elements. In terms of directional evolution of MPF2-like promoters, CRMs are significantly more conserved than flanking regions, hence, bearing the signatures for purifying selection. Thus, CRMs are the pervasive feature of STMADS11 genes and mutations and/or appearance of new transcription factor binding sites and position of the CRMs are responsible for the divergence in expression patterns in this clade. These results have implications in understanding functional evolution of cis-regulatory modules in plants.

MPF2-like MADS-box genes affecting expression of SOC1 and MAF1 are recruited to control flowering time

A complex and intricate network of genes responding to various developmental and environmental signals control floral transition in plants. MADS-box genes are the key regulators and major contributors with regard to flowering time determination. Previously, MPF2-like genes belonging to the STMADS11 superclade were duplicated into MPF2-like-A and MPF2-like-B in Withania (WSA206 and WSB206) and Tubocapsicum (TAB 201). The present study was conducted to determine the effect of MPF2-like genes on flowering time by analyzing 35S:MPF2-like transgenic Arabidopsis plants as well as to probe their effects on the expression of SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1, a floral promoter) and MADS AFFECTING FLOWERING 1 (MAF1, a floral repressor) genes. The overexpression of WSA206 (35S:MPF2-like-A) moderately promoted flowering, while that of WSB206 and TAB 201 (35S:MPF2-like-B) exhibited no effects on floral transition. Concomitantly, an elevation in SOC1 transcript abundance and a reduction for MAF1 transcript levels were observed in 35S:WSA206 transgenic plants. Nucleotide diversity analysis indicated an extraordinary 8 aa extension at the C-terminus of the WSA206 protein. Ectopic expression of a truncated WSA206-version without these 8 aa (WSA206ΔC246) and of MPF2-like-B-versions elongated by these 8 aa (WSB206∇C257 and TAB 201∇C257) in Arabidopsis revealed an ambiguous role of the 8 aa signature in floral transition. It may influence a protein's ability to modulate flowering time but is neither sufficient nor strictly necessary for early flowering. Nevertheless, the 8 aa extension influences the expression of SOC1 and MAF1 in MPF2-like derivative constructs. Our studies provide insight into the role of MPF2-like genes in phase transition by interacting with SOC1 and MAF1 genes, thereby also pointing to their significance as potential candidates for modifying flowering in crop plants in the future.

Reciprocal loss of CArG-boxes and auxin response elements drives expression divergence of MPF2-Like MADS-box genes controlling calyx inflation

Expression divergence is thought to be a hallmark of functional diversification between homologs post duplication. Modification in regulatory elements has been invoked to explain expression divergence after duplication for several MADS-box genes, however, verification of reciprocal loss of cis-regulatory elements is lacking in plants. Here, we report that the evolution of MPF2-like genes has entailed degenerative mutations in a core promoter CArG-box and an auxin response factor (ARF) binding element in the large 1(st) intron in the coding region. Previously, MPF2-like genes were duplicated into MPF2-like-A and -B through genome duplication in Withania and Tubocapsicum (Withaninae). The calyx of Withania grows exorbitantly after pollination unlike Tubocapsicum, where it degenerates. Besides inflated calyx syndrome formation, MPF2-like transcription factors are implicated in functions both during the vegetative and reproductive development as well as in phase transition. MPF2-like-A of Withania (WSA206) is strongly expressed in sepals, while MPF2-like-B (WSB206) is not. Interestingly, their combined expression patterns seem to replicate the pattern of their closely related hypothetical progenitors from Vassobia and Physalis. Using phylogenetic shadowing, site-directed mutagenesis and motif swapping, we could show that the loss of a conserved CArG-box in MPF2-like-B of Withania is responsible for impeding its expression in sepals. Conversely, loss of an ARE in MPF2-like-A relaxed the constraint on expression in sepals. Thus, the ARE is an active suppressor of MPF2-like gene expression in sepals, which in contrast is activated via the CArG-box. The observed expression divergence in MPF2-like genes due to reciprocal loss of cis-regulatory elements has added to genetic and phenotypic variations in the Withaninae and enhanced the potential of natural selection for the adaptive evolution of ICS. Moreover, these results provide insight into the interplay of floral developmental and hormonal pathways during ICS development and add to the understanding of the importance of polyploidy in plants.

Evaluation of wheat landrace genotypes for salinity tolerance at vegetative stage by using morphological and molecular markers

Identification of new sources of salt tolerance is particularly important to develop crop varieties suitable for saline soils. We evaluated 129 Pakistani and 58 exotic wheat landraces/cultivars grown in Hoagland's hydroponic nutrient solution, under control (tap water equivalent to 10 mM salt) and salt stress (200 mM NaCl) conditions. Forty-four genotypes were also tested under 250 mM NaCl stress. High heritability and positive correlations suggested that number of tillers per plant, root length, root fresh and dry weights, and shoot fresh and dry weights are associated with salt tolerance and could be used as selection criteria. SSR markers revealed high genetic variation in the wheat genotypes. Twelve SSR markers (cfd 1, cfd 9, cfd 18, cfd 46, cfd 49, cfd 183, wmc 11, wmc 17, wmc 18, wmc 154, wmc 432, and wmc 503) were found to be associated with salt tolerance because they were amplified in tolerant genotypes only. Five markers, cfd 9, cfd 18, cfd 183, wmc 96, and wmc 405, were identified as most suitable to evaluate salt tolerance because they were associated with four or more salt tolerance traits studied. Cultivars Pasban 90, accessions 10790, 10828, 10823, and 4098805 from Pakistan and Sakha-92 from Egypt performed best at both stress levels.

Application of proteomics to investigate stress-induced proteins for improvement in crop protection

Proteomics has contributed to defining the specific functions of genes and proteins involved in plant-pathogen interactions. Proteomic studies have led to the identification of many pathogenicity and defense-related genes and proteins expressed during phytopathogen infections, resulting in the collection of an enormous amount of data. However, the molecular basis of plant-pathogen interactions remains an intensely active area of investigation. In this review, the role of differential analysis of proteins expressed during fungal, bacterial, and viral infection is discussed, as well as the role of JA and SA in the production of stress related proteins. Resistance acquired upon induction of stress related proteins in intact plant leaves is mediated by potentiation of pathogens via signal elicitors. Stress related genes extensively used in biotechnology had been cited. Stress related proteins identified must be followed through for studying the molecular mechanism for plant defense against pathogens.

Proteomic analysis of rice leaf sheath during drought stress

Drought is one of the most severe limitations on the productivity of rainfed lowland and upland rice. To investigate the initial response of rice to drought stress, changes in protein expression were analyzed using a proteomic approach. Two-week-old rice seedlings were exposed to drought conditions from 2 to 6 days, and proteins were extracted from leaf sheaths, separated by two-dimensional polyacrylamide gel electrophoresis and stained with Coomassie brilliant blue. After drought stress for 2 to 6 days, 10 proteins increased in abundance and the level of 2 proteins decreased. The functional categories of these proteins were identified as defense, energy, metabolism, cell structure, and signal transduction. In addition to drought stress, accumulations of protein were analyzed under several different stress conditions. The levels of an actin depolymerizing factor, a light harvesting complex chain II, a superoxidase dismutase and a salt-induced protein were changed by drought and osmotic stresses, but not cold or salt stresses, or abscisic acid treatment. The effect of drought stress on protein in the leaf sheaths of drought-tolerant rice cultivar was also analyzed. The light harvesting complex chain II and the actin depolymerizing factor were present at high levels in a drought-tolerant rice cultivar before stress application. With drought stress, actin depolymerizing factor was expressed in leaf blades, leaf sheaths, and roots. These results suggest that actin depolymerizing factor is one of the target proteins induced by drought stress.

Clinical presentation and CAT scan findings in mycetoma of the head

Nine cases comprising seven males and two females with mycetoma of the cranium were studied between January 1990 and June 1997. Streptomyces somaliensis was the most common causative organism. The source of the infection was thought to be known in only three cases. The common mode of presentation was headache and scalp swelling. The next common presentation was epilepsy. Other focal neurological disorders also occur. CT scan findings of the cranium showed osteosclerotic rather than osteolytic changes.

Results of echocardiographic examinations in a regional hospital of central Sudan

Sixty-seven patients were examined with a small portable echocardiograph in Wad Medani Teaching Hospital in central Sudan. The cardiac alterations detected in the referred patients, namely valvular disease and pericardial effusion, suggested a high prevalence of inflammatory heart disease in this area. Other findings were dilatative cardiomyopathy, congenital heart disease, mitral valve prolapse and a cardiac mass. Echocardiographic examination of patients with advanced hepatosplenic schistosomiasis revealed no evidence of cardiac alterations or abnormal right heart function. For echocardiography a general purpose ultrasound scanner, as defined by the World Health Organization, was used, additionally equipped with M mode facilities. It was concluded that echocardiography is applicable even in remote tropical areas and that its value, considering costs, therapeutic consequences and clinical benefit in developing countries, can be substantial. It was particularly helpful with pericardial disease.

Renal function in Sudanese school children with Schistosoma mansoni infection

Renal function was investigated in 218 school children with Schistosoma mansoni infection in the Providence of Gezira in central Sudan and in 65 Sudanese and 65 German age-matched controls. Serum creatinine was normal in all children. A pathological urinary protein-creatinine ratio was found in 3% of S. mansoni-infected children and in 5% of Sudanese controls but in none of the European children. Characterization of pathological proteinuria using albumin nephelometry, alpha-1 microglobulin immunodiffusion and SDS-polyacrylamide gel electrophoresis in these children showed glomerular, tubular or mixed glomerulotubular patterns. One, 4 and 6 months following treatment of schistosomiasis with praziquantel, stools were re-examined; 57% of patients were cured, 16% were found to be reinfected and 27% had persistent egg excretion. Six months after therapy, pathological urinary protein-creatinine ratios were encountered in 3% of S. mansoni patients and in none of the 34 reinvestigated controls. Proteinuria was similar in patients with persistent S. mansoni egg excretion and in children cured of schistosomiasis infection. It is concluded that there was no evidence for S. mansoni associated glomerulonephritis in this group of Sudanese children. The high rate of pathological proteinuria in S. mansoni-infected and non-infected Sudanese children may be due to other causes.