Muhammad Faisal

Background: Mung bean is an important leguminous crop, which is reported to face devastating yield losses of up to 70% due to Cercospora leaf spot (CLS) disease. Traditional methods, such as the application of agrochemicals and fungicides, have been used to control CLS, but their intensive use has toxic effects on edible crops. Methods: To find out a sustainable alternative, this study characterizes a strain, Bacillus subtilis Medicinal_04, isolated from Cannabis sativa rhizosphere and explores its role as an eco-friendly biofungicide and biostimulant. The species level identification of the isolate was confirmed by Average Nucleotide Identity (ANIb) and a digital DNA–DNA hybridization (dDDH). The antagonistic efficacy of B. subtilis Medicinal_04 against Cercospora canescens was evaluated in vitro as well as in planta assays. Results: ANIb of 97.80% and a dDDH score of 85.90% against the reference B. subtilis str. 168. confirmed this isolate as B. subtilis. The in-vitro results showed that B. subtilis robustly inhibited C. canescens growth by 81.5%, strongly correlated with positive chitinolytic activity and a diverse genomic array of secondary metabolite biosynthetic gene clusters. The in planta results demonstrated that B. subtilis seed priming reduced disease incidence by 80 and 71.4%, while foliar application resulted in reductions of 90 and 85.7% for NM-51 and NM-20-21 varieties, respectively. Furthermore, fungicide application successfully reduced disease, however it caused noticeable phytotoxic reductions in root-shoot architecture and chlorophyll content. In contrast, biological interventions completely bypassed these trade-offs as B. subtilis application displayed improved root-shoot length, pod number, and chlorophyll content, while simultaneously enhancing antioxidative enzyme activities (SOD, POD, and CAT) and PR-1 gene expression. Conclusion: These findings demonstrate that B. subtilis Medicinal_04 has the potential to serve as a multifunctional biocontrol agent and is capable of securing high-level disease suppression and optimizing plant productivity, offering a valuable toolkit for climate-smart, sustainable agriculture.

Background: Pathogenic variants in the COL4A4 gene lead to Alport syndrome, a hereditary kidney disorder characterized by deficiencies in the glomerular basement membrane (GBM), progressive renal failure, and associated visual and auditory dysfunctions. Objective: This study is aimed at detecting genetic variants and conducting an integrative network analysis to elucidate their involvement in Alport syndrome and chronic kidney disease (CKD). Methodology: The enrolled patients were biological sisters. Clinical and pathological data were collected using laboratory tests. Genetic testing was performed to identify the variants via whole‐exome sequencing (WES). The pathogenicity of the detected variant was confirmed using different computational approaches. The detected variants were classified according to the ACMG criteria. The interaction networks of CKD, Alport syndrome, and COL4A4 were examined using STRING v11.5, whereas pathways were analyzed by KEGG and STRING pathways analysis. Results: Patients were diagnosed with CKD of Stage 5. The ultrasound results were not clear due to kidney fibrosis. WES revealed an 18‐base pair deletion in the COL4A4 gene (chr2: g.227958874_227958891del). The detected variant was classified as pathogenic by ACMG criteria. Online Mendelian Inheritance in Man (OMIM) reveals that the variant in COL4A4 is due to autosomal recessive Alport syndrome 2. Sensorineural hearing loss was observed in two family members of the patients. These results show the existence of Alport syndrome in their family. The disease–protein interaction by STRING reveals that the COL4A4 protein is strongly associated with both CKD and Alport syndrome diseases. KEGG analysis indicates a consistent association of PI3K‐Akt and AGE‐RAGE pathways among both diseases. Conclusion: Dysfunction of COL4A4 leads to disruptions in GBM structure and signaling, which hasten CKD in Alport syndrome. Genetic testing is essential for identifying the exact cause of the disease, which aids in early diagnosis and control to spread within families.

Introduction and importance: Chronic kidney disease (CKD) is recognized as one of the leading causes of human death. This case highlights the importance of whole-exome sequencing (WES) and genetic diagnosis in families. Case Presentation: A 4-year-old girl (subject) was diagnosed with CKD along with her father, grandfather, and grandmother. The subject was first evaluated at 4 years of age because of black urine problem. On early diagnosis, it was kidney stones. She was suspected to be affected with kidney disorder by ultrasound and is being evaluated for the presence genetic variations by WES. We identified a missense variation in GRHPR gene c.494 G>A in subject, and her 27-year-old father was also identified with the same variation in the GRHPR gene. On follow-up, kidney stones were removed via extracorporeal shock wave lithotripsy (ESWL). Following ESWL sections, the subject was stable and sent home. Clinical discussion: Genetic diagnoses are essential for identifying diseases, which aid in early diagnosis and control to spread within families. This case highlights the value of advanced genetic testing in nephrology for precision diagnosis and family risk assessment. Conclusion: A multidisciplinary approach and timely intervention in CKD are vital to prevent complications in families.

Leguminous crops are usually sensitive to saline stress during germination and plant growth stages. The Salt Overly Sensitive (SOS) pathway is one of the key signaling pathways involved in salt translocation and tolerance in plants however, it is obscure in soybean. The current study describes the potential of calcium application on the mitigation of salinity stress and its impact on seed germination, morphological, physiological and biochemical attributes of soybean. The seeds from previously reported salt-tolerant and salt-susceptible soybean varieties were primed with water, calcium (10 and 20 mM), and stressed under 60, 80 and 100 mM NaCl and evaluated in various combinations. Results show that germination increased by 7% in calcium primed non-stressed seeds under non-stressing, whereas an improvement of 15%-25% was observed in germination under NaCl stress. Likewise, improvement in seedling length (3%-8%), plant height (9%-18%), number of nodes (3%-14%), SOD activity (20%) and Na⁺/K⁺ concentration (3%-5% reduction) in calcium primed plants, indicates alleviation of salinity-induced negative effects. In addition, this study also included in silico identification and confirmation of presence of Arabidopsis thaliana SOS genes orthologs in soybean. The research of amino acid sequences of SOS proteins from Arabidopsis thaliana (AtSOSs) within Glycine max genome displayed protein identity (60–80%) thus these identified homologs were called as GmSOS. Further phylogeny and in silico analyses showed that GmSOS orthologs contain similar gene structures, close evolutionary relationship, and same conserved motifs, reinforcing that GmSOSs belong to SOS family and they share many common features with orthologs from other species thus may perform similar functions. This is the first study that reports role of SOSs in salt-stress mitigation in soybean.

Mung bean is one of the economically important leguminous crops generally grown in arid region of Pakistan. Mung bean grows best at 30-35℃ and is a nutrient enriched crop with higher amounts of starch (50%), proteins (18-25%), fat (3%) and fiber (3-4.5%). Many biotic factors affect crop production. Yield losses due to biotic factors are up to 40-80% in mung bean. Cercospora leaf spot (CLS) is very common disease in mung bean caused by hemi-biotrophic fungal pathogen Cercospora canescens. For sustainable agrocontrol there is need to develop alternative solutions for conventional methods. Green synthesized nanoparticles offer promising solution to mitigate adverse effect of agrochemicals and fungicides. In this review green synthesized TiO2 nanoparticles used to mitigate the disease severity by seed priming with 50mgL-1 and 150mgL-1 nanoparticles (NPs) suspension solution in mung bean. The result shows that 50mgL-1 Tio2-NPs inhibit fungal growth by 87.85% in in vitro and 74.07% in in vivo experiment. Tio2-NPs application improve root, shoot, leaf surface area, chlorophyll content, stomatal conductance and boost plant immunity by enhancing expression of the Pathogenesis-related (PR-1) gene in response stress. Therefore, present study indicates that green synthesized Tio2-NPs is an effective way to enhance the growth and productivity of mung bean by inhibiting C. canescens.

Phytonanotechnology plays a crucial part in the production of good quality and high-yield food. It can also alter the plant's production systems, hence permitting the efficient, controlled and stable release of agrochemicals such as fertilizers and pesticides. An advanced understanding of nanomaterials interaction with plant responses like localization and uptake, etc. could transfigure the production of crops with high disease resistance and efficient nutrients utilization. In agriculture, the use of nanomaterials has gained acceptance due to their wide-range applications. However, their toxicity and bioavailability are the major hurdles for their massive employment. Undoubtedly, nanoparticles positively influence seeds germination, growth and development, stress management and post-harvest handling of vegetables and fruits. These nanoparticles may also cause toxicity in plants through oxidative stress by generation of excessive reactive oxygen species thus affecting the cellular biomolecules and targeting different channels. Nanoparticles have shown to exert various effects on plants that are mainly affected by various attributes such as physicochemical features of nanomaterials, coating materials for nanoparticles, type of plant, growth stages and growth medium for plants. This article discusses the interaction, accretion and toxicity of nanomaterials in plants. The factors inducing nanotoxicity and the mechanisms followed by nanomaterials causing toxicity are also instructed. At the end, detoxification mechanism of plant is also presented.

Cyperus rotundus is rapidly growing plant can quickly form dense colonies through the extensive underground system of tuber and rhizomes. It is highly competitive for resources and causes a significant yield reduction in field crops. The nonchemical method has recently been practiced to control this noxious weed species. The current study was conducted to determine the effect of sowing depths (4, 8, 12, and 16 cm) and water regimes (deficit irrigation, medium irrigation, and frequent irrigation treatments) on C. rotundus shoot growth and underground growth of tubers in pots soil. Weed emergence, i.e., mean emergence time (MET), emergence index (EI), final emergence percentage (FEP), and shoot growth traits i.e. shoot density, shoot fresh weight, shoot dry weight, and tuber growth traits i.e. tuber density, tuber weight, root density, and root weight were recorded under the completely randomized (CRD) factorial design. The greatest suppression of C. rotundus emergence and growth was found at 16 cm sowing depth. The mean emergence time (MET) of C. rotundus was increased by increasing the sowing depth. Minimum value of shoot densty (9.5 g) and tuber density (15.75 g) were recorded at 16 cm sowing depth under deficit irrigation treatment respectively.While shoot and tuber desnity traits were also drastically suppressed by increasing sowing depth at the deficit irrigation level. It is concluded that sowing depths and deficit irrigation methods can be included as a reliable approach for controlling purple nutsedge shoot and tuber growth.

Kabupaten Garut menggambarkan wilayah sesuatu sedang berkembang dimana pembangunan dan peningkatan infrastruktur. Terlebih lagi Kota garut merupakan kota wisata yang banyak terhubung dengan jalan lokal hingga jalan provinsi sehingga menyebabkan banyaknya kerusakan seperti jalan yang berlubang kondisi serta drainase yang kurang baik. Oleh karna itu, Pemerintah Provinsi Jawa Barat melakukan pembangunan jalan serta rehabilitasi agar membasmi masalah tertentu. Penelitian ini berguna agar menganalisis perbedaan antara metode Bina Marga dan metode AASHTO dalam merencanakan ketebalan perkerasan kaku. Lokasi penelitian ini yaitu pada Ruas Jalan Jend. Sudirman Sta. 0+000 – Sta. 0+135. Jalan ini diklasifikasikan sebagai jalan arteri dengan status jalan provinsi yang mempunyai lebar 6 meter. Direncanakan lintasan beton pada bagian lintasan Jend. Sudirman ini memakai mutu beton K-350 dan menggunakan lama direncana 2.0 tahun. Perhitungan ketebalan lintasan semen agartidaknya methode BinaMarga dan methode ASHTO, memiliki perbedaan yang sangat signifikan dengan mengacu pada parameter yang berbeda. Faktor yang mempengaruhi perbedaan hasil ketebalan tersebut antara lain pada metode AASHTO memasukkan banyak faktor selain dari beban lalu-lintas dan kekuatan tanah dasar, yaitu seperti koefisien drainase, reliabilty, serviceability hingga faktor tingkat kelayanan dalam metode ini sangat diperhatikan. Hal tersebut membuat ketebalan yang dihasilkan metode AASHTO lebih besar dibandingkan dengan metode Bina Marga.

Background: The Arabidopsis CONSTITUTIVE EXPRESSER of PATHOGENESIS-RELATED GENES 5 (CPR5) has recently been shown to play a role in gating as part of the nuclear pore complex (NPC). Mutations in CPR5 cause multiple defects, including aberrant trichomes, reduced ploidy levels, reduced growth and enhanced resistance to bacterial and fungal pathogens. The pleiotropic nature of cpr5 mutations implicates that the CPR5 protein affects multiple pathways. However, little is known about the structural features that allow CPR5 to affect the different pathways. Results: Our in silico studies suggest that in addition to three clusters of putative nuclear localization signals and four or five transmembrane domains, CPR5 contains two putative alternative translation start sites. To test the role of the methionine-encoding nucleotides implicated in those sites, metCPR5 cDNAs, in which the relevant nucleotides were changed to encode glutamine, were fused to the CPR5 native promoter and the constructs transformed to cpr5–2 plants to complement cpr5-compromised phenotypes. The control and metCPR5 constructs were able to complement all cpr5 phenotypes, although the extent of complementation depended on the specific complementing plant lines. Remarkably, plants transformed with metCPR5 constructs showed larger leaves and displayed reduced resistance when challenged to Pseudomonas syringae pv Pst DC3000, as compared to control plants. Thus, the methionine-encoding nucleotides regulate growth and resistance. We propose that structural features of the CPR5 N-terminus are implicated in selective gating of proteins involved in regulating the balance between growth and resistance. Conclusion: Plants need to carefully balance the amount of resources used for growth and resistance. The Arabidopsis CPR5 protein regulates plant growth and immunity. Here we show that N-terminal features of CPR5 are involved in the regulation of the balance between growth and resistance. These findings may benefit efforts to improve plant yield, while maintaining optimal levels of disease resistance.

Rapid and cost-efficient whole-genome sequencing of SARS-CoV-2, the virus that causes COVID-19, is critical for understanding viral transmission dynamics. Here we show that using a new multiplexed set of primers in conjunction with the Oxford Nanopore Rapid Barcode library kit allows for faster, simpler, and less expensive SARS-CoV-2 genome sequencing. This primer set results in amplicons that exhibit lower levels of variation in coverage compared to other commonly used primer sets. Using five SARS-CoV-2 patient samples with C _q values between 20 and 31, we show that high-quality genomes can be generated with as few as 10,000 reads (approximately 5 Mbp of sequence data). We also show that mis-classification of barcodes, which may be more likely when using the Oxford Nanopore Rapid Barcode library prep, is unlikely to cause problems in variant calling. This method reduces the time from RNA to genome sequence by more than half compared to the more standard ligation-based Oxford Nanopore library preparation method at considerably lower costs.