Effect of naringenin on post-thaw quality, fertility-associated gene expression and fertilization potential of buffalo (Bubalus bubalis) bull sperm.

Our objectives were to explore the effect of naringenin addition in the semen extender on the post-thaw 1) sperm quality, 2) fertility-associated gene expression, and 3) fertilization potential of buffalo bull sperm. In experiment 1, semen samples (n = 32) from four Nili-Ravi buffalo bulls were pooled (n = 8) and diluted with the tris-citric acid (TCF-EY) extender containing different concentrations of naringenin, i.e., placebo (DMSO), 0 (control), 50, 100, 150 and 200 µM naringenin. After dilution, semen samples were packed in 0.5 mL French straws, cryopreserved and analyzed for post-thawed sperm quality and gene expression. Computer-assisted Semen Analysis, Hypo-osmotic Swelling test, Normal Apical Ridge assay, Rhodamine 123, Acridine orange, Propidium iodide staining and Thiobarbituric Acid Reactive Substances assay were performed to assess sperm motility parameters, plasma membrane functionality, acrosome integrity, mitochondrial membrane potential, DNA integrity, viability and lipid peroxidation, respectively. Expression levels of sperm acrosome-associated SPACA3, DNA condensation-related PRM1, anti-apoptotic BCL2, pro-apoptotic BAX, and oxidative stress-associated ROMO1 genes were evaluated through qPCR. Results revealed that total and progressive motility, plasma membrane functionality, acrosome integrity, mitochondrial membrane potential, DNA integrity and viability were higher (P < 0.05) with 50, 100 and 150 µM naringenin compared to 200 µM naringenin, placebo and control groups. Moreover, all naringenin-treated groups improved catalase activity, and reduced lipid peroxidation compared to placebo and control groups (P < 0.05). Relative expression levels of SPACA3 and PRM1 genes were higher (P < 0.05) with 150 µM naringenin compared to all groups except 100 µM (P > 0.05). No difference (P > 0.05) in the expression level of BCL2 gene was observed among all groups. Furthermore, BAX gene was expressed higher (P < 0.05) in the 200 µM naringenin group, whereas no difference (P > 0.05) in expression was noticed among the remaining groups. In addition, ROMO1 gene was expressed lower (P < 0.05) in all naringenin-treated groups compared to the control. In experiment 2, the in vivo fertility of semen doses (n = 400; 200/group) containing optimum concentration of naringenin (150 µM; depicted better in vitro sperm quality in experiment 1) was compared with control during the breeding season. Buffaloes were inseminated 24 h after the onset of natural estrus and palpated transrectal for pregnancy at least 60 days post-insemination. The fertility rate of 150 µM naringenin group was higher (P = 0.0366) compared to the control [57.00 ± 0.03 % (114/200) vs. 46.50 ± 0.04 % (93/200), respectively]. Taken together, it is concluded that naringenin supplementation in semen extender improves post-thaw quality, fertility-associated gene expression and fertilization potential of buffalo bull sperm, more apparently at 150 µM concentration.

The spectrum of novel ABCB11 gene variations in children with progressive familial intrahepatic cholestasis type 2 in Pakistani cohorts.

Progressive familial intrahepatic cholestasis (PFIC) is a rare childhood manifested disease associated with impaired bile secretion with severe pruritus yellow stool, and sometimes hepatosplenomegaly. PFIC is caused by mutations in ATP8B1, ABCB11, ABCB4, TJP2, NR1H4, SLC51A, USP53, KIF12, ZFYVE19, and MYO5B genes depending on its type. ABCB11 mutations lead to PFIC2 that encodes the bile salt export pump (BSEP). Different mutations of ABCB11 have been reported in different population groups but no data available in Pakistani population being a consanguineous one. We sequenced coding exons of the ABCB11 gene along with its flanking regions in 66 unrelated Pakistani children along with parents with PFIC2 phenotype. We identified 20 variations of ABCB11: 12 in homozygous form, one compound heterozygous, and seven heterozygous. These variants include 11 missenses, two frameshifts, two nonsense mutations, and five splicing variants. Seven variants are novel candidate variants and are not detected in any of the 120 chromosomes from normal ethnically matched individuals. Insilico analysis revealed that four homozygous missense variations have high pathogenic scores. Minigene analysis of splicing variants showed exon skipping and the addition of exon. This data is a useful addition to the disease variants genomic database and would be used in the future to build a diagnostic algorithm.

Signatures of selection in Angus and Hanwoo beef cattle using imputed whole genome sequence data.

In this study, we detected signatures of selection in Hanwoo and Angus beef cattle using allele frequency and haplotype-based methods based on imputed whole genome sequence variants. Our dataset included 13,202 Angus animals with 10,057,633 imputed SNPs and 10,437 Hanwoo animals with 13,241,550 imputed SNPs. The dataset was subset down to 6,873,624 SNPs in common between the two populations to identify within population (runs of homozygosity, extended haplotype homozygosity) and between population signals of selection (allele fixation index, extended haplotype homozygosity). Assuming these selection signals were complementary to each other, they were combined into a decorrelated composite of multiple signals to identify regions under selection for each of the breeds. 27 genomic regions spanning 25.15 Mb and harboring 360 genes were identified in Angus on chromosomes 1,3, 4, 5, 6, 7, 8, 12, 13, 14, 16, 20, 21 and 28. Similarly, in Hanwoo, 59 genes and 17 genomic regions spanning 5.21 Mb on chromosomes 2, 4, 5, 6, 7, 8, 9, 10, 13, 17, 20 and 24 were identified. Apart from a small region on chromosome 13, there was no major overlap of selection signals between the two breeds reflecting their largely different selection histories, environmental challenges, breeding objectives and breed characteristics. Positional candidate genes identified in selected genomic regions in Angus have been previously associated with growth, immunity, reproductive development, feed efficiency and adaptation to environment while the candidate genes identified in Hanwoo included important genes regulating meat quality, fat deposition, cholesterol metabolism, lipid synthesis, neuronal development, and olfactory reception.

Ultrasound guidance to replicate transuterine BioGlue injection in the fetal hydrocephalus sheep model.

INTRODUCTION: Congenital hydrocephalus often results in irreversible and severe damage to the brain despite postnatal interventions. The potential for prenatal intervention to mitigate these deleterious effects underscores the importance of a suitable animal model. We aimed assess the results of an ultrasound guided transuterine approach to replicate the BioGlue injection fetal hydrocephalus model. METHODS: Pregnant ewes were anesthetized at 95 days of gestation and BioGlue was injected into the fetal cisterna magna under ultrasound guidance through the uterus. Ventriculomegaly was assessed by MRI and histology. RESULTS: Nine pregnant ewes were included in the study, and their fetuses were divided into the the BioGlue intervention group (n=9 fetuses) or the control group (n=7 fetuses) who were not injected. Although hydrocephalus was noted in 5 of 9 fetuses in the intervention group, the ability to induce hydrocephalus went from 0% to 100% in the last 3 fetuses following technical modifications. None of the controls developed hydrocephalus. Fetal brains with hydrocephalus demonstrated increased IBA1+ compared to control animals. CONCLUSIONS: While technical challenges were noted, the ultrasound guided transuterine approach to replicate the BioGlue fetal hydrocephalus model in sheep showed consistent and reproducible results. This model offers the advantage of directly visualizing the location of the needle tip and injection of the BioGlue. This technique offers an alternative for testing novel approaches for prenatal congenital hydrocephalus treatment.

Potassium and zinc improves physiological performance, nutrient use efficiency, and productivity of wheat.

Despite the critical role of balanced nutrition in crop productivity, the use of potash (K) and zinc (Zn) is not much practiced by Pakistani farmers. The reduced nutrient uptake and crop productivity together increase the costs associated with fertilization and revisit farmers' confidence in the efficacy and profitability of fertilizers. To address this problem, a field study was conducted in the research area of the MNS-University of Agriculture, Multan, in collaboration with Engro Fertilizers Limited. The research plan consisted of five treatments, including T1 = control (without N, P, K, and Zn fertilizers), T2 = NP in practice (NP at 32-23-0 kg acre-1), T3 = recommended NP (NP at 48-34.5 kg acre-1), T4 = balanced NPK (NP+K at 48-34.5-30 kg acre-1), and T5 = balanced NPK + Zn (NPK+Zn at 48-34.5-30 + 7.5 kg acre-1). Wheat was used as a test crop, and its growth, yield, and physiological and nutritional parameters were studied. The results indicated that NPK+Zn balanced nutrition increased plant height, spike length, photosynthetic rate, water use efficiency, transpiration rate, stomatal conductance, and grain yield by 13%, 15%, 44%, 60%, 63%, 39%, and 78%, respectively, compared with the control. It was found that the combined application of NP, K, and Zn improved the recovery efficiency of applied nutrients, i.e., nitrogen recovery efficiency (NRE) by 230%, phosphorus recovery efficiency (PRE) by 136%, potassium recovery efficiency (KRE) by 135%, and zinc recovery efficiency (ZnRE) by 136% compared to NP-alone application. Agronomic use efficiency of applied fertilizers, such as potassium agronomic use efficiency (KAUE) by 71%, phosphorus agronomic use efficiency (PAUE) by 72%, nitrogen agronomic use efficiency (NAUE) by 70%, and zinc agronomic use efficiency (ZnAUE) by 72%, was observed compared to NP-alone application. The results showed that NPUE, PPUE, NPUE, and ZnPUE were reduced by 5%, 3%, 3%, and 5%, respectively, compared to NP-alone application. Our findings suggest that K and Zn should be made an essential part of wheat nutrition management for higher yield and better quality of produce.

Inhibiting AGTR1 reduces AML burden and protects the heart from cardiotoxicity in mouse models.

Clinical treatment of acute myeloid leukemia (AML) largely relies on intensive chemotherapy. However, the application of chemotherapy is often hindered by cardiotoxicity. Patient sequence data revealed that angiotensin II receptor type 1 (AGTR1) is a shared target between AML and cardiovascular disease (CVD). We found that inhibiting AGTR1 sensitized AML to chemotherapy and protected the heart against chemotherapy-induced cardiotoxicity in a human AML cell-transplanted mouse model. These effects were regulated by the AGTR1-Notch1 axis in AML cells and cardiomyocytes from mice. In mouse cardiomyocytes, AGTR1 was hyperactivated by AML and chemotherapy. AML leukemogenesis increased the expression of the angiotensin-converting enzyme and led to increased production of angiotensin II, the ligand of AGTR1, in an MLL-AF9-driven AML mouse model. In this model, the AGTR1-Notch1 axis regulated a variety of genes involved with cell stemness and chemotherapy resistance. AML cell stemness was reduced after Agtr1a deletion in the mouse AML cell transplant model. Mechanistically, Agtr1a deletion decreased γ-secretase formation, which is required for transmembrane Notch1 cleavage and release of the Notch1 intracellular domain into the nucleus. Using multiomics, we identified AGTR1-Notch1 signaling downstream genes and found decreased binding between these gene sequences with Notch1 and chromatin enhancers, as well as increased binding with silencers. These findings describe an AML/CVD association that may be used to improve AML treatment.

Effect of supplementing epinephrine in maturation media on in-vitro developmental competence of cattle and buffalo oocytes.

During in-vitro maturation, the oocyte experiences stressful conditions that likely compromise its development. Epinephrine is a catecholamine that plays a vital role during cellular stress by scavenging free radicals. The hypothesis is that epinephrine addition in maturation media improves the developmental competence of oocytes in cattle and buffalo. The objectives of the experiments were to investigate the effect of epinephrine addition in maturation media on nuclear maturation, developmental competence, and oocyte mRNA abundance of genes related to antioxidants and growth pathways in cattle and buffalo. In experiment 1, cattle oocytes were matured for 24 h in maturation media supplemented with increasing concentrations of epinephrine 0, 0.01, 1.0, and 100 µM. Oocytes were cultured to assess cleavage at 48 h and blastocyst on day 7 of the culture. The cumulus-oocyte complexes (COCs) expansion, nuclear maturation, and oocyte mRNA abundance of genes (SOD1, GPX4, GDF9, CASP9) were evaluated. In experiment 2, buffalo oocytes were matured and assessed for development and mRNA abundance as described for cattle. In addition, the blastomere number was counted in the hatched blastocyst. The data were analyzed using GLIMMIX and MIXED procedures of SAS. Results revealed that the supplementation of epinephrine increased (P ≤ 0.03) the COCs expansion, nuclear maturation, and developmental competence of oocytes in cattle. Interestingly, all the responses were maximized (quadratic effect; P ≤ 0.08) at 1 µM concentrations. The mRNA abundance of genes in cattle oocytes was not affected by the treatment. The experiment in buffalo revealed that epinephrine increased blastocyst formation without affecting COCs expansion, and nuclear maturation. The higher blastocyst was achieved at 0.01 µM concentrations of epinephrine. Interestingly, the addition of epinephrine increased the mRNA abundance of genes related to antioxidant pathways (SOD1, GPX4). Moreover, supplementation of epinephrine increased the blastomere count of the hatched blastocyst in buffalo. In conclusion, epinephrine addition in maturation media benefited oocyte development in cattle and blastocyst yield in buffalo at 1 and 0.01 µM concentrations, respectively. It appears that the addition of epinephrine affected different cellular pathways, COCs expansion, and nuclear maturation in cattle and increased antioxidant genes for buffalo.

Molecular identification of Coxiella burnetii in raw milk samples collected from farm animals in districts Kasur and Lahore of Punjab, Pakistan.

Coxiella burnetii is the worldwide zoonotic infectious agent for Q fever in humans and animals. Farm animals are the main reservoirs of C. burnetii infection, which is mainly transmitted via tick bites. In humans, oral, percutaneous, and respiratory routes are the primary sources of infection transmission. The clinical signs vary from flu-like symptoms to endocarditis for humans' acute and chronic Q fever. While it is usually asymptomatic in livestock, abortion, stillbirth, infertility, mastitis, and endometritis are its clinical consequences. Infected farm animals shed C. burnetii in birth products, milk, feces, vaginal mucus, and urine. Milk is an important source of infection among foods of animal origin. This study aimed to determine the prevalence and molecular characterization of C. burnetii in milk samples of dairy animals from two districts in Punjab, Pakistan, as it has not been reported there so far. Using a convenience sampling approach, the current study included 304 individual milk samples from different herds of cattle, buffalo, goats, and sheep present on 39 farms in 11 villages in the districts of Kasur and Lahore. PCR targeting the IS1111 gene sequence was used for its detection. Coxiella burnetii DNA was present in 19 of the 304 (6.3%) samples. The distribution was 7.2% and 5.2% in districts Kasur and Lahore, respectively. The results showed the distribution in ruminants as 3.4% in buffalo, 5.6% in cattle, 6.7% in goats, and 10.6% in sheep. From the univariable analysis, the clinical signs of infection i.e. mastitis and abortion were analyzed for the prevalence of Coxiella burnetii. The obtained sequences were identical to the previously reported sequence of a local strain in district Lahore, Sahiwal and Attock. These findings demonstrated that the prevalence of C. burnetii in raw milk samples deserves more attention from the health care system and veterinary organizations in Kasur and Lahore of Punjab, Pakistan. Future studies should include different districts and human populations, especially professionals working with animals, to estimate the prevalence of C. burnetii.

Demand-side load forecasting in smart grids using machine learning techniques.

Electrical load forecasting remains an ongoing challenge due to various factors, such as temperature and weather, which change day by day. In this age of Big Data, efficient handling of data and obtaining valuable information from raw data is crucial. Through the use of IoT devices and smart meters, we can capture data efficiently, whereas traditional methods may struggle with data management. The proposed solution consists of two levels for forecasting. The selected subsets of data are first fed into the "Daily Consumption Electrical Networks" (DCEN) network, which provides valid input to the "Intra Load Forecasting Networks" (ILFN) network. To address overfitting issues, we use classic or conventional neural networks. This research employs a three-tier architecture, which includes the cloud layer, fog layer, and edge servers. The classical state-of-the-art prediction schemes usually employ a two-tier architecture with classical models, which can result in low learning precision and overfitting issues. The proposed approach uses more weather features that were not previously utilized to predict the load. In this study, numerous experiments were conducted and found that support vector regression outperformed other methods. The results obtained were 5.055 for mean absolute percentage error (MAPE), 0.69 for root mean square error (RMSE), 0.37 for normalized mean square error (NRMSE), 0.0072 for mean squared logarithmic error (MSLE), and 0.86 for R2 score values. The experimental findings demonstrate the effectiveness of the proposed method.

National guidelines for the diagnosis and treatment of hilar cholangiocarcinoma.

A consensus meeting of national experts from all major national hepatobiliary centres in the country was held on May 26, 2023, at the Pakistan Kidney and Liver Institute & Research Centre (PKLI & RC) after initial consultations with the experts. The Pakistan Society for the Study of Liver Diseases (PSSLD) and PKLI & RC jointly organised this meeting. This effort was based on a comprehensive literature review to establish national practice guidelines for hilar cholangiocarcinoma (hCCA). The consensus was that hCCA is a complex disease and requires a multidisciplinary team approach to best manage these patients. This coordinated effort can minimise delays and give patients a chance for curative treatment and effective palliation. The diagnostic and staging workup includes high-quality computed tomography, magnetic resonance imaging, and magnetic resonance cholangiopancreatography. Brush cytology or biopsy utilizing endoscopic retrograde cholangiopancreatography is a mainstay for diagnosis. However, histopathologic confirmation is not always required before resection. Endoscopic ultrasound with fine needle aspiration of regional lymph nodes and positron emission tomography scan are valuable adjuncts for staging. The only curative treatment is the surgical resection of the biliary tree based on the Bismuth-Corlette classification. Selected patients with unresectable hCCA can be considered for liver transplantation. Adjuvant chemotherapy should be offered to patients with a high risk of recurrence. The use of preoperative biliary drainage and the need for portal vein embolisation should be based on local multidisciplinary discussions. Patients with acute cholangitis can be drained with endoscopic or percutaneous biliary drainage. Palliative chemotherapy with cisplatin and gemcitabine has shown improved survival in patients with irresectable and recurrent hCCA.

Successful application of modified crude DNA extraction from muscle tissues for various types of PCR amplifications.

BACKGROUND: One of the most challenging aspects of nucleic acid amplification tests is the extraction of genomic DNA. However, achieving satisfactory quality and quantity of genomic DNA is not always easy, while the demand for rapid, low-cost and less laborious DNA isolation methods is ever-increasing. METHODS AND RESULTS: We have developed a rapid (⁓2 min) crude DNA extraction method leading to direct-PCR that requires minimum reagents and laboratory equipment. It was developed by eliminating the time-consuming purification steps of DNA extraction, by processing the sample in optimized amounts of Taq KCl PCR buffer and DNARelease Additive/Proteinase K in only two minutes and carrying out amplification using conventional Taq DNA polymerase. The DNA preparation method was validated on muscle tissue samples from 12 different species as well as 48 cooked meat samples. Its compatibility was also successfully tested with different types of PCR amplification platforms extensively used for genetic analysis, such as simplex PCR, PCR-RFLP (Restriction Fragment Length Polymorphism), multiplex PCR, isothermal amplification, real-time PCR and DNA sequencing. CONCLUSIONS: The developed protocol provides sufficient amount of crude DNA from muscle tissues of different species for PCR amplifications to identify species-of-origin via different techniques coupled with PCR. The simplicity and robustness of this protocol make nucleic acid amplification assays more accessible and affordable to researchers and authorities for both laboratory and point-of-care tests.

Characterization and expression analysis of GLABRA3 (GL3) genes in cotton: insights into trichome development and hormonal regulation.

BACKGROUND: GLABRA3 (GL3) and ENHANCER OF GLABRA3 (EGL3) genes encode a typical helix-loop-helix (bHLH) transcription factors that primarily regulate trichome branching and root hair development, DNA endoreduplication, trichoblast size, and stomatal formation. The functions of GL3 genes in cotton crop have been poorly characterized. In this study, we performed comprehensive genome-wide scans for GL3 and EGL3 homologs to enhance our comprehension of their potential roles in trichome and fiber development in cotton crop. METHODS AND RESULTS: Our findings paraded that Gossypium hirsutum and G. barbadense have 6 GL3s each, unevenly distributed on 4 chromosomes whereas, G. arboreum, and G. raimondii have 3 GL3s each, unevenly distributed on 2 chromosomes. Gh_A08G2088 and Gb_A09G2187, despite having the same bHLH domain as the other GL3 genes, were excluded due to remarkable short sequences and limited number of motifs, indicating a lack of potential functional activity. The phylogenetic analysis categorized remaining 16 GL3s into three subfamilies (Group I-III) closely related to A. thaliana. The 16 GL3s have complete bHLH domain, encompassing 590-631 amino acids, with molecular weights (MWs) ranging from 65.92 to 71.36 kDa. Within each subfamily GL3s depicted shared similar gene structures and motifs, indicating conserved characteristics within respective groups. Promoter region analysis revealed 27 cis-acting elements, these elements were responsive to salicylic acid, abscisic acid (ABA), methyl jasmonate (MeJA), and gibberellin. The expression of GL3 genes was analyzed across 12 tissues in both G. barbadense and G. hirsutum using the publicly available RNA-seq data. Among GL3s, Gb_D11G0219, Gb_D11G0214, and Gb_D08G2182, were identified as relatively highly expressed across different tissues, consequently selected for hormone treatment and expression validation in G. barbadense. RT-qPCR results demonstrated significant alterations in the expression levels of Gb_D11G0219 and Gb_D11G0214 following MeJA, GA, and ABA treatment. Subcellular localization prediction revealed that most GL3 proteins were predominantly expressed in the nucleus, while a few were localized in the cytoplasm and chloroplasts. CONCLUSIONS: In summary, this study lays the foundation for subsequent functional validation of GL3 genes by identifying hormonal regulation patterns and probable sites of action in cotton trichome formation and fiber development. The results stipulate a rationale to elucidate the roles and regulatory mechanisms of GL3 genes in the intricate process of cotton fibre and trichome development.

Toxicodynamic of combined mycotoxins: MicroRNAs and acute-phase proteins as diagnostic biomarkers.

Mycotoxins, ubiquitous contaminants in food, present a global threat to human health and well-being. Mitigation efforts, such as the implementation of sound agricultural practices, thorough food processing, and the advancement of mycotoxin control technologies, have been instrumental in reducing mycotoxin exposure and associated toxicity. To comprehensively assess mycotoxins and their toxicodynamic implications, the deployment of effective and predictive strategies is imperative. Understanding the manner of action, transformation, and cumulative toxic effects of mycotoxins, moreover, their interactions with food matrices can be gleaned through gene expression and transcriptome analyses at cellular and molecular levels. MicroRNAs (miRNAs) govern the expression of target genes and enzymes that play pivotal roles in physiological, pathological, and toxicological responses, whereas acute phase proteins (APPs) exert regulatory control over the metabolism of therapeutic agents, both endogenously and posttranscriptionally. Consequently, this review aims to consolidate current knowledge concerning the regulatory role of miRNAs in the initiation of toxicological pathways by mycotoxins and explores the potential of APPs as biomarkers following mycotoxin exposure. The findings of this research highlight the potential utility of miRNAs and APPs as indicators for the detection and management of mycotoxins in food through biological processes. These markers offer promising avenues for enhancing the safety and quality of food products.

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.

Association of Oral Submucous Fibrosis Risk with GSTM1 and GSTT1 Gene Polymorphisms.

OBJECTIVE: To determine the association of GSTM1 and GSTT1 polymorphisms with oral submucous fibrosis (OSF). STUDY DESIGN: A case-control study. Place and Duration of the Study: Department of Human Genetics and Molecular Biology, University of Health Sciences, Lahore and Oral and Maxillofacial Surgery Department, de Montmorency, College of Dentistry/ Punjab Dental Hospital, Lahore, Pakistan, from 1st April 2019 to 31st April 2020. METHODOLOGY: OSF patients were diagnosed with different clinical staging of mouth opening by Vernier caliper with the help of a professional dentist in the Department of Oral and Maxillofacial, de Montmorency, College of Dentistry, Lahore. One hundred and eight blood samples of OSF patients and 108 samples of normal controls were collected. Genomic DNA was obtained from whole-blood extraction. Multiplex PCR amplification using GSTM1, GSTT1, and ß -Globin gene primers was performed. RESULTS: GSTM1 and GSTT1 null genotypes frequencies were found in 43.5% (47/108) and 13.9% (15/108) of controls, whereas 54.6% (59/108) and 25.9% (28/108) of OSF patients, respectively. OSF patients had a greater frequency rate of GSTM1 and GSTT1 null genotypes than controls [OR 1.56, 95% CI 0.91-2.67 (p=0.13)] and [OR 2.17, 95% CI 1.08-4.34 (p=0.04)], respectively. The GSTT1 genotype was found statistically significant with OSF (p=0.05), and risk was also determined. The cumulative effect of null genotypes of GSTM1/GSTT1 did not show any association with the controls and in OSF patients. Proportions of active and null alleles of the patient group were; 86.1%/13.9%; and in control, it was 92.6%/7.4% (OR = 2.01; CI: 0.82-4.97; p=0.18), respectively. CONCLUSION: The study determined a statistically significant association of GSTT1 gene polymorphism with OSF. KEY WORDS: Oral submucous fibrosis, GSTM1, GSTT1, Gene polymorphisms, Genetic risk.

Cold plasma: A success road to mycotoxins mitigation and food value edition.

Mycotoxins are common in many agricultural products and may harm both animals and humans. Dietary mycotoxins are reduced via physical, chemical, and thermal decontamination methods. Chemical residues are left behind after physical and chemical treatments that decrease food quality. Since mycotoxins are heat-resistant, heat treatments do not completely eradicate them. Cold plasma therapy increases food safety and shelf life. Cold plasma-generated chemical species may kill bacteria quickly at room temperature while leaving no chemical residues. This research explains how cold plasma combats mold and mycotoxins to guarantee food safety and quality. Fungal cells are damaged and killed by cold plasma species. Mycotoxins are also chemically broken down by the species, making the breakdown products safer. According to a preliminary cold plasma study, plasma may enhance food shelf life and quality. The antifungal and antimycotoxin properties of cold plasma benefit fresh produce, agricultural commodities, nuts, peppers, herbs, dried meat, and fish.

3D-QSAR pharmacophore modeling, virtual screening, molecular docking, MD simulations, in vitro and in vivo studies to identify potential anti-hyperplasia drugs.

Psoriasis is a common immune-mediated skin condition characterized by aberrant keratinocytes and cell proliferation. The purpose of this study was to explore the FDA-approved drugs by 3D-QSAR pharmacophore model and evaluate their efficiency by in-silico, in vitro, and in vivo psoriasis animal model. A 3D-QSAR pharmacophore model was developed by utilizing HypoGen algorithm using the structural features of 48 diaryl derivatives with diverse molecular patterns. The model was validated by a test set of 27 compounds, by cost analysis method, and Fischer's randomization test. The correlation coefficient of the best model (Hypo2) was 0.9601 for the training set while it was 0.805 for the test set. The selected model was taken as a 3D query for the virtual screening of over 3000 FDA-approved drugs. Compounds mapped with the pharmacophore model were further screened through molecular docking. The hits that showed the best docking results were screened through in silico skin toxicity approach. Top five hits were selected for the MD simulation studies. Based on MD simulations results, the best two hit molecules, that is, ebastine (Ebs) and mebeverine (Mbv) were selected for in vitro and in vivo antioxidant studies performed in mice. TNF-α and COX pro-inflammatory mediators, biochemical assays, histopathological analyses, and immunohistochemistry observations confirmed the anti-inflammatory response of the selected drugs. Based on these findings, it appeared that Ebs can effectively treat psoriasis-like skin lesions and down-regulate inflammatory responses which was consistent with docking predictions and could potentially be employed for further research on inflammation-related skin illnesses such as psoriasis.

The GaKAN2, a KANADI transcription factor, modulates stem trichomes in Gossypium arboreum.

KEY MESSAGE: GaKAN2, a member of the KANADI family, was found to be widely expressed in the cotton tissues and regulates trichome development through complex pathways. Cotton trichomes are believed to be the defense barrier against insect pests. Cotton fiber and trichomes are single-cell epidermal extensions with shared regulatory mechanisms. Despite several studies underlying mechanism of trichome development remains elusive. The KANADI is one of the key transcription factors (TFs) family, regulating Arabidopsis trichomes growth. However, the function of KANADI genes in cotton remains unknown. In the current study genome-wide scanning, transcriptomic analysis, gene silencing, subcellular localization, and yeast two-hybrid techniques were employed to decipher the function of KANADI TFs family genes in cotton crop. A total of 7 GaKAN genes were found in the Gossypium arboreum. Transcriptomic data revealed that these genes were significantly expressed in stem and root. Moreover, GaKAN2 was widely expressed in other tissues also. Subsequently, we selected GaKAN2 to validate the function of KANADI genes. Silencing of GaKAN2 resulted in a 24.99% decrease in single-cell trichomes and an 11.33% reduction in internodal distance, indicating its potential role in regulating trichomes and plant growth. RNA-Seq analysis elucidated that GaSuS and GaERS were the downstream genes of GaKAN2. The transcriptional activation and similarity in silencing phenotype between GaKAN2 and GaERS suggested that GaKAN2 regulates trichomes development through GaERS. Moreover, KEGG analysis revealed that a significant number of genes were enriched in the biosynthesis of secondary metabolites and plant hormone signal transduction pathways, thereby suggesting that GaKAN2 regulates the stem trichomes and plant growth. The GFP subcellular localization and yeast transcriptional activation analysis elucidated that GaKAN2 was located in the nucleus and capable of regulating the transcription of downstream genes. This study elucidated the function and characteristics of the KANADI gene family in cotton, providing a fundamental basis for further research on GaKAN2 gene in cotton plant trichomes and plant developmental processes.

Development and validation of a universal primer pair for the taxonomic and phylogenetic studies of vertebrates.

BACKGROUND: Recent studies in the field of molecular identification have described 16S rRNA gene as a highly informative fragment of mitochondrial DNA for species discrimination. This study presents a newly developed universal primer pair yielding an approximately 350 bp fragment of mitochondrial 16S rRNA, variable enough to encompass and identify all vertebrate classes. METHODS AND RESULTS: The primers were designed by aligning and analyzing over 1500 16S rRNA sequences downloaded from the NCBI nucleotide database. A total of 93 vertebrate species, spanning 27 orders and 55 families, were PCR-amplified to validate the primers. All the target species were successfully amplified and identified when aligned with reference sequences from the NCBI nucleotide database. Using the Kimura 2-parameter model, low intra-species genetic divergence of the target region was observed - from 0 to 4.63%, whereas relatively higher inter-species genetic divergence was observed, ranging from 4.88% to 69.81%. Moreover, the newly developed primers were successfully applied to a direct PCR protocol, making the workflow very cost-effective, time-saving and less laborious in comparison to conventional PCR. CONCLUSIONS: The short length, high variability and conserved priming sites of the target fragment across all vertebrate species make it a highly desirable marker for species identification and discrimination.

GNAS mutation inhibits growth and induces phosphodiesterase 4D expression in colorectal cancer cell lines.

Approximately 5% of colorectal cancers (CRCs) have a gain-of-function mutation in the GNAS gene, which leads to the activation of cAMP-dependent signaling pathways and associates with poor prognosis. We investigated the effect of an activating GNAS mutation in CRC cell lines on gene expression and cell proliferation in vitro, and tumor growth in vivo. GNAS-mutated (GNASmt) HCT116 cells showed stimulated synthesis of cAMP as compared to parental (Par) cells. The most upregulated gene in the GNASmt cells was cAMP-hydrolyzing phosphodiesterase 4D (PDE4D) as detected by RNA sequencing. To further validate our finding, we analyzed PDE4D expression in a set of human CRC tumors (n = 35) and demonstrated overexpression in GNAS mutant CRC tumors as compared to GNAS wild-type tumors. The GNASmt HCT116 cells proliferated more slowly than the Par cells. PDE4 inhibitor Ro 20-1724 and PDE4D subtype selective inhibitor GEBR-7b further suppressed the proliferation of GNASmt cells without an effect on Par cells. The growth inhibitory effect of these inhibitors was also seen in the intrinsically GNAS-mutated SK-CO-1 CRC cell line having high levels of cAMP synthesis and PDE4D expression. In vivo, GNASmt HCT116 cells formed smaller tumors than the Par cells in nude mice. In conclusion, our findings demonstrate that GNAS mutation results in the growth suppression of CRC cells. Moreover, the GNAS mutation-induced overexpression of PDE4D provides a potential avenue to impede the proliferation of CRC cells through the use of PDE4 inhibitors.