Identification of potential miRNA-mRNA regulatory network contributing to pathogenesis of polycystic ovarian syndrome.

BACKGROUND: Polycystic ovarian syndrome (PCOS), a gynae-endocrine disorder, has a relatively high risk of differential expression of miRNA (DE-miRNA) in the disease progression. AIMS: To identify the DE-miRNA in the progression of PCOS in the ovarian cumulus cells. METHODS: The microarray dataset GSE72274 was analysed for PCOS-associated DE-miRNAs. miRNet identifies the target genes. Protein-protein interaction (PPI) network was constructed and hub genes were analysed by topology and module analysis. Transcription factors (TFs) and protein kinases (PKs) regulating the hub genes were identified using X2K tool. Biological functions were analysed using DAVID software. Finally, the DGIdb drug-gene interaction tool identifies the candidate medications. RESULTS: A total of 1577 DE-miRNAs linked to PCOS were identified, with 13 meeting the specified criteria. Subsequently, its 2053 target genes were retrieved through miRNet. Topology and module analysis identified the hub genes VEGFA, SOX2, KRAS, AKT1, and SMAD4 that are implicated in ovarian regulation. Notably, the study highlighted the significant role of the wnt signalling pathway, which is involved in ovarian function, specifically in follicle development, corpus luteum formation, and steroid production. Additionally, six TFs and PKs were identified as important regulators of these hub genes, and the potential medication interactions identified 11 medicines for VEGFA, KRAS, AKT1, and SMAD4 genes, while no suitable drug for SOX2 was identified. CONCLUSION: Identified, hub genes are known to associate with the regulation of ovarian function such as oocyte development, and steroid synthesis via the wnt signalling pathway.

A hypothesis: MiRNA-124 mediated regulation of sirtuin 1 and vitamin D receptor gene expression accelerates aging.

Objectives: Specific miRNAs are evident to be overexpressed with age, lifestyle, and environmental changes. Previous studies reported miR-124 overexpression in different scenarios in aged skin, age-related cognitive impairment, ischemic heart disease, muscle atrophy, and fractures. Thus miR-124 was considered to be a reliable miRNA target to establish a hypothesis on aging epigenome. Parallelly the hypothesis focuses on the expression of SIRT1 and VDR genes as a target for this specific miRNA expression as these genes were believed to be related to aging. This study aims to derive facts and evidence from past studies on aging. The objective was to establish a hypothetical linkage between miR-124 with age-related genes like SIRT1 and VDR. Methods: An in silico search was performed in the TargetScan and miRbase databases to analyze the aging-associated miRNAs and their gene targets, the Python seaborn library was used, and the results were represented in terms of a bar plot. Results: Based on an in silico analysis and studies available in the literature, we identified that miR-124-3p.1 and miR-124-3p.2 targets 3' UTR of VDR and SIRT1 genes, and hence thereby indicates that the miR-124 can regulate the expression of these genes. Further, few in vitro research studies have observed that miR-124 overexpression leads to the downregulation of VDR and SIRT1 gene expression. These results indicate that the suppression of these target genes accelerates early aging and age-related disorders. Conclusions: Overall, this study hypothesizes that the overexpression of miR-124 diminishes the expression of VDR and SIRT1 genes, and thereby advances the process of aging, resulting in the development of age-associated complications.

Extent of Virulence and Antibiotic Resistance Genes in Helicobacter pylori and Campylobacteria.

Helicobacter pylori, a member of the clade campylobacteria, is the leading cause of chronic gastritis and gastric cancer. Virulence and antibiotic resistance of H. pylori are of great concern to public health. However, the relationship between virulence and antibiotic resistance genes in H. pylori in relation to other campylobacteria remains unclear. Using the virulence and comprehensive antibiotic resistance databases, we explored all available 354 complete genomes of H. pylori and compared it with 90 species of campylobacteria for virulence and antibiotic resistance genes/proteins. On average, H. pylori had 129 virulence genes, highest among Helicobacter spp. and 71 antibiotic resistance genes, one of the lowest among campylobacteria. Just 2.6% of virulence genes were shared by all campylobacterial members, whereas 9.4% were unique to H. pylori. The cytotoxin-associated genes (cags) seemed to be exclusive to H. pylori. Majority of the isolates from Asia and South America were cag2-negative and many antibiotic resistance genes showed isolate-specific patterns of occurrence. Just 15 (8.8%) antibiotic resistance genes, but 103 (66%) virulence genes including 25 cags were proteomically identified in H. pylori. Arcobacterial members showed large variation in the number of antibiotic resistance genes and there was a positive relation with the genome size. Large repository of antibiotic resistance genes in campylobacteria and a unique set of virulence genes might have important implications in shaping the course of virulence and antibiotic resistance in H. pylori.

Repurposing EORTC QLQ-H&N43 and NCCN Distress Thermometer and Problem List: Adaptation and Validation in Kannada.

To translate, validate and test the reliability of Kannada version of "EORTC QLQ-H&N43" and "NCCN Distress Thermometer and Problem list" version 2.2022. The English version of "EORTC QLQ H&N43" and "NCCN Distress thermometer and Problem List" version 2.2022 tools were translated into Kannada language according to standard guideline. The translated version was validated by EORTC and by using content validity index (CVI). Further, the reliability of validated tools was established via test-retest and internal consistency method whereas construct was determined via spearman rank correlation. The Cronbach alpha value > 0.7 and correlation coefficients (ρ) < 0.05 was considered as significant. The Kannada version of "EORTC QLQ-H&N43" was validated by EORTC as well as by experts whereas  NCCN distress tool was validated only by experts with average CVI score of 1 and 0.97 respectively. Out of total 80 patients, 50% were head and neck cancer (HNC) patients and 50% belonged to other cancer types. Kannada version of EORTC QLQ-H&N43 and NCCN distress tool was found to be reliable among HNC and general cancer patients respectively with the Cronbach alpha value between 0.819-1 and 0.71-1 for all the domains. Further, only 7.72% of EORTC QLQ-H&N43 and 13.33% of NCCN distress tool construct were significantly correlated with construct of EORTC QLQ-C30 (p < 0.05). The Kannada version of QoL and distress instrument was found to be valid and reliable to use among HNC and/ general cancer patients respectively. Thus, this method of translation, validation and reliability testing can be used as a novel practice in healthcare. Supplementary Information: The online version contains supplementary material available at 10.1007/s12070-023-04366-0.

Clinicopathological Study of Lesions of Upper Gastrointestinal Tract.

Conditions affecting the upper digestive system are often seen in clinical practice and are associated with a high rate of death and disability. Histopathological confirmation is one of the foundations for good treatment planning and the definite diagnosis of illnesses of the upper gastrointestinal tract. The numerous methods employed in the diagnosis of gastrointestinal lesions have come a long way in the previous 25 years. The identification and diagnosis of gastrointestinal lesions have been substantially aided by the development of endoscopy, endoscopic biopsy, and other surgical techniques. This research aimed to examine the variety of gastrointestinal tract (GI) lesions and to draw connections between the clinical and pathological manifestations of these conditions. Materials and Methods: A two-year cross-sectional study was conducted in the Department of Pathology, from June 2018 to May 2020, which included surgical specimens of 140 cases from the upper gastrointestinal tract, of which 111 cases were biopsy, and 29 cases were resected surgical specimens. The data were analyzed using SPSS software. Furthermore, P values, sensitivity, specificity, positive predictive value, and negative predictive value were calculated. Results: This study was a two-year cross-sectional study conducted in the Department of Pathology during the period of June 2018-May 2020.

Prevalence of Epstein Barr Virus and Herpes Simplex Virus Among Human Papillomavirus Negative Oral Cancer Patients: A Cross-Sectional Study from South India.

The high incidence of oral carcinomas is due to its multifactorial etiology and the presence of various risk factors. Human Papillomavirus (HPV) has a proven role in the pathogenesis of oral carcinomas, but in the recent times there has been an increasing incidence of oral cancers who are negative for HPV infection. Also, these patients are non-smokers and non-drinkers so it could be speculated that these oral cancers are due to some other etiological factor probably of other viral infections. Therefore, this study examined the prevalence of Epstein Barr Virus (EBV) and Herpes Simplex Virus (HSV) among oral cancer patients. This cross-sectional study was conducted from January 2019 to June 2020. Biopsy samples from 47 newly diagnosed untreated patients with oral malignancies were collected along with their demographic and clinicopathological information. DNA extracted from the biopsies was processed for nested PCR for the detection of EBV and HSV. All the samples tested negative for HPV and HSV infection. Nested PCR detected 29 cases (70.7%) to be positive for EBV. The non-cancerous adjacent tissues also were negative for HPV, EBV and HSV. The prevalence of EBV was found to be more in males (62.1%) and the highest number of cases was of the left buccal mucosa compromising 34% of the total cases. From the present study it can be concluded that EBV but not HSV infection is associated with an increased risk of developing oral cancers. Although, 70.7% of the patients were found to be positive for EBV whether the viral infection played any role in the driving the malignancy needs to be further elucidated.

Trabecular bone score in adults with type 1 diabetes: a meta-analysis.

Type 1 diabetes mellitus (T1DM) is associated with a disproportionately high fracture rate despite a minimal decrease in bone mineral density. Though trabecular bone score (TBS), an indirect measure of bone architecture, is lower in adults with T1DM, the modest difference is unlikely to account for the large excess risk and calls for further exploration. INTRODUCTION: Fracture rates in type 1 diabetes mellitus (T1DM) are disproportionately high compared to the modestly low bone mineral density (BMD). Distortion of bone microarchitecture compromises bone quality in T1DM and is indirectly measured by trabecular bone score (TBS). TBS could potentially be used as a screening tool for skeletal assessment; however, there are inconsistencies in the studies evaluating TBS in T1DM. We performed this meta-analysis to address this knowledge gap. METHODS: An electronic literature search was conducted using PubMed, Scopus, and Web of Science resources (all-year time span) to identify studies relating to TBS in T1DM. Cross-sectional and retrospective studies in adults with T1DM were included. TBS and BMD data were extracted for pooled analysis. Fracture risk could not be analyzed as there were insufficient studies reporting it. RESULT: Data from six studies were included (T1DM: n = 378 and controls: n = 286). Pooled analysis showed a significantly lower TBS [standardized mean difference (SMD) = - 0.37, 95% CI - 0.52 to - 0.21; p < 0.00001] in T1DM compared to controls. There was no difference in the lumbar spine BMD (6 studies, SMD - 0.06, 95% CI - 0.22 to 0.09; p = 0.43) and total hip BMD (6 studies, SMD - 0.17, 95% CI - 0.35 to 0.01; p = 0.06) in the case and control groups. CONCLUSIONS: Adults with T1DM have a lower TBS but similar total hip and lumbar spine BMD compared to controls. The risk attributable to the significant but limited difference in TBS falls short of explaining the large excess propensity to fragility fracture in adults with T1DM. Further studies on clarification of the mechanism and whether TBS is suited to screen for fracture risk in adults with T1DM are necessary.

Factors determining success and the cost of materials used in securing intravenous access in an emergency setting: A prospective observational study.

INTRODUCTION: Multiple failed attempts at securing intravenous catheter access cause increased patient dissatisfaction and higher costs. We aimed to identify the factors leading to multiple failed attempts and estimate the cost of resources wasted. METHODS: Participants were recruited from the emergency department for a prospective, observational study. Healthcare workers inserting peripheral intravenous catheters were observed. Patient characteristics and the number of attempts needed were recorded. RESULTS: Three hundred thirty-four patients were enrolled, and an average of 1.74 ± 1.026 (Range: 1 - 5) access attempts were needed per patient. Only 56.28% of the insertions were successful on the first attempt. On multivariate linear regression with attempts as the outcome variable, age (ß = 0.01, 95%CI 0.004 - 0.014, p = 0.0006), catheter calibre (ß 20G = -0.25, 95%CI -0.45 - -0.07, p = 0.008), visibility (ß = 0.23, 95%CI 0.02 - 0.44, p = 0.026) and palpability (ß = 0.44, 95%CI 0.21 - 0.66, p = 0.0001) of the vein were statistically significant predictors. The average total cost of materials required was $6.4 USD per patient, of which $1.76 USD was spent towards unsuccessfully inserted catheters that were consequently thrown away. CONCLUSIONS: Our study shows that securing IV access often requires multiple attempts, with nearly 30% of the total cost amounting towards materials wasted. The risk of multiple attempts is highest for older patients with invisible and non-palpable veins.

Extracellular Vesicles from Stromal Vascular Fraction of Human Adipose Tissue in the Development of Non-antibiotic Therapy.

BACKGROUND: Antibiotic-resistant microorganisms (ARMS) are the leading cause of socio- economic loss in the world, with historical evidence linking them to increased mortality and morbidity. METHODOLOGY: In this systematic review, we highlight a new treatment approach for antibiotic-resistant infections using 'Extracellular vesicle (EVs)-based therapy,' also known as cell- and drug-free therapy. Here, we categorize and summarize studies on EVs derived from various human sources, such as tissues, bodily fluids, or their condition media, emphasizing their anti-infective properties in the treatment of various infections. In addition, we contend that human adipose tissue (HAT) is a superior source of antimicrobial EVs (aEVs) and investigate the distinct antimicrobial properties of aEVs derived from a stromal vascular fraction (SVF) of human adipose tissue. In light of this, we described the limited literature and research gaps that are essential for using SVF-aEVs as personalized precision medicine. RESULT AND DISCUSSION: The notion behind adipose-derived SVF-EVs is supported by extensive literature searches that demonstrate growing trends in EV-based medical treatments as well as the larger therapeutic potential of HAT because of its extensive history of usage in regenerative medicine. CONCLUSION: Additionally, the underlying science that explains how the inflammatory process aids in the clearance of infections and the restoration of homeostasis after the host immune system successfully defends against foreign pathogens, as well as the fact that adipose-derived SVF is a noninvasive, cost-effective source of a variety of parent immune cells that produces a good yield of EVs with the same genetic make-up as their parent cells, make this concept worthwhile. This research may thereby increase survival rates and survival quality in cases of resistant infections. Vocabulary: Drug- and cell-free therapy = Nano molecules (extracellular vesicles) used as a therapeutic source without the need for chemical drugs or cell transplantation. Anti-infection EVs (aEVs) = Nature's own anti-infection powered EVs (unmodified).

Association of pro-fibrinolytic receptor AnnexinA2 with tissue plasminogen activator/Inhibitor-1 in pre-eclampsia.

Background: The clinical manifestations of pre-eclampsia are related to placental anti-angiogenic factor alteration. These variations are mainly due to the alteration of plasminolytic components. The study aims to compare the expression of plasminolytic components in the placenta of women with and without pre-eclampsia. Material and Methods: The study included pregnant women with pre-eclampsia as PE group (n = 30) and without pre-eclampsia as a control group (n = 30). Placental bed biopsy tissues were collected. AnxA2, tPA, PAI-1 expression in the placental villous tissue was quantitatively evaluated using immunohistochemistry, western blot, and real time-PCR analysis. Results: The results of the study showed a significant decrease in the expression of ANXA2 and increased expression of tPA and PAI-1 in PE group compared to control group (p<0.005). AnxA2 expression showed positive correlation with tPA (r=+0.895, p=0.002) and negative correlation with PAI-1(r=-0.905, p=0.020) in control group whereas in the PE group AnxA2 expression was negatively correlated with tPA ((r=-0.801, p=0.016) and PAI-1 (R=-0.831, P=0.010). Conclusion: Decreased AnxA2 with increased expression of PAI-1 and tPA may be responsible for the altered fibrinolytic activity and play a significant role in pre-eclampsia pathogenesis.

Tissue plasminogen activator receptor ANXA2 and its complementary regulator anti-inflammatory ANXA1 as prognostic indicators of inflammatory response in COVID-19 pathogenesis.

COVID-19 patients demonstrating hyperactive immunologic response appear to have a severe illness with a poor prognosis. This study hypothesizes that the pro-inflammatory Annexin A2 (ANXA2) has role in COVID-19 pathogenesis. In thisobservational study, serum levels of ANXA2 along with interleukin 1 beta (IL1ß), IL6, tumour necrosis factor-alpha (TNFα), and anti-inflammatory ANXA1 were determined by sandwich ELISA in 20 each control, mild, moderate, and severe COVID-19 subjects.The ANXA2 levels (130 ng/mL, p < 0.001) were significantly elevated in severe COVID-19 subjects, compared to mild, moderate and controls. Similarly, all the other pro-inflammatory biomarkers levels were also significantly correlated with disease severity (p < 0.0001). However, ANXA1 showed significantly negative correlation with disease severity (p < 0.0001). Furthermore, the pro-inflammatory ANXA2 showed utility in mortality prediction with 86% sensitivity and specificity, and 57% positive predictive value at a serum threshold of 94 ng/mL. Overall,ANXA2 and ANXA1 along with IL1ß, IL6, TNFα, would be beneficial biomarkers in assessing the COVID-19 severity and mortality prediction.

Integrated molecular-network analysis reveals infertility-associated key genes and transcription factors in the non-obstructive azoospermia.

BACKGROUND: Male infertility is a multifactorial reproductive health problem with complex causes. Non-obstructive azoospermia (NOA) is characterized by failure of spermatogenesis, leading to the absence of spermatozoa in ejaculates. The molecular mechanism underlying the NOA is still not well understood. OBJECTIVES: This study aims to identify the key genes involved in male infertility that could be a potential biomarker in the diagnosis and prognosis of azoospermia. STUDY DESIGN: The microarray expression profiles dataset GSE45885 and GSE45887 were downloaded from the NCBI's Gene Expression Omnibus (GEO) database and analyzed for male infertility-associated differentially expressed genes (DEGs) using the GEO2R tool. The common DEGs between the two datasets were combined and their protein-protein interaction (PPI) network was constructed using Cytoscape to reveal the hub genes by topology and module analysis. In addition, transcription factors (TFs) and protein kinases regulating the hub genes were identified using the X2K tool. Then, the expression of the hub genes was validated by analyzing the GSE190752 microarray dataset. Further, the PPI network was screened for biological roles and enriched pathways using DAVID software. RESULTS: About 256 DEGs associated with NOA were identified and constructed the PPI network to find the infertility-associated proteins. The biological processes linked with these proteins were spermatogenesis, cell differentiation, flagellated sperm motility, and spermatid development. The topology and module analysis of the infertility-associated protein network identified the hub genes TEX38, FAM71F, PRR30, FAM166A, LYZL6, TPPP2, ARMC12, SPACA4, and FAM205A, which were found to be upregulated in the non-obstructive azoospermia. In addition, a total of 23 transcription factors and 3 protein kinases that are regulating these key hub genes were identified. Further these hub genes expression was validated using the microarray data and found that their expression was increased in the testicular biopsies obtained from NOA subjects, compared to healthy individuals. CONCLUSION: The identified key genes and its associated transcription factors are known to regulate the infertility-related processes in the non-obstructive azoospermia. Also, the clinical sample-based microarray data validation for the expression of these key hub genes indicates their potentiality to develop them as diagnostic or prognostic biomarkers for NOA.

Theranostic Potential of EFNB2 for Cetuximab Resistance in Head and Neck Cancer.

Only 13% of head and neck cancer (HNC) patients respond to cetuximab therapy despite its target (EGFR) is expressed in about 80-90% of HNC patients. However, this problem remained unresolved till date despite of numerous efforts. Thus, the current study aimed to establish hub genes involved in cetuximab resistance via series of bioinformatics approach. The GSE21483 dataset was analysed for differentially expressed genes (DEGs) using GEO2R and enrichment analysis was carried out using DAVID. STRING 11.5 and Cytoscape 3.7.2 were used for protein-protein interactions and hub genes respectively. The significant hub genes (p < 0.05) were validated using ULCAN and Human protein atlas. Validated genes were further queried for tumor infiltration using TIMER2.0. Out of total 307 DEGs, 38 hub genes were identified of which IL1A, EFNB2, SPRR1A, ROBO1 and SOCS3 were the significant hub genes associated with both mRNA expression and overall survival. IL1A, ROBO1, and SOCS3 were found to be downregulated whereas EFNB2 and SPRR1A were found to be upregulated in our study. However, using UALCAN, we found that high expression of IL1A, EFNB2, SOCS3 negatively affects overall survival whereas high expression of SPRR1A and ROBO1 positively affects overall survival. Protein level for EFNB2 and SPRR1A expression was significant in tumor HNC tissue as compared to normal HNC tissue. EFNB2 was found to be a key regulator of CTX resistance among HNC patients. Targeting EFNB2 and associated PPI circuits might improve the response rate to CTX. Thus, EFNB2 has potential to be theranostic marker for CTX resistance. Supplementary Information: The online version contains supplementary material available at 10.1007/s12070-023-03739-9.

Efficacy of HDAC inhibitors and epigenetic modulation in the amelioration of synovial inflammation, cellular invasion, and bone erosion in rheumatoid arthritis pathogenesis.

Rheumatoid arthritis (RA), an auto-immune disorder affected 1 % of the population around the globe. The pathophysiology of RA is highly concerted process including synovial hyperplasia, pannus formation, bone erosion, synovial cell infiltration in joints, and cartilage destruction. However, recent reports suggest that epigenetics play a pivotal role in the formation and organization of immune response in RA. Particularly, altered DNA methylation and impaired microRNA (miRNA) were detected in several immune cells of RA patients, such as T regulatory cells, fibroblast-like synoviocytes, and blood mononuclear cells. All these processes can be reversed by regulating the ubiquitous or tissue-based expression of histone deacetylases (HDACs) to counteract and terminate them. Hence, HDAC inhibitors (HDACi) could serve as highly potent anti-inflammatory regulators in the uniform amelioration of inflammation. Therefore, this review encompasses the information mainly focussing on the epigenetic modulation in RA pathogenesis and the efficacy of HDACi as an alternative therapeutic option for RA treatment. Overall, these studies have reported the targeting of HDAC1, 2 & 6 molecules would attenuate synoviocyte inflammation, cellular invasion, and bone erosion. Further, the inhibitors such as trichostatin A, suberoyl bis-hydroxamic acid, suberoyl anilide hydroxamic acid, and other compounds are found to attenuate synovial inflammatory immune response, clinical arthritis score, paw swelling, bone erosion, and cartilage destruction. Insight to view this, more clinical studies are required to determine the efficacy of HDACi in RA treatment and to unravel the underlying molecular mechanisms.

System Biology Approach to Identify the Hub Genes and Pathways Associated with Human H5N1 Infection.

INTRODUCTION: H5N1 is a highly pathogenic avian influenza virus that can infect humans and has an estimated fatality rate of 53%. As shown by the current situation of the COVID-19 pandemic, emerging and re-emerging viruses such as H5N1 have the potential to cause another pandemic. Thus, this study outlined the hub genes and pathways associated with H5N1 infection in humans. METHODS: The genes associated with H5N1 infection in humans were retrieved from the NCBI Gene database using "H5N1 virus infection" as the keyword. The genes obtained were investigated for protein-protein interaction (PPI) using STRING version 11.5 and studied for functional enrichment analysis using DAVID 2021. Further, the PPI network was visualised and analysed using Cytoscape 3.7.2, and the hub genes were obtained using the local topological analysis method of the cytoHubba plugin. RESULTS: A total of 39 genes associated with H5N1 infection in humans significantly interacted with each other, forming a PPI network with 38 nodes and 149 edges modulating 74 KEGG pathways, 76 biological processes, 13 cellular components, and 22 molecular functions. Further, the PPI network analysis revealed that 33 nodes interacted, forming 1056 shortest paths at 0.282 network density, along with a 1.947 characteristic path length. The local topological analysis predicted IFNA1, IRF3, CXCL8, CXCL10, IFNB1, and CHUK as the critical hub genes in human H5N1 infection. CONCLUSION: The hub genes associated with the H5N1 infection and their pathways could serve as diagnostic, prognostic, and therapeutic targets for H5N1 infection among humans.

Identification of signature genes and drug candidates for primary plasma cell leukemia: An integrated system biology approach.

BACKGROUND: Plasma cell leukemia (PCL) is one of the rare cancer which is characterized by the uncontrolled proliferation of plasma cells in peripheral blood and bone marrow. The aggressive behavior of the disease and high mortality rate among PCL patients makes it a thirst area to be explored. METHODS: The dataset for PCL was obtained from the GEO database and was analyzed using GEO2R for differentially expressed genes. Further, the functional enrichment analysis was carried out for DEGs using DAVID. The protein-protein interactions (PPI) for DEGs were obtained using STRING 11.5 and were analyzed in Cytoscape 3.7.2. to obtain the key hub genes. These key hub genes were investigated for their interaction with suitable drug candidates using DGIdb, DrugMAP, and Schrodinger's version 2022-1. RESULTS: Out of the total of 104 DEGs, 39 genes were up-regulated whereas 65 genes were down-regulated. A total of 11 biological processes, 2 cellular components, and 5 molecular functions were enriched along with the 7 KEGG pathways for the DEGs. Further, a total of 11 hub genes were obtained from the PPI of DEGs of which TP53, MAPK1, SOCS1, MBD3, and YES1 were the key hub genes. Oxaliplatin, mitoxantrone, and ponatinib were found to have the highest binding affinity towards the p53, MAPK1, and YES1 proteins respectively. CONCLUSION: TP53, MAPK1, SOCS1, MBD3, and YES1 are the signature hub genes that might be responsible for the aggressive prognosis of PCL leading to poor survival rate. However, p53, MAPK1, and YES1 can be targeted with oxaliplatin, mitoxantrone, and ponatinib.

Molecular detection of monkeypox and related viruses: challenges and opportunities.

The recent widespread emergence of monkeypox (mpox), a rare and endemic zoonotic disease by monkeypox virus (MPXV), has made global headlines. While transmissibility (R0 ≈ 0.58) and fatality rate (0-3%) are low, as it causes prolonged morbidity, the World Health Organization has declared monkeypox as a public health emergency of international concern. Thus, effective containment and disease management require quick and efficient detection of MPXV. In this bioinformatic overview, we summarize the numerous molecular tests available for MPXV, and discuss the diversity of genes and primers used in the polymerase chain reaction-based detection. Over 90 primer/probe sets are used for the detection of poxviruses. While hemagglutinin and A-type inclusion protein are the most common target genes, tumor necrosis factor receptor and complement binding protein genes are frequently used for distinguishing Clade I and Clade II of MPXV. Problems and possibilities in the detection of MPXV have been discussed.

First report of Lasiodiplodia theobromae causing stem canker of pomegranate (Punica granatum L.) in India.

In March 2022, cankers and lesions appeared on the branches of 2-3-year-old pomegranate plants grown in four orchards of Hanumangarh, Rajasthan, India. The disease incidence ranged from 5-15%. Field symptoms such as dark brown lesions on one side of the branches, cracked lesions, vascular tissue discoloration and drooping of the plants were noticed. To identify the causative agent, 2 diseased branch samples, showing typical symptoms collected from each orchard 25-30 km apart. The samples were washed with distilled water and small sections of tissue were excised from both symptomatic and asymptomatic areas using a sterile scalpel. Sections were surface sterilized with 1% sodium hypochlorite for 30 sec and 70% ethanol for 2 min followed by rinsing with sterilized water thrice. Sterile sections were dried on sterile filter paper and then transferred onto potato dextrose agar (PDA) amended with streptomycin (100 mgL-1) and incubated at 24±1°C in the dark. Samples (n=5) collected from different orchards produced similar colonies, with greyish white aerial mycelia, which became dark black after 5-7 days. The morphological characteristics of all isolates were observed under microscope. Immature conidia (6.3±1.05*14.7±0.98 µm: average of 50 measurements) were single celled, hyaline, ellipsoid or ovoid, apex rounded and truncated at the base while the matured conidia (8.4±1.41*15.3±1.17 µm: average of 50 measurements) had two cells with dark septa. The conidial morphology of all isolates was in accordance with Lasiodiplodia sp. (Alves et al; 2008) therefore, one representative isolate (HSC-1) was used for molecular identification at species level. Three loci viz., ITS, EF1-a and ß tubulin of fungal genomic DNA were PCR amplified using ITS-1/4, EF-F/R and TUB-2A/2B primers, respectively. The amplicons were sequenced and deposited in GenBank, NCBI database with accession no. ON598885 (ITS), ON605203 (EF) and ON605204 (TUB). BLASTn analysis showed similarity with the sequences of Lasiodiplodia theobromae isolates: ITS showed 100% with MK530071.1 (492 bases), EF 99.77% with MT975688.1 (436 bases) and BT 99.76% with MW287586.1 (422 bases). Phylogenetic analysis using Neighbour Joining method revealed close association among L. theobromae isolates. Thus, causative agent associated with stem canker of pomegranate was confirmed as L. theobromae. Further, the same isolate was used for pathogenicity tests on 1-year-old pomegranate plants (n=6). Briefly, 2 cm wound was created in the main stem with a sterile scalpel and a same-size mycelial plug was placed in the wound and wrapped with parafilm. Six plants that were wrapped with uncultured PDA served as control. The inoculated plants were maintained at 26°C and 65-70% RH in a polyhouse. After 4 days parafilm was removed from all plants. The experiment was repeated twice. Inoculated plants produced lesions (0.7 x 5.5 cm; average of 6 measurements) similar to field symptoms after 10-15 days and no such symptoms developed on control plants. The difference between control and inoculated plants was statistically significant (p=0.0001). The fungus was re-isolated from symptomatic tissue and colonies were morphologically similar to HSC-1, thus fulfilling the Koch's postulates. The fungus, L. theobromae causes stem canker and dieback on different host plants and is mainly distributed in tropical and subtropical regions and has been reported on pomegranate from Florida (Xavier et al 2017). To the best of our knowledge, this is the first report of L. theobromae causing stem canker of pomegranate in India.

Implicative role of epidermal growth factor receptor and its associated signaling partners in the pathogenesis of Alzheimer's disease.

Epidermal growth factor receptor (EGFR) plays a pivotal role in early brain development, although its expression pattern declines in accordance with the maturation of the active nervous system. However, recurrence of EGFR expression in brain cells takes place during neural functioning decline and brain atrophy in order to maintain the homeostatic neuronal pool. As a consequence, neurotoxic lesions such as amyloid beta fragment (Aß1-42) formed during the alternative splicing of amyloid precursor protein in Alzheimer's disease (AD) elevate the expression of EGFR. This inappropriate peptide deposition on EGFR results in the sustained phosphorylation of the downstream signaling axis, leading to extensive Aß1-42 production and tau phosphorylation as subsequent pathogenesis. Recent reports convey that the pathophysiology of AD is correlated with EGFR and its associated membrane receptor complex molecules. One such family of molecules is the annexin superfamily, which has synergistic relationships with EGFR and is known for membrane-bound signaling that contributes to a variety of inflammatory responses. Besides, Galectin-3, tissue-type activated plasminogen activator, and many more, which lineate the secretion of pro-inflammatory cytokines (TNF-α, IL-1ß, IL-6, and IL-18) result in severe neuronal loss. Altogether, we emphasized the perspectives of cellular senescence up-regulated by EGFR and its associated membrane receptor molecules in the pathogenesis of AD as a target for a therapeutical alternative to intervene in AD.