Systematic characterization of Gossypium GLN family genes reveals a potential function of GhGLN1.1a regulates nitrogen use efficiency in cotton.

The enzyme glutamine synthetase (GLN) is mainly responsible for the assimilation and reassimilation of nitrogen (N) in higher plants. Although the GLN gene has been identified in various plants, there is little information about the GLN family in cotton (Gossypium spp.). To elucidate the roles of GLN genes in cotton, we systematically investigated and characterized the GLN gene family across four cotton species (G. raimondii, G. arboreum, G. hirsutum, and G. barbadense). Our analysis encompassed analysis of members, gene structure, cis-element, intragenomic duplication, and exploration of collinear relationships. Gene duplication analysis indicated that segmental duplication was the primary driving force for the expansion of the GhGLN gene family. Transcriptomic and quantitative real-time reverse-transcription PCR (qRT-PCR) analyses indicated that the GhGLN1.1a gene is responsive to N induction treatment and several abiotic stresses. The results of virus-induced gene silencing revealed that the accumulation and N use efficiency (NUE) of cotton were affected by the inactivation of GhGLN1.1a. This study comprehensively analyzed the GhGLN genes in Gossypium spp., and provides a new perspective on the functional roles of GhGLN1.1a in regulating NUE in cotton.

The function of microbial enzymes in breaking down soil contaminated with pesticides: a review.

The use of pesticides and the subsequent accumulation of residues in the soil has become a worldwide problem. Organochlorine (OC) pesticides have spread widely in the environment and caused contamination from past agricultural activities. This article reviews the bioremediation of pesticide compounds in soil using microbial enzymes, including the enzymatic degradation pathway and the recent development of enzyme-mediated bioremediation. Enzyme-mediated bioremediation is divided into phase I and phase II, where the former increases the solubility of pesticide compounds through oxidation-reduction and hydrolysis reactions, while the latter transforms toxic pollutants into less toxic or nontoxic products through conjugation reactions. The identified enzymes that can degrade OC insecticides include dehalogenases, phenol hydroxylase, and laccases. Recent developments to improve enzyme-mediated bioremediation include immobilization, encapsulation, and protein engineering, which ensure its stability, recyclability, handling and storage, and better control of the reaction.

Predominance of MGMT promoter methylation among Pakistani glioblastoma patients.

BACKGROUND: Glioblastoma multiforme (GBM), the most prevalent subgroup of neuroepithelial tumors, is characterized by dismal overall survival (OS). Several studies have linked O6-methylguanine-DNA-methyltransferase (MGMT) promoter methylation to OS in GBM patients. However, MGMT methylation frequencies vary geographically and across ethnicities, with limited data for South Asian populations, including Pakistan. This study aimed to analyze MGMT promoter methylation in Pakistani GBM patients. METHODS: Consecutive primary GBM patients diagnosed ≥ 18 years-of-age, with no prior chemotherapy or radiotherapy history, were retrospectively selected. DNA was isolated from formalin-fixed-paraffin-embedded tissues. MGMT promoter methylation was analyzed using methylation-specific PCR. Clinical, pathological, and treatment data were assessed using Fisher's exact/Chi-squared tests. OS was calculated using Kaplan-Meier analysis in SPSS 27.0.1. RESULTS: The study included 48 GBM patients, comprising 38 (79.2%) males and 10 (20.8%) females. The median diagnosis age was 49.5 years (range 18-70). MGMT methylation was observed in 87.5% (42/48) of all cases. Patients with MGMT methylation undergoing radiotherapy or radiotherapy plus chemotherapy exhibited significantly improved median OS of 7.2 months (95% CI, 3.7-10.7; P < 0.001) and 16.9 months (95% CI, 15.9-17.9; P < 0.001), respectively, compared to those undergoing surgical resection only (OS: 2.2 months, 95% CI, 0.8-3.6). CONCLUSION: This is the first comprehensive study highlighting a predominance of MGMT methylation in Pakistani GBM patients. Furthermore, our findings underscore the association of MGMT methylation with improved OS across diverse treatment modalities. Larger studies are imperative to validate our findings for better management of Pakistani GBM patients.

Conducting nationwide cohort COVID-19 serology surveys on a nation with limited resources and decentralized governance: Evidence from Indonesia.

Knowing the level of SARS-CoV-2 transmission is crucial for decision-making on Coronavirus disease (COVID-19) handling. Guidelines for measuring SARS-CoV-2 antibodies to estimate seroprevalence are conceptually straightforward and internationally available. However, challenges exist for developing countries with limited laboratory capacity, diverse geographical topography, fragmented health information systems and limited resources such as Indonesia. One year after the first case was confirmed in Indonesia, approximately ten infections were undiagnosed or underreported for every reported case. Under those circumstances, we described the method and lessons learned in conducting nationwide cohort COVID-19 serology surveys in a nation with limited resources, such as Indonesia. •Strong cross-sectoral collaboration between ministries and levels of governance (central and subnational) enables strategic use of civil registration database for efficient sampling.•All agglomeration districts (highly dense population and urban area) were selected as study sites, and additional non-agglomeration districts were selected using probability-proportional-to-size (PPS).•Involving the experienced phlebotomist in community health service provider and district laboratory cut down preparation time.

Brachyolmia, dental anomalies and short stature (DASS): Phenotype and genotype analyses of Egyptian and Pakistani patients.

Brachyolmia is a heterogeneous group of developmental disorders characterized by a short trunk, short stature, scoliosis, and generalized platyspondyly without significant deformities in the long bones. DASS (Dental Abnormalities and Short Stature), caused by alterations in the LTBP3 gene, was previously considered as a subtype of brachyolmia. The present study investigated three unrelated consanguineous families (A, B, C) with Brachyolmia and DASS from Egypt and Pakistan. In our Egyptian patients, we also observed hearing impairment. Exome sequencing was performed to determine the genetic causes of the diverse clinical conditions in the patients. Exome sequencing identified a novel homozygous splice acceptor site variant (LTBP3:c.3629-1G > T; p. ?) responsible for DASS phenotypes and a known homozygous missense variant (CABP2: c.590T > C; p.Ile197Thr) causing hearing impairment in the Egyptian patients. In addition, two previously reported homozygous frameshift variants (LTBP3:c.132delG; p.Pro45Argfs*25) and (LTBP3:c.2216delG; p.Gly739Alafs*7) were identified in Pakistani patients. This study emphasizes the vital role of LTBP3 in the axial skeleton and tooth morphogenesis and expands the mutational spectrum of LTBP3. We are reporting LTBP3 variants in seven patients of three families, majorly causing brachyolmia with dental and cardiac anomalies. Skeletal assessment documented short webbed neck, broad chest, evidences of mild long bones involvement, short distal phalanges, pes planus and osteopenic bone texture as additional associated findings expanding the clinical phenotype of DASS. The current study reveals that the hearing impairment phenotype in Egyptian patients of family A has a separate transmission mechanism independent of LTBP3.

Causes and outcome of pregnancy related acute kidney injury.

Objective: To determine frequencies of causes and renal outcomes of pregnancy related acute kidney injury. Method: This descriptive case series study was conducted in Nephrology unit of a tertiary care hospital of Peshawar, from 1st August 2021 to 31st July 2022.A total of 100 patients with acute kidney injury secondary to obstetric conditions were enrolled via non-probability consecutive sampling technique. While patients with pre-existing renal disease, those with renal stones, or having bilateral small kidneys on ultrasound were excluded from the study. Patients were followed till 12 weeks postpartum period. Underlying obstetrical causes and outcome at 12 weeks postnatal period were determined. Results: The mean age of sample of 100 cases was 29.29 ± 6.45. Mean serum creatinine at presentation was 6.5± 3.13. Majority of patient, 89% were multigravidas. Seventy eight percent patients required hemodialysis. Primary postpartum hemorrhage remained the commonest underlying cause of pregnancy related acute kidney injury in this study. The frequency of persistent renal failure in Pr-AKI (pregnancy related acute kidney injury) in this study was 14%. In about 66% of cases complete recovery occurred. All the underlying obstetrical causes, when adjusted for age, gravidity, place and mode of delivery, had no association with persistent renal failure. Conclusion: Primary postpartum hemorrhage is the predominant cause of pregnancy related acute kidney injury. By the end of 12 weeks postpartum, two third patients recover completely from pregnancy related acute renal injury.

Molecular insight into CREBBP and TANGO2 variants causing intellectual disability.

BACKGROUND: Intellectual disability (ID) can be associated with different syndromes such as Rubinstein-Taybi syndrome (RSTS) and can also be related to conditions such as metabolic encephalomyopathic crises, recurrent,with rhabdomyolysis, cardiac arrhythmias and neurodegeneration. Rare congenital RSTS1 (OMIM 180849) is characterized by mental and growth retardation, significant and duplicated distal phalanges of thumbs and halluces, facial dysmorphisms, and an elevated risk of malignancies. Microdeletions and point mutations in the CREB-binding protein (CREBBP) gene, located at 16p13.3, have been reported to cause RSTS. By contrast, TANGO2-related metabolic encephalopathy and arrhythmia (TRMEA) is a rare metabolic condition that causes repeated metabolic crises, hypoglycemia, lactic acidosis, rhabdomyolysis, arrhythmias and encephalopathy with cognitive decline. Clinicians need more clinical and genetic evidence to detect and comprehend the phenotypic spectrum of this disorder. METHODS: Exome sequencing was used to identify the disease-causing variants in two affected families A and B from District Kohat and District Karak, Khyber Pakhtunkhwa. Affected individuals from both families presented symptoms of ID, developmental delay and behavioral abnormalities. The validation and co-segregation analysis of the filtered variant was carried out using Sanger sequencing. RESULTS: In the present study, two families (A and B) exhibiting various forms of IDs were enrolled. In Family A, exome sequencing revealed a novel missense variant (NM 004380.3: c.4571A>G; NP_004371.2: p.Lys1524Arg) in the CREBBP gene, whereas, in Family B, a splice site variant (NM 152906.7: c.605 + 1G>A) in the TANGO2 gene was identified. Sanger sequencing of both variants confirmed their segregation with ID in both families. The in silico tools verified the aberrant changes in the CREBBP protein structure. Wild-type and mutant CREBBP protein structures were superimposed and conformational changes were observed likely altering the protein function. CONCLUSIONS: RSTS and TRMEA are exceedingly rare disorders for which specific clinical characteristics have been clearly established, but more investigations are underway and required. Multicenter studies are needed to increase our understanding of the clinical phenotypes, mainly showing the genotype-phenotype associations.

Method of moments solution to ethylene glycol based Al2O3 nanofluid flow through expanding/contracting rectangular channel.

In this study, we present a comprehensive analysis of the laminar time-dependent magnetohydrodynamic (MHD) flow of ethylene glycol-based aluminum oxide nanofluid through a rectangular channel with contracting/expanding porous walls. We investigate the influence of aggregation/non-aggregation of nanoparticles, as well as the presence of thermal radiation. By imposing self-similarities in space and time, we obtain a system of nonlinear ordinary differential equations governing the flow. To solve these equations, we employ a well-known semi-analytical technique known as the Method of Moments (MoM). Additionally, we compare our results with the outcomes achieved through an application of another commonly utilized numerical approach (shooting technique with the Runge-Kutta-Fehlberg scheme). The comparison shows an excellent agreement that endorses the accuracy of the calculated solutions. The velocity and temperature profiles obtained from our analysis exhibit variations due to the changes in involved dimensionless parameters. We present these variations through graphical representations along with their explanations. Interestingly, our study reveals that the aggregation of nanoparticles influences the fluctuations caused by other parameters, and to some extent, suppresses them. Consequently, we observe less deviation among the velocity and temperature curves for the aggregation case compared to the non-aggregation case. These findings have significant implications in real-world engineering and industry. The understanding of the flow behavior of nanofluids through expanding/contracting rectangular channels can aid in the design and optimization of various engineering systems, such as heat exchangers and microfluidic devices. Additionally, our study provides valuable insights into the effects of nanoparticle aggregation and thermal radiation in such systems, offering opportunities for enhancing their efficiency and performance.

Prevalence of BRCA1 and BRCA2 germline variants in an unselected pancreatic cancer patient cohort in Pakistan.

BACKGROUND: BRCA1 and BRCA2 (BRCA1/2) are the most frequently investigated genes among Caucasian pancreatic cancer patients, whereas limited reports are available among Asians. We aimed to investigate the prevalence of BRCA1/2 germline variants in Pakistani pancreatic cancer patients. METHODS: One hundred and fifty unselected and prospectively enrolled pancreatic cancer patients were comprehensively screened for BRCA1/2 germline variants using denaturing high-performance liquid chromatography and high-resolution melting analyses, followed by DNA sequencing of the variant fragments. The novel variants were analyzed for their pathogenic effect using in-silico tools. Potentially functional variants were further screened in 200 cancer-free controls. RESULTS: Protein truncating variant was detected in BRCA2 only, with a prevalence of 0.7% (1/150). A frameshift BRCA2 variant (p.Asp946Ilefs*14) was identified in a 71-year-old male patient of Pathan ethnicity, with a family history of abdominal cancer. Additionally, we found a novel variant in BRCA2 (p.Glu2650Gln), two previously reported variants in BRCA1 (p.Thr293Ser) and BRCA2 (p.Ile2296Leu) and a recurrent nonsense variant in BRCA2 (p.Lys3326Ter). These variants were classified as variants of uncertain significance (VUS). It is noteworthy that none of these VUS carriers had a family history of pancreatic or other cancers. CONCLUSIONS: In this first study, BRCA1/2 pathogenic variant is identified with a low frequency in pancreatic cancer patients from Pakistan. Comprehensive multigene panel testing is recommended in the Pakistani pancreatic cancer patients to enhance genetic understanding in this population.

Intelligent Levenberg-Marquardt neural network solution to flow of carbon nanotubes in a nozzle of liquid rocket engine.

In this research, we utilized artificial neural networks along with the Levenberg-Marquardt algorithm (ANN-LMA) to interpret numerical computations related to the efficiency of heat transfer in a regenerative cooling channel of a rocket engine. We used a mixture of Kerosene and carbon nanotubes (CNTs) for this purpose, examining both single-wall carbon nanotubes and multi-wall carbon nanotubes. The primary equations were converted into a dimensionless form using a similarity transformation technique. To establish a reference dataset for ANN- LMA and to analyze the movement and heat transfer properties of CNTs, we employed a numerical computation method called bvp4c, which is a solver for boundary value problems in ordinary differential equations using finite difference schemes combined with the Lobatto IIIA algorithm in MATLAB mathematical software. The ANN- LMA method was trained, tested and validated using these reference datasets to approximate the solutions of the flow model under different scenarios involving various significant physical parameters. We evaluated the accuracy of the proposed ANN- LMA model by comparing its results with the reference outcomes. We validated the performance of ANN- LMA in solving the Kerosene-based flow with CNTs in a rocket engine through regression analysis, histogram studies, and the calculation of the mean square error. The comprehensive examination of parameters undertaken in this research endeavor is poised to provide invaluable support to aerospace engineers as they endeavor to craft regenerative equipment with optimal efficiency. The pragmatic implications of our study are wide-ranging, encompassing domains as diverse as aerospace technology, materials science, and artificial intelligence. This research holds the potential to catalyze progress across multiple sectors and foster the evolution of increasingly efficient and sustainable systems.

Impact analysis of moisture stress on growth and yield of cotton using DSSAT-CROPGRO-cotton model under semi-arid climate.

Adequate soil moisture around the root zone of the crops is essential for optimal plant growth and productivity throughout the crop season, whereas excessive as well as deficient moisture is usually detrimental. A field experiment was conducted on cotton (Gossipium hirsuttum) with three water regimes (viz. well-watered (control); rainfed after one post-sowing irrigation (1-POSI) and rainfed after two post-sowing irrigations (2-POSI)) in main plots and application of eight osmoprotectants in sub plots of Split plot design to quantify the loss of seed cotton yield (SCY) under high and mild moisture stress. The DSSAT-CROPGRO-cotton model was calibrated to validate the response of cotton crop to water stress. Results elucidated that in comparison of well watered (control) crop, 1-POSI and 2-POSI reduced plant height by 13.5-28.4% and lower leaf area index (LAI) by 21.6-37.6%. Pooled analysis revealed that SCY under control was higher by 1,127 kg ha-1 over 1-POSI and 597 kg ha-1 than 2-POSI. The DSSAT-CROPGRO-cotton model fairly simulated the cotton yield as evidenced by good accuracy (d-stat ≥ 0.92) along with lower root mean square error (RMSE) of ≤183.2 kg ha-1; mean absolute percent error (MAPE) ≤6.5% under different irrigation levels. Similarly, simulated and observed biomass also exhibited good agreement with ≥0.98 d-stat; ≤533.7 kg ha-1 RMSE; and ≤4.6% MAPE. The model accurately simulated the periodical LAI, biomass and soil water dynamics as affected by varying water regimes in conformity with periodical observations. Both the experimental and the simulated results confirmed the decline of SCY with any degree of water stress. Thus, a well calibrated DSSAT-CROPGRO-cotton model may be successfully used for estimating the crop performance under varying hydro-climatic conditions.

Structural and functional implications of SLC13A3 and SLC9A6 mutations: an in silico approach to understanding intellectual disability.

BACKGROUND: Intellectual disability (ID) is a condition that varies widely in both its clinical presentation and its genetic underpinnings. It significantly impacts patients' learning capacities and lowers their IQ below 70. The solute carrier (SLC) family is the most abundant class of transmembrane transporters and is responsible for the translocation of various substances across cell membranes, including nutrients, ions, metabolites, and medicines. The SLC13A3 gene encodes a plasma membrane-localized Na+/dicarboxylate cotransporter 3 (NaDC3) primarily expressed in the kidney, astrocytes, and the choroid plexus. In addition to three Na + ions, it brings four to six carbon dicarboxylates into the cytosol. Recently, it was discovered that patients with acute reversible leukoencephalopathy and a-ketoglutarate accumulation (ARLIAK) carry pathogenic mutations in the SLC13A3 gene, and the X-linked neurodevelopmental condition Christianson Syndrome is caused by mutations in the SLC9A6 gene, which encodes the recycling endosomal alkali cation/proton exchanger NHE6, also called sodium-hydrogen exchanger-6. As a result, there are severe impairments in the patient's mental capacity, physical skills, and adaptive behavior. METHODS AND RESULTS: Two Pakistani families (A and B) with autosomal recessive and X-linked intellectual disorders were clinically evaluated, and two novel disease-causing variants in the SLC13A3 gene (NM 022829.5) and the SLC9A6 gene (NM 001042537.2) were identified using whole exome sequencing. Family-A segregated a novel homozygous missense variant (c.1478 C > T; p. Pro493Leu) in the exon-11 of the SLC13A3 gene. At the same time, family-B segregated a novel missense variant (c.1342G > A; p.Gly448Arg) in the exon-10 of the SLC9A6 gene. By integrating computational approaches, our findings provided insights into the molecular mechanisms underlying the development of ID in individuals with SLC13A3 and SLC9A6 mutations. CONCLUSION: We have utilized in-silico tools in the current study to examine the deleterious effects of the identified variants, which carry the potential to understand the genotype-phenotype relationships in neurodevelopmental disorders.

Exploring the recuperative potential of brassinosteroids and nano-biochar on growth, physiology, and yield of wheat under drought stress.

Drought stress as a result of rapidly changing climatic conditions has a direct negative impact on crop production especially wheat which is the 2nd staple food crop. To fulfill the nutritional demand under rapidly declining water resources, there is a dire need to adopt a precise, and efficient approach in the form of different amendments. In this regard, the present study investigated the impact of nano-biochar (NBC) and brassinosteroids (BR) in enhancing the growth and productivity of wheat under different drought stress conditions. The field study comprised different combinations of amendments (control, NBC, BR, and NBC + BR) under three irrigation levels (D0, D1 and D2). Among different treatments, the synergistic approach (NBC + BR) resulted in the maximum increase in different growth and yield parameters under normal as well as drought stress conditions. With synergistic approach (NBC + BR), the maximum plant height (71.7 cm), spike length (17.1), number of fertile tillers m-2 (410), no. of spikelets spike-1 (19.1), no. of grains spike-1 (37.9), 1000 grain weight (37 g), grain yield (4079 kg ha-1), biological yield (10,502 kg ha-1), harvest index (43.5). In the case of physiological parameters such as leaf area index, relative water contents, chlorophyll contents, and stomatal conductance were maximally improved with the combined application of NBC and BR. The same treatment caused an increase of 54, 10, and 7% in N, P, and K contents in grains, respectively compared to the control treatment. Similarly, the antioxidant response was enhanced in wheat plants under drought stress with the combined application of NBC and BR. In conclusion, the combined application of NBC and BR caused a significant increase in the growth, physiological and yield attributes of wheat under drought stress.

Psychometric properties of the Malay version of the difficulties in Emotion Regulation Scale-18 in Malaysian adolescents.

OBJECTIVE: The Difficulties in Emotion Regulation Scale-18 (DERS-18) is an instrument used to measure deficits in emotion regulation. However, the instrument has not been adapted to Malaysians and has never been validated in the Malay language. This study aimed to examine the psychometric properties of the Malay version of DERS-18. METHOD: The DERS-18 underwent forward-backward translation and assessment of face and content validity. Both Malay version of the DERS-18 and DASS-21 were completed by 701 adolescents (44.4% boys) aged 13 and 14 years old. To assess its dependability, a floor and ceiling effect evaluation and Cronbach's analysis were both performed. A series of confirmatory factor analyses (CFA), bivariate correlation, and regression were performed to evaluate the construct and criterion validity, respectively. RESULTS: The Malay version of DERS-18, after excluding "Awareness", indicated excellent reliability (Cronbach's α = 0.93), and acceptable internal consistency for each subscale (range of α from 0.63 to 0.82). Floor or ceiling effects were observed at item level and subscale level, but not at total level. CFA results revealed that the Malay version of the DERS-18 bifactor model (excluding "Awareness") portrayed the best construct validity (χ2/df = 2.673, RMSEA = 0.049, CFI = 0.977, TLI = 0.968) compared to a single factor, a correlated factor, and a higher-order factor model. The DERS-18 subscales (except "Awareness") and DERS-18 total scores were significantly correlated with stress, anxiety, and depression in a positive direction (r ranged from 0.62 to 0.64, p < 0.01). The general factor of the DERS-18 and its specific factors ("Clarity", "Goals", and "Non-Acceptance") significantly predicted the symptoms of stress, anxiety, and depression (R2 ranged from 0.44 to 0.46, p < 0.001). CONCLUSION: The Malay version of the DERS-18, excluding "Awareness", possessed good reliability, construct validity, and criterion validity to assess emotion dysregulation among Malaysian adolescents.

Multiple-Genome-Based Simple Sequence Repeat Is an Efficient and Successful Method in Genotyping and Classifying Different Jujube Germplasm Resources.

Jujube (Ziziphus jujuba Mill.) is a commercially important tree native to China, known for its high nutritional value and widespread distribution, as well as its diverse germplasm resources. Being resilient to harsh climatic conditions, the cultivation of jujube could provide a solution to food insecurity and income for people of arid and semi-arid regions in and outside of China. The evaluation of germplasm resources and genetic diversity in jujube necessitates the use of Simple Sequence Repeat (SSR) markers. SSR markers are highly polymorphic and can be used to evaluate the genetic diversity within and between cultivars of Chinese jujube, and are important for conservation biology, breeding programs, and the discovery of important traits for Chinese jujube improvement in China and abroad. However, traditional methods of SSR development are time-consuming and inadequate to meet the growing research demands. To address this issue, we developed a novel approach called Multiple-Genome-Based SSR identification (MGB-SSR), which utilizes the genomes of three jujube cultivars to rapidly screen for polymorphic SSRs in the jujube genome. Through the screening process, we identified 12 pairs of SSR primers, which were then used to successfully classify 249 jujube genotypes. Based on the genotyping results, a digital ID card was established, enabling the complete identification of all 249 jujube plants. The MGB-SSR approach proved efficient in rapidly detecting polymorphic SSRs within the jujube genome. Notably, this study represents the first successful differentiation of jujube germplasm resources using 12 SSR markers, with 4 markers successfully identifying triploid jujube genotypes. These findings offer valuable information for the classification of Chinese jujube germplasm, thereby providing significant assistance to jujube researchers and breeders in identifying unknown jujube germplasm.

Contribution of constitutional BRCA1 promoter methylation to early-onset and familial breast cancer patients from Pakistan.

PURPOSE: Constitutional BRCA1 promoter methylation has been identified as a potential risk factor for breast cancer (BC) in the Caucasian population. However, this data is lacking for BC patients of Asian origin. Therefore, we assessed the contribution of constitutional BRCA1 promoter methylation in Pakistani BC patients. METHODS: A total of 385 BRCA1/2-negative index BC patients (197 early-onset BC (≤ 30 years), 152 familial BC, 17 familial BC and ovarian cancer, 19 male BC) and 107 healthy controls were screened for the constitutional BRCA1 promoter methylation by methylation-sensitive high-resolution melting assay. Overall, 131 patients displayed triple-negative BC (TNBC) and 254 non-TNBC phenotypes. The prevalence of BRCA1 promoter methylation was calculated based on clinicopathological characteristics using univariable and multivariable logistic regression models. RESULTS: Constitutional BRCA1 promoter methylation was identified in 19.5% (75/385) of BC patients and 13.1% (14/107) of controls. The frequency of methylation was higher in early-onset BC (23.4% vs. 13.1%, P = 0.035) and TNBC patients (29.0% vs. 13.1%, P = 0.004) compared to controls. Methylation was also more prevalent in patients with high-grade than low-grade tumors (21.7% vs. 12.2%, P = 0.034) and progesterone receptor (PR)-negative than PR-positive tumors (26.0% vs. 13.9%, P = 0.004). Constitutional BRCA1 promoter methylation remained independently associated with TNBC phenotype (odds ratio 1.99; 95% CI 1.12-3.54; P = 0.02) after adjusting for BC diagnosis age, tumor grade, ER, and PR status. CONCLUSION: Constitutional BRCA1 promoter methylation is associated with TNBC and can serve as a non-invasive blood-based biomarker for Pakistani TNBC patients.

Digital Tomosynthesis: Review of Current Literature and Its Impact on Diagnostic Bronchoscopy.

Bronchoscopy has garnered increased popularity in the biopsy of peripheral lung lesions. The development of navigational guided bronchoscopy systems along with radial endobronchial ultrasound (REBUS) allows clinicians to access and sample peripheral lesions. The development of robotic bronchoscopy improved localization of targets and diagnostic accuracy. Despite such technological advancements, published diagnostic yield remains lower compared to computer tomography (CT)-guided biopsy. The discordance between the real-time location of peripheral lesions and anticipated location from preplanned navigation software is often cited as the main variable impacting accurate biopsies. The utilization of cone beam CT (CBCT) with navigation-based bronchoscopy has been shown to assist with localizing targets in real-time and improving biopsy success. The resources, costs, and radiation associated with CBCT remains a hindrance in its wider adoption. Recently, digital tomosynthesis (DT) platforms have been developed as an alternative for real-time imaging guidance in peripheral lung lesions. In North America, there are several commercial platforms with distinct features and adaptation of DT. Early studies show the potential improvement in peripheral lesion sampling with DT. Despite the results of early observational studies, the true impact of DT-based imaging devices for peripheral lesion sampling cannot be determined without further prospective randomized trials and meta-analyses.

Autosomal recessive variants c.953A>C and c.97-1G>C in NSUN2 causing intellectual disability: a molecular dynamics simulation study of loss-of-function mechanisms.

Introduction: Intellectual disability (ID) is a clinically and genetically heterogeneous disorder. It drastically affects the learning capabilities of patients and eventually reduces their IQ level below 70. Methods: The current genetic study ascertained two consanguineous Pakistani families suffering from autosomal recessive intellectual developmental disorder-5 (MRT5). We have used exome sequencing followed by Sanger sequencing to identify the disease-causing variants. Results and discussion: Genetic analysis using whole exome sequencing in these families identified two novel mutations in the NSUN2 (NM_017755.5). Family-A segregated a novel missense variant c.953A>C; p.Tyr318Ser in exon-9 of the NSUN2. The variant substituted an amino acid Tyr318, highly conserved among different animal species and located in the functional domain of NSUN2 known as "SAM-dependent methyltransferase RsmB/NOP2-type". Whereas in family B, we identified a novel splice site variant c.97-1G>C that affects the splice acceptor site of NSUN2. The identified splice variant (c.97-1G>C) was predicted to result in the skipping of exon-2, which would lead to a frameshift followed by a premature stop codon (p. His86Profs*16). Furthermore, it could result in the termination of translation and synthesis of dysfunctional protein, most likely leading to nonsense-mediated decay. The dynamic consequences of NSUN2 missense variant was further explored together with wildtype through molecular dynamic simulations, which uncovered the disruption of NSUN2 function due to a gain in structural flexibility. The present molecular genetic study further extends the mutational spectrum of NSUN2 to be involved in ID and its genetic heterogeneity in the Pakistani population.

Transcriptome-wide expression analysis of MYB gene family leads to functional characterization of flavonoid biosynthesis in fruit coloration of Ziziphus Mill.

The Ziziphus mauritiana Lam. and Z. jujuba Mill. are the two most economically important members of the genus Ziziphus. The fruit color of Z. mauritiana remains green throughout fruit development in the majority of commercial cultivars, whereas its close relative, Z. jujuba Mill. turns from green to red in all cultivars. However, the lack of transcriptomic and genomic information confines our understanding of the molecular mechanisms underlying fruit coloration in Z. mauritiana (Ber). In the present study, we performed the transcriptome-wide analysis of MYB transcription factors (TFs) genes in Z. mauritiana and Z. jujuba, and identified 56 ZmMYB and 60 ZjMYB TFs in Z. mauritiana and Z. jujuba, respectively. Through transcriptomic expression analysis, four similar MYB genes (ZmMYB/ZjMYB13, ZmMYB/ZjMYB44, ZmMYB/ZjMYB50, and ZmMYB/ZjMYB56) from Z. mauritiana and Z. jujuba were selected as candidate key genes regulating flavonoid biosynthesis. Among these genes, the ZjMYB44 gene was transiently highly expressed in fruit, and flavonoid content accumulation also increased, indicating that this gene can influence flavonoid content during the period of fruit coloration in Z. jujuba. The current study adds to our understanding of the classification of genes, motif structure, and predicted functions of the MYB TFs, as well as identifying MYBs that regulate flavonoid biosynthesis in Ziziphus (Z. mauritiana and Z. jujuba). Based on this information, we concluded that MYB44 is involved in the flavonoids biosynthesis pathway during the fruit coloring of Ziziphus. Our research results provide an important understanding of the molecular mechanism of flavonoid biosynthesis resulting in fruit coloration and laying a foundation for further genetic improvement of fruit color in Ziziphus.

Biallelic Variants in Seven Different Genes Associated with Clinically Suspected Bardet-Biedl Syndrome.

Bardet-Biedl syndrome (BBS) is a rare clinically and genetically heterogeneous autosomal recessive multi-systemic disorder with 22 known genes. The primary clinical and diagnostic features include six different hallmarks, such as rod-cone dystrophy, learning difficulties, renal abnormalities, male hypogonadism, post-axial polydactyly, and obesity. Here, we report nine consanguineous families and a non-consanguineous family with several affected individuals presenting typical clinical features of BBS. In the present study, 10 BBS Pakistani families were subjected to whole exome sequencing (WES), which revealed novel/recurrent gene variants, including a homozygous nonsense mutation (c.94C>T; p.Gln32Ter) in the IFT27 (NM_006860.5) gene in family A, a homozygous nonsense mutation (c.160A>T; p.Lys54Ter) in the BBIP1 (NM_001195306.1) gene in family B, a homozygous nonsense variant (c.720C>A; p.Cys240Ter) in the WDPCP (NM_015910.7) in family C, a homozygous nonsense variant (c.505A>T; p.Lys169Ter) in the LZTFL1 (NM_020347.4) in family D, pathogenic homozygous 1 bp deletion (c.775delA; p.Thr259Leufs*21) in the MKKS/BBS5 (NM_170784.3) gene in family E, a pathogenic homozygous missense variant (c.1339G>A; p.Ala447Thr) in BBS1 (NM_024649.4) in families F and G, a pathogenic homozygous donor splice site variant (c.951+1G>A; p?) in BBS1 (NM_024649.4) in family H, a pathogenic bi-allelic nonsense variant in MKKS (NM_170784.3) (c.119C>G; p.Ser40*) in family I, and homozygous pathogenic frameshift variants (c.196delA; p.Arg66Glufs*12) in BBS5 (NM_152384.3) in family J. Our findings extend the mutation and phenotypic spectrum of four different types of ciliopathies causing BBS and also support the importance of these genes in the development of multi-systemic human genetic disorders.