Biallelic NUDT2 variants defective in mRNA decapping cause a neurodevelopmental disease.

Dysfunctional RNA processing caused by genetic defects in RNA processing enzymes has a profound impact on the nervous system, resulting in neurodevelopmental conditions. We characterized a recessive neurological disorder in 18 children and young adults from 10 independent families typified by intellectual disability, motor developmental delay and gait disturbance. In some patients peripheral neuropathy, corpus callosum abnormalities and progressive basal ganglia deposits were present. The disorder is associated with rare variants in NUDT2, a mRNA decapping and Ap4A hydrolysing enzyme, including novel missense and in-frame deletion variants. We show that these NUDT2 variants lead to a marked loss of enzymatic activity, strongly implicating loss of NUDT2 function as the cause of the disorder. NUDT2-deficient patient fibroblasts exhibit a markedly altered transcriptome, accompanied by changes in mRNA half-life and stability. Amongst the most up-regulated mRNAs in NUDT2-deficient cells, we identified host response and interferon-responsive genes. Importantly, add-back experiments using an Ap4A hydrolase defective in mRNA decapping highlighted loss of NUDT2 decapping as the activity implicated in altered mRNA homeostasis. Our results confirm that reduction or loss of NUDT2 hydrolase activity is associated with a neurological disease, highlighting the importance of a physiologically balanced mRNA processing machinery for neuronal development and homeostasis.

Bi-allelic ACBD6 variants lead to a neurodevelopmental syndrome with progressive and complex movement disorders.

The acyl-CoA-binding domain-containing protein 6 (ACBD6) is ubiquitously expressed, plays a role in the acylation of lipids and proteins and regulates the N-myristoylation of proteins via N-myristoyltransferase enzymes (NMTs). However, its precise function in cells is still unclear, as is the consequence of ACBD6 defects on human pathophysiology. Using exome sequencing and extensive international data sharing efforts, we identified 45 affected individuals from 28 unrelated families (consanguinity 93%) with bi-allelic pathogenic, predominantly loss-of-function (18/20) variants in ACBD6. We generated zebrafish and Xenopus tropicalis acbd6 knockouts by CRISPR/Cas9 and characterized the role of ACBD6 on protein N-myristoylation with myristic acid alkyne (YnMyr) chemical proteomics in the model organisms and human cells, with the latter also being subjected further to ACBD6 peroxisomal localization studies. The affected individuals (23 males and 22 females), aged 1-50 years, typically present with a complex and progressive disease involving moderate-to-severe global developmental delay/intellectual disability (100%) with significant expressive language impairment (98%), movement disorders (97%), facial dysmorphism (95%) and mild cerebellar ataxia (85%) associated with gait impairment (94%), limb spasticity/hypertonia (76%), oculomotor (71%) and behavioural abnormalities (65%), overweight (59%), microcephaly (39%) and epilepsy (33%). The most conspicuous and common movement disorder was dystonia (94%), frequently leading to early-onset progressive postural deformities (97%), limb dystonia (55%) and cervical dystonia (31%). A jerky tremor in the upper limbs (63%), a mild head tremor (59%), parkinsonism/hypokinesia developing with advancing age (32%) and simple motor and vocal tics were among other frequent movement disorders. Midline brain malformations including corpus callosum abnormalities (70%), hypoplasia/agenesis of the anterior commissure (66%), short midbrain and small inferior cerebellar vermis (38% each) as well as hypertrophy of the clava (24%) were common neuroimaging findings. Acbd6-deficient zebrafish and Xenopus models effectively recapitulated many clinical phenotypes reported in patients including movement disorders, progressive neuromotor impairment, seizures, microcephaly, craniofacial dysmorphism and midbrain defects accompanied by developmental delay with increased mortality over time. Unlike ACBD5, ACBD6 did not show a peroxisomal localization and ACBD6-deficiency was not associated with altered peroxisomal parameters in patient fibroblasts. Significant differences in YnMyr-labelling were observed for 68 co- and 18 post-translationally N-myristoylated proteins in patient-derived fibroblasts. N-myristoylation was similarly affected in acbd6-deficient zebrafish and X. tropicalis models, including Fus, Marcks and Chchd-related proteins implicated in neurological diseases. The present study provides evidence that bi-allelic pathogenic variants in ACBD6 lead to a distinct neurodevelopmental syndrome accompanied by complex and progressive cognitive and movement disorders.

Clinical and genetic investigation of 14 families with various forms of short stature syndromes.

Skeletal dysplasias are a heterogeneous group of disorders presenting mild to lethal defects. Several factors, such as genetic, prenatal, and postnatal environmental may contribute to reduced growth. Fourteen families of Pakistani origin, presenting the syndromic form of short stature either in the autosomal recessive or autosomal dominant manner were clinically and genetically investigated to uncover the underlying genetic etiology. Homozygosity mapping, whole exome sequencing, and Sanger sequencing were used to search for the disease-causing gene variants. In total, we have identified 13 sequence variants in 10 different genes. The variants in the HSPG2 and XRCC4 genes were not reported previously in the Pakistani population. This study will expand the mutation spectrum of the identified genes and will help in improved diagnosis of the syndromic form of short stature in the local population.

A Novel Coated Suture Displays Antimicrobial Activity Without Compromising Structural Properties.

BACKGROUND: Treated or coated sutures promise to prevent contamination of wounds. PURPOSE: The purpose of the study was to coat surgical sutures with a new quaternary ammonium silane (QAS) antimicrobial compound at two different application temperatures and then to evaluate the resulting structural, physical, mechanical, and biological properties. STUDY DESIGN, SETTING, SAMPLE: In vitro and in vivo studies were conducted using male albino Wistar rats approved by the Joint Ethical Committee of IMU and Postgraduate Medical Institute, Lahore. Only suture samples, coated uniformly with verified presence of the compound and of adequate length were used. Samples which were not coated uniformly and with inadequate length or damaged were excluded. PREDICTOR VARIABLE: Predictor variables were sutures with and without QAS coatings and different temperatures. Sutures were coated with QAS at 0.5 and 1.0% wt/vol using the dip coating technique and sutures with and without QAS coating were tested at 25 and 40 °C temperatures. MAIN OUTCOME VARIABLE(S): Outcome variables of structural and physico-mechanical properties of QAS-coated and non-coated sutures were measured using Fourier transform infrared spectroscopy (for structural changes), confocal laser and scanning electron (for diameter changes), and tensile strength/modulus (for mechanical testing). Biologic outcome variables were tested (bacterial viability); macrophage cultures from Wistar rats were tested (M1/M2 polarization detecting IL-6 and IL-10). Macrophage cells were analyzed with CD80+ (M1) and CD163+ (M2). Chemotaxis index was calculated as a ratio of quantitative fluorescence of cells. COVARIATES: Not applicable. ANALYSES: Ordinal data among groups were compared using the Wilcoxon Mann-Whitney U test along with the comparison of histological analysis using the Wilcoxon Sign-rank test (P < .05). RESULTS: Fourier transform infrared spectroscopy peak at 1490 cm-1 confirmed the presence of QAS on suture's surfaces with a significant increase (P < .05) in diameter (0.99 ± 0.5-mm) and weight (0.77 ± 0.02-mg) observed for 1% QAS groups treated at 40 °C. Non-coated samples heated at 25 °C had significantly (P < .05) less diameters (0.22 ± 0.03-mm) and weights (0.26 ± 0.06-mg). Highest tensile strength/modulus was observed for 0.5% QAS-coated samples which also had significantly higher antibacterial characteristics than other sutures (P < .05). QAS-coated sutures significantly increased M1 and M2 markers. CONCLUSION AND RELEVANCE: QAS coating conferred antibacterial action properties without compromising the physical and mechanical properties of the suture.

Melamine-based hyper-cross-linked resin for efficient removal of total petroleum hydrocarbons (C10-C32) from aqueous solutions.

Petroleum hydrocarbons (PHCs) are produced from industrial discharges, storage leakages, accidental spills, and operational failures. The hazardous nature of PHCs causes serious health risks and threatens the entire aquatic habitat. In this research work, the investigation of the removal of total petroleum hydrocarbons (TPHs) from the contaminated water is carried out utilizing a novel hypercross-linked resin, MAICY, which is generated by condensation of commercially available precursors. The chemical structures of MAICY have been examined extensively by FESEM, FT-IR, solid (CP-MAS) 13C-NMR, and TGA. A comprehensive analysis for adsorption parameters of TPHs has been performed, and different models such as Langmuir and Freundlich isotherms have been employed where the Freundlich isotherm was found to be the best fit for removal of THPs (R2= 0.9991). The results revealed that the performance of MAICY for the adsorption of TPHs from contaminated water gives a maximum adsorption capacity (qe) of 146 mg.g-1. The results of various parameters hinted that the contact time (0.25-4 h), the dosage of adsorbent (0.17 g/L), pH (7), and concentration of TPHs (26.5 mg/L) have controlled the overall adsorptive performance. Moreover, the kinetic data of qe(expt.) and qe(calc.) for adsorption of TPHs disclosed the regression values (R2) for pseudo-first order (R2= 0.9921) and pseudo-second order (R2= 0.9891). Additionally, based on CHI factor (X2) error estimations, the data was shown to be more consistent with pseudo-first-order kinetics. Moreover, MAICY demonstrated excellent reusability and recycling properties for up to four consecutive adsorption-desorption cycles.

Toxic effects of lead on plants: integrating multi-omics with bioinformatics to develop Pb-tolerant crops.

MAIN CONCLUSION: Lead disrupts plant metabolic homeostasis and key structural elements. Utilizing modern biotechnology tools, it's feasible to develop Pb-tolerant varieties by discovering biological players regulating plant metabolic pathways under stress. Lead (Pb) has been used for a variety of purposes since antiquity despite its toxic nature. After arsenic, lead is the most hazardous heavy metal without any known beneficial role in the biological system. It is a crucial inorganic pollutant that affects plant biochemical and morpho-physiological attributes. Lead toxicity harms plants throughout their life cycle and the extent of damage depends on the concentration and duration of exposure. Higher levels of lead exposure disrupt numerous key metabolic activities of plants including oxygen-evolving complex, organelles integrity, photosystem II connectivity, and electron transport chain. This review summarizes the detrimental effects of lead toxicity on seed germination, crop growth, and yield, oxidative and ultra-structural alterations, as well as nutrient absorption, transport, and assimilation. Further, it discusses the Pb-induced toxic modulation of stomatal conductance, photosynthesis, respiration, metabolic-enzymatic activity, osmolytes accumulation, and antioxidant activity. It is a comprehensive review that reports on omics-based studies along with morpho-physiological and biochemical modifications caused by lead stress. With advances in DNA sequencing technologies, genomics and transcriptomics are gradually becoming popular for studying Pb stress effects in plants. Proteomics and metabolomics are still underrated and there is a scarcity of published data, and this review highlights both their technical and research gaps. Besides, there is also a discussion on how the integration of omics with bioinformatics and the use of the latest biotechnological tools can aid in developing Pb-tolerant crops. The review concludes with core challenges and research directions that need to be addressed soon.

Microplastics and Nanoplastics Effects on Plant-Pollinator Interaction and Pollination Biology.

Microplastics and nanoplastics (MNPs) contamination is an emerging environmental and public health concern, and these particles have been reported both in aquatic and terrestrial ecosystems. Recent studies have expanded our understanding of the adverse effects of MNPs pollution on human, terrestrial, and aquatic animals, insects, and plants. In this perspective, we describe the adverse effects of MNPs particles on pollinator and plant health and discuss the mechanisms by which MNPs disrupt the pollination process. We discuss the evidence and integrate transcriptome studies to investigate the negative effects of MNPs on the molecular biology of pollination, which may cause delay or inhibit the pollination services. We conclude by addressing challenges to plant-pollinator health from MNPs pollution and argue that such harmful effects disrupt the communication between plant and pollinator for a successful pollination process.

The impact of partner's behaviour on pregnancy related outcomes and safe child-birth in Pakistan.

BACKGROUND: Pakistan is one of the nations with the worst statistics for pregnancy-related outcomes. Health programmes in underdeveloped nations frequently ignore the role of partners in maternal health, which is a crucial contributing factor in these worst situations. This research study aims to explore the role of husbands in maternity care and safe childbirth in Pakistan. METHODS: The data for this study comes from the Pakistan Maternal Mortality Survey 2019. The k-Modes clustering algorithm was implemented to generate clusters from the dataset. Cluster profiling was used to identify the problems in pregnancy-related outcomes in cases where women live away from their partners. The chi-square test and logistic regression model were fitted to identify the significant factors associated with women's health and safe childbirth. RESULTS: The finding of the study reveals that the partner's support during and after pregnancy plays a vital role in maternal health and safe child-birth. It was revealed that the women living away from their partners have certain health problems during pregnancy. These problems include Vaginal bleeding, Excessive vomiting, Chest pain, Cough, High B.P, Excessive weight gain, Body aches, Swelling of feet, and Swelling of the face. This also leads to complications and health problems in the postpartum period. Due to a lack of antenatal care from the spouse during pregnancy, the women who lived away from their partners lost their pregnancies. CONCLUSION: The study concludes that the husband's emotional and financial support substantially impacts the overall health of expecting mothers and the safety of delivery in Pakistan. Given its potential advantages for mother and child health outcomes, male engagement in health education must be acknowledged and addressed. The finding of the study is of immense importance, as it guides the policymakers to arrange various awareness programs for the male partners to support their pregnant spouse and provide proper antenatal care.

Assessment of fall-associated risk factors in the Muslim community-dwelling older adults of Peshawar, Khyber Pakhtunkhwa, Pakistan.

BACKGROUND: Falls are the third-leading cause of disability among the elderly population worldwide. It is multifactorial, and the occurrence of falls depends on different factors, which can be different from context to context, and individual to individual. Therefore, regular assessment of fall risk factors is required to develop a strategy for fall prevention. The study aimed to identify fall-related risk factors in Pakistani healthy older adults at risk of developing physical disabilities. It also aimed to create a risk-predictive model for fall occurrence, offering evidence for preventive strategies. METHODS: Data were collected from 140 Muslim older adults from two residential areas of Peshawar, Khyber Pakhtunkhwa, from July 2022 to August 25, 2022, after obtaining permission from the Zhengzhou University Ethical Review Board (ZZUIRB #202,254), and the District Health Department Office (DHO #14,207). Participants were informed, and consent was obtained before data collection. Data were collected using the Time Up and Go Test (TUGT) checklist, the Cognitive Screening Scores (CS-10) checklist, interviews regarding the prayer practice, fall history in the last six months, visual equity questions, and demographic variables. RESULTS: Factors associated with falls were; age, gender, education, cognitive status, poor walking speed, lack of physical activity, poor vision, and history of falls in the last six months, with a significant P value of (P. < 0.05) in the Pearson correlation coefficient test. Poor cognition, low visual equity, poor walking speed, and lack of exercise increase the risk of falling in the future, with a prediction value of (P < 0.005) in Omnibus, Lemeshow score of (0.77). CONCLUSION: Hence, our study provides a road map for future risk assessment of falls by adding the four mentioned risk factors in the proposed model to facilitate timely action to prevent fall-related infirmities in Pakistani healthy older adults.

Sea Conch Peptides Hydrolysate Alleviates DSS-Induced Colitis in Mice through Immune Modulation and Gut Microbiota Restoration.

Inflammatory bowel disease (IBD) is a persistent, lifelong inflammation of the digestive system. Dextran sulfate sodium is commonly used to induce colitis in experimental animal models, which causes epithelial damage, intestinal inflammation, mucin depletion, and dysbiosis of the gut microbiota. Various prebiotics, polysaccharides, and polypeptides are used for IBD treatment. In this study, we used a murine model utilizing BALB/c mice, with 10 mice per group, to investigate the treatment effect of sea conch peptide hydrolysate (CPH) on DSS-induced colitis mice. Colitis was induced through the administration of 2.5% DSS in drinking water over a seven-days period. Furthermore, on the eighth day of the experiment, sea conch peptide hydrolysate (CPH) at low (100 mg/kg), medium (200 mg/kg), and high (400 mg/kg) doses, which were continued for 14 days, were assessed for medicinal purposes in DSS-induced colitis mice. Our results showed that CPH treatment significantly alleviated the severity and symptoms of colitis. The epithelial integrity and histological damage were improved. Intestinal inflammation and inflammatory cell infiltration were improved. Furthermore, the expression of pro-inflammatory cytokines was reduced, and intestinal barrier integrity was restored by elevating the tight junction proteins. Moreover, 16s RNA sequencing revealed dysbiosis of the gut microbiota was observed upon DSS treatment, which was reinstated after CPH treatment. An increased level of Firmicutes and Lactobacillus was observed in the treatment groups. Finally, our results suggest that CPH would be recommended as a functional food source and also have the potential to be used as a medicinal product for different gastrointestinal disorders.

Comparative microbiome analysis of Diaphorina citri and its associated parasitoids Tamarixia radiata and Diaphorencyrtus aligarhensis reveals Wolbachia as a dominant endosymbiont.

Microbiome analysis in a host-parasitoid interaction network was conducted to compare the taxonomic composition of bacterial communities of Diaphornia citri, Tamarixia radiata, and Diaphorencyrtus aligarhensis. The comparative analysis revealed differences in the composition and diversity of the symbiont populations across the host and its associated parasitoids. Proteobacteria was the most dominant phylum, representing 67.80% of the total bacterial community, while Candidatus Profftella armature and Wolbachia were the dominant genera across the host and parasitoids. There were clear differences observed in alpha and beta diversity of microbiota through the host and its associated parasitoids. The function prediction of bacterial communities and Pearson correlation analysis showed that specific bacterial communities displayed positive correlations with the carbohydrate metabolism pathway. Furthermore, when symbiotic bacteria were eliminated using a broad-spectrum antibiotic, tetracycline hydrochloride, the parasitoids' median survival time and longevity were significantly reduced. We confirmed the physiological effects of symbiotic bacteria on the fitness of parasitoids and demonstrated the effect of antibiotics in decreasing the food intake and measurement of amino acids in the hemolymph. This study sheds light on basic information about the mutualism between parasitoids and bacteria, which may be a potential source for biocontrol strategies for citrus psyllid, especially D. citri.

Opium Poppy Mosaic Virus Has an Xrn-Resistant, Translated Subgenomic RNA and a BTE 3' CITE.

Opium poppy mosaic virus (OPMV) is a recently discovered umbravirus in the family Tombusviridae OPMV has a plus-sense genomic RNA (gRNA) of 4,241 nucleotides (nt) from which replication protein p35 and p35 extension product p98, the RNA-dependent RNA polymerase (RdRp), are expressed. Movement proteins p27 (long distance) and p28 (cell to cell) are expressed from a 1,440-nt subgenomic RNA (sgRNA2). A highly conserved structure was identified just upstream from the sgRNA2 transcription start site in all umbraviruses, which includes a carmovirus consensus sequence, denoting generation by an RdRp-mediated mechanism. OPMV also has a second sgRNA of 1,554 nt (sgRNA1) that starts just downstream of a canonical exoribonuclease-resistant sequence (xrRNAD). sgRNA1 codes for a 30-kDa protein in vitro that is in frame with p28 and cannot be synthesized in other umbraviruses. Eliminating sgRNA1 or truncating the p30 open reading frame (ORF) without affecting p28 substantially reduced accumulation of OPMV gRNA, suggesting a functional role for the protein. The 652-nt 3' untranslated region of OPMV contains two 3' cap-independent translation enhancers (3' CITEs), a T-shaped structure (TSS) near its 3' end, and a Barley yellow dwarf virus-like translation element (BTE) in the central region. Only the BTE is functional in luciferase reporter constructs containing gRNA or sgRNA2 5' sequences in vivo, which differs from how umbravirus 3' CITEs were used in a previous study. Similarly to most 3' CITEs, the OPMV BTE links to the 5' end via a long-distance RNA-RNA interaction. Analysis of 14 BTEs revealed additional conserved sequences and structural features beyond the previously identified 17-nt conserved sequence.IMPORTANCEOpium poppy mosaic virus (OPMV) is an umbravirus in the family Tombusviridae We determined that OPMV accumulates two similarly sized subgenomic RNAs (sgRNAs), with the smaller known to code for proteins expressed from overlapping open reading frames. The slightly larger sgRNA1 has a 5' end just upstream from a previously predicted xrRNAD site, identifying this sgRNA as an unusually long product produced by exoribonuclease trimming. Although four umbraviruses have similar predicted xrRNAD sites, only sgRNA1 of OPMV can code for a protein that is an extension product of umbravirus ORF4. Inability to generate the sgRNA or translate this protein was associated with reduced gRNA accumulation in vivo We also characterized the OPMV BTE structure, a 3' cap-independent translation enhancer (3' CITE). Comparisons of 13 BTEs with the OPMV BTE revealed additional stretches of sequence similarity beyond the 17-nt signature sequence, as well as conserved structural features not previously recognized in these 3' CITEs.

Transcriptomics for Drought Stress Mediated by Biological Processes in-relation to Key Regulated Pathways in Gossypium darwinii.

BACKGROUND: Wild cotton Gossypium darwinii, an allotetraploid harbours important traits useful for tolerating abiotic stress, i.e., drought, salt and good genetic stability, hence these characteristics can be transferred to cultivated cotton for genetic improvement. MATERIALS AND METHODS: In this study, we analyzed the RNA-seq transcriptomes from leaves of G. darwinii seedlings with and without drought stress. A total of 86.7 million valid reads with an average length of 95.79 bp were generated from the two samples and 58,960 transcripts with a length of more than 500 bp were assembled. We searched the known proteins on the strength of sequence similarity; these transcripts were annotated with COG, KEGG and GO functional categories. According to gene expression abundance RPKM value, we carried out RT-qPCR analysis to determine the expression pattern of the obtained transcription factors. RESULTS: A total of 58,960 genes was differentially expressed (DEG), with 32,693 and 25,919 genes found to be upregulated and downregulated, respectively. Through gene ontology and KEGG pathways, the upregulated genes were found to associate with all the GO terms, molecular functions (MF), biological process (BP) and cellular components (CC), which are highly linked to enhancing drought stress tolerance. CONCLUSION: The study provides an in-depth knowledge of regulation of pathways and genes involved in photosynthesis during drought stress in G. darwinii. These pathways and genes were found to be significantly downregulated and this information could be further utilized by cotton breeders in developing a more drought tolerant cotton germplasm.

Prevalence and Risk Factors of Dental Trauma in Ha'il, Saudi Arabia.

AIM: This study will aid in determining the prevalence and risk factors for dental trauma. This will assist in developing a treatment budget plan, thereby, fend off complications. MATERIALS AND METHODS: This study was an observational study, having a cross-sectional design, in which information was obtained from 555 participants. Data were obtained using a non-probability convenient sampling technique. A validated questionnaire was used as a study tool. Data were analyzed using the statistical package for the social sciences (SPSS, version 20). Descriptive and inferential statistics were used. Data were displayed as numbers and percentages, and the Chi-squared test was used to measure the association. RESULTS: Dental trauma was found to be 44% prevalent. Most of the injuries occurred in the 6-9-years age-group (19.1%) and were more common in boys (54.13%) than in girls. The majority of respondents (61%) identified "falls" as the most common cause of dental trauma, and the frequent location for the occurrence of dental injuries was found to be "home" (64.44%). Only 18% of parents reported that their kid's experienced nail-biting concerns, with the majority claimed that their kids never developed oral habits. Most dental injuries occurred during the summer season (48%). CONCLUSION: Young aged group and male gender group were more prone to dental injuries; dental injuries along with fall were found as the most common cause of dental trauma, whereas most of the dental traumas were reported to have occurred at home. CLINICAL SIGNIFICANCE: The study evaluated risk factors and the prevalence of dental trauma in the population of Ha'il, Saudi Arabia. It will be an effective tool for determining the need for treatment facilities.

A Critical Review: Recent Advancements in the Use of CRISPR/Cas9 Technology to Enhance Crops and Alleviate Global Food Crises.

Genome editing (GE) has revolutionized the biological sciences by creating a novel approach for manipulating the genomes of living organisms. Many tools have been developed in recent years to enable the editing of complex genomes. Therefore, a reliable and rapid approach for increasing yield and tolerance to various environmental stresses is necessary to sustain agricultural crop production for global food security. This critical review elaborates the GE tools used for crop improvement. These tools include mega-nucleases (MNs), such as zinc-finger nucleases (ZFNs), and transcriptional activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR). Specifically, this review addresses the latest advancements in the role of CRISPR/Cas9 for genome manipulation for major crop improvement, including yield and quality development of biotic stress- and abiotic stress-tolerant crops. Implementation of this technique will lead to the production of non-transgene crops with preferred characteristics that can result in enhanced yield capacity under various environmental stresses. The CRISPR/Cas9 technique can be combined with current and potential breeding methods (e.g., speed breeding and omics-assisted breeding) to enhance agricultural productivity to ensure food security. We have also discussed the challenges and limitations of CRISPR/Cas9. This information will be useful to plant breeders and researchers in the thorough investigation of the use of CRISPR/Cas9 to boost crops by targeting the gene of interest.

Direct maternal morbidity and the risk of pregnancy-related deaths, stillbirths, and neonatal deaths in South Asia and sub-Saharan Africa: A population-based prospective cohort study in 8 countries.

BACKGROUND: Maternal morbidity occurs several times more frequently than mortality, yet data on morbidity burden and its effect on maternal, foetal, and newborn outcomes are limited in low- and middle-income countries. We aimed to generate prospective, reliable population-based data on the burden of major direct maternal morbidities in the antenatal, intrapartum, and postnatal periods and its association with maternal, foetal, and neonatal death in South Asia and sub-Saharan Africa. METHODS AND FINDINGS: This is a prospective cohort study, conducted in 9 research sites in 8 countries of South Asia and sub-Saharan Africa. We conducted population-based surveillance of women of reproductive age (15 to 49 years) to identify pregnancies. Pregnant women who gave consent were include in the study and followed up to birth and 42 days postpartum from 2012 to 2015. We used standard operating procedures, data collection tools, and training to harmonise study implementation across sites. Three home visits during pregnancy and 2 home visits after birth were conducted to collect maternal morbidity information and maternal, foetal, and newborn outcomes. We measured blood pressure and proteinuria to define hypertensive disorders of pregnancy and woman's self-report to identify obstetric haemorrhage, pregnancy-related infection, and prolonged or obstructed labour. Enrolled women whose pregnancy lasted at least 28 weeks or those who died during pregnancy were included in the analysis. We used meta-analysis to combine site-specific estimates of burden, and regression analysis combining all data from all sites to examine associations between the maternal morbidities and adverse outcomes. Among approximately 735,000 women of reproductive age in the study population, and 133,238 pregnancies during the study period, only 1.6% refused consent. Of these, 114,927 pregnancies had morbidity data collected at least once in both antenatal and in postnatal period, and 114,050 of them were included in the analysis. Overall, 32.7% of included pregnancies had at least one major direct maternal morbidity; South Asia had almost double the burden compared to sub-Saharan Africa (43.9%, 95% CI 27.8% to 60.0% in South Asia; 23.7%, 95% CI 19.8% to 27.6% in sub-Saharan Africa). Antepartum haemorrhage was reported in 2.2% (95% CI 1.5% to 2.9%) pregnancies and severe postpartum in 1.7% (95% CI 1.2% to 2.2%) pregnancies. Preeclampsia or eclampsia was reported in 1.4% (95% CI 0.9% to 2.0%) pregnancies, and gestational hypertension alone was reported in 7.4% (95% CI 4.6% to 10.1%) pregnancies. Prolonged or obstructed labour was reported in about 11.1% (95% CI 5.4% to 16.8%) pregnancies. Clinical features of late third trimester antepartum infection were present in 9.1% (95% CI 5.6% to 12.6%) pregnancies and those of postpartum infection in 8.6% (95% CI 4.4% to 12.8%) pregnancies. There were 187 pregnancy-related deaths per 100,000 births, 27 stillbirths per 1,000 births, and 28 neonatal deaths per 1,000 live births with variation by country and region. Direct maternal morbidities were associated with each of these outcomes. CONCLUSIONS: Our findings imply that health programmes in sub-Saharan Africa and South Asia must intensify their efforts to identify and treat maternal morbidities, which affected about one-third of all pregnancies and to prevent associated maternal and neonatal deaths and stillbirths. TRIAL REGISTRATION: The study is not a clinical trial.

Attitude toward personal genomics: A nation-wide survey of public and professionals in Pakistan.

With the emergence of modern genetic testing and profiling techniques, it has become imperative to assess the general public awareness and attitudes toward such developments. The public's perspective and possible responses are necessary for planning commercial, legal, medical, or healthcare initiatives. The purpose of this study was to assess the perception of the general public and professionals about the personal genome testing and genetic profiling. A questionnaire-based survey was conducted to investigate the attitudes of 2954 adults (56.4% male and 43.6% female) from more than 120 different educational, research, and professional organizations of Pakistan. The aim of the study was to assess interest in genomic testing. The findings of this survey will feed into the larger Genome Projects in Pakistan and will be helpful for the national bioethical committee, healthcare agencies, diagnostic companies, and other institutions for making policy decisions.

Next-generation sequencing studies on the E1-HVR1 region of hepatitis C virus (HCV) from non-high-risk HCV patients living in Punjab and Khyber Pakhtunkhwa, Pakistan.

The incidence rate of hepatitis C virus (HCV) infection in Pakistan is very high. In this study, we evaluated the genetic heterogeneity of HCV hypervariable region 1 (HVR1) from the HCV-infected Pakistani population and compare the isolated genotypes with representative sequences from internationally diverse geographic regions. We also investigated potential transmission events in non-high-risk HCV patients. Next-generation sequencing (NGS) data from the E1-HVR1 region from 30 HCV patients were used for phylogenetic analysis. Reference sequences were retrieved from the Los Alamos HCV and GenBank databases. NGS data were analyzed to examine HCV HVR1 sequence diversity and identify transmission links among HCV-infected individuals using Global Hepatitis Outbreak and Surveillance Technology (GHOST). Phylogenetic analysis showed the predominance of HCV genotype 3a (86.6%), followed by 1a (6.6%), 1b (3.3%), and 3b (3.3%). NGS of HVR1 displayed significant genetic heterogeneity of HCV populations within each patient. The average nucleotide sequence diversity for HVR1 was 0.055. JR781281 was found to be the most diverse (0.14) of the specimens. Phylogenetic analysis demonstrated that all HCV specimens sequenced in this study were more similar to each other and showed variations from the representative sequences. The GHOST results suggested genetic relatedness between two (6.6%) HCV cases, possibly defining an incipient outbreak in a non-high-risk population. We urge rigorous countrywide investigation of outbreaks to identify transmission clusters and their sources to incorporate preventive measures for disease control.

Machine learning guided postnatal gestational age assessment using new-born screening metabolomic data in South Asia and sub-Saharan Africa.

BACKGROUND: Babies born early and/or small for gestational age in Low and Middle-income countries (LMICs) contribute substantially to global neonatal and infant mortality. Tracking this metric is critical at a population level for informed policy, advocacy, resources allocation and program evaluation and at an individual level for targeted care. Early prenatal ultrasound examination is not available in these settings, gestational age (GA) is estimated using new-born assessment, last menstrual period (LMP) recalls and birth weight, which are unreliable. Algorithms in developed settings, using metabolic screen data, provided GA estimates within 1-2 weeks of ultrasonography-based GA. We sought to leverage machine learning algorithms to improve accuracy and applicability of this approach to LMICs settings. METHODS: This study uses data from AMANHI-ACT, a prospective pregnancy cohorts in Asia and Africa where early pregnancy ultrasonography estimated GA and birth weight are available and metabolite screening data in a subset of 1318 new-borns were also available. We utilized this opportunity to develop machine learning (ML) algorithms. Random Forest Regressor was used where data was randomly split into model-building and model-testing dataset. Mean absolute error (MAE) and root mean square error (RMSE) were used to evaluate performance. Bootstrap procedures were used to estimate confidence intervals (CI) for RMSE and MAE. For pre-term birth identification ROC analysis with bootstrap and exact estimation of CI for area under curve (AUC) were performed. RESULTS: Overall model estimated GA had MAE of 5.2 days (95% CI 4.6-6.8), which was similar to performance in SGA, MAE 5.3 days (95% CI 4.6-6.2). GA was correctly estimated to within 1 week for 85.21% (95% CI 72.31-94.65). For preterm birth classification, AUC in ROC analysis was 98.1% (95% CI 96.0-99.0; p < 0.001). This model performed better than Iowa regression, AUC Difference 14.4% (95% CI 5-23.7; p = 0.002). CONCLUSIONS: Machine learning algorithms and models applied to metabolomic gestational age dating offer a ladder of opportunity for providing accurate population-level gestational age estimates in LMICs settings. These findings also point to an opportunity for investigation of region-specific models, more focused feasible analyte models, and broad untargeted metabolome investigation.

Genetic diversity of Paramecium species on the basis of multiple loci analysis and ITS secondary structure models.

Among ciliates, Paramecium has become a privileged model for the study of "species problem" particularly in the case of the "Paramecium aurelia complex" that has been intensely investigated. Despite extensive studies, the taxonomy of Paramecium is still challenging. The major problem is an uneven sampling of Paramecium with relatively few representatives of each species. To investigate species from the less discovered region (Pakistan), 10 isolates of Paramecium species including a standing-alone FT8 strain previously isolated by some of us were subjected to molecular characterization. Fragments of 18S recombinant DNA (rDNA), ITS1-5.8S-ITS2-5'LSU rDNA, cytochrome c oxidase subunit II, and hsp70 genes were used as molecular markers for phylogenetic analysis of particular isolates. The nucleotide sequences of polymerase chain reaction products of all markers were compared with the available sequences of relevant markers of other Paramecium species from GenBank. Phylogenetic trees based on all molecular markers showed that all the nine strains had a very close relationship with Paramecium primaurelia except for the FT8 strain. FT8 consistently showed its unique position in comparison to all other species in the phylogenetic trees. Available sequences of internal transcribed spacer 1 (ITS1) and ITS2 and some other ciliate sequences from GenBank were used for the construction of secondary models. Two highly conserved helices supported by compensatory base changes among all ciliates of ITS2 secondary structures were found similar to other eukaryotes. Therefore, the most conserved 120 to 180 base pairs regions were identified for their comparative studies. We found that out of the three helices in ITS1 structure, helix B was more conserved in Paramecium species. Despite various substitutions in the primary sequence, it was observed that secondary structures of ITS1 and ITS2 could be helpful in interpreting the phylogenetic relationships both at species as well as at generic level.