Long COVID in Pakistan: a cross-sectional analysis of health and psychosocial outcomes.

According to the World Health Organization-led Delphi consensus, long COVID corresponds to the occurrence of symptoms beyond twelve weeks after the onset of acute COVID-19 illness that cannot be explained by alternate diagnosis. This cross-sectional study aimed to analyse the impacts of long COVID on general health and psychosocial well-being. For this study, the participants were interviewed either face to face or via telephone, and their responses were recorded on a questionnaire capturing information on demographics, COVID-19 status, duration of symptoms and long COVID symptoms. The psychosocial impacts of the pandemic were assessed using scales like Short Mood and feeling questionnaire (sMFQ), Warwick-Edinburgh Mental Well-being Scale (WEMWBS), Generalized Anxiety Disorder Assessment (GAD-7) and Perceived Stress Scale (PSS). Regression analysis was conducted to analyse the predictors of long COVID. A total of 300 participants were interviewed, of which 155 (52%) had COVID-19 illness. Of these 54 (35%) had persistent symptoms for a period of more than 12 weeks classified as long COVID. Muscle problems and fatigue were the most frequent (14.7%) symptoms encountered, followed by breathing problems (12.6%) and cognitive issues (12.6%). The symptoms of decrease in appetite and confusion or disorientation during the initial phase of the infection were associated with long COVID. The majority of the participants (83.3%) had moderate level of perceived stress, while moderate to severe levels of stress were observed in 17.3% of the individuals. Moreover, a high level of positive mental well-being was also observed. This study highlights the need for further research into the clinical aspects and implications of long COVID in Pakistan and emphasizes the importance of ongoing support for affected individuals.

Allelopathy: an alternative tool for sustainable agriculture.

Population increase, poverty, environmental degradation, and the use of synthetic herbicides are interdependent and closely linked and hence influence global food safety and stability of world agriculture. On the one hand, varied weeds, insects, and other pests have caused a tremendous loss in agricultural crop productivity annually. On the other hand, the use of synthetic insecticides, herbicides, fungicides, and other pesticides significantly disturbed the ecology of biotic communities in agricultural and natural ecosystems. Eventually, it destroyed the ecological balance in food chains. Interestingly, natural products released by the plants (allelochemicals) are secondary metabolites involved in ecological interactions and could be an important source of alternative agrochemicals. Mainly released by the plants as an outcome of acquaintances with other plants in their vicinity, these allelochemicals can also be used as eco-friendly substitutes for synthetic herbicides and other pesticides. Despite these facts, agrochemicals are either preferred over allelochemicals or the latter are not known in the direction of their use in achieving sustainability in agriculture. Given this, considering recent reports, this paper aims to: (1) emphasize allelochemicals; (2) overview the major biochemistry of allelochemicals; (3) critically discuss the role of allelopathy (and underlying major mechanisms) in the management of noxious weeds, insect pests, and major plant pathogens; and (4) enlighten the significant aspects so far not or least explored in the current context.

Immunological characterization of chitosan adjuvanted outer membrane proteins of Salmonella enterica serovar Typhi as multi-epitope typhoid vaccine candidate.

BACKGROUND: Outer membrane proteins (OMPs) of Gram-negative bacteria have been known as potential vaccine targets due to their antigenic properties and host specificity. Here, we focused on the exploration of the immunogenic potential and protective efficacy of total OMPs of Salmonella enterica serovar Typhi due to their multi epitope properties, adjuvanted with nanoporous chitosan particles (NPCPs). The study was designed to extrapolate an effective, low cost prophylactic approach for typhoid fever being getting uncontrolled in Pakistan due to emergence of extensively drug resistant (XDR) strains. METHODS & RESULTS: The OMPs of two S. Typhi variants (with and without Vi capsule) alone and with nanoporous chitosan particles as adjuvant were comparatively analyzed for immunogenic potential in mice. Adaptive immunity was evaluated by ELISA and relative quantification of cytokine gene expression (IL4, IL6, IL9, IL17, IL10, TNF, INF and PPIA as house keeping gene) using RT-qPCR. Statistical analysis was done using Welch's test. The protection was recorded by challenging the immunized mice with 50% ×LD50 of S. Typhi. The Vi + ve-OMPs of S. Typhi showed the most promising results by ELISA and significantly high expression of IL-6, IL-10 and IL-17 and 92.5% protective efficacy with no detectable side effects. CONCLUSION: We can conclude that the OMPs of Vi + ve S. Typhi are the most promising candidates for future typhoid vaccines because of cost effective preparation without expensive purification steps and multi-epitope properties. Chitosan adjuvant may have applications for oral protein based vaccines but found less effective in injectable preparations.

Silencing of Curlin Protein via M13 Phagemid-Mediated Synthetic sRNA Expression Reduces Virulence in the Avian Pathogenic E. coli (APEC).

Curli fimbriae, a virulent factor of the Avian Pathogenic Escherichia coli (APEC), is responsible for adhesion, biofilm formation, and colonization of pathogen. Major curli fimbriae protein is encoded by csgA gene. APEC is one of the leading causes of colibacillosis in poultry flocks and due to excessive use of antibiotics and vaccines in poultry, the emergence of various multi-drug resistant (MDR) bacterial strainsare is frequently reported. The growing concern of MDR bacterial strains necessitate novel antibacterial approaches to combat colibacillosis in poultry. RNA-based gene silencing is a very specific and robust strategy to target specific bacterial factors involved in pathogenicity and virulence. In this study, a phagemid-mediated sRNA expression system to target a vital gene, csgA, is employed. This comprises an M13 phagemid harboring a sRNA expression cassette and a pre-designed GUIDE sequences for the csgA target gene. To target the csgA gene at the mRNA level, a GUIDE sequence was computationally designed for pre-designed sRNA expression cassette. Online web tools were used to predict the binding energy, secondary structure, and off-target binding potential of the sRNA to optimize its expression. Results showed that the designed sRNA has a binding energy of - 29.60 kcal/mol with zero off-targets. After expression of the sRNA in the APEC cells, Ì´ 45% reduction in the csgA level was observed via RT-PCR in the CS-APEC-O1 strains compared to the wt-APEC-O1. Similarly, the biofilm forming ability decreased by 40% in the CS-APEC-O1 strains. The swarming motility and hemagglutination efficiency were not affected by the sRNA expression. Future studies investigating the in vivo efficiency of M13 phagemid delivery are required to evaluate its candidacy in phage therapy.

Optimized Protocol for Proportionate CNS Cell Retrieval as a Versatile Platform for Cellular and Molecular Phenomapping in Aging and Neurodegeneration.

Efficient purification of viable neural cells from the mature CNS has been historically challenging due to the heterogeneity of the inherent cell populations. Moreover, changes in cellular interconnections, membrane lipid and cholesterol compositions, compartment-specific biophysical properties, and intercellular space constituents demand technical adjustments for cell isolation at different stages of maturation and aging. Though such obstacles are addressed and partially overcome for embryonic premature and mature CNS tissues, procedural adaptations to an aged, progeroid, and degenerative CNS environment are underrepresented. Here, we describe a practical workflow for the acquisition and phenomapping of CNS neural cells at states of health, physiological and precocious aging, and genetically provoked neurodegeneration. Following recent, unprecedented evidence of post-mitotic cellular senescence (PoMiCS), the protocol appears suitable for such de novo characterization and phenotypic opposition to classical senescence. Technically, the protocol is rapid, efficient as for cellular yield and well preserves physiological cell proportions. It is suitable for a variety of downstream applications aiming at cell type-specific interrogations, including cell culture systems, Flow-FISH, flow cytometry/FACS, senescence studies, and retrieval of omic-scale DNA, RNA, and protein profiles. We expect suitability for transfer to other CNS targets and to a broad spectrum of engineered systems addressing aging, neurodegeneration, progeria, and senescence.

Isolation and phylogenetic analysis of Avian orthoavulavirus 1 sub-genotypes VII.2 and XXI.1.2 from caged birds in the Lahore district, Pakistan - Short communication.

In this study, the prevalence of Avian orthoavulavirus-1 (AOAV-1) (also commonly known as Newcastle disease virus) was investigated in caged birds kept in bird markets in the Lahore district of Pakistan. A total of 354 swab samples were obtained from 14 different species of clinically healthy birds. The overall virus prevalence was 12.7% in 9 out of the 14 species. Phylogenetic analysis of the complete fusion protein (F) gene showed that 23 isolates from different avian species belonged to sub-genotype VII.2 while three isolates of pigeon origin clustered with sub-genotype XXI.1.2. The VII.2 viruses isolated had a high nucleotide identity to viruses repeatedly isolated from poultry in Pakistan from 2011 to 2018. To date, sub-genotype XXI.1.2 viruses have only been identified in Pakistan. These findings suggest that the Newcastle disease (ND) outbreaks occurring in Pakistan involve multiple hosts and environments. The study emphasises the importance of continuing to monitor multiple avian species for the presence of AOAV-1s and implementing effective ND control strategies.

Genomic and biological characteristics of Avian Orthoavulavirus-1 strains isolated from multiple wild birds and backyard chickens in Pakistan.

Circulation of the dominant sub-genotype VII.2 of Avian Orthoavulavirus-1 (AOAV-1) is affecting multiple poultry and non-poultry avian species and causing significant economic losses to the poultry industry worldwide. In countries where ND is endemic, continuous monitoring and characterization of field strains are necessary. In this study, genetic characteristics of eleven AOAV-1 strains were analyzed isolated from wild birds including parakeets (n = 3), lovebird parrot (n = 1), pheasant (n = 1), peacock (n = 1), and backyard chickens (n = 5) during 2015-2016. Genetic characterization (genome size [15,192 nucleotides], the presence of typical cleavage site [112-RRQKRF-117]) and biological assessment (HA log 27 to 29 and intracerebral pathogenicity index [ICPI] value ranging from 1.50 to 1.86) showed virulent AOAV-1. Phylogenetic analysis showed that the studied isolates belonged to sub-genotype VII.2 and genetically very closely related (> 98.9%) to viruses repeatedly isolated (2011-2018) from commercial poultry. These findings provide evidence for the existence of epidemiological links between poultry and wild bird species in the region where the disease is prevalent. The deduced amino acid analysis revealed several substitutions in critical domains of fusion and hemagglutinin-neuraminidase genes. The pathogenesis and transmission potential of wild bird-origin AOAV-1 strain (AW-Pht/2015) was evaluated in 21-day-old chickens that showed the strain was highly virulent causing clinical signs and killed all chickens. High viral loads were detected in different organs of the infected chickens correlating with the severity of lesions developed. The continuous monitoring of AOAV-1 isolates in different species of birds will improve our knowledge of the evolution of these viruses, thereby preventing possible panzootic.

Clearing the Clutter: Antiatherosclerotic activity of Eucalyptus camaldulensis crude extract.

Plant components have been extensively evaluated for their pharmacological activities. This study provides scientific rationale towards the therapeutic effect of Eucalyptus camaldulensis aqueous bark extract against induced atherosclerosis and hyperlipidemia in pigeons. Phytochemical components of Eucalyptus bark extract possess a great antioxidant activity that potentially reduced the risk of heart diseases. A total of 42 Pigeons of both sexes were distributed into negative control (fed normal grain diet), hyperlipidemic control (fed HFD 1% animal fat oil and 0.1% cholesterol for 3 months), test groups of variable doses (0.05, 0.1, 0.2 to 0.4 gms/kg BW for 21 days) and the group received atorvastatin daily after induction used. At the end of the experiment biochemical and histological evaluation has been performed. After HFD induction the serum levels of liver enzyme AST, glucose, urea, cholesterol, LDL, VLDL, and TG were significantly increased with the reduction in HDL levels. The atherogenic index was also found significantly raised. Microscopic examination of the liver and aorta showed the appearance of lipid-filled foam cells all over the liver parenchyma and intima after the HFD induction. Thus it was concluded that Eucalyptus aqueous bark extract can be effective against atherosclerosis and hyperlipidemia.

Extrachromosomal Circular DNA: Current Knowledge and Implications for CNS Aging and Neurodegeneration.

Still unresolved is the question of how a lifetime accumulation of somatic gene copy number alterations impact organ functionality and aging and age-related pathologies. Such an issue appears particularly relevant in the broadly post-mitotic central nervous system (CNS), where non-replicative neurons are restricted in DNA-repair choices and are prone to accumulate DNA damage, as they remain unreplaced over a lifetime. Both DNA injuries and consecutive DNA-repair strategies are processes that can evoke extrachromosomal circular DNA species, apparently from either part of the genome. Due to their capacity to amplify gene copies and related transcripts, the individual cellular load of extrachromosomal circular DNAs will contribute to a dynamic pool of additional coding and regulatory chromatin elements. Analogous to tumor tissues, where the mosaicism of circular DNAs plays a well-characterized role in oncogene plasticity and drug resistance, we suggest involvement of the "circulome" also in the CNS. Accordingly, we summarize current knowledge on the molecular biogenesis, homeostasis and gene regulatory impacts of circular extrachromosomal DNA and propose, in light of recent discoveries, a critical role in CNS aging and neurodegeneration. Future studies will elucidate the influence of individual extrachromosomal DNA species according to their sequence complexity and regional distribution or cell-type-specific abundance.

Pharmacological basis for sedative and hypnotic like effects of Pyrus pashia using in vivo experimental models.

OBJECTIVE: Pyrus pashia has traditionally been used as a therapeutic agent including sedative. In this regard, hydroethanolic extract of Pyrus pashia (HEPP) was screened for phytochemical investigation, acute toxicity, and sedative-hypnotic activity to provide a scientific rationale to its ethno-medicinal uses. METHODS: Mice were used in acute toxicity test; sedative potential was observed in open field test while thiopental-induced sleeping time and barbiturate-induced sleeping time tests were used for the assessment of hypnotic like effects of HEPP. Various phytochemical groups were detected in preliminary phytochemical tests. RESULTS: In acute toxicity study, the extract was found safe up to 1g/kg while the extract caused 50% death at 1500 mg/kg. In all animal models, the extract had shown sedative and hypnotic effects but the most significant effect observed at increased dose in comparison with standard diazepam-treated group. In open field test, the extract at doses of 200 and 400 mg/kg, there is mild decrease in number of lines crossed by tested animals (mice) while significant reduction shown at 600 mg/kg compared with diazepam-treated group at dose 0.5 mg/kg. In phytochemical investigation HEPP subjected to different phytochemical tests. From the thoroughly study, it is revealed that these constituents mainly participating in sedation and hypnosis. CONCLUSIONS: The results of the present study showed significant sedative-hypnotic effects of the HEPP in mice and that the central benzodiazepine receptors are involved in the sedative-hypnotic effects of this plant.

Probiotics and Their Use in Inflammatory Bowel Disease.

Context • Crohn's disease and ulcerative colitis result in similar gastrointestinal (GI) symptoms, including pain, diarrhea, stools with mucus or blood, and ulceration or tissue damage within the alimentary canal. Gut microbiota play a crucial role in triggering, maintaining, and exacerbating inflammatory bowel disease (IBD). Probiotics might help to rebalance the gut flora in a positive way, shifting from pro- to anti-inflammatory. Objectives • The study intended to investigate the safety and use of probiotics and the biological effects of probiotic bacteria on IBD. Design • The research team performed a literature review. The team conducted a database search in April 2015 using Google Scholar and PubMed to find studies relevant to probiotics and their use in IBD. Only papers that were published in English were considered, and all available years in each database were searched. The initial search identified 38 published articles, for which the research team obtained full texts and independently read them in full to identify those papers suitable for inclusion in the review. Setting • The study took place in the main library of the University of Lahore (Islamabad, Pakistan). Results • Many strains of probiotics exist, but the most common strains available today are (1) the Bifidobacterium species, (2) Enterococcus faecium, (4) the Lactobacillus strains, (4) Saccharomyces boulardii, (5) the Bacillus species, and (6) Pediococcus, all used to produce beneficial health effects. These species showed their beneficial effects on the host using different mechanisms involving (1) production of proteins, quorum sensing signaling inhibitors, butyrate, immunoglobulin A, and short-chain fatty acids; (2) decreased production of tumor necrosis factor alpha and interleukin 8; (3) increased expression of mucin 2; and (4) increased upregulation of defensin. Conclusions • Studies on probiotics in animal models of IBD are promising, and clinical results in IBD patients are encouraging; however, the data are limited, and few studies are placebo controlled. Additional placebo-controlled, double-blind studies in IBD are required before recommendations can be offered for routine use of probiotics in IBD. Additional organisms may eventually be developed through genetic engineering. The current evidence also indicates that probiotic effects are strain specific; they do not act through the same mechanisms nor are all probiotics indicated for the same health conditions. More research is needed to determine what strains and at what dose probiotics become more useful as part of a clinical intervention.

Antifertility effect of methanolic leaf extract of Chenopodium ambrosioides Hook. in male Sprague Dawley rats.

This study evaluated the antifertility activity of methanolic extract of Chenopodium ambrosioides leaf on male rats. During the experiment, different doses of extract (0, 50, 100 and 150 mg/kg) were orally administered to rats for 28 days. Analysis of sperm parameters revealed a dose-dependent decrease in sperm motility, viability and daily sperm production (DSP). While, increased oxidative stress in reproductive organs; and impaired testicular and epididymal histology was also evident in high dose regimen. Furthermore, a reduction in concentrations of plasma testosterone, follicle stimulating hormone (FSH) and luteinizing hormone (LH) was also recorded. Reduced pregnancy outcome and small litter size in the females paired with treated male rats after 30 days of treatment withdrawn was noted in higher doses. From these findings, it is concluded that the methanolic leaf extract of C. ambrosioides is quite effective in reversible suppression of male fertility.

Synthesis, pharmacological screening and computational analysis of some 2-(1H-Indol-3-yl)-N'-[(un)substituted phenylmethylidene] acetohydrazides and 2-(1H-Indol-3-yl)-N'-[(un)substituted benzoyl/2-thienylcarbonyl]acetohydrazides.

The undertaken research was initiated by transforming 2-(1H-Indol-3-yl)acetic acid (1) in catalytic amount of sulfuric acid and ethanol to ethyl 2-(1H-Indol-3-yl)acetate (2), which was then reacted with hydrazine monohydrate in methanol to form 2-(1H-Indol-3-yl)acetohydrazide (3). Further, The reaction scheme was designed into two pathways where, first pathway involved The reaction of 3 with substituted aromatic aldehydes (4a-o) in methanol with few drops of glacial acetic acid to generate 2-(1H-Indol-3-yl)-N'-[(un)substitutedphenylmethylidene]acetohydrazides (5a-o) and in second pathway 3 was reacted with acyl halides (6a-e) in basic aqueous medium (pH 9-10) to afford 2-(1H-Indol-3-yl)-N'-[(un)substitutedbenzoyl/2-thienylcarbonyl]acetohydrazides (7a-e). All The synthesized derivatives were characterized by IR, EI-MS and 1H-NMR spectral techniques and evaluated for their anti-bacterial potentials against Gram positive and Gram negative bacterial strains and it was found that compounds 7a-d exhibited antibacterial activities very close to standard Ciprofloxacin. The synthesized derivatives demonstrated moderate to weak anti-enzymatic potential against α-Glucosidase and Butyrylcholinesterase (BChE) where, compounds 7c and 5c exhibited comparatively better inhibition against these enzymes respectively. Compounds 7a, 7d and 7e showed excellent anti-enzymatic potentials against Lipoxygenase (LOX) and their IC50 values were much lower than the reference standard Baicalein. Enzyme inhibitory activities were also supported by computational docking results. Compounds 5c, 7a, 7b and 7c also showed low values of % hemolytic activity as well, showing that these molecules were not toxic, indicating that these molecules can be utilized as potential therapeutic agents against inflammatory ailments.

Phytochemical analysis of Hibiscus caesius using high performance liquid chromatography coupled with mass spectrometry.

Various species in genus Hibiscus are traditionally known for their therapeutic attributes. The present study focused on the phytochemical analysis of a rather unexplored species Hibiscus caesius (H. caesius), using high-pressure liquid chromatography coupled with mass spectrometry (HPLC-MS). The analysis revealed five major compounds in the aqueous extract, viz. vanillic acid, protocatechoic acid, quercetin, quercetin glucoside and apigenin, being reported for the first time in H. caesius. Literature suggests that these compounds have important pharmacological traits such as anti-cancer, anti-inflammatory, anti-bacterial and hepatoprotective etc. however, this requires further pharmacological investigations at in vitro and in vivo scale. The above study concluded the medicinal potential of H. caesius.

A DFT approach to correlate the physical characteristics of novel chalcopyrites ASbN2(A = Li, Na) for green technology.

Semiconductor chalcopyrite compounds have been a subject of research interest due to their diverse range of physical properties that have captured the attention of scientists. In this ongoing research, we have examined the physical characteristics of LiSbN2 and NaSbN2 chalcopyrites using DFT. The modified Becke-Johnson (mBJ) potential is utilized for the computation of electronic structures. The stability is attained with negative formation energies and optimization curves. A bandgap of 2.60 eV in LiSbN2 and 3.15 eV in NaSbN2 has been achieved, which is further endorsed by the density of states. An in-depth analysis of the optical properties unveils the potential utility of LiSbN2 and NaSbN2 in various photovoltaic devices, attributed to its pronounced absorption in the UV spectrum. The transport characteristics are also assessed through various transport characteristics. The large electrical conductivity and ZT values for both chalcopyrite compounds are attained. Due to their remarkable capability to convert heat into electricity, these materials display potential for use in thermoelectric devices.

Genetic and clinical characteristics of patients with lipoprotein lipase deficiency from Slovenia and Pakistan: case series and systematic literature review.

Introduction: Hypertriglyceridemia (HTG) is a complex disorder caused by genetic and environmental factors that frequently results from loss-of-function variants in the gene encoding lipoprotein lipase (LPL). Heterozygous patients have a range of symptoms, while homozygous LPL deficiency presents with severe symptoms including acute pancreatitis, xanthomas, and lipemia retinalis. Methods: We described the clinical characteristics of three Slovenian patients (an 8-year-old female, an 18-year-old man, and a 57-year-old female) and one Pakistani patient (a 59-year-old male) with LPL deficiency. We performed next-generation sequencing (NGS) targeting all coding exons and intron-exon boundaries of the LPL gene, and Sanger sequencing for variant confirmation. In addition, we performed a systematic literature review of all cases with three identified variants and described their clinical characteristics. Results: Two Slovenian patients with a heterozygous pathogenic variant NM_000237.3:c.984G>T (p.Met328Ile) were diagnosed within the first three years of life and had triglyceride (TG) values of 16 and 20 mmol/L. An asymptomatic Pakistani patient with TG values of 36.8 mmol/L until the age of 44 years, was identified as heterozygous for a pathogenic variant NM_000237.3:c.724G>A (p.Asp242Asn). His TG levels dropped to 12.7 mmol/L on dietary modifications and by using fibrates. A Slovenian patient who first suffered from pancreatitis at the age of 18 years with a TG value of 34 mmol/L was found to be homozygous for NM_000237.3:c.337T>C (p.Trp113Arg). Conclusions: Patients with LPL deficiency had high TG levels at diagnosis. Homozygous patients had worse outcomes. Good diet and medication compliance can reduce severity.

High resistance of fluoroquinolone and macrolide reported in avian pathogenic Escherichia coli isolates from the humid subtropical regions of Pakistan.

OBJECTIVES: This study aimed to assess the antimicrobial resistance profile, virulence potential, and genetic characterization of avian pathogenic Escherichia coli (APEC) that cause colibacillosis in poultry. METHODS: Antibiotic susceptibility testing (AST) was measured via the Kirby-Bauer disc diffusion method against 27 commonly used antibiotics. Phylogrouping, virulence-associated gene detection, and hybrid strain detection via multiplex polymerase chain reaction (PCR) and genetic diversity were analysed via ERIC-PCR fingertyping method. RESULTS: AST analysis showed 100% of isolates were multidrug-resistant (MDR) and highest resistance was against penicillin, tetracycline, and macrolide classes of antibiotics. The mcr-1 gene was present in 40% of the isolates, though only 4% of isolates were showing phenotypic resistance. Despite the scarce use of fluoroquinolone, carbapenem, and cephalosporin in the poultry sector, resistance was evident because of the high prevalence of extended-spectrum ß-lactamase (ESBL) (53.7%) and other ß-lactamases in APEC isolates. ß-lactamase genotyping of APEC isolates revealed that 85.7% of isolates contained either blaCTX or blaTEM and around 38% of isolates were complement resistant. Growth in human urine was evident in 67.3% of isolates. Phylogroup B1 (51%) was the most prevalent group followed by phylogroups A (30.6%), D (13.61%), and B2 (4.76%). The most prevalent virulence-associated genes were fimH, iss, and tatT. Results showed that 26 isolates (17.69%) can be termed hybrid strains and APEC/EHEC (enterohemorrhagic E. coli) was the most prevalent hybrid E. coli pathotype. ERIC-PCR fingerprinting genotype analysis clustered APEC isolates in 40 groups (E1-E40). This study provides insights into the antibiotic resistance and virulence profiling of the APEC isolates in Pakistan. CONCLUSIONS: The findings of this study provide insights into that the antibiotic resistance and virulence profiling of the APEC isolates in Pakistan. This data can inform future studies designed to better estimate the severity of the colibacillosis in poultry farms.

Does mainstream BRCA testing affect surgical decision-making in newly-diagnosed breast cancer patients?

BACKGROUND: Germline pathogenic variants mutations) in the BRCA1 and BRCA2 genes cause an increased risk of breast cancer and ovarian cancer. Mainstream cancer genetic testing (MCG) was introduced for breast cancer patients in our unit in 2013. Non-geneticist clinicians have been trained to offer genetic testing during initial treatment planning. We assessed the impact of timely test results on surgical decision-making. METHODS: Women who had undergone mainstream genetic testing for breast cancer between September 2013 and September 2018 were identified from a prospective database. Surgical data were collected retrospectively. RESULTS: 580 eligible women had mainstream genetic testing. For 474 this was their first breast cancer diagnosis. The median age was 46 years (interquartile range (IQR) 38-57). The indications were: age ≤45 years for 233 (49%); triple negative disease for 192 women (40.5%); bilateral breast cancer age <60 for 39 (8%) and other for 72 (14%) women. The median time for test initiation to result was 18 days (IQR 15-21). 302 (64% received results before surgery. 88% of those found to have a BRCA mutation before surgery opted for bilateral mastectomy (compared to 5% with BRCA wild type). An additional 106 patients had a new diagnosis on a background of previous treatment. Of these all with a pathogenic variant chose bilateral mastectomy. CONCLUSION: Timely BRCA gene testing influences surgeons' and patients' choice of surgery. It reassures women with a negative result and allows those with a positive result to take an active decision about the management of their future risk.

Mapping of familial hypercholesterolemia and dyslipidemias basic management infrastructure in Pakistan: a cross-sectional study.

Background: Familial hypercholesterolemia (FH) is an autosomal inherited disorder characterised by elevated low-density lipoprotein cholesterol and premature cardiovascular events. Despite being declared as a public health priority, FH remains highly underdiagnosed, generally due to the lack of awareness and shortcomings in the available infrastructure, particularly in lower income countries. Methods: To map the existing infrastructure for the management of FH, a survey was conducted among 128 physicians (cardiologists, paediatricians, endocrinologists, and internal medicine specialists) from different regions of Pakistan. Findings: The respondents encountered a limited number of adults or children with diagnosed FH. A very small proportion of the population had access to free cholesterol and genetic testing even when indicated by a physician. In general, cascade screening of the relatives was not performed. Uniform diagnostic criteria for FH had not been established even within the same institution or province. The use of statins and ezetimibe in addition to lifestyle changes were the most common recommended treatment option for FH patients. The respondents considered lack of financial resources as a major barrier for the management of FH and stressed on taking relevant measures for a uniform FH screening programs around the country. Interpretation: National FH screening programmes are not in place worldwide hence FH is commonly undiagnosed, and many individuals are at a high risk for cardiovascular diseases. Timely screening of population for FH requires knowledge about FH among the clinicians and the availability of fundamental infrastructure coupled with sufficient financial resources. Funding: The authors confirm independence from the sponsor. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results. FS received funding from Higher Education Commission, Pakistan (Grant 20-15760) and UG received grants from Slovenian Research Agency (J3-2536, P3-0343).

A distinct circular DNA profile intersects with proteome changes in the genotoxic stress-related hSOD1G93A model of ALS.

BACKGROUND: Numerous genes, including SOD1, mutated in familial and sporadic amyotrophic lateral sclerosis (f/sALS) share a role in DNA damage and repair, emphasizing genome disintegration in ALS. One possible outcome of chromosomal instability and repair processes is extrachromosomal circular DNA (eccDNA) formation. Therefore, eccDNA might accumulate in f/sALS with yet unknown function. METHODS: We combined rolling circle amplification with linear DNA digestion to purify eccDNA from the cervical spinal cord of 9 co-isogenic symptomatic hSOD1G93A mutants and 10 controls, followed by deep short-read sequencing. We mapped the eccDNAs and performed differential analysis based on the split read signal of the eccDNAs, referred as DifCir, between the ALS and control specimens, to find differentially produced per gene circles (DPpGC) in the two groups. Compared were eccDNA abundances, length distributions and genic profiles. We further assessed proteome alterations in ALS by mass spectrometry, and matched the DPpGCs with differentially expressed proteins (DEPs) in ALS. Additionally, we aligned the ALS-specific DPpGCs to ALS risk gene databases. RESULTS: We found a six-fold enrichment in the number of unique eccDNAs in the genotoxic ALS-model relative to controls. We uncovered a distinct genic circulome profile characterized by 225 up-DPpGCs, i.e., genes that produced more eccDNAs from distinct gene sequences in ALS than under control conditions. The inter-sample recurrence rate was at least 89% for the top 6 up-DPpGCs. ALS proteome analyses revealed 42 corresponding DEPs, of which 19 underlying genes were itemized for an ALS risk in GWAS databases. The up-DPpGCs and their DEP tandems mainly impart neuron-specific functions, and gene set enrichment analyses indicated an overrepresentation of the adenylate cyclase modulating G protein pathway. CONCLUSIONS: We prove, for the first time, a significant enrichment of eccDNA in the ALS-affected spinal cord. Our triple circulome, proteome and genome approach provide indication for a potential importance of certain eccDNAs in ALS neurodegeneration and a yet unconsidered role as ALS biomarkers. The related functional pathways might open up new targets for therapeutic intervention.