Elucidation of population stratifying markers and selective sweeps in crossbred Landlly pig population using genome-wide SNP data.

The present study was aimed at the identification of population stratifying markers from the commercial porcine SNP 60K array and elucidate the genome-wide selective sweeps in the crossbred Landlly pig population. Original genotyping data, generated on Landlly pigs, was merged in various combinations with global suid breeds that were grouped as exotic (global pig breeds excluding Indian and Chinese), Chinese (Chinese pig breeds only), and outgroup pig populations. Post quality control, the genome-wide SNPs were ranked for their stratifying power within each dataset in TRES (using three different criteria) and FIFS programs and top-ranked SNPs (0.5K, 1K, 2K, 3K, and 4K densities) were selected. PCA plots were used to assess the stratification power of low-density panels. Selective sweeps were elucidated in the Landlly population using intra- and inter-population haplotype statistics. Additionally, Tajima's D-statistics were calculated to determine the status of balancing selection in the Landlly population. PCA plots showed 0.5K marker density to effectively stratify Landlly from other pig populations. The A-score in DAPC program revealed the Delta statistic of marker selection to outperform other methods (informativeness and FST methods) and that 3000-marker density was suitable for stratification of Landlly animals from exotic pig populations. The results from selective sweep analysis revealed the Landlly population to be under selection for mammary (NAV2), reproductive efficiency (JMY, SERGEF, and MAP3K20), body conformation (FHIT, WNT2, ASRB, DMGDH, and BHMT), feed efficiency (CSRNP1 and ADRA1A), and immunity (U6, MYO3B, RBMS3, and FAM78B) traits. More than two methods suggested sweeps for immunity and feed efficiency traits, thus giving a strong indication for selection in this direction. The study is the first of its kind in Indian pig breeds with a comparison against global breeds. In conclusion, 500 markers were able to effectively stratify the breeds. Different traits under selective sweeps (natural or artificial selection) can be exploited for further improvement.

COVID-19 and renal allograft rejection: insight from controlled and non-controlled studies.

AIM: Kidney transplant recipients (KTRs), due to their immunosuppressed status, are potentially more susceptible to both the severe effects of COVID-19 and complications in their transplanted organ. The aim of this study is to investigate whether COVID-19 infection increases the risk of rejection in kidney transplant recipients (KTRs). METHODS: This study involved a detailed literature review, conducted using PubMed, with the search being completed by September 7th, 2023. The search strategy incorporated a combination of relevant keywords: 'COVID', 'Renal', 'Kidney', 'Transplant', and 'Rejection'. The results from controlled and uncontrolled studies were separately collated and analyzed. RESULTS: A total of 11 studies were identified, encompassing 1,179 patients. Among these, two controlled studies reported the incidence of rejection in KTRs infected with COVID-19. Pooling data from these studies revealed no significant statistical correlation between COVID-19 infection and biopsy-proven rejection (p = 0.26). In addition, nine non-controlled studies were found, with rejection incidences ranging from 0% to 66.7%. The majority of these studies (eight out of nine) had small sample sizes, ranging from 3 to 75 KTRs, while the largest included 372 KTRs. The combined rejection rate across these studies was calculated to be 11.8%. CONCLUSION: In conclusion, the limited number of published controlled studies revealed no statistically significant association between COVID-19 infection and biopsy-proven rejection among KTRs. However, the broader analysis of non-controlled studies showed a variable rejection incidence with a pooled rejection rate of 11.8%. There is insufficient high-quality data to explore the association of COVID-19 infection and rejection.

Read-depth based approach on whole genome resequencing data reveals important insights into the copy number variation (CNV) map of major global buffalo breeds.

BACKGROUND: Elucidating genome-wide structural variants including copy number variations (CNVs) have gained increased significance in recent times owing to their contribution to genetic diversity and association with important pathophysiological states. The present study aimed to elucidate the high-resolution CNV map of six different global buffalo breeds using whole genome resequencing data at two coverages (10X and 30X). Post-quality control, the sequence reads were aligned to the latest draft release of the Bubaline genome. The genome-wide CNVs were elucidated using a read-depth approach in CNVnator with different bin sizes. Adjacent CNVs were concatenated into copy number variation regions (CNVRs) in different breeds and their genomic coverage was elucidated. RESULTS: Overall, the average size of CNVR was lower at 30X coverage, providing finer details. Most of the CNVRs were either deletion or duplication type while the occurrence of mixed events was lesser in number on a comparative basis in all breeds. The average CNVR size was lower at 30X coverage (0.201 Mb) as compared to 10X (0.013 Mb) with the finest variants in Banni buffaloes. The maximum number of CNVs was observed in Murrah (2627) and Pandharpuri (25,688) at 10X and 30X coverages, respectively. Whereas the minimum number of CNVs were scored in Surti at both coverages (2092 and 17,373). On the other hand, the highest and lowest number of CNVRs were scored in Jaffarabadi (833 and 10,179 events) and Surti (783 and 7553 events) at both coverages. Deletion events overnumbered duplications in all breeds at both coverages. Gene profiling of common overlapped genes and longest CNVRs provided important insights into the evolutionary history of these breeds and indicate the genomic regions under selection in respective breeds. CONCLUSION: The present study is the first of its kind to elucidate the high-resolution CNV map in major buffalo populations using a read-depth approach on whole genome resequencing data. The results revealed important insights into the divergence of major global buffalo breeds along the evolutionary timescale.

Allelic to genome wide perspectives of swine genetic variation to litter size and its component traits.

Litter size is a complex and sex limited trait that depends on various biological, managemental and environmental factors. Owing to its low heritability it is inefficaciously selected by traditional methods. However, due to higher heritability of ovulation rate and embryo survival, selection based on component traits of litter size is advocated. QTL analysis and candidate gene approach are among the various supplementary/alternate strategies for selection of litter size. QTL analysis is aimed at identifying genomic regions affecting trait of interest significantly. Candidate gene approach necessitates identification of genes potentially affecting the trait. There are various genes that significantly affect litter size and its component traits viz. ESR, LEP, BF, IGFBP, RBP4, PRLR, CTNNAL1, WNT10B, TCF12, DAZ, and RNF4. These genes affect litter size in a complex interacting manner. Lately, genome wide association study (GWAS) have been utilized to unveil the genetic and biological background of litter traits, and elucidate the genes governing litter size. Favorable SNPs in these genes have been identified and offers a scope for inclusion in selection programs thereby increasing breeding efficiency and profit in pigs. The review provides a comprehensive coverage of investigations carried out globally to unravel the genetic variation in litter size and its component traits in pigs, both at allelic and genome wide level. It offers a current perspective on different strategies including the profiling of candidate genes, QTLs, and genome wide association studies as an aid to efficient selection for litter size and its component traits.

Impact of body condition on sow and litter performance, postpartum physiological, hematological, and biochemical parameters in Landlly crossbred pigs.

A total of 32 Landlly crossbred sows were categorized into three groups based on their body condition score (BCS) on the 90th day of gestation viz. low, moderate, and high body condition groups. BCS assessments were subsequently conducted on the 102nd day, at farrowing, and on the 7th, 17th, 27th, and 42nd day postpartum, along with measurements of ultrasonic backfat thickness and body weight. Key reproductive performance traits, including total number born (TNB) and alive (TLA), stillbirths, mummification, and litter weight at birth and weaning, were recorded. Several physiological, health, biochemical, and hematological parameters were also estimated at different lactation stages. Analysis of the data revealed that TNB, TLA (P<0.04), and weaned piglets (P<0.01), as well as litter weight at birth (P<0.08) and weaning (P<0.08), were significantly higher in the low BCS group. Meanwhile, the weaning to estrous interval (P<0.04) was optimized in the high and moderate BCS groups. However, sows with high body condition exhibited higher stillbirths and pre-weaning mortality. Additionally, the order of increasing body condition correlated with superior colostrum quality, characterized by higher IgG levels (P<0.02), and increased average milk yield during early and mid-lactation (P<0.03). A high occurrence of postpartum dysgalactia syndrome (PDS) was evident in obese sows (P<0.001). Moreover, a positive correlation was found between the body condition of sows at late gestation and cortisol concentration throughout lactation across the three BCS groups (P<0.0001). Furthermore, a strong positive correlation was observed between the postpartum serum concentration of T3 (thyroid hormone) (P<0.002) and the prepartum body condition of sows. Based on these findings, maintaining sows with a moderate body condition (BCS of 3) and a backfat thickness of 21 mm in the breeding herd is recommended for enhancing profitability and productivity at the farm level.

Transplantation of Patients With Long Dialysis Vintage in the Current Deceased Donor Kidney Allocation System (KAS).

RATIONALE & OBJECTIVE: In 2014 the wait-time calculation for deceased donor kidney transplantation in the United States was changed from the date of first waitlisting to the date of first maintenance dialysis treatment with the aim of minimizing disparities in access to transplantation. This study examined the impact of this policy on access to transplantation, patient survival, and transplant outcomes among patients treated with maintenance dialysis for a prolonged duration before waitlisting. STUDY DESIGN: Retrospective cohort study. SETTING & PARTICIPANTS: Patients identified in the US Renal Data System between 2008 and 2018 aged 18-70 years and in the 95th percentile of dialysis treatment duration (≥6.5 years) before waitlisting. EXPOSURE: Waitlisting for transplantation before versus after implementation of the policy. OUTCOME: Time from date of waitlisting to deceased donor transplantation and death, and from date of transplantation to all cause graft loss. ANALYTICAL APPROACH: Univariate and multivariable time to event analyses. RESULTS: Patients waitlisted after the policy change had a higher likelihood of deceased donor transplantation (HR, 3.12 [95% CI, 2.90-3.37]) and lower risk of death (HR, 0.74 [95% CI, 0.63-0.87]). The risk of graft loss was lower in the post-kidney allocation system (KAS) cohort (HR, 0.66 [95% CI, 0.55-0.80]). The proportion of adult patients treated with dialysis ≥6.5 years who were never waitlisted for transplantation remained high (73%) and did not decrease after the policy implementation. LIMITATIONS: Cannot determine causality in this observational study. CONCLUSIONS: The policy change was associated with an increase in deceased donor transplantation and marked improvement in patient survival for patients waitlisted after long periods of dialysis treatment without decreasing the utility of available deceased donor kidney supply. The policy was not associated with increased waitlisting of this disadvantaged population.

Livestock and poultry farm wastewater treatment and its valorization for generating value-added products: Recent updates and way forward.

Livestock and poultry wastewater poses a potent risk for environmental pollution accelerating disease load and premature deaths. It is characterized by high chemical oxygen demand, biological oxygen demand, suspended solids, heavy metals, pathogens, and antibiotics, among other contaminants. These contaminants have a negative impact on the quality of soil, groundwater, and air, and is a potential hazard to human health. Depending on the specific characteristics of wastewater, such as the type and concentration of pollutants present; several physical, chemical and biological strategies have been developed for its treatment. This review aims at providing comprehensive overview of the profiling of livestock wastewater from the dairy, swine and poultry sub-sectors along with the biological, physico-chemical, AI-based and integrated treatment methodologies, and valorisation for the generation of value-added products such as bioplastics, biofertilizers, biohydrogen and microalgal-microbial fuel cells. Additionally, future perspectives for efficient and sustainable wastewater treatment are contemplated.

Histiocytic necrotising lymphadenitis (Kikuchi-Fujimoto disease) of axillary lymph nodes.

Kikuchi-Fujimoto disease (KFD) or histiocytic necrotising lymphadenitis is a rare entity, occurring most commonly in young Asian adults. KFD is characterised by fever with tender lymph node enlargement. The cervical group of lymph nodes is most commonly involved, and the diagnosis is conclusively made by lymph node biopsy and histopathology. KFD is a self-limiting condition, which usually resolves over 1-4 months. Symptomatic treatment with antipyretics and/or non-steroidal anti-inflammatory drugs is recommended. Here we describe an uncommon presentation of KFD in a young woman in which only the axillary lymph nodes were enlarged.

Bullous pemphigoid associated with dipeptidyl peptidase IV inhibitors. A case report and review of literature.

BACKGROUND: Bullous pemphigoid is a cutaneous autoimmune blistering disorder. The etiology for what precipitates this disease is not entirely clear at this point, although it has been associated with certain medications. MAIN OBSERVATION: We describe the case of a 70-year-old male with a past medical history of diabetes type 2 who developed a diffuse eruption of bullae with skin biopsy positive for bullous pemphigoid. He had previously been prescribed sitagliptin 50 mg daily for at least one year prior to onset of his disease. The medication was discontinued and the patient was treated with first IV and then oral steroids with good clinical outcome. There have been a few reports that have explored the relationship between DPP-IV inhibitors (gliptins) and bullous pemphigoid, including three case series and a report on sitagliptin associated allergic skin reactions submitted to the Adverse Event Reports System database of the FDA. According to the Naranjo ADR probability score there is a "possible" cause and effect relationship for this case. CONCLUSION: The enzyme DPP-IV is ubiquitously expressed in almost every organ system, including the skin. The exact mechanism at this time is unknown but is believed to be multifactorial involving many aspects of the immune system. Our case and the findings from our literature review further demonstrate a link between dipeptidyl peptidase-IV inhibitors and the development of bullous pemphigoid.