Unveiling novel genetic variants in 370 challenging medically relevant genes using the long read sequencing data of 41 samples from 19 global populations.

BACKGROUND: A large number of challenging medically relevant genes (CMRGs) are situated in complex or highly repetitive regions of the human genome, hindering comprehensive characterization of genetic variants using next-generation sequencing technologies. In this study, we employed long-read sequencing technology, extensively utilized in studying complex genomic regions, to characterize genetic alterations, including short variants (single nucleotide variants and short insertions and deletions) and copy number variations, in 370 CMRGs across 41 individuals from 19 global populations. RESULTS: Our analysis revealed high levels of genetic variants in CMRGs, with 68.73% exhibiting copy number variations and 65.20% containing short variants that may disrupt protein function across individuals. Such variants can influence pharmacogenomics, genetic disease susceptibility, and other clinical outcomes. We observed significant differences in CMRG variation across populations, with individuals of African ancestry harboring the highest number of copy number variants and short variants compared to samples from other continents. Notably, 15.79% to 33.96% of short variants were exclusively detectable through long-read sequencing. While the T2T-CHM13 reference genome significantly improved the assembly of CMRG regions, thereby facilitating variant detection in these regions, some regions still lacked resolution. CONCLUSION: Our results provide an important reference for future clinical and pharmacogenetic studies, highlighting the need for a comprehensive representation of global genetic diversity in the reference genome and improved variant calling techniques to fully resolve medically relevant genes.

Systematic review and meta-analysis of single-stage vs two-stage revision for periprosthetic joint infection: a call for a prospective randomized trial.

BACKGROUND: Periprosthetic joint infection (PJI) is a severe complication of joint arthroplasty that causes significant pain and economic loss. This study aimed to determine whether the current evidence supports single-stage revision for PJI based on reinfection and reoperation rates. METHODS: We searched the PubMed, EBSCO, Medline, and Cochrane Library databases from inception to 30 May 2023 to identify studies that compared single-stage revision and two-stage revision for PJI. Data on reinfection and reoperation rates were pooled. RESULTS: This meta-analysis included a total of 40 studies with 8711 patients. Overall, there was no significant difference between single- and two-stage revision regarding the postoperative reinfection rate and reoperation rate. Subgroup analysis by surgery period and different surgical sites revealed no difference between the two groups in the reinfection and reoperation rates. CONCLUSIONS: Based on the available evidence, our study did not identify a significant difference in reinfection and reoperation rates between single- and two-stage revision for PJI. Given the limitations in inclusion/exclusion criteria and the observed heterogeneity, we acknowledge the complexity of drawing strong conclusions. Therefore, we suggest that the choice between single- and two-stage revision should be carefully considered on an individual basis, taking into account patient-specific factors and further research developments.

Purple sweet potato polysaccharide ameliorates concanavalin A-induced hepatic injury by inhibiting inflammation and oxidative stress.

BACKGROUND: Autoimmune hepatitis (AIH) is a prevalent liver disease that can potentially lead to hepatic fibrosis and cirrhosis. The prolonged administration of immunosuppressive medications carries significant risks for patients. Purple sweet potato polysaccharide (PSPP), a macromolecule stored in root tubers, exhibits anti-inflammatory, antioxidant, immune-enhancing, and intestinal flora-regulating properties. Nevertheless, investigation into the role and potential mechanisms of PSPP in AIH remains notably scarce. PURPOSE: Our aim was to explore the possible protective impacts of PSPP against concanavalin A (Con A)-induced liver injury in mice. METHODS: Polysaccharide was isolated from purple sweet potato tubers using water extraction and alcohol precipitation, followed by purification through DEAE-52 cellulose column chromatography and Sephadex G-100 column chromatography. A highly purified component was obtained, and its monosaccharide composition was characterized by high performance liquid chromatography (HPLC). Mouse and cellular models induced by Con A were set up to investigate the impacts of PSPP on hepatic histopathology, apoptosis, as well as inflammation- and oxidative stress-related proteins in response to PSPP treatment. RESULTS: The administration of PSPP significantly reduced hepatic pathological damage, suppressed elevation of ALT and AST levels, and attenuated hepatic apoptosis in Con A-exposed mice. PSPP was found to mitigate Con A-induced inflammation by suppressing the TLR4-P2X7R/NLRP3 signaling pathway in mice. Furthermore, PSPP alleviated Con A-induced oxidative stress by activating the PI3K/AKT/mTOR signaling pathway in mice. Additionally, PSPP demonstrated the ability to reduce inflammation and oxidative stress in RAW264.7 cells induced by Con A in vitro. CONCLUSION: PSPP has the potential to ameliorate hepatic inflammation via the TLR4-P2X7R/NLRP3 pathway and inhibit hepatic oxidative stress through the PI3K/AKT/mTOR pathway during the progression of Con A-induced hepatic injury. The results of this study have unveiled the potential hepatoprotective properties of purple sweet potato and its medicinal value for humans. Moreover, this study serves as a valuable reference, highlighting the potential of PSPP-1 as a drug candidate for the treatment of immune liver injury.

The spotted parrotfish genome provides insights into the evolution of a coral reef dietary specialist (Teleostei: Labridae: Scarini: Cetoscarus ocellatus).

With over 600 valid species, the wrasses (family Labridae) are among the largest and most successful families of the marine teleosts. They feature prominently on coral reefs where they are known not only for their impressive diversity in colouration and form but also for their functional specialisation and ability to occupy a wide variety of trophic guilds. Among the wrasses, the parrotfishes (tribe Scarini) display some of the most dramatic examples of trophic specialisation. Using abrasion-resistant biomineralized teeth, parrotfishes are able to mechanically extract protein-rich micro-photoautotrophs growing in and among reef carbonate material, a dietary niche that is inaccessible to most other teleost fishes. This ability to exploit an otherwise untapped trophic resource is thought to have played a role in the diversification and evolutionary success of the parrotfishes. In order to better understand the key evolutionary innovations leading to the success of these dietary specialists, we sequenced and analysed the genome of a representative species, the spotted parrotfish (Cetoscarus ocellatus). We find significant expansion, selection and duplications within several detoxification gene families and a novel poly-glutamine expansion in the enamel protein ameloblastin, and we consider their evolutionary implications. Our genome provides a useful resource for comparative genomic studies investigating the evolutionary history of this highly specialised teleostean radiation.

Enhancement of the anticancer potential and biosafety of BSA-modified, bacterial membrane-coated curcumin nanoparticles.

Bacteria and bacterial components have been widely used as bionanocarriers to deliver drugs to treat tumors. In this study, we isolated bacterial outer membrane vesicles (OMVs) with good stability and high yield for macrophage polarization and cell recruitment. Using ultrasound baths, these bacterial OMVs were combined with curcumin nanoparticles (OMV CUR NPs), following which these nanoparticles were modified with bovine serum albumin (BSA) to achieve high biosafety and tumor-targeting effects. The particle size, PDI, and zeta potential of the BSA-OMV CUR NPs were 157.9 nm, 0.233, and -15.1 mV, respectively. The BSA-OMV CUR NPs exhibited high storage stability, low cytotoxicity, sustained release, enhanced cellular uptake of CUR, induction of tumor cell apoptosis, and inhibition of tumor cell proliferation and migration. By determining the survival rate, body length, heart rate, head size, eye size, and pericardium size of the zebrafish, we found that the BSA-OMV CUR NPs were safe for application in vivo. Moreover, an increase in antiproliferation, antiangiogenic and antimetastatic effects of BSA-OMV CUR NPs was demonstrated in wild-type and transgenic tumor-transplanted zebrafish embryos.

Integrative functional genomic analyses identify genetic variants influencing skin pigmentation in Africans.

Skin color is highly variable in Africans, yet little is known about the underlying molecular mechanism. Here we applied massively parallel reporter assays to screen 1,157 candidate variants influencing skin pigmentation in Africans and identified 165 single-nucleotide polymorphisms showing differential regulatory activities between alleles. We combine Hi-C, genome editing and melanin assays to identify regulatory elements for MFSD12, HMG20B, OCA2, MITF, LEF1, TRPS1, BLOC1S6 and CYB561A3 that impact melanin levels in vitro and modulate human skin color. We found that independent mutations in an OCA2 enhancer contribute to the evolution of human skin color diversity and detect signals of local adaptation at enhancers of MITF, LEF1 and TRPS1, which may contribute to the light skin color of Khoesan-speaking populations from Southern Africa. Additionally, we identified CYB561A3 as a novel pigmentation regulator that impacts genes involved in oxidative phosphorylation and melanogenesis. These results provide insights into the mechanisms underlying human skin color diversity and adaptive evolution.

Cervical Spondylosis as a Potential Cause of Venous Hypertensive Myelopathy: A Case Report.

BACKGROUND Venous hypertensive myelopathy (VHM) is generally closely related to spinal vascular malformations, but a small number of other causes of VHM have been reported. CASE REPORT This rare case report describes a 74-year-old man with a C3 to C7 disc herniation, posterior spondylolisthesis (degree I) with spinal stenosis, exhibiting comparatively swift decline in neurological function as well as abnormal expansion of the high-signal intensity region on T2-weighted magnetic resonance imaging (MRI), which progressed to the medulla oblongata. Whether spinal cord degeneration is caused by cervical spondylotic myelopathy remains uncertain. Lumbar puncture was not performed because of spinal stenosis. An acute inflammatory process was also considered and the patient received hormone therapy. However, the effect was not significant, and his symptoms worsened after his hormone levels decreased. Repeat cervical MRI demonstrated interval development of diffuse intramedullary increased T2 signal in the spinal cord, which gradually increased to the pons, with cord swelling and degeneration more apparent. His medical history, negative laboratory results, evoked potential examination results, and poor effects of hormone therapy indicated a low probability of spinal inflammatory disease. Posterior C3-C6 expansive open-door cervical laminoplasty with lateral mass screw insertion and C2 and C7 decompression surgeries were performed. The neurological symptoms and abnormal T2-weighted MRI signals significantly improved after the operation. CONCLUSIONS VHM can be caused by spondylotic cord compression, leading to spinal cord injury. Therefore, an accurate diagnosis and timely surgery are essential.