Inflammatory and Immune Mechanisms for Atherosclerotic Cardiovascular Disease in HIV.

Atherosclerotic vascular disease disproportionately affects persons living with HIV (PLWH) compared to those without. The reasons for the excess risk include dysregulated immune response and inflammation related to HIV infection itself, comorbid conditions, and co-infections. Here, we review an updated understanding of immune and inflammatory pathways underlying atherosclerosis in PLWH, including effects of viral products, soluble mediators and chemokines, innate and adaptive immune cells, and important co-infections. We also present potential therapeutic targets which may reduce cardiovascular risk in PLWH.

The Chromosome-Scale Genome of Chitala ornata Illuminates the Evolution of Early Teleosts.

Teleosts are the most prolific vertebrates, occupying the vast majority of aquatic environments, and their pectoral fins have undergone remarkable physiological transformations throughout their evolution. Studying early teleost fishes, such as those belonging to the Osteoglossiformes order, could offer crucial insights into the adaptive evolution of pectoral fins within this group. In this study, we have assembled a chromosomal-level genome for the Clown featherback (Chitala ornata), achieving the highest quality genome assembly for Osteoglossiformes to date, with a contig N50 of 32.78 Mb and a scaffold N50 of 40.73 Mb. By combining phylogenetic analysis, we determined that the Clown featherback diverged approximately 202 to 203 million years ago (Ma), aligning with continental separation events. Our analysis revealed the intriguing discovery that a unique deletion of regulatory elements is adjacent to the Gli3 gene, specifically in teleosts. This deletion might be tied to the specialized adaptation of their pectoral fins. Furthermore, our findings indicate that specific contractions and expansions of transposable elements (TEs) in teleosts, including the Clown featherback, could be connected to their adaptive evolution. In essence, this study not only provides a high-quality genomic resource for Osteoglossiformes but also sheds light on the evolutionary trajectory of early teleosts.

Hepatoprotective effect of diammonium glycyrrhizinate and neuroprotective effect of piperazine ferulate on AmB-induced liver and kidney injury by suppressing apoptosis in vitro and in vivo.

Amphotericin B (AmB) induced liver and kidney injury is often responsible for hepatic and renal dysfunction. Therefore, the protection strategy on liver and renal functions in patients treated with AmB should be emphasized. In this paper, diammonium glycyrrhizinate (DG) and piperazine ferulate (PF) were taken as the research object to study its hepatoprotective and neuroprotective effect on AmB-induced liver and kidney damage in vitro and in vivo. The microplate method and ELISA kits were employed for the biochemical detection in the serum and urine of mice. Flow cytometric analysis and western blotting analysis were conducted to study the mechanism of DG and PF. Our results confirmed the prevention capacity of DG and PF on AmB-induced liver and kidney injury through the alleviation of pathological changes and enzyme reducing action. Furthermore, DG and PF suppressed ROS-mediated mitochondrial apoptosis in AmB-treated mice and cells through Caspase pathway and Caspase-independent AIF pathway. In summary, DG and PF could protect AmB-induced hepatotoxicity and nephrotoxicity by disrupting oxidative stress and apoptosis.

A chromosome-level genome of electric catfish (Malapterurus electricus) provided new insights into order Siluriformes evolution.

The electric catfish (Malapterurus electricus), belonging to the family Malapteruridae, order Siluriformes (Actinopterygii: Ostariophysi), is one of the six branches that has independently evolved electrical organs. We assembled a 796.75 Mb M. electricus genome and anchored 88.72% sequences into 28 chromosomes. Gene family analysis revealed 295 expanded gene families that were enriched on functions related to glutamate receptors. Convergent evolutionary analyses of electric organs among different lineage of electric fishes further revealed that the coding gene of rho guanine nucleotide exchange factor 4-like (arhgef4), which is associated with G-protein coupled receptor (GPCR) signaling pathway, underwent adaptive parallel evolution. Gene identification suggests visual degradation in catfishes, and an important role for taste in environmental adaptation. Our findings fill in the genomic data for a branch of electric fish and provide a relevant genetic basis for the adaptive evolution of Siluriformes. Supplementary Information: The online version contains supplementary material available at 10.1007/s42995-023-00197-8.

Chromosome-level genome of butterflyfish unveils genomic features of unique colour patterns and morphological traits.

Chaetodontidae, known as butterflyfishes, are typical fish in coral ecosystems, exhibiting remarkable interspecific differences including body colour patterns and feeding ecology. In this study, we report genomes of three butterflyfish species (Chelmon rostratus, Chaetodon trifasciatus and Chaetodon auriga) and a closely related species from the Pomacanthidae family, Centropyge bicolour, with an average genome size of 65,611 Mb. Chelmon rostratus, comprising 24 chromosomes assembled to the chromosome level, could be served as a reference genome for butterflyfish. By conducting a collinearity analysis between butterflyfishes and several fishes, we elucidated the specific and conserved genomic features of butterflyfish, with particular emphasis on novel genes arising from tandem duplications and their potential functions. In addition to the two melanocyte-specific tyr genes commonly found in fish, we found the gene tyrp3, a new tyrosinase-related proteins gene in the reef fish, including butterflyfish and clownfish, implicating their involvement in the pigmentation diversity of fish. Additionally, we observed a tandem duplication expansion of three copies of nell1 gene in C. rostratus genome, which likely contribute to its unique jaw development and distinctive morphology of its sharp mouth. These results provided valuable genomic resources for further investigations into the genetic diversity and evolutionary adaptations of reef fish.

Bi-DCNet: Bilateral Network with Dilated Convolutions for Left Ventricle Segmentation.

Left ventricular segmentation is a vital and necessary procedure for assessing cardiac systolic and diastolic function, while echocardiography is an indispensable diagnostic technique that enables cardiac functionality assessment. However, manually labeling the left ventricular region on echocardiography images is time consuming and leads to observer bias. Recent research has demonstrated that deep learning has the capability to employ the segmentation process automatically. However, on the downside, it still ignores the contribution of all semantic information through the segmentation process. This study proposes a deep neural network architecture based on BiSeNet, named Bi-DCNet. This model comprises a spatial path and a context path, with the former responsible for spatial feature (low-level) acquisition and the latter responsible for contextual semantic feature (high-level) exploitation. Moreover, it incorporates feature extraction through the integration of dilated convolutions to achieve a larger receptive field to capture multi-scale information. The EchoNet-Dynamic dataset was utilized to assess the proposed model, and this is the first bilateral-structured network implemented on this large clinical video dataset for accomplishing the segmentation of the left ventricle. As demonstrated by the experimental outcomes, our method obtained 0.9228 and 0.8576 in DSC and IoU, respectively, proving the structure's effectiveness.

[Response of Soil Fungal Communities in Diversified Rotations of Wheat and Different Crops].

Crop-soil microorganism interactions and feedback are critical to soil health and crop production. The aim of this study was to clarify the difference in soil fungal communities under diversified rotations of wheat and different crops in the North China Plain and to provide a theoretical basis for the construction and optimization of ecological sustainable planting systems. The soil fungal community abundance, composition, and diversity of continuous winter wheat-summer maize M, winter wheat-summer peanut (summer maize) PM, and winter wheat-summer soybean (summer maize) SM treatments were studied using real-time quantitative PCR and high-throughput sequencing technology. The results showed that, compared with those of the continuous winter wheat-summer maize treatment, the peanut rotation treatment PM2 and soybean rotation treatment SM2 significantly reduced soil fungal ITS sequence copy numbers (P<0.05); there was no significant difference in soil fungal ITS sequence copy numbers between other rotation treatments and those of the control (P>0.05). Rotation treatments with peanut or soybean increased soil fungal community richness (Chao1 and ACE indices) and diversity (Shannon and InvSimson indices), in which the community richness of all rotation treatments and the community diversity of SM1/SM2 treatments varied significantly (P<0.05). The result of non-metric multidimensional scaling (NMDS) analysis showed that the soil fungal community among different rotation crops were obviously separated. The rotation crops significantly affected soil fungal community structure (PERMANOVA:r2=0.350, P=0.001; ANOSIM:r=0.478, P=0.001). Ascomycota (73.67%-85.48%) was the dominant phylum, whereas Sordariomycetes (30.53%-48.19%) and Eurotiomycetes (11.12%-31.19%) were the dominant classes of the fungal communities of sandy-loam fluvo-aquic soil in the North China Plain. There were significantly different taxa of soil fungal communities in different rotations. Potential pathogens such as Neocosmospora, Plectosphaerella, and Gibellulopsis were significantly enriched in the rotations of winter wheat-summer peanut (summer maize), whereas potential beneficial fungi such as Penicillium and Zopfiella were significantly enriched in the rotations of winter wheat-summer soybean (summer maize). Compared with that under the continuous winter wheat-summer maize treatment, rotations with peanut or soybean increased the relative abundance of pathotroph, pathotroph-symbiotroph, and saprotroph-symbiotroph fungi and decreased the relative abundance of saprotroph fungi. The soil fungal community richness and structure were significantly related to soil organic carbon and available nutrients, and the Shannon diversity index was significantly related to soil mineral nitrogen and available phosphorus. In summary, on the basis of continuous winter wheat-summer maize rotation in the North China Plain, adding summer peanut or summer soybean instead of summer maize for rotations with different interval years could increase the richness and diversity of soil fungal communities and significantly change soil fungal community structure. In particular, summer soybean as the preceding crop had a positive effect on the enrichment of potential beneficial fungi.

Genomic basis of evolutionary adaptation in a warm-blooded fish.

Few fishes have evolved elevated body temperatures compared with ambient temperatures, and only in opah (Lampris spp) is the entire body affected. To understand the molecular basis of endothermy, we analyzed the opah genome and identified 23 genes with convergent amino acid substitutions across fish, birds, and mammals, including slc8b1, which encodes the mitochondrial Na+/Ca2+ exchanger and is essential for heart function and metabolic heat production. Among endothermic fishes, 44 convergent genes with suggestive metabolic functions were identified, such as glrx3, encoding a crucial protein for hemoglobin maturation. Numerous genes involved in the production and retention of metabolic heat were also found to be under positive selection. Analyses of opah's unique inner-heat-producing pectoral muscle layer (PMI), an evolutionary key innovation, revealed that many proteins were co-opted from dorsal swimming muscles for thermogenesis and oxidative phosphorylation. Thus, the opah genome provides valuable resources and opportunities to uncover the genetic basis of thermal adaptations in fish.

Initial data release and announcement of the 10,000 Fish Genomes Project (Fish10K).

BACKGROUND: With more than 30,000 species, fish-including bony, jawless, and cartilaginous fish-are the largest vertebrate group, and include some of the earliest vertebrates. Despite their critical roles in many ecosystems and human society, fish genomics lags behind work on birds and mammals. This severely limits our understanding of evolution and hinders progress on the conservation and sustainable utilization of fish. RESULTS: Here, we announce the Fish10K project, a portion of the Earth BioGenome Project aiming to sequence 10,000 representative fish genomes in a systematic fashion within 10 years, and we officially welcome collaborators to join this effort. As a step towards this goal, we herein describe a feasible workflow for the procurement and storage of biospecimens, as well as sequencing and assembly strategies. CONCLUSIONS: To illustrate, we present the genomes of 10 fish species from a cohort of 93 species chosen for technology development.

MAP7 interacts with RC3H1 and cooperatively regulate cell-cycle progression of cervical cancer cells via activating the NF-κB signaling.

Ensconsin is encoded by the MAP7 gene and belongs to the microtubule-associated proteins. This study aimed to explore its functional roles and partners in cell-cycle progression in cervical cancer. Data from the Cancer Genome Atlas-Cervical & Endocervical Cancer (TCGA-CESC) and the Genotype-Tissue Expression project were used for bioinformatic analysis. SiHa cells were used for in-vitro and in-vivo analysis. Co-immunoprecipitation (Co-IP) assay was conducted to explore the proteins interacted with MAP7. Results showed that MAP7 mRNA expression might serve as an independent biomarker of shorter survival. MAP7 overexpression elevated cyclin D1/cyclin B1 expression, facilitated cell-cycle progression and promoted SiHa cell growth in a xenograft tumor model. Co-IP experiments confirmed a novel interaction between MAP7 and RC3H1. Knockdown of either RC3H1 or MAP7 significantly attenuated cyclin D1/cyclin B1 upregulation, and cell-cycle progression induced by the other partner. MAP7 overexpression led to increased expression of P-IKK (Ser176/177) and P-p65 (Ser536). RC3H1 inhibition abrogated MAP7 induced upregulation of P-IKK and P-p65. Data in TCGA-CESC showed that MAP7 expression was positively correlated with its copy number segments, but was negatively correlated with the methylation level of three CpG sites within the gene locus. Demethylation treatment by 5-Aza-dC elevated both MAP7 mRNA and protein expression in a dose-dependent manner. In conclusion, this study revealed a novel interaction between MAP7 and RC3H1 in cervical cancer cells, which cooperatively enhanced cyclin D1/cyclin B1 expression and facilitated cell-cycle progression. These effects were at least partly mediated by activated canonical IKK/NF-kB signaling.

[Effects of postponing nitrogen application on photosynthetic characteristics and grain yield of winter wheat subjected to water stress after heading stage].

A pot culture experiment was conducted to study the effects of postponing nitrogen (N) application on photosynthetic characteristics and grain yield of winter wheat subjected to water stress after heading stage. Equal in the total N rate in winter wheat growth season, N application was split before sowing, and/or at jointing and /or at anthesis at the ratio of 10:0:0 (N1), 6:4:0 (N2) and 4:3:3 (N3), combined with unfavorable water condition (either waterlogged or drought) with the sufficient water condition as control. The results showed that, under each of the water condition, both N2 and N3 treatments significantly improved the leaf photosynthetic rate and the SPAD value of flag leaf compared with N1 treatment during grain filling stage, and also the crop ear number, grain number per spike and above-ground biomass were increased. Although postponing nitrogen application increased water consumption, both grain yield and water use efficiency were increased. Compared with sufficient water supply, drought stress and waterlogging stress significantly reduced the photosynthetic rate of flag leaves at anthesis and grain filling stages, ear number, 1000-grain mass and yield under all of the N application patterns. The decline of photosynthetic rate under either drought stress or waterlogging stress was much less in N2 and N3 than in N1 treatments, just the same as the grain yield. The results indicated that postponing nitrogen application could regulate winter wheat yield as well as its components to alleviate the damages, caused by unfavorable water stress by increasing flag leaf SPAD and maintaining flag leaf photosynthetic rate after anthesis, and promoting above-ground dry matter accumulation.