Graph-pMHC: graph neural network approach to MHC class II peptide presentation and antibody immunogenicity.

Antigen presentation on MHC class II (pMHCII presentation) plays an essential role in the adaptive immune response to extracellular pathogens and cancerous cells. But it can also reduce the efficacy of large-molecule drugs by triggering an anti-drug response. Significant progress has been made in pMHCII presentation modeling due to the collection of large-scale pMHC mass spectrometry datasets (ligandomes) and advances in machine learning. Here, we develop graph-pMHC, a graph neural network approach to predict pMHCII presentation. We derive adjacency matrices for pMHCII using Alphafold2-multimer and address the peptide-MHC binding groove alignment problem with a simple graph enumeration strategy. We demonstrate that graph-pMHC dramatically outperforms methods with suboptimal inductive biases, such as the multilayer-perceptron-based NetMHCIIpan-4.0 (+20.17% absolute average precision). Finally, we create an antibody drug immunogenicity dataset from clinical trial data and develop a method for measuring anti-antibody immunogenicity risk using pMHCII presentation models. Our model increases receiver operating characteristic curve (ROC)-area under the ROC curve (AUC) by 2.57% compared to just filtering peptides by hits in OASis alone for predicting antibody drug immunogenicity.

In silico tools for accurate HLA and KIR inference from clinical sequencing data empower immunogenetics on individual-patient and population scales.

Immunogenetic variation in humans is important in research, clinical diagnosis and increasingly a target for therapeutic intervention. Two highly polymorphic loci play critical roles, namely the human leukocyte antigen (HLA) system, which is the human version of the major histocompatibility complex (MHC), and the Killer-cell immunoglobulin-like receptors (KIR) that are relevant for responses of natural killer (NK) and some subsets of T cells. Their accurate classification has typically required the use of dedicated biological specimens and a combination of in vitro and in silico efforts. Increased availability of next generation sequencing data has led to the development of ancillary computational solutions. Here, we report an evaluation of recently published algorithms to computationally infer complex immunogenetic variation in the form of HLA alleles and KIR haplotypes from whole-genome or whole-exome sequencing data. For both HLA allele and KIR gene typing, we identified tools that yielded >97% overall accuracy for four-digit HLA types, and >99% overall accuracy for KIR gene presence, suggesting the readiness of in silico solutions for use in clinical and high-throughput research settings.

A chromosome-level genome assembly of the striped catfish (Pangasianodon hypophthalmus).

Striped catfish (Pangasianodon hypophthalmus), belonging to the Pangasiidae family, has become an economically important fish with wide cultivation in Southeast Asia. Owing to the high-fat trait, it is always considered as an oily fish. In our present study, a high-quality genome assembly of the striped catfish was generated by integration of Illumina short reads, Nanopore long reads and Hi-C data. A 731.7-Mb genome assembly was finally obtained, with a contig N50 of 3.5 Mb, a scaffold N50 of 29.5 Mb, and anchoring of 98.46% of the assembly onto 30 pseudochromosomes. The genome contained 36.9% repeat sequences, and a total 18,895 protein-coding genes were predicted. Interestingly, we identified a tandem triplication of fatty acid binding protein 1 gene (fabp1; thereby named as fabp1-1, fabp1-2 and fabp1-3 respectively), which may be related to the high fat content in striped catfish. Meanwhile, the FABP1-2 and -3 isoforms differed from FABP1-1 by several missense mutations including R126T, which may affect the fatty acid binding properties. In summary, we report a high-quality chromosome-level genome assembly of the striped catfish, which provides a valuable genetic resource for biomedical studies on the high-fat trait, and lays a solid foundation for practical aquaculture and molecular breeding of this international teleost species.

Ketogenic diet induces autophagy to alleviate bleomycin-induced pulmonary fibrosis in murine models.

AIM OF THE STUDY: Ketogenic diet (KD) has been identified as an effective strategy in treating multiple diseases. KD is capable of inducing autophagy which is an important therapeutic target for pulmonary fibrosis (PF). This study aimed to investigate the effect of KD treatment on PF progression. Materials and Methods: Intratracheal instillation of bleomycin (BLM, 5 mg/kg) to establish PF model in male Kunming mice fed either KD or standard diet. The survival of mice was recorded every day for 3 weeks. The pulmonary tissues were weighed on day 21 and the pulmonary index was calculated. The histopathological changes of pulmonary tissues were analyzed by hematoxylin and eosin staining and Masson staining, and the collagen deposition by hydroxyproline assay. Then the content of proinflammatory factors in pulmonary tissues was measured using enzyme-linked immunosorbent assay, and the expression of profibrogenic cytokines, autophagy markers and PI3K/AKT/mTOR pathway-related proteins in pulmonary tissues using western blotting or immunohistochemistry. Results: KD treatment significantly restored the BLM-induced increase of pulmonary index and had a tendency to increase the survival rate of PF mice. Furthermore, KD treatment restored the BLM-induced damage of alveolar structure, infiltration of inflammatory cells and collagen deposition and decreased hydroxyproline content. In addition, the BLM-induced secretion of tumor necrosis factor-alpha, interleukin-6 and interleukin-1ß and expression of transforming growth factor ß1, phospho-Smad2/3, connective tissue growth factor, α-smooth muscle actin and collagen type III alpha 1 chain were inhibited by KD. KD treatment also up-regulated the expression of light chain 3 II/I and Beclin1 and down-regulated the expression of p62, phospho-AKT, phospho-mTOR and phospho-p70S6K, suggesting that KD induced autophagy and suppressed the BLM-induced activation of PI3K/AKT/mTOR signaling pathway. Conclusions: These findings indicate that KD can alleviate PF in vivo by regulating autophagy and PI3K/AKT/mTOR signaling pathway, which provides a novel therapeutic strategy for PF.

An integrated map of structural variation in 2,504 human genomes.

Structural variants are implicated in numerous diseases and make up the majority of varying nucleotides among human genomes. Here we describe an integrated set of eight structural variant classes comprising both balanced and unbalanced variants, which we constructed using short-read DNA sequencing data and statistically phased onto haplotype blocks in 26 human populations. Analysing this set, we identify numerous gene-intersecting structural variants exhibiting population stratification and describe naturally occurring homozygous gene knockouts that suggest the dispensability of a variety of human genes. We demonstrate that structural variants are enriched on haplotypes identified by genome-wide association studies and exhibit enrichment for expression quantitative trait loci. Additionally, we uncover appreciable levels of structural variant complexity at different scales, including genic loci subject to clusters of repeated rearrangement and complex structural variants with multiple breakpoints likely to have formed through individual mutational events. Our catalogue will enhance future studies into structural variant demography, functional impact and disease association.

High throughput screening of small immune peptides and antimicrobial peptides from the Fish-T1K database.

Analyses of transcriptomic datasets have the potential to reveal genetic markers underlying ecological adaptations. In the present study, we leverage the expanding dataset generated by the Fish-T1K Project (Transcriptomes of 1000 Fishes) to characterize small peptides that may be implicated in the immune system of fishes. We focused our analyses on sequences smaller than 360 bp obtained from gill transcriptomes of 87 ray-finned fishes (Actinopterygii). Functional annotation of short transcripts revealed that the number of small immune peptides varied significantly among the studied species. High-throughput screening of antimicrobial peptides (AMPs) with homologous searches was used to characterize the composition of innate immune defense factors present in fishes. We analyzed the putative effects of habitat, climatic zone and genetic system on the distribution of small peptides among species. Our results highlight the utility of large transcriptomic datasets such as Fish-T1K to explore patterns of variation at macroevolutionary scales and to discover novel peptides that may be used for further investigation and drug development.

Transcriptomic evidence of adaptive tolerance to high environmental ammonia in mudskippers.

Mudskippers are typical amphibious fishes and possess various strategies to ameliorate ammonia toxicity during exposure to environmental ammonia. The present study aimed to provide transcriptomic evidence through profiling the gill and liver transcriptomes of Boleophthalmus pectinirostris (BP) and Periophthalmus magnuspinnatus (PM), which were subjected to treatment with high environmental ammonia for up to 72 h. The results of gene function annotation showed that most of the differentially expressed genes were involved in metabolic pathways. After ammonia exposure, the protein and amino acid metabolism related genes in mudskippers were down-regulated, and PM had more down-regulated genes than BP. The expression levels of several representative genes involved in ammonia excretion in the gill were commonly increased. Interestingly, NH4+ transporting and H+ excreting related genes, including Na+/K+(NH4+)/2Cl- cotransporter (nkcc), Na+/K+(NH4+)-ATPase (nka), carbonic anhydrase 2 (ca2), H+-ATPase, Na+/H+ (NH4+)-exchanger (nhe), and carbonic anhydrase 15 (ca15), were up-regulated more significantly in BP than PM; however, the transcription levels of Rhesus glucoprotein b (Rhbg) and Rhesus glucoprotein c1 (Rhcg1), which constitute the NH3 transporting channels, were up-regulated more significantly in PM than BP. Furthermore, the present study provides molecular evidence for how mudskippers adopt partial amino acid catabolism to decrease the production of endogenous ammonia under high environmental ammonia loading.

The Sinocyclocheilus cavefish genome provides insights into cave adaptation.

BACKGROUND: An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively. RESULTS: The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes. CONCLUSION: As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology.

Interpretation of genomic variants using a unified biological network approach.

The decreasing cost of sequencing is leading to a growing repertoire of personal genomes. However, we are lagging behind in understanding the functional consequences of the millions of variants obtained from sequencing. Global system-wide effects of variants in coding genes are particularly poorly understood. It is known that while variants in some genes can lead to diseases, complete disruption of other genes, called 'loss-of-function tolerant', is possible with no obvious effect. Here, we build a systems-based classifier to quantitatively estimate the global perturbation caused by deleterious mutations in each gene. We first survey the degree to which gene centrality in various individual networks and a unified 'Multinet' correlates with the tolerance to loss-of-function mutations and evolutionary conservation. We find that functionally significant and highly conserved genes tend to be more central in physical protein-protein and regulatory networks. However, this is not the case for metabolic pathways, where the highly central genes have more duplicated copies and are more tolerant to loss-of-function mutations. Integration of three-dimensional protein structures reveals that the correlation with centrality in the protein-protein interaction network is also seen in terms of the number of interaction interfaces used. Finally, combining all the network and evolutionary properties allows us to build a classifier distinguishing functionally essential and loss-of-function tolerant genes with higher accuracy (AUC = 0.91) than any individual property. Application of the classifier to the whole genome shows its strong potential for interpretation of variants involved in mendelian diseases and in complex disorders probed by genome-wide association studies.

Fabrication and Application of Grinding Wheels with Soft and Hard Composite Structures for Silicon Carbide Substrate Precision Processing.

In silicon carbide processing, the surface and subsurface damage caused by fixed abrasive grinding significantly affects the allowance of the next polishing process. A novel grinding wheel with a soft and hard composite structure was fabricated for the ultra-precision processing of SiC substrates, and the grinding performance of the grinding wheel was assessed in this study. Different types of gels, heating temperatures, and composition ratios were used to fabricate the grinding wheel. The grinding performance of the grinding wheel was investigated based on the surface integrity and subsurface damage of SiC substrates. The results showed that the grinding wheel with a soft and hard composite structure was successfully fabricated using freeze-dried gel with a heating temperature of 110 °C, and the component ratio of resin to gel was 4:6. A smooth SiC substrate surface with almost no cracks was obtained after processing with the grinding wheel. The abrasive exposure height was controlled by manipulating the type and ratio of the gel. Furthermore, the cutting depth in nanoscale could be achieved by controlling the abrasive exposure height. Therefore, the fabrication and application of the grinding wheels with soft and hard composite structures is important for the ultra-precision processing of large-size SiC substrates.

Genomics comparisons of three chromosome-level mudskipper genome assemblies reveal molecular clues for water-to-land evolution and adaptation.

INTRODUCTION: Mudskippers are a large group of amphibious fishes that have developed many morphological and physiological capacities to live on land. Genomics comparisons of chromosome-level genome assemblies of three representative mudskippers, Boleophthalmus pectinirostris (BP), Periophthalmus magnuspinnatus (PM) and P. modestus (PMO), may be able to provide novel insights into the water-to-land evolution and adaptation. METHODS: Two chromosome-level genome assemblies for BP and PM were respectively sequenced by an integration of PacBio, Nanopore and Hi-C sequencing. A series of standard assembly and annotation pipelines were subsequently performed for both mudskippers. We also re-annotated the PMO genome, downloaded from NCBI, to obtain a redundancy-reduced annotation. Three-way comparative analyses of the three mudskipper genomes in a large scale were carried out to discover detailed genomic differences, such as different gene sizes, and potential chromosomal fission and fusion events. Comparisons of several representative gene families among the three amphibious mudskippers and some other teleosts were also performed to find some molecular clues for terrestrial adaptation. RESULTS: We obtained two high-quality haplotype genome assemblies with 23 and 25 chromosomes for BP and PM respectively. We also found two specific chromosome fission events in PM. Ancestor chromosome analysis has discovered a common fusion event in mudskipper ancestor. This fusion was then retained in all the three mudskipper species. A loss of some SCPP (secretory calcium-binding phosphoprotein) genes were identified in the three mudskipper genomes, which could lead to reduction of scales for a part-time terrestrial residence. The loss of aanat1a gene, encoding an important enzyme (arylalkylamine N-acetyltransferase 1a, AANAT1a) for dopamine metabolism and melatonin biosynthesis, was confirmed in PM but not in PMO (as previously reported existence in BP), suggesting a better air vision of PM than both PMO and BP. Such a tiny variation within the genus Periophthalmus exemplifies to prove a step-by-step evolution for the mudskippers' water-to-land adaptation. CONCLUSION: These high-quality mudskipper genome assemblies will become valuable genetic resources for in-depth discovery of genomic evolution for the terrestrial adaptation of amphibious fishes.

The FIB-4 scores in the emergency department to predict the outcomes of COVID-19 patients in taiwan.

Objective: We aimed to determine the reliability of using the Fibrosis-4 (FIB-4) index in COVID-19 patients without underlying liver illness. Method: We employed multivariate logistic regression to identify variables that exhibited statistically significant influence on the ultimate outcome. Multilayer perceptron analysis was employed to develop a prediction model for the FIB-4 index concerning ICU admission and intubation rates. However, the scarcity of cases rendered the assessment of the mortality rate unfeasible. We plotted ROC curves to analyze the predictive strength of the FIB-4 index across various age groups. Result: In univariate logistic regression, only the FIB-4 index and respiratory rate demonstrated statistical significance on all poor outcomes. The FIB-4 index for mortality prediction had an ROC and AUC of 0.863 (95% CI: 0.781-0.9444). It demonstrates predictive power across age groups, particularly for age ≥65 (AUC: 0.812, 95% CI: 0.6571-0.9673) and age <65 (AUC: 0.878, 95% CI: 0.8012-0.9558). Its sensitivity for intubation and ICU admission prediction is suboptimal. Conclusion: FIB-4 index had promising power in prediction of mortality rate in all age groups.

Construction of high-density genetic linkage maps for orange-spotted grouper Epinephelus coioides using multiplexed shotgun genotyping.

BACKGROUND: Orange-spotted grouper, Epinephelus coioides, is one of the most valuable fish species in China. Commercial production of orange-spotted grouper could be increased by developing higher growth rates and improving commercially important traits. Information on genetic markers associated with quantitative trait loci (QTL) can be used in breeding programs to identify and select individuals carrying desired traits. A high-density genetic linkage map is the basis for QTL study, and multiplexed shotgun genotyping (MSG) facilitates the development of single nucleotide polymorphisms (SNPs) and genotyping. In this study, the first high-density genetic linkage maps for groupers were generated on the basis of the MSG method. RESULTS: The sex-averaged map contained a total of 4,608 SNPs, which spanned 1581.7 cM, with a mean distance between SNPs of 0.34 cM. The 4,608 SNPs were located in 2,849 unique locations on the linkage map, with an average inter-location space at 0.56 cM. There were 2,516 SNPs on the female map, and the number of unique locus was 1,902. However, the male map contained more numbers of SNP (2,939) and unique locations (2,005). The total length of the female and male maps was 1,370.9 and 1,335.5 cM, respectively. CONCLUSIONS: The high-resolution genetic linkage maps will be very useful for QTL analyses and marker-assisted selection (MAS) for economically important traits in molecular breeding of the orange-spotted grouper.

Degradation performance of methylene blue in metal nanoparticle modified 3D mesoporous wood microchannels.

Wood has a rich three-dimensional pore structure and many bottom-up nanochannels. However, the structure of wood itself has limited ability to adsorb dyes, so the effective combination of the unique structure of wood and Pd NPs was studied to achieve efficient degradation of dyes. First, the three-dimensional structure of natural wood is optimized by combining the complex pore structure of wood with Pd NPs to improve the contact process between the dye and Pd NPs. Then, Pd (II) ion can be well reduced to Pd NPs by wood lignin. In addition, Pd NPs can be fixed by hydroxyl groups on cellulose in wood. The flow state inside Pd NPs/wood film and the contact area between catalyst and dye were discussed in detail by hydrodynamic simulation, which filled the gap. It provides reference for composite structure. When Pd NPs/wood membrane was used to treat methylene blue (MB), the degradation efficiency was up to 96.7%, which was 90% higher than that of natural wood. Its TOF value was 1.82 molMB molPd-1min-1, which was higher than that in the previous literature. Therefore, the novelty of this study is that the mechanism of catalytic degradation of MB by Pd nanoparticles/wood composites is reported for the first time. The internal flow mode and contact condition of the new material are understood, which has a good application prospect.

Ag3PO4-anchored La2Ti2O7 nanorod as a Z-Scheme heterostructure composite with boosted photogenerated carrier separation and enhanced photocatalytic performance under natural sunlight.

Developing wide spectra-responsive photocatalysts has attracted considerable attention in the photocatalytic technology to achieve excellent catalytic activity. Ag3PO4, with strong response to light spectra shorter than 530 nm, shows extremely outstanding photocatalytic oxidation ability. Unfortunately, the photocorrosion of Ag3PO4 is still the biggest obstacle to its application. Herein, the La2Ti2O7 nanorod was used to anchor Ag3PO4 nanoparticles in this study, and a novel Z-Scheme La2Ti2O7/Ag3PO4 heterostructure composite was constructed. Remarkably, the composite showed strong responsive to most of the spectra in natural sunlight. The Ag0 formed in-situ acted as the recombination center of photogenerated carriers, which promoted their efficient separation and contributed to the improved photocatalytic performance of the heterostructure. When the mass ratio of Ag3PO4 in the La2Ti2O7/Ag3PO4 catalyst was 50%, the degradation rate constant of Rhodamine B (RhB), methyl orange (MO), chloroquine phosphate (CQ), tetracycline (TC), and phenol under natural sunlight irradiation were 0.5923, 0.4463, 0.1399, 0.0493, and 0.0096 min-1, respectively. Furthermore, the photocorrosion of the composite was greatly inhibited, 76.49% of CQ and 83.96% of RhB were still degraded after four cycles. Besides, the holes and O2•- played a significant role in RhB degradation, and it included multiple mechanisms of deethylation, deamination, decarboxylation, and cleavage of ring-structures. Moreover, the treated solution can also show safety to the water receiving environment. Overall, the synthesized Z-Scheme La2Ti2O7/Ag3PO4 composite exhibited immense potential for removing various organic pollutants through photocatalytic technology under natural sunlight irradiation.

Effects of Building Directions on Microstructure, Impurity Elements and Mechanical Properties of NiTi Alloys Fabricated by Laser Powder Bed Fusion.

For NiTi alloys prepared by the Laser Powder Bed Fusion (LPBF), changes in the building directions will directly change the preferred orientation and thus directly affect the smart properties, such as superelasticity, as well as change the distribution state of defects and impurity elements to affect the phase transformation behaviour, which in turn affects the smart properties at different temperatures. In this study, the relationship between impurity elements, the building directions, and functional properties; the effects of building directions on the crystallographic anisotropy; phase composition; superelastic properties; microhardness; geometrically necessary dislocation (GND) density; and impurity element content of NiTi SMAs fabricated by LPBF were systematically studied. Three building directions measured from the substrate, namely, 0°, 45° and 90°, were selected, and three sets of cylindrical samples were fabricated with the same process parameters. Along the building direction, a strong <100>//vertical direction (VD) texture was formed for all the samples. Because of the difference in transformation temperature, when tested at 15 °C, the sample with the 45° orientation possessed the highest strain recovery of 3.2%. When tested at the austenite phase transformation finish temperature (Af)+10 °C, the 90° sample had the highest strain recovery of 5.83% and a strain recovery rate of 83.3%. The sample with the 90° orientation presented the highest microhardness, which was attributed to its high dislocation density. Meanwhile, different building directions had an effect on the contents of O, C, and N impurity elements, which affected the transformation temperature by changing the Ni/Ti ratio. This study innovatively studied the impurity element content and GND densities of compressive samples with three building directions, providing theoretical guidance for LPBFed NiTi SMA structural parts.

Genetic structure of the Han Chinese population revealed by genome-wide SNP variation.

Population stratification is a potential problem for genome-wide association studies (GWAS), confounding results and causing spurious associations. Hence, understanding how allele frequencies vary across geographic regions or among subpopulations is an important prelude to analyzing GWAS data. Using over 350,000 genome-wide autosomal SNPs in over 6000 Han Chinese samples from ten provinces of China, our study revealed a one-dimensional "north-south" population structure and a close correlation between geography and the genetic structure of the Han Chinese. The north-south population structure is consistent with the historical migration pattern of the Han Chinese population. Metropolitan cities in China were, however, more diffused "outliers," probably because of the impact of modern migration of peoples. At a very local scale within the Guangdong province, we observed evidence of population structure among dialect groups, probably on account of endogamy within these dialects. Via simulation, we show that empirical levels of population structure observed across modern China can cause spurious associations in GWAS if not properly handled. In the Han Chinese, geographic matching is a good proxy for genetic matching, particularly in validation and candidate-gene studies in which population stratification cannot be directly accessed and accounted for because of the lack of genome-wide data, with the exception of the metropolitan cities, where geographical location is no longer a good indicator of ancestral origin. Our findings are important for designing GWAS in the Chinese population, an activity that is expected to intensify greatly in the near future.

Singapore Genome Variation Project: a haplotype map of three Southeast Asian populations.

The Singapore Genome Variation Project (SGVP) provides a publicly available resource of 1.6 million single nucleotide polymorphisms (SNPs) genotyped in 268 individuals from the Chinese, Malay, and Indian population groups in Southeast Asia. This online database catalogs information and summaries on genotype and phased haplotype data, including allele frequencies, assessment of linkage disequilibrium (LD), and recombination rates in a format similar to the International HapMap Project. Here, we introduce this resource and describe the analysis of human genomic variation upon agglomerating data from the HapMap and the Human Genome Diversity Project, providing useful insights into the population structure of the three major population groups in Asia. In addition, this resource also surveyed across the genome for variation in regional patterns of LD between the HapMap and SGVP populations, and for signatures of positive natural selection using two well-established metrics: iHS and XP-EHH. The raw and processed genetic data, together with all population genetic summaries, are publicly available for download and browsing through a web browser modeled with the Generic Genome Browser.