PIGOME: An Integrated and Comprehensive Multi-omics Database for Pig Functional Genomics Studies.

In addition to being a major source of animal protein, pigs are an important model for the study of development and diseases in humans. During the past two decades, thousands of high-throughput sequencing studies in pigs have been performed using a variety of tissues from different breeds and developmental stages. However, the multi-omics database specifically used for pig functional genomic research is still limited.

The effect of hypersensitive C-reactive protein to albumin ratio on the risk of fragility fracture in the Chinese male population.

Unlabelled: This study explored the association between the hypersensitive C-reactive protein to albumin ratio (CAR) and fragility fractures in Chinese males. Results show that elevated levels of CAR were associated with an increased risk of fragility fractures and that this association was robust to adjustment for multiple potential confounders.

Purpose: This study investigates the relationship between the hypersensitive C-reactive protein to albumin ratio (CAR) and fragility fractures in a Chinese male population.

The cumulative exposure to triglyceride-glucose index and the risk of onset fragility fractures.

Objective: To investigate the association between the cumulative exposure to triglyceride-glucose index (cumTyG index) and fragility fractures in the general population.

Methods: This prospective cohort study analyzed active and retired employees of Kailuan Group who participated in three consecutive health examinations in 2006, 2008 and 2010, and were followed up until 31st December 2022. The cohort comprised 55,824 participants who met the inclusion and exclusion criteria and were grouped using the cumTyG index quartiles.

Serendipitous Discovery of Dearomatized Dimers in Anthracene Derivative Oxidation.

We present the serendipitous discovery of an unusual dimer formed from anthracene-derived polyarenes. Unlike the typical oxidative coupling of substituted aromatic scaffolds, the reaction yielded a dearomatized enone dimer as the sole product. This dearomatized motif, notably, does not undergo the commonly observed rearomatization, and no biaryl products were detected.

Quantifying information stored in synaptic connections rather than in firing patterns of neural networks.

A cornerstone of our understanding of both biological and artificial neural networks is that they store information in the strengths of connections among the constituent neurons. However, in contrast to the well-established theory for quantifying information encoded by the firing patterns of neural networks, little is known about quantifying information encoded by its synaptic connections. Here, we develop a theoretical framework using continuous Hopfield networks as an exemplar for associative neural networks, and data that follow mixtures of broadly applicable multivariate log-normal distributions.

Quantifying information stored in synaptic connections rather than in firing patterns of neural networks.

A cornerstone of our understanding of both biological and artificial neural networks is that they store information in the strengths of connections among the constituent neurons. However, in contrast to the well-established theory for quantifying information encoded by the firing patterns of neural networks, little is known about quantifying information encoded by its synaptic connections. Here, we develop a theoretical framework using continuous Hopfield networks as an exemplar for associative neural networks, and data that follow mixtures of broadly applicable multivariate log-normal distributions.

The miR-6240 target gene Igf2bp3 promotes myoblast fusion by enhancing myomaker mRNA stability.

Background: Myoblast fusion plays a crucial role in myogenesis. Insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) functions as an RNA N-methyladenosine reader and exerts important roles in various biological processes. While our prior study suggested Igf2bp3 contributes to myogenesis, its molecular regulatory mechanism is largely unclear.

Suppressing IGF2R mitigates hypoxia-induced apoptosis by reducing the expression of pro-apoptotic factor BAX.

Oxidative stress caused by hypoxia can lead to serious bodily damage and functional degradation. Our previous study in pigs showed that the insulin-like growth factor II receptor (IGF2R) gene might participate in the process of hypoxia adaptability. To investigate the function and mechanism of IGF2R in cellular hypoxia tolerance, we analyze the effect of IGF2R on cell survival capacity under hypoxia conditions in intestinal porcine enterocyte cell line (IPEC-J2) cells.

The Spatial-Temporal Alternative Splicing Profile Reveals the Functional Diversity of FXR1 Isoforms in Myogenesis.

Alternative splicing (AS) is a fundamental mechanism contributing to proteome diversity, yet its comprehensive landscape and regulatory dynamics during skeletal muscle development remain largely unexplored. Here, the temporal AS profiles are investigated during myogenesis in five vertebrates, conducting comprehensive profiling across 27 developmental stages in skeletal muscle and encompassing ten tissues in adult pigs. The analysis reveals a pervasive and evolutionarily conserved pattern of alternative exon usage throughout myogenic differentiation, with hundreds of skipped exons (SEs) showing developmental regulation, particularly within skeletal muscle.

A comprehensive atlas of pig RNA editome across 23 tissues reveals RNA editing affecting interaction mRNA-miRNAs.

RNA editing is a co-transcriptional/post-transcriptional modification that is mediated by the ADAR enzyme family. Profiling of RNA editing is very limited in pigs. In this study, we collated 3813 RNA-seq data from the public repositories across 23 tissues and carried out comprehensive profiling of RNA editing in pigs.

Production of constrained L-cyclo-tetrapeptides by epimerization-resistant direct aminolysis.

The synthesis of constrained 12-membered rings is notably difficult. The main challenges result from constraints during the linear peptide cyclization. Attempts to overcome constraints through excessive activation frequently cause peptidyl epimerization, while insufficient activation of the C-terminus hampers cyclization and promotes intermolecular oligomer formation.

Polypeptide Preparation by β-Lactone-Mediated Chemical Ligation.

Native chemical ligation (NCL) represents a cornerstone strategy in accessing synthetic peptides and proteins, remaining one of the most efficacious methodologies in this domain. The fundamental requisites for achieving a proficient NCL reaction involve chemoselective coupling between a C-terminal thioester peptide and a thiol-bearing N-terminal peptide. However, achieving coupling at sterically congested residues remains challenging.

Haplotype-resolved assembly of a pig genome using single-sperm sequencing.

Single gamete cell sequencing together with long-read sequencing can reliably produce chromosome-level phased genomes. In this study, we employed PacBio HiFi and Hi-C sequencing on a male Landrace pig, coupled with single-sperm sequencing of its 102 sperm cells. A haplotype assembly method was developed based on long-read sequencing and sperm-phased markers.

CRISPR Screen Identifies the RNA-Binding Protein Eef1a1 as a Key Regulator of Myogenesis.

Skeletal muscle myogenesis hinges on gene regulation, meticulously orchestrated by molecular mechanisms. While the roles of transcription factors and non-coding RNAs in myogenesis are widely known, the contribution of RNA-binding proteins (RBPs) has remained unclear until now. Therefore, to investigate the functions of post-transcriptional regulators in myogenesis and uncover new functional RBPs regulating myogenesis, we employed CRISPR high-throughput RBP-KO (RBP-wide knockout) library screening.

Wnt5a deficiency in osteocalcin-expressing cells could not alleviate the osteoarthritic phenotype in a mouse model of post-traumatic osteoarthritis.

Objectives: Wnt5a, which regulates the activities of osteoblasts and osteoclasts, is reportedly overexpressed in osteoarthritis (OA) tissues. The purpose of this study was to elucidate its role in the development of OA by deleting Wnt5a in osteocalcin (OCN)-expressing cells.

Materials And Methods: Knee OA was induced by anterior cruciate ligament transection (ACLT) in knockout (Wnt5a-cKO) mice and control littermates.

Circular RNA transcriptome across multiple tissues reveal skeletal muscle-specific circPSME4 regulating myogenesis.

There are significant differences in meat production, growth rate and other traits between Western commercial pigs and Chinese local pigs. Comparative transcriptome approaches have identified many coding and non-coding candidate genes associated various traits. However, the expression and function of circular RNAs (circRNAs) in different pig tissues are largely unknown.

Rapid and Direct Assessment of Asphalt Volatile Organic Compound Emission Based on Carbon Fiber Ionization Mass Spectrometry.

Due to the complicacy of asphalt fumes, the analytical methods for investigating volatile organic compounds (VOCs) are very limited. In this study, a direct and real-time analysis method based on carbon fiber ionization mass spectrometry (CFI-MS), an ambient mass spectrometric technique, was established and successfully applied in the analysis of asphalt VOCs. The asphalt VOCs can be directly detected in the open atmosphere without the collection step of asphalt fumes, and the mass spectra of one asphalt sample can be obtained in a few seconds in both positive and negative ion modes.

Dielectric Metalens for Superoscillatory Focusing Based on High-Order Angular Bessel Function.

The phenomenon of optical superoscillation provides an unprecedented way to solve the problem of optical far-field label-free super-resolution imaging. Numerous optical devices that enable superoscillatory focusing were developed based on scalar and vector diffraction theories in the past several years. However, these reported devices are designed according to the half-wave zone method in spatial coordinates.

Integration of multi-omics data reveals cis-regulatory variants that are associated with phenotypic differentiation of eastern from western pigs.

Background: The genetic mechanisms that underlie phenotypic differentiation in breeding animals have important implications in evolutionary biology and agriculture. However, the contribution of cis-regulatory variants to pig phenotypes is poorly understood. Therefore, our aim was to elucidate the molecular mechanisms by which non-coding variants cause phenotypic differences in pigs by combining evolutionary biology analyses and functional genomics.

circRNAome profiling reveals circFgfr2 regulates myogenesis and muscle regeneration via a feedback loop.

Background: Circular RNAs (circRNAs) represent a novel class of non-coding RNAs formed by a covalently closed loop and play crucial roles in many biological processes. Several circRNAs associated with myogenesis have been reported. However, the dynamic expression, function, and mechanism of circRNAs during myogenesis and skeletal muscle development are largely unknown.

The genome variation and developmental transcriptome maps reveal genetic differentiation of skeletal muscle in pigs.

Natural and artificial directional selections have resulted in significantly genetic and phenotypic differences across breeds in domestic animals. However, the molecular regulation of skeletal muscle diversity remains largely unknown. Here, we conducted transcriptome profiling of skeletal muscle across 27 time points, and performed whole-genome re-sequencing in Landrace (lean-type) and Tongcheng (obese-type) pigs.

Influence of an L-type SALMFamide neuropeptide on locomotory performance and muscle physiology in the sea cucumber Apostichopus japonicus.

Neuropeptides in the SALMFamide family serve as muscle relaxants in echinoderms and may affect locomotion, as the motor behavior in sea cucumbers involves alternating contraction and extension of the body wall, which is under the control of longitudinal muscle. We evaluated the effect of an L-type SALMFamide neuropeptide (LSA) on locomotory performance of Apostichopus japonicus. We also investigated the metabolites of longitudinal muscle tissue using ultra performance liquid chromatography and quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) to assess the potential physiological mechanisms underlying the effect of LSA.

Landscape of tissue-specific RNA Editome provides insight into co-regulated and altered gene expression in pigs ().

RNA editing generates genetic diversity in mammals by altering amino acid sequences, miRNA targeting site sequences, influencing the stability of targeted RNAs, and causing changes in gene expression. However, the extent to which RNA editing affect gene expression via modifying miRNA binding site remains unexplored. Here, we first profiled the dynamic A-to-I RNA editome across tissues of Duroc and Luchuan pigs.

-Mediated circRNA Regulates Myogenesis by Targeting Ribosomal Protein Rpl7.

Circular RNAs (circRNAs) represent a class of covalently closed single-stranded RNA molecules that are emerging as essential regulators of various biological processes. The circRNA originates from exon 2 of the gene in mice and was reported to be involved in acute promyelocytic leukemia and myocardial injury. However, the functions and mechanisms of in myogenesis are largely unknown.

Photoacoustic dual-scan mammoscope: results from 38 patients.

We have developed a photoacoustics-based imaging system, the dual-scan mammoscope (DSM), that combines optical contrasts with acoustic detection, to obtain the angiographic features in human breast. In this study, we investigated whether the system can differentiate malignant tumor and healthy breast. We have imaged 38 patients with various tumor types and compared results of tumor-bearing breast with healthy breast for each patient.