Variation and evolution analysis of SARS-CoV-2 using self-game sequence optimization.

Introduction: The evolution of SARS-CoV-2 has precipitated the emergence of new mutant strains, some exhibiting enhanced transmissibility and immune evasion capabilities, thus escalating the infection risk and diminishing vaccine efficacy. Given the continuous impact of SARS-CoV-2 mutations on global public health, the economy, and society, a profound comprehension of potential variations is crucial to effectively mitigate the impact of viral evolution. Yet, this task still faces considerable challenges.

Characterization of chicken gene: mRNA expression and response to reproductive hormone treatment in ovarian granulosa cells, and single nucleotide polymorphisms associated with egg laying traits in hens.

As a protein structurally similar to insulin, relaxin3 (RLN3) plays a role in promoting arousal, suppressing depressive or anxious behaviors. Two studies revealed the increase of RLN3 expression during chicken follicle selection. In this study, by real-time quantitative PCR and luciferase assay, mRNA expression and single nucleotide polymorphisms (SNPs) of chicken were investigated.

TMT-labeled quantitative malonylome analysis on the longissimus dorsi muscle of Laiwu pigs reveals the role of ACOT7 in fat deposition.

The Laiwu pig is an indigenous fatty pig breed distributed in North China, characterized by an extremely high level of intramuscular fat (IMF) content (9% ∼ 12%), but the regulatory mechanism underlying intramuscular fat deposition in skeletal muscle is still unknown. In this study, the TMT-labeled quantitative malonylome of the longissimus dorsi muscle in Laiwu pigs at the fastest IMF deposition stage (240 d vs 120 d) was compared to analyze the molecular mechanism of IMF variation in pigs. In Laiwu pigs aged 240 days/120 days, we identified 291 malonylated lysine sites across 188 proteins in the longissimus dorsi muscle.

ActionCLIP: Adapting Language-Image Pretrained Models for Video Action Recognition.

The canonical approach to video action recognition dictates a neural network model to do a classic and standard 1-of-N majority vote task. They are trained to predict a fixed set of predefined categories, limiting their transferability on new datasets with unseen concepts. In this article, we provide a new perspective on action recognition by attaching importance to the semantic information of label texts rather than simply mapping them into numbers.

Expression and regulation of Noggin4 gene in chicken ovarian follicles and its role in the proliferation and differentiation of granulosa cells.

As a member of Noggin family, Noggin4 is reported to play an important role in the formation of head structure during the embryo development of Xenopus laevis and chicken. We previously detected an increase of Noggin4 transcript in the granulosa cells of chicken hierarchal follicles (Post-GCs) compared to pre-hierarchal follicles (Pre-GCs) by ONT transcriptome sequencing. To further clarify the role of Noggin4 in chicken follicle selection, in this study, we investigated its expression, regulation and function in follicles and granulosa cells.

Long-read sequencing reveals the effect of follicle-stimulating hormone on the mRNA profile of chicken granulosa cells from prehierarchical follicles.

Follicle selection is an important step in the laying process of chicken, which is closely related to the laying performance and fecundity of hens. Follicle selection mainly depends on the regulation of follicle-stimulating hormone (FSH) secreted by pituitary gland and the expression of follicle stimulation hormone receptor. To uncover the role of FSH in chicken follicle selection, in this study, we analyzed the changes in the mRNA transcriptome profiles of FSH-treated chicken granulosa cells from prehierarchical follicles by long-read sequencing Oxford Nanopore Technologies (ONT) approach.

Identification of genes involved in chicken follicle selection by ONT sequencing on granulosa cells.

In chickens, follicle selection is an important process affecting laying traits, which is characterized by the differentiation of granulosa cells and the synthesis of progesterone by granulosa cells from hierarchical follicles. By using Oxford Nanopore Technologies (ONT) approach, we compared the transcriptomes of granulosa cells between pre-hierarchical (Pre-GCs) and hierarchical follicles (Post-GCs) to identify genes underlying chicken follicle selection. A total of 2,436 differentially expressed genes (DEGs), 3,852 differentially expressed transcripts (DETs) and 925 differentially expressed lncRNA transcripts were identified between chicken Pre-GCs and Post-GCs.

AFTGAN: prediction of multi-type PPI based on attention free transformer and graph attention network.

Motivation: Protein-protein interaction (PPI) networks and transcriptional regulatory networks are critical in regulating cells and their signaling. A thorough understanding of PPIs can provide more insights into cellular physiology at normal and disease states. Although numerous methods have been proposed to predict PPIs, it is still challenging for interaction prediction between unknown proteins.

Comparative Transcriptomic Analysis of mRNAs, miRNAs and lncRNAs in the Muscles between Fat-Type and Lean-Type Pigs.

In pigs, meat quality and production are two important traits affecting the pig industry and human health. Compared to lean-type pigs, fat-type pigs contain higher intramuscular fat (IMF) contents, better taste and nutritional value. To uncover genetic factors controlling differences related to IMF in pig muscle, we performed RNA-seq analysis on the transcriptomes of the Longissimus dorsi (LD) muscle of Laiwu pigs (LW, fat-type pigs) and commercial Duroc × Landrace × Yorkshire pigs (DLY, lean-type pigs) at 150 d to compare the expression profiles of mRNA, miRNA and lncRNA.

Identification of nucleotide polymorphisms in the key promoter region of chicken annexins A2 gene associatied with egg laying traits.

Annexin A2 () is a member of the A subfamily of a multifunctional calcium dependent membrane phospholipid binding protein family. The mRNA expression of is consistent with ovary function and egg laying in chickens. In this study, six nucleotide polymorphisms in the key promoter region of chicken gene (-2861bp to -1394bp), i.

Hesitant fuzzy multi-attribute decision making based on binary connection number of set pair analysis.

To objectively evaluate the influence of hesitant fuzziness on the ranking of alternatives in multi-attribute decision making with hesitant fuzzy or probabilistic hesitant fuzzy information, the binary connection number of set pair analysis is applied to hesitant fuzzy multi-attribute decision making. The hesitant or probabilistic hesitant fuzzy set is transformed to the binary connection number. A hesitant fuzzy multi-attribute decision making model based on binary connection number is then established.