iAVPs-ResBi: Identifying antiviral peptides by using deep residual network and bidirectional gated recurrent unit

Human history is also the history of the fight against viral diseases. From the eradication of viruses to coexistence, advances in biomedicine have led to a more objective understanding of viruses and a corresponding increase in the tools and methods to combat them. More recently, antiviral peptides (AVPs) have been discovered, which due to their superior advantages, have achieved great impact as antiviral drugs. Therefore, it is very necessary to develop a prediction model to accurately identify AVPs. In this paper, we develop the iAVPs-ResBi model using k-spaced amino acid pairs (KSAAP), encoding based on grouped weight (EBGW), enhanced grouped amino acid composition (EGAAC) based on the N5C5 sequence, composition, transition and distribution (CTD) based on physicochemical properties for multi-feature extraction. Then we adopt bidirectional long short-term memory (BiLSTM) to fuse features for obtaining the most differentiated information from multiple original feature sets. Finally, the deep model is built by combining improved residual network and bidirectional gated recurrent unit (BiGRU) to perform classification. The results obtained are better than those of the existing methods, and the accuracies are 95.07, 98.07, 94.29 and 97.50% on the four datasets, which show that iAVPs-ResBi can be used as an effective tool for the identification of antiviral peptides. The datasets and codes are freely available at https://github.com/yunyunliang88/iAVPs-ResBi

Povezanost polimorfizma pojedinačnog nukleotida gena ARID4A i kvalitete sperme kineskog vodenog bivola

ARID4A (AT-rich interaction domain 4A) is closely related to animal sperm quality traits. In the present study, the association between ARID4A gene polymorphisms of Chinese water buffalo (Bubalus bubalis) with sperm quality traits was examined, including ejaculate volume, sperm concentration, post-thaw sperm motility, and sperm abnormality of buffalo semen. Seven single-nucleotide polymorphisms (SNPs) of ARID4A gene were detected in 156 Chinese water buffaloes by Sanger sequencing and identifying overlap peaks. Among the SNPs, six were associated with at least one sperm quality trait. In brief, g.21192G>C, g.21285C>G, and g.21364A>G could be used as potential markers for selecting semen with low sperm abnormality, high ejaculate volume, sperm concentration, and sperm motility. Furthermore, 10 haplotypes (H1: -CTCGG, H2: GTGGCA, H3: GCGGCA, H4: GCTGCA, H5: GCTCGA, H6: GTGGGG, H7: GCTCCG, H8: -CGGGA, H9: GCGGCG, and H10: GTTGCA) were formed by the six SNPs through linkage disequilibrium analysis, and then 14 different combined haplotypes were collected. Correlation analysis showed that the combined H1H2 haplotype had the highest genotype frequency. Notably, the combined H1H2 haplotype had low sperm concentration, low sperm motility, and high sperm abnormality. The combined H2H3 haplotype could be used as a potential molecular marker for selecting semen with high sperm motility. In general, we illustrated a significant correlation between SNPs in ARID4A and sperm quality traits of Chinese water buffalo, which may be useful in the marker-assisted selection of buffalo breeding. This study was the first to analyze the genetic polymorphisms of ARID4A and association with sperm qualities of Chinese buffalo.Gen ARID4A (engl AT-rich interaction domain 4A) usko je povezan s kvalitetom sperme. U ovom je radu istraživana povezanost polimorfizma gena ARID4A u kineskih vodenih bivola (Bubalus bubalis) s kvalitetom sperme, uključujući volumen ejakulata, koncentraciju sperme, pokretljivost spermija nakon odmrzavanja i abnormalnost spermija u sjemenu bivola. U 156 kineskih vodenih bivola otkriveno je sedam polimorfizama pojedinačnog nukleotida (SNPs) gena ARID4A Sangerovim sekvenciranjem i identifikacijom preklopljenih vrhova. Među SNP-ovima njih je šest bilo povezano s barem jednim svojstvom kvalitete spermija. Ukratko, g. 21192G>C, g. 21285C>G i g. 21364A>G mogu se upotrijebiti kao potencijalni markeri za selekciju sjemena s niskom abnormalnošću spermija, većim volumenom ejakulata, većom koncentracijom i pokretljivošću spermija. Nadalje, šest SNP-ova formiralo je 10 haplotipova (H1: -CTCGG, H2: GTGGCA, H3: GCGGCA, H4: GCTGCA, H5: GCTCGA, H6: GTGGGG, H7: GCTCCG, H8: -CGGGA, H9: GCGGCG i H10: GTTGCA) analizom povezanosti nepodudarnosti te je ustanovljeno 14 različitih kombiniranih haplotipova. Analiza korelacije pokazala je da kombinirani haplotip H1H2 ima najveću učestalost. Kombinirani haplotip H1H2 imao je najmanju koncentraciju sperme, slabu pokretljivost seprmija i znatnu abnormalnost spermija. Kombinirani haplotip H2H3 može se upotrijebiti kao potencijalni molekularni marker za odabir sjemena s većom pokretljivošću. Općenito je pokazana znakovita korelacija između SNP-ova u ARID4A i kvalitete sperme kineskog vodenog bivola, što može biti korisno u selekciji bivola potpomognutoj markerima. Ovo je prvo istraživanje koje je analiziralo genske polimorfizme ARID4A i njihovu povezanost s kvalitetom sjemena kineskih vodenih bivola

Progress on Research and Application of Postbiotics

Postbiotics are a preparation of inanimate microorganisms and/or their components are beneficial to the health of the host, with multiple advantages such as safety, stability, easy storage and production, and clear chemical structure. This article reviews the major bioactive ingredients, probiotic functions and current application status of postbiotics; elaborates the health benefits of inactivated bacterial cells, bacterial components and bacterial metabolites to the host; summarizes recent progress in understanding the health benefits of postbiotics such as enhancing immunity, regulating gastrointestinal function, alleviating obesity, maintaining oral health, and preventing osteoporosis; outlines commercially available postbiotic products in Japan, the United States, Germany and China; and proposes the challenges and new research directions of postbiotics

KIF2A silencing inhibits the proliferation and migration of breast cancer cells and correlates with unfavorable prognosis in breast cancer

Background; Kinesin family member 2a (KIF2A), a type of motor protein found in eukaryotic cells, is associated with development and progression of various human cancers. The role of KIF2A during breast cancer tumorigenesis and progression was studied. Methods; Immunohistochemical staining, real time RT-PCR and western blot were used to examine the expression of KIF2A in cancer tissues and adjacent normal tissues from breast cancer patients. Patients’ survival in relation to KIF2A expression was estimated using the Kaplan–Meier survival and multivariate analysis. Breast cancer cell line, MDA-MB-231 was used to study the proliferation, migration and invasion of cells following KIF2A-siRNA transfection. Results; The expression of KIF2A in cancer tissues was higher than that in normal adjacent tissues from the same patient (P < 0.05). KIF2A expression in cancer tissue with lymph node metastasis and HER2 positive cancer were higher than that in cancer tissue without (P < 0.05). A negative correlation was found between KIF2A expression levels in breast cancer and the survival time of breast cancer patients (P < 0.05). In addition, multivariate analysis indicated that KIF2A was an independent prognostic for outcome in breast cancer (OR: 16.55, 95% CI: 2.216-123.631, P = 0.006). The proliferation, migration and invasion of cancer cells in vitro were suppressed by KIF2A gene silencing (P < 0.05). Conclusions; KIF2A may play an important role in breast cancer progression and is potentially a novel predictive and prognostic marker for breast cancer

Amine-responsive bilayer films with improved illumination stability and electrochemical writing property for visual monitoring of meat spoilage

Amine-responsive bilayer films were developed by using agar (AG), anthocyanins (AN), gellan gum (GG) and TiO2 nanoparticles for visual monitoring of meat spoilage. The AG-AN layer worked as the sensing layer to volatile amines, while GG-TiO2 layer served as the light barrier layer and simultaneously the conducting layer to improve the illumination stability and electrochemical writing ability of the AG-AN layer, respectively. The Scanning electron microscopy (SEM) images and X-ray diffraction (XRD) spectra indicated the successful fabrication of bilayer films. Illumination experiments showed that the incorporation of TiO2 in the GG-TiO2 layer significantly improved the illumination stability of AN in the AG-AN layer. Meanwhile, electrochemical writing process could be easily conducted on the AG-AN layer in the presence of GG-TiO2 layer, indicating the feasibility of ink-free printing on bilayer biopolymer films. The AG-AN/GG-2%TiO2 film presented a limit of detection of 0.018 mM to trimethylamine (TMA), a typical basic gas generated during meat spoilage. Based on its good illumination stability and sensing ability to basic gases, the AG-AN/GG-2%TiO2 film exhibited rose red-to-green color changes along with the spoilage of pork and silver carp, indicating its great potential for monitoring meat spoilage in intelligent food packaging