Phylogenetic Evolution and Phylogeography of Tibetan Sheep Based on mtDNA D-Loop Sequences

The molecular and population genetic evidence of the phylogenetic status of the Tibetan sheep (Ovis aries) is not well understood, and little is known about this species’ genetic diversity. Phylogenetic relationship and phylogeography of 636 individual Tibetan sheep which were collected from the Qinghai-Tibetan Plateau area in China and were assessed using 642 complete sequences of the mitochondrial DNA D-loop. Reference data were obtained from the six reference breed sequences available in GenBank. Phylogeography analysis showed that all four previously defined haplogroups were found in the 15 Tibetan sheep populations but that only one haplogroup was found in Linzhou sheep. Furthermore, clustering analysis divided the 636 individual Tibetan sheep into at least two clusters. The estimated genetic distance and genetic differentiation associate with altitude, suggesting geographic and adaptive effects in Tibetan sheep. These results contribute to the knowledge of Tibetan sheep populations and will help inform future conservation programs about the Tibetan sheep native to the Qinghai-Tibetan Plateau in China

Proteomic Analysis of Bacillus thuringiensis Strain 4.0718 at Different Growth Phases

The growth process of Bacillus thuringiensis Bt4.0718 strain was studied using proteomic technologies. The proteins of Bt whole cells at three phases—middle vegetative, early sporulation, and late sporulation—were extracted with lysis buffer, followed with separation by 2-DE and identified by MALDI-TOF/TOF MS. Bioactive factors such as insecticidal crystal proteins (ICPs) including Cry1Ac(3), Cry2Aa, and BTRX28, immune inhibitor (InhA), and InhA precursor were identified. InhA started to express at the middle vegetative phase, suggesting its contribution to the survival of Bt in the host body. At the early sporulation phase, ICPs started their expression. CotJC, OppA, ORF1, and SpoIVA related to the formation of crystals and spores were identified, the expression characteristics of which ensured the stable formation of crystals and spores. This study provides an important foundation for further exploration of the stable expression of ICPs, the smooth formation of crystals, and the construction of recombinant strains

SCFM: Social and crowdsourcing factorization machines for recommendation

With the rapid development of social networks, the exponential growth of social information has attracted much attention. Social information has great value in recommender systems to alleviate the sparsity and cold start problem. On the other hand, the crowd computing empowers recommender systems by utilizing human wisdom. Internal user reviews can be exploited as the wisdom of the crowd to contribute information. In this paper, we propose social and crowdsourcing factorization machines, called SCFM. Our approach fuses social and crowd computing into the factorization machine model. For social computing, we calculate the influence value between users by taking users’ social information and user similarity into account. For crowd computing, we apply LDA (Latent Dirichlet Allocation) on people review to obtain sets of underlying topic probabilities. Furthermore, we impose two important constraints called social regularization and domain inner regularization. The experimental results show that our approach outperforms other state-of-the-art methods.This project is supported by the National Natural Science Foundation of China (Nos. 61672340, 61472240, 61572268)

A Wolf in Sheep's Clothing: Generalized Nested Jailbreak Prompts can Fool Large Language Models Easily

Large Language Models (LLMs), such as ChatGPT and GPT-4, are designed to provide useful and safe responses. However, adversarial prompts known as 'jailbreaks' can circumvent safeguards, leading LLMs to generate harmful content. Exploring jailbreak prompts can help to better reveal the weaknesses of LLMs and further steer us to secure them. Unfortunately, existing jailbreak methods either suffer from intricate manual design or require optimization on another white-box model, compromising generalization or jailbreak efficiency. In this paper, we generalize jailbreak prompt attacks into two aspects: (1) Prompt Rewriting and (2) Scenario Nesting. Based on this, we propose ReNeLLM, an automatic framework that leverages LLMs themselves to generate effective jailbreak prompts. Extensive experiments demonstrate that ReNeLLM significantly improves the attack success rate while greatly reducing the time cost compared to existing baselines. Our study also reveals the inadequacy of current defense methods in safeguarding LLMs. Finally, we offer detailed analysis and discussion from the perspective of prompt execution priority on the failure of LLMs' defense. We hope that our research can catalyze both the academic community and LLMs vendors towards the provision of safer and more regulated Large Language Models

Comparative Proteomic Analysis of saccharopolyspora spinosa SP06081 and PR2 strains reveals the differentially expressed proteins correlated with the increase of spinosad yield

<p>Abstract</p> <p>Background</p> <p><it>Saccharopolyspora spinosa </it>produces the environment-friendly biopesticide spinosad, a mixture of two polyketide-derived macrolide active ingredients called spinosyns A and D. Therefore considerable interest is in the improvement of spinosad production because of its low yield in wild-type <it>S. spinosa</it>. Recently, a spinosad-hyperproducing PR2 strain with stable heredity was obtained from protoplast regeneration of the wild-type <it>S. spinosa </it>SP06081 strain. A comparative proteomic analysis was performed on the two strains during the first rapid growth phase (RG1) in seed medium (SM) by using label-free quantitative proteomics to investigate the underlying mechanism leading to the enhancement of spinosad yield.</p> <p>Results</p> <p>In total, 224 proteins from the SP06081 strain and 204 proteins from the PR2 strain were unambiguously identified by liquid chromatography-tandem mass spectrometry analysis, sharing 140 proteins. A total of 12 proteins directly related to spinosad biosynthesis were identified from the two strains in RG1. Comparative analysis of the shared proteins revealed that approximately 31% of them changed their abundance significantly and fell in all of the functional groups, such as tricarboxylic acid cycles, glycolysis, biosynthetic processes, catabolic processes, transcription, translation, oxidation and reduction. Several key enzymes involved in the synthesis of primary metabolic intermediates used as precursors for spinosad production, energy supply, polyketide chain assembly, deoxysugar methylation, and antioxidative stress were differentially expressed in the same pattern of facilitating spinosad production by the PR2 strain. Real-time reverse transcriptase polymerase chain reaction analysis revealed that four of five selected genes showed a positive correlation between changes at the translational and transcriptional expression level, which further confirmed the proteomic analysis.</p> <p>Conclusions</p> <p>The present study is the first comprehensive and comparative proteome analysis of <it>S. spinosa </it>strains. Our results highlight the differentially expressed proteins between the two <it>S. spinosa </it>strains and provide some clues to understand the molecular and metabolic mechanisms that could lead to the increased spinosad production yield.</p

Maternal Fecal Microbes Contribute to Shaping the Early Life Assembly of the Intestinal Microbiota of Co-inhabiting Yak and Cattle Calves

The Qinghai-Tibetan Plateau offers one of the most extreme environments for yaks (Bos grunniens). Although the genetic adaptability of yak and rumen metagenomes is increasingly understood, the relative contribution of host genetics and maternal symbiotic microbes throughout early intestinal microbial successions in yaks remains elusive. In this study, we assessed the intestinal microbiota succession of co-inhabiting yak and cattle (Bos taurus) calves at different weeks after birth as well as the modes of transmission of maternal symbiotic microbes (i.e., rumen fluid, feces, oral cavity, and breast skin) to their calves’ intestinal microbiota colonization. We found that the fecal microbiota of yak and cattle calves after birth was dominated by members of the familiesRuminococcaceae, Bacteroidaceae, and Lachnospiraceae. The Source Tracker model revealed that maternal fecal microbes played an important role (the average contribution was about 80%) in the intestinal microbial colonization of yak and cattle calves at different weeks after birth. Unlike cattle calves, there was no significant difference in the fecal microbiota composition of yak calves between 5 and 9 weeks after birth (Wilcoxon test, P &gt; 0.05), indicating that yak may adapt to its natural extreme environment to stabilize its intestinal microbiota composition. Additionally, our results also find that theintestinal microbial composition of yak and cattle calves, with age, gradually tend to become similar, and the differences between species gradually decrease. The findings of this study are vital for developing strategies to manipulate the intestinal microbiota in grazing yaks and cattle for better growth and performance on the Qinghai-Tibetan Plateau

Lactobacillus rhamnosus CY12 Enhances Intestinal Barrier Function by Regulating Tight Junction Protein Expression, Oxidative Stress, and Inflammation Response in Lipopolysaccharide-Induced Caco-2 Cells

he intestinal barrier is vital for preventing inflammatory bowel disease (IBD). The objectives of this study were to assess whether the Lactobacillus rhamnosus CY12 could alleviate oxidative stress, inflammation, and the disruption of tight junction (TJ) barrier functions induced by lipopolysaccharide (LPS), and therefore to explore the potential underlying molecular mechanisms. Our results showed that LPS-induced Cancer coli-2 (Caco-2) cells significantly increased the levels of reactive oxygen species (ROS), lactate dehydrogenase, inflammatory cytokines interleukin-1β, interleukin-6, interleukin-8, and tumor necrosis factor-α (IL-1β, IL-6, IL-8, and TNF-α), and the cell apoptosis rate while decreasing the levels of TJ proteins occludin, zonula occludens-1 (ZO-1), and claudin and antioxidant enzymes, such as catalase, superoxide dismutase, and glutathione peroxidase(CAT, SOD, and GSH-Px) (p &lt; 0.05). However, Lactobacillus rhamnosus CY12 could relieve cytotoxicity, apoptosis, oxidative stress, and pro-inflammatory cytokine expressions, and also inhibit the Toll-like receptor 4/nuclear factor kappa-B(TLR4/NF-κB) signaling pathway. Furthermore, the gene expression of antioxidant enzymes, as well as the mRNA and protein expressions of TJ proteins, was improved. Particularly, the concentration of 108 cfu/mL significantly prevented the inflammatory injury induced by LPS in Caco-2 cells (p &lt; 0.05). These findings support a potential application of Lactobacillus rhamnosus CY12 as a probiotic to prevent LPS-induced intestinal injury and treat intestinal barrier dysfunction

Fast dynamic color switching in temperature-responsive plasmonic films

This research was supported by UK Engineering and Physical Sciences Research Council grants EP/G060649/1 and EP/L027151/1 , and ERC grant LINASS 320503 . F.B. thanks the supports from the Winton Programme for the Physics of Sustainability.Publisher PDFPeer reviewe

Fecal Microbiota Dynamics Reveal the Feasibility of Early Weaning of Yak Calves under Conventional Grazing System

Background: The gut microbiota plays an important role in the health and production of animals. However, little information is available on the dynamic variations and comparison of intestinal microbiota in post-weaning yak calves living on the QTP. Methods: We explored the fecal bacterial microbiota succession of yak calves at different months after early weaning (60 d) compared with cattle calves by 16S rRNA gene amplicon sequencing and functional composition prediction. Results: We found no significant difference in blood biochemical parameters related to glucose and lipid metabolism between yaks and calves in different months after weaning. The core fecal bacterial microbiota from both species of calves was dominated by Ruminococcaceae, Rikenellaceae, and Bacteroidaceae. The fecal microbial community has a great alteration within the time after weaning in both cattle and yak calves, but cattle showed a larger change. After five months, the microbiota achieves a stable and concentrated state. This is also similar to the functional profile. Conclusions: Based on the exploration of dynamic changes in the fecal microbiota at an early stage of life, our results illustrated that there were no negative effects of intestinal microbiota succession on yak calves when early weaning was employed

Age-dependent variations in rumen bacterial community of Mongolian cattle from weaning to adulthood

BackgroundRumen microbes play an important role in ruminant energy supply and animal performance. Previous studies showed that the rumen microbiome of Mongolian cattle has adapted to degrade the rough forage to provide sufficient energy to tolerate the harsh desert ecological conditions. However, little is known about the succession of rumen microbes in different developmental stages of post-weaning Mongolian cattle.MethodsHere, we examined the succession of the rumen microbial composition and structure of 15 post-weaning Mongolian cattle at three developmental stages i.e., 5 months (RM05), 18 months (RM18) and, 36 months (RM36) by using the 16S rRNA gene sequencing method.ResultsWe did not find any age-dependent variations in the ruminal concentrations of any volatile fatty acid (VFA) of Mongolian cattle. The diversity of the rumen bacterial community was significantly lower in RM05 group, which reached to stability with age. Bacteroidetes and Firmicutes were the two dominant phyla among all age groups. Phylum Actinobacteria was significantly higher in RM05 group, phyla Spirochaetes, and Tenericutes were highly abundant in RM18 group, and phyla Proteobacteria and Epsilonbacteraeota were enriched in RM36 group. Genera Prevotella_1, Bacteroides, and Bifidobacterium were abundant in RM05 group. The short chain fatty acid (SCFA) producing bacteria Rikenellaceae_RC9_gut_group showed high abundance in RM18 group and fiber degrading genus Alloprevotella was highly abundant in RM36 group. Random forest analysis identified Alloprevotella, Ileibacterium, and Helicobacter as important age discriminatory genera. In particular, the genera Ruminococcaceae_UCG-005, Bacteroides, Saccharofermentans, and Fibrobacter in RM05, genera [Eubacterium] coprostanoligenes_group, Erysipelotrichaceae_UCG-004, Helicobacter, Saccharofermentans, Papillibacter, and Turicibacter in RM18, and genera Rikenellaceae_RC9_gut_group, Lachnospiraceae_AC2044_group, and Papillibacter in RM36 showed the top interactions values in the intra-group interaction network.ConclusionsThe results showed that rumen microbiota of Mongolian cattle reached to stability and maturity with age after weaning. This study provides some theoretical evidence about the importance of functional specific rumen bacteria in different age groups. Further studies are needed to determine their actual roles and interactions with the hos