Reconstruction of Microbial Haplotypes by Integration of Statistical and Physical Linkage in Scaffolding

DNA sequencing technologies provide unprecedented opportunities to analyze within-host evolution of microorganism populations. Often, within-host populations are analyzed via pooled sequencing of the population, which contains multiple individuals or “haplotypes.” However, current next-generation sequencing instruments, in conjunction with single-molecule barcoded linked-reads, cannot distinguish long haplotypes directly. Computational reconstruction of haplotypes from pooled sequencing has been attempted in virology, bacterial genomics, metagenomics, and human genetics, using algorithms based on either cross-host genetic sharing or within-host genomic reads. Here, we describe PoolHapX, a flexible computational approach that integrates information from both genetic sharing and genomic sequencing. We demonstrated that PoolHapX outperforms state-of-the-art tools tailored to specific organismal systems, and is robust to within-host evolution. Importantly, together with barcoded linked-reads, PoolHapX can infer whole-chromosome-scale haplotypes from 50 pools each containing 12 different haplotypes. By analyzing real data, we uncovered dynamic variations in the evolutionary processes of within-patient HIV populations previously unobserved in single position-based analysis.     

Analysis of geographic centrality and genetic diversity in the declining grasshopper species Bryodemella tuberculata (Orthoptera: Oedipodinae)

Human-induced ecological and climatic changes have led to the decline and even local extinction of many formerly widely distributed temperate and cold-adapted species. Determining the exact causes of this decline remains difficult. Bryodemella tuberculata was a widely distributed orthopteran species before the mid-19th century. Since then, many European populations have suffered drastic declines and are now considered extinct or critically endangered. We used ecological niche modelling based on a large dataset of extant and extinct occurrence data to investigate whether poor climatic suitability in the periphery of its global range was a possible cause of the local extinction of the European populations of B. tuberculata. We also used population genetics based on the COI marker to estimate and compare the genetic diversity of extant populations. We found that Europe still provides highly suitable habitats close to the climatic optimum, contradicting the assumption of climate change as major driver of this decline. Instead, changes in land-cover and other anthropogenic modifications of the habitats at the local scale seem to be the major reasons for local extinctions. Genetic analysis suggests Central Asia as center of diversity with a stable population size, whereas the effective sizes of the remaining European populations are decreasing. We found European genetic lineages nested within Central Asian lineages, suggesting a Central Asian source distribution area. Our results suggest that the declining European populations represent relics of a formerly wider distribution, which was fragmented by changes in land-use. These relics are now threatened by limited connectivity and small effective population sizes. Specific conservation actions, such as the restoration of former or potential new habitats, and translocation of individuals from extant populations to these restored sites may help slow, stall, or even revert the extinction process.

     

The management effectiveness of protected areas in Kenya

Merely designating new and/or expanding existing protected areas (PAs) does not guarantee the protection of critical ecosystems and species. The management of PAs must be effective to sustain meaningful conservational outcomes. We inferred the management effectiveness of PAs in Kenya based on the representation of ranges and distribution of multiple diversity dimensions of terrestrial mammals and their association with governance and designation types. We hypothesized that different governance types underlie variable management efficacies, such that stricter-managed PAs have better habitats that attract more wildlife, translating to higher species diversity compared to less strictly-managed PAs, especially for focal species groups (large carnivores, large herbivores, and endangered species). The results showed nearly all terrestrial mammals in Kenya represented in at least one PA. However, the relative proportion of represented ranges were low, and analysis of spatial conservation prioritization showed significant expansion beyond current PAs needed to achieve a one third coverage of focal species’ ranges in a best-solution reserve system. Differences in PA governance and designation types were not systematically associated with diversity variances, and while there were more unique species in state-managed PAs than in privately-managed ones, averaged diversity coefficients were comparable between categories. Diversity variances explained by PA size and status year were low in a combined species pool but increased in focal species groups. These findings suggest that success in terrestrial mammal conservation in PAs in Kenya require clearly and formally streamlined definition, performance feedback, and collaboration terms between state-managed and privately-managed PAs.

     

Low NLRP3 expression predicts a better prognosis of colorectal cancer

Background: NOD-like receptor pyrin domain-3 (NLRP3) inflammasome activation is a double-edged sword in tumorigenesis. Whether NLRP3 is involved in the progression and prognosis of colorectal cancer (CRC) remains elucidated and is the focus of the present study.Methods: Immunohistochemistry (IHC) was applied on tissue microarray (TMA) to determine the expression of NLRP3 in CRC patients. All 100 patients were divided into the low NLRP3 group and the high NLRP3 group according to their NLRP3 IHC scoring. Additionally, CRC xenografts were established by injecting HCT116 or RKO cells subcutaneously into nude mice. Cell proliferation and apoptosis were determined in HCT116 cells after treatment with NLRP3 inhibitor MCC950.Results: NLRP3 expression was up-regulated in colon adenocarcinoma tissues compared with that in paracancerous tissues in CRC patients, HCT116 xenograft, and RKO xenograft. High NLRP3 level correlated with the advanced TNM classification of malignant tumors, the occurrence of distant metastasis, vascular invasion, and positive lymph nodes. Furthermore, Kaplan–Meier survival analysis revealed that a high NLRP3 level was associated with a low 5-year survival rate and even a low 10-year survival rate. Moreover, the multivariable Cox proportional hazards regression model implied that NLRP3 expression level was an independent risk factor for CRC prognosis. Inhibition of NLRP3 by MCC950 suppressed cell proliferation, induced cell apoptosis, and decreased mRNA levels of interleukin 1β (IL1β) and interleukin 18 (IL18) in HCT116 cells.Conclusions: High level of NLRP3 predicts poor survival in CRC patients. NLRP3 is a putative prognostic biomarker and a potential therapeutic target in CRC treatments.     

革兰氏阴性菌Ⅵ型分泌系统及其参与金属离子转运的研究进展

细菌通过其分泌系统将特定的效应蛋白输送到外界环境或进入靶细胞中,从而在细菌和宿主、细菌和微生物群落的相互作用中占据适应性优势。Ⅵ型分泌系统（The type VI secretion system,T6SS）是革兰氏阴性菌中广泛存在的大分子分泌装置,其结构和功能类似于可收缩的噬菌体尾针样,通过细胞间直接接触将细菌各种酶或毒素效应蛋白转运到原核和真核生物中,从而介导细菌间竞争以及对宿主的致病过程。有些效应蛋白还可通过非接触依赖的方式进入胞外环境来帮助细菌获取稀缺金属离子,并且它们对应激条件下细胞内金属稳态的维持至关重要。这篇综述总结了Ⅵ型分泌系统的结构、组装及其分泌的效应蛋白,并重点阐述了Ⅵ型分泌系统在多种金属离子转运机制中作用的研究进展,有助于理解T6SS在细菌间相互作用和细菌感染过程中发挥的重要作用。     

Biochar application to rice with 15N-labelled fertilizers,enhanced leaf nitrogen concentration and assimilation by improving morpho-physiological traits and soil quality

Leaf nitrogen (N) concentration plays an important role in biochemical and physiological functions, and N availability directly influences rice yield. However, excessive N fertilization is considered to be a root cause of environmental issues and low nitrogen use efficiency. Therefore, the selection of appropriate nutrient management practices and organic amendments is key to maximizing nitrogen uptake and maintaining high and sustainable rice production. Here, we evaluated the effects of different ¹⁵N-labelled nitrogen sources (urea, ammonium nitrate, and ammonium sulfate at 315 kg ha⁻¹) with or without biochar (30 t ha⁻¹) on paddy soil properties, root growth, leaf gas exchange, N metabolism enzymes, and N uptake in the early and late seasons of 2019. We found significant differences among N fertilizer sources applied with or without biochar (P < 0.05). Across the seasons, the combination of biochar with N fertilizers significantly increased soil organic carbon by 51.21% and nitrogen availability by 27.51% compared with N fertilizers alone. Correlation analysis showed that rice root morphological traits were strongly related to soil chemical properties, and higher root growth was measured in the biochar treatments. Similarly, net leaf photosynthetic rate averaged 9.34% higher, chlorophyll (Chl) a concentration 12.91% higher, and Chl b concentration 10.05% higher in the biochar treatments than in the biochar-free treatments across the seasons. Notably, leaf ¹⁵N concentration was 23.19% higher in the biochar treatments in both seasons. These results illustrated higher activities of N metabolism enzymes such as NR, GS, and GOGAT by an average 23.44%, 11.26% and 18.16% in the biochar treatments across the seasons, respectively. The addition of biochar with synthetic N fertilizers is an ecological nutrient management strategy that can increase N uptake and assimilation by ameliorating soil properties and improving the morpho-physiological factors of rice.     

Targeting Human Hippo TEAD Binding Interface with YAP/TAZ-Derived,Flexibility-Reduced Peptides in Gastric Cancer

International Journal of Peptide Research and Therapeutics - Human Hippo signaling pathway plays an important role in the tumorigenesis of diverse cancers and has been recognized as an attractive...     

Effect of emodin on long non-coding RNA-mRNA networks in rats with severe acute pancreatitis-induced acute lung injury

Long non-coding RNAs (lncRNAs) contribute to disease pathogenesis and drug treatment effects. Both emodin and dexamethasone (DEX) have been used for treating severe acute pancreatitis-associated acute lung injury (SAP-ALI). However, lncRNA regulation networks related to SAP-ALI pathogenesis and drug treatment are unreported. In this study, lncRNAs and mRNAs in the lung tissue of SAP-ALI and control rats, with or without drug treatment (emodin or DEX), were assessed by RNA sequencing. Results showed both emodin and DEX were therapeutic for SAP-ALI and that mRNA and lncRNA levels differed between untreated and treated SAP-ALI rats. Gene expression profile relationships for emodin-treated and control rats were higher than DEX-treated and -untreated animals. By comparison of control and SAP-ALI animals, more up-regulated than down-regulated mRNAs and lncRNAs were observed with emodin treatment. For DEX treatment, more down-regulated than up-regulated mRNAs and lncRNAs were observed. Functional analysis demonstrated both up-regulated mRNA and co-expressed genes with up-regulated lncRNAs were enriched in inflammatory and immune response pathways. Further, emodin-associated lncRNAs and mRNAs co-expressed modules were different from those associated with DEX. Quantitative polymerase chain reaction demonstrates selected lncRNA and mRNA co-expressed modules were different in the lung tissue of emodin- and DEX-treated rats. Also, emodin had different effects compared with DEX on co-expression network of lncRNAs Rn60_7_1164.1 and AABR07062477.2 for the blue lncRNA module and Nrp1 for the green mRNA module. In conclusion, this study provides evidence that emodin may be a suitable alternative or complementary medicine for treating SAP-ALI.     

Sertoli cell-derived exosomal MicroRNA-486-5p regulates differentiation of spermatogonial stem cell through PTEN in mice

Self-renewal and differentiation of spermatogonial stem cell (SSC) are critical for male fertility and reproduction, both of which are highly regulated by testicular microenvironment. Exosomal miRNAs have emerged as new components in intercellular communication. However, their roles in the differentiation of SSC remain unclear. Here, we observed miR-486-5p enriched in Sertoli cell and Sertoli cell-derived exosomes. The exosomes mediate the transfer of miR-486-5p from Sertoli cells to SSCs. Exosomes release miR-486-5p, thus up-regulate expression of Stra8 (stimulated by retinoic acid 8) and promote differentiation of SSC. And PTEN was identified as a target of miR-486-5p. Overexpression of miR-486-5p in SSCs down-regulates PTEN expression, which up-regulates the expression of STRA8 and SYCP3, promotes SSCs differentiation. In addition, blocking the exosome-mediated transfer of miR-486-5p inhibits differentiation of SSC. Our findings demonstrate that miR-486-5p acts as a communication molecule between Sertoli cells and SSCs in modulating differentiation of SSCs. This provides a new insight on molecular mechanisms that regulates SSC differentiation and a basis for the diagnosis, treatment, and prevention of male infertility.