Meta-network: optimized species-species network analysis for microbial communities

Background

The explosive growth of microbiome data provides ample opportunities to gain a better understanding of the microbes and their interactions in microbial communities. Given these massive data, optimized data mining methods become important and necessary to perform deep and comprehensive analysis. Among the various priorities for microbiome data mining, the examination of species-species co-occurrence patterns becomes one of the key themes in urgent need.

Results

Hence, in this work, we propose the Meta-Network framework to lucubrate the microbial communities. Rooted in loose definitions of network (two species co-exist in a certain samples rather than all samples) as well as association rule mining (mining more complex forms of correlations like indirect correlation and mutual information), this framework outperforms other methods in restoring the microbial communities, based on two cohorts of microbial communities: (a) the loose definition strategy is capable to generate more reasonable relationships among species in the species-species co-occurrence network; (b) important species-species co-occurrence patterns could not be identified by other existing approaches, but could successfully generated by association rule mining.

Conclusions

Results have shown that the species-species co-occurrence network we generated are much more informative than those based on traditional methods. Meta-Network has consistently constructed more meaningful networks with biologically important clusters, hubs, and provides a general approach towards deciphering the species-species co-occurrence networks.

     

自身代谢缓解甲氨蝶呤对小鼠体内成熟卵母细胞副作用的研究

甲氨蝶呤(methotrexate,MTX)作为抗叶酸代谢类药物,在临床上应用广泛.其副作用之一表现为损伤卵母细胞质量.那么,对于有妊娠需求的女性服药者,停药后多久才适合受孕呢?该文结合双光子荧光成像与三维重构技术研究此问题.通过单次腹腔注射生理盐水及5 mg/kg MTX建立了对照组和MTX组小鼠,随后建立了MTX注...     

干旱半干旱区地下水埋深对沙地植物土壤系统演变的驱动作用综述

在干旱半干旱生态脆弱区,地下水是限制植物种类组成、数量和生长发育的关键因素之一。近年来由于气候变化与土地利用强度的增加,我国北方普遍出现以极端气候变化、地表水体萎缩和地下水位下降为特征的生态过程,对区域生态系统安全和可持续发展构成严重威胁。而有关干旱半干旱区地下水埋深变化驱动退化植被恢复和稳定性维持方面的系统研究尚存不足。系统总结了地下水埋深变化分别对植物、土壤产生的影响及其三者间相互作用关系,比较分析了前人的研究成果,归纳总结了地下水埋深变化的驱动作用和影响因素,以及干旱半干旱区地下水埋深变化对植物土壤系统影响的预测模型研究,以期为今后应对地下水埋深变化制定生态保护策略提供理论指导依据。对本研究做了展望。     

A ubiquitin-like protein unleashes ubiquitin ligases

Modification of cullin-RING ubiquitin ligases by the ubiquitin-like molecule Nedd8 promotes substrate ubiquitination. A crystal structure of a cullin modified by Nedd8 recently reported in Cell (Duda et al., 2008) and a biochemical study in Molecular Cell (Saha and Deshaies, 2008) reveal the dramatic impact on the ligase machinery by conjugation of ubiquitin or ubiquitin-like proteins.     

黑龙江省野生和栽培大豆异黄酮与其组分相关性分析

利用高效液相色谱法（HPLC）检测了黑龙江省556份不同生态区以及不同类型大豆的异黄酮、大豆苷和染料木苷含量,其中野生大豆243份,栽培大豆313份。结果表明：野生大豆异黄酮含量高于栽培大豆,同时筛选出高异黄酮含量种质3份,低异黄酮含量种质2份。异黄酮、大豆苷和染料木苷含量三者问的相关分析表明,大豆异黄酮含量与大豆苷含量及染料木苷含量、大豆苷含量与染料木苷含量均呈极显著正相关。     

Adiponectin alleviated Alzheimer‐like pathologies via autophagy‐lysosomal activation

Adiponectin (APN) deficiency has also been associated with Alzheimer‐like pathologies. Recent studies have illuminated the importance of APN signaling in reducing Aβ accumulation, and the Aβ elimination mechanism remains rudimentary. Therefore, we aimed to elucidate the APN role in reducing Aβ accumulation and its associated abnormalities by targeting autophagy and lysosomal protein changes. To assess, we performed a combined pharmacological and genetic approach while using preclinical models and human samples. Our results demonstrated that the APN level significantly diminished in the plasma of patients with dementia and 5xFAD mice (6 months old), which positively correlated with Mini‐Mental State Examination (MMSE), and negatively correlated with Clinical Dementia Rating (CDR), respectively. APN deficiency accelerated cognitive impairment, Aβ deposition, and neuroinflammation in 5xFAD mice (5xFAD*APN KO), which was significantly rescued by AdipoRon (AR) treatment. Furthermore, AR treatment also markedly reduced Aβ deposition and attenuated neuroinflammation in APP/PS1 mice without altering APP expression and processing. Interestingly, AR treatment triggered autophagy by mediating AMPK‐mTOR pathway signaling. Most importantly, APN deficiency dysregulated lysosomal enzymes level, which was recovered by AR administration. We further validated these changes by proteomic analysis. These findings reveal that APN is the negative regulator of Aβ deposition and its associated pathophysiologies. To eliminate Aβ both extra‐ and intracellular deposition, APN contributes via the autophagic/lysosomal pathway. It presents a therapeutic avenue for AD therapy by targeting autophagic and lysosomal signaling.     

Enzymatic synthesis of galactosyl lactic ethyl ester and its polymer for use as biomaterials

Lactate-based chemicals and polymers including poly(lactic acid) (PLA) are highly valuable materials for biomedical, food and general-purpose applications. Chemical synthesis, albeit the high reaction velocities achieved with it, often leaves chemical residues that are subject to health and safety concerns. Alternative biosynthesis is preferred in order to overcome these problems. Herein we report a novel enzymatic synthesis for the preparation of beta-d-galactosyl-l-lactic acid ethyl ester (GLAEE). Such a product, which may find applications in food and personal care products, is generally difficult to synthesize via traditional chemical routes because the reactions have to be highly selective due to the multiple hydroxyl groups of sugars. We further explore the enzymatic polymerization of GLAEE to form a unique biopolymer, poly(beta-d-galactoside-co-l-lactic acid) (PGLA). Novozyme 435 was found efficient in catalyzing the polymerization reaction in acetone with a conversion yield of 60% within 100 h. The molecular weight of the polymer product ranged from about 800-2000 as analyzed by using ESI-MS. It is expected that a variety of sugar-hydroxyl acids copolymers can be prepared through the same approach and a new class of biomaterials can thus be developed.     

Temperature Response of Soil Respiration in a Chinese Pine Plantation: Hysteresis and Seasonal vs. Diel Q 10

Although the temperature response of soil respiration (R_s) has been studied extensively, several issues remain unresolved, including hysteresis in the R_s–temperature relationship and differences in the long- vs. short-term R_s sensitivity to temperature. Progress on these issues will contribute to reduced uncertainties in carbon cycle modeling. We monitored soil CO₂ efflux with an automated chamber system in a Pinus tabulaeformis plantation near Beijing throughout 2011. Soil temperature at 10-cm depth (T_s) exerted a strong control over R_s, with the annual temperature sensitivity (Q ₁₀) and basal rate at 10°C (R_{s 10}) being 2.76 and 1.40 µmol m⁻² s⁻¹, respectively. Both R_s and short-term (i.e., daily) estimates of R_{s 10} showed pronounced seasonal hysteresis with respect to T_s, with the efflux in the second half of the year being larger than that early in the season for a given temperature. The hysteresis may be associated with the confounding effects of microbial population dynamics and/or litter input. As a result, all of the applied regression models failed to yield unbiased estimates of R_s over the entire annual cycle. Lags between R_s and T_s were observed at the diel scale in the early and late growing season, but not in summer. The seasonality in these lags may be due to the use of a single T_s measurement depth, which failed to represent seasonal changes in the depth of CO₂ production. Daily estimates of Q ₁₀ averaged 2.04, smaller than the value obtained from the seasonal relationship. In addition, daily Q ₁₀ decreased with increasing T_s, which may contribute feedback to the climate system under global warming scenarios. The use of a fixed, universal Q ₁₀ is considered adequate when modeling annual carbon budgets across large spatial extents. In contrast, a seasonally-varying, environmentally-controlled Q ₁₀ should be used when short-term accuracy is required.