基于宏基因组学解析不同质量等级中温大曲微生物组的异质性

【目的】中温大曲是浓香型白酒酿造中的糖化发酵剂和生香剂，目前其质量评价主要依赖于感官和理化特征。已有研究采用扩增子测序初步探索了大曲质量等级与微生物群落组成之间的关联性，但是微生物群落功能对大曲质量的影响尚缺乏深入研究。【方法】本研究采用宏基因组学解析和对比了不同质量等级大曲的微生物群落组成和潜在功能的差异，结合理化性质，聚焦分析了酶活、乳酸和乙酸代谢相关的关键酶基因丰度。【结果】两种等级大曲的真菌群落组成差异显著。一级大曲含有更高相对丰度的丝状真菌，主要分布在曲霉属(Aspergillus, 21.6%)、罗萨氏菌属(Rasamsonia, 6.8%)、拟青霉属(Paecilomyces, 5.0%)和篮状菌属(Talaromyces, 4.4%)等。一级大曲中与环境信息处理和细胞过程相关途径的基因相对丰度普遍显著高于二级大曲。一级大曲中薄层菌属(Hymenobacter)和曲霉属等提供了更高基因丰度的α-淀粉酶，使其具有显著较高的液化力。二级大曲则含有更高相对丰度的横梗霉属(Lichtheimia, 11.8%)、根霉属(Rhizopus, 13.4%)和毕赤酵母属(Pichia, 7.2%)以及乳酸菌类微生物，如伴生乳杆菌属(Companilactobacillus)、魏斯氏菌属(Weissella)和黏液乳杆菌属(Limosilactobacillus)等。二级大曲中与代谢相关途径的基因相对丰度显著较高，如碳水化合物代谢、能量代谢和核苷酸代谢等。二级大曲中较多的乳酸菌类群有利于提高乙醇脱氢酶基因丰度，同时，糖多孢菌属(Saccharopolyspora)、葡萄球菌属(Staphylococcus)、曲霉属和高温放线菌属(Thermoactinomyces)等提供了更多的羧酸酯酶基因丰度，分别使其具有较高的发酵力和酯化力。此外，二级大曲中较多的乳酸菌还可能产生更多的乳酸脱氢酶，降解乳酸，且更高基因丰度的乙酸代谢相关酶类可促进乙酸分解代谢，使得二级大曲酸度显著低于一级大曲。【结论】本研究在基因水平上研究了不同质量等级大曲酶活和酸度差异的微生物基础，可为建立完善的大曲质量评价体系以及理性地调控群落功能提供理论支撑。     

SSVEP次谐波的诱发影响因素及其功率变化——建模及实验研究*

稳态视觉诱发电位(steady-state visual evoked potential, SSVEP)在大脑的感知、认知研究中具有广泛应用。目前，对SSVEP次谐波的诱发机制尚未清楚。为此，本文通过视皮层网络模型进行SSVEP次谐波的诱发因素和功率变化的研究；进一步，测试20名受试者的头表SSVEP，对建模仿真结果进行验证。仿真和实验结果表明，刺激频率、刺激强度和噪声强度是影响SSVEP的1/2次谐波诱发和功率变化的三个重要参数。次谐波诱发是三个参数协同作用的结果：（1）在刺激频率和噪声强度相同时，1/2次谐波功率随刺激强度的变化曲线与Sigma函数相似，存在无诱发区、线性增长区和饱和区：在无诱发区，1/2次谐波功率近似为0；在线性增长区，1/2次谐波功率和刺激强度成正比；在饱和区，1/2次谐波功率趋于恒定；（2）在噪声强度相同时，能明显诱发出1/2次谐波的刺激参数区域呈现非线性同步中的阿诺德舌头变化规律，即能诱发1/2次谐波的有效刺激频率范围随刺激强度的增大而增宽；（3）在刺激参数相同时，噪声强度的大小决定了1/2次谐波能否被诱发；噪声强度越大，对1/2次谐波的诱发及功率抑制作用就越强。本文的实验和仿真结果基本一致，说明了模型仿真的可行性。研究结果为理解SSVEP次谐波的产生机制及其有效应用提供有意义的理论和实验依据。     

A mini review of MAR-binding proteins

Genomic DNA encompasses several levels of organization, the nuclear matrix mediates the formation of DNA loop domains that are anchored to matrix attachment regions (MARs). By means of specific interaction with MAR binding proteins (MARBPs), MAR plays an important regulation role in enhancing transgene expression, decreasing expression variation among individuals of different transformants and serving as the replication origin. Through these years, some MARBPs have been identified and characterized from humans, plants, animals and algae so far and the list is growing. Most of MARBPs exist in a co-repressor/co-activator complex and involve in chromosome folding, regulation of gene expression, influencing cell development and inducing cell apoptosis. This review covers recent advances that have contributed to our understanding of MARBPs.     

Ovular development and perisperm formation in Phytolacca americana (Phytolaccaceae) and their systematic significance in Caryophyllales

Phytolacca is the biggest and most original genus in Phytolaccaceae and an important genus in plant systematic studies. Light microscopy results show that the Phytolacca americana L. ovule arises from the caulis (floral receptacle). The perisperm and hypostase are simultaneously initiated from the top several layers of cells of chalaza after fertilization, and the perisperm is located between the nucellus and hypostase. In the early stages of development, the hypostase cells are thin-walled with dense cytoplasm, clear nuclei, and some reserve granules.Later, at the heart-shaped embryo stage, the hypostase cells are dead and thick-walled. The main functions of the hypostase may be to maintain cellular division and perisperm growth without delivering nutrient materials to the perisperm. An evolutionary picture of placentation in Caryophyllales is also presented.     

虚拟视觉刺激引起幼年斑马鱼捕食行为放弃的研究

目的 当动物重复某种行为以逃避危险或获取奖励而无法成功时，会产生放弃。放弃是一种常见且基本的行为，在小鼠等模式动物中已经被广泛研究，但是其部分神经机制仍未被阐明。幼年斑马鱼适合进行全脑光学成像，是神经科学领域的重要模式生物。已经有研究者通过持续电击等消极刺激诱发斑马鱼放弃行为，然而奖励刺激能否引起斑马鱼放弃尚无报道。本文对奖励刺激引起的斑马鱼放弃行为进行了探究。方法 通过给予斑马鱼虚拟的食物视觉刺激，检验斑马鱼对虚拟食物的捕食情况，比较斑马鱼捕食频率和单次捕食时长随时间的变化。结果 虚拟的食物视觉刺激可以引起斑马鱼的捕食行为，接受25 min虚拟刺激后，8日龄以上斑马鱼的捕食频率和单次捕食时长均出现显著下降。结论 此研究丰富了斑马鱼放弃行为的研究范式，实验结果表明，缺失真实奖励的虚拟食物刺激可以诱导斑马鱼放弃捕食行为，这将进一步加深对动物放弃行为的理解，推动对其神经机制的研究。     

A consensus protocol for the recovery of mercury methylation genes from metagenomes

Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce “marky-coco”, a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.     

Genetic diversity and structure of Rhododendron meddianum,a plant species with extremely small populations

Rhododendron meddianum is a critically endangered species with important ornamental value and is also a plant species with extremely small populations. In this study, we used double digest restriction-site-associated DNA sequencing (ddRAD) technology to assess the genetic diversity, genetic structure and demographic history of the three extant populations of R. meddianum. Analysis of SNPs indicated that R. meddianum populations have a high genetic diversity (π = 0.0772 ± 0.0024, H_E = 0.0742 ± 0.002). Both F_ST values (0.1582–0.2388) and AMOVA showed a moderate genetic differentiation among the R. meddianum populations. Meanwhile, STRUCTURE, PCoA and NJ trees indicated that the R. meddianum samples were clustered into three distinct genetic groups. Using the stairway plot, we found that R. meddianum underwent a population bottleneck about 70,000 years ago. Furthermore, demographic models of R. meddianum and its relative, Rhododendron cyanocarpum, revealed that these species diverged about 3.05 (2.21–5.03) million years ago. This divergence may have been caused by environmental changes that occurred after the late Pliocene, e.g., the Asian winter monsoon intensified, leading to a drier climate. Based on these findings, we recommend that R. meddianum be conserved through in situ, ex situ approaches and that its seeds be collected for germplasm.     

Trade-offs in carbon-degrading enzyme activities limit long-term soil carbon sequestration with biochar addition

Biochar amendment is one of the most promising agricultural approaches to tackle climate change by enhancing soil carbon (C) sequestration. Microbial-mediated decomposition processes are fundamental for the fate and persistence of sequestered C in soil, but the underlying mechanisms are uncertain. Here, we synthesise 923 observations regarding the effects of biochar addition (over periods ranging from several weeks to several years) on soil C-degrading enzyme activities from 130 articles across five continents worldwide. Our results showed that biochar addition increased soil ligninase activity targeting complex phenolic macromolecules by 7.1%, but suppressed cellulase activity degrading simpler polysaccharides by 8.3%. These shifts in enzyme activities explained the most variation of changes in soil C sequestration across a wide range of climatic, edaphic and experimental conditions, with biochar-induced shift in ligninase:cellulase ratio correlating negatively with soil C sequestration. Specifically, short-term (<1 year) biochar addition significantly reduced cellulase activity by 4.6% and enhanced soil organic C sequestration by 87.5%, whereas no significant responses were observed for ligninase activity and ligninase:cellulase ratio. However, long-term (≥1 year) biochar addition significantly enhanced ligninase activity by 5.2% and ligninase:cellulase ratio by 36.1%, leading to a smaller increase in soil organic C sequestration (25.1%). These results suggest that shifts in enzyme activities increased ligninase:cellulase ratio with time after biochar addition, limiting long-term soil C sequestration with biochar addition. Our work provides novel evidence to explain the diminished soil C sequestration with long-term biochar addition and suggests that earlier studies may have overestimated soil C sequestration with biochar addition by failing to consider the physiological acclimation of soil microorganisms over time.