Organelle association visualized by three-dimensional ultrastructural imaging of the yeast cell

This study was aimed at a better understanding of organelle organization in the yeast Saccharomyces cerevisiae with special emphasis on the interaction and physical association of organelles. For this purpose, a computer aided method was employed to generate three-dimensional ultrastructural reconstructions of chemically and cryofixed yeast cells. This approach showed at a high level of resolution that yeast cells were densely packed with organelles that had a strong tendency to associate at a distance of <30 nm. The methods employed here also allowed us to measure the total surface area and volume of organelles, the number of associations between organelles, and the ratio of associations between organelles per surface area. In general, the degree of organelle associations was found to be much higher in chemically fixed cells than in cryofixed cells, with endoplasmic reticulum/plasma membrane, endoplasmic reticulum/mitochondria and lipid particles/nuclei being the most prominent pairs of associated fractions. In cryofixed cells, similar preferences for organelle association were seen, although at lower frequency. The occurrence of specific organelle associations is believed to be important for intracellular translocation and communication. Membrane contact as a possible means of interorganelle transport of cellular components, especially of lipids, is discussed.     

喀斯特常绿落叶阔叶林个体死亡对空间格局及种间关联性的影响

树木死亡作为森林生态系统中一个重要的生态学过程,研究其如何影响物种的空间分布格局及种间关联性,可以为揭示树木死亡机制及群落动态变化规律提供重要参考。本研究根据木论25 hm²喀斯特常绿落叶阔叶林动态监测样地两次木本植物调查数据,采用点格局分析方法,分析了树木死亡前后空间格局和种间关系的变化。结果表明: 样地内个体死亡前后主要表现为聚集分布,但死亡后聚集分布的物种比例较死亡前略微下降,小尺度上呈现随机分布的物种比例有所增加,个体的死亡呈非随机性死亡。在物种水平上,13个优势种的死树和活树之间在0～30 m各尺度上呈显著正关联,表明样地内优势物种个体之间种内和种间竞争作用不激烈;树木死亡前后种间关联性主要为正关联,且大部分物种种间关系在死亡前后并未发生变化,表明群落已发展到相对稳定的阶段;死亡后,在1～30 m尺度上表现为正关联的物种对比例有所增加,负关联和无关联的物种对在大部分尺度上有所减少,说明个体死亡发生后,各个物种之间的竞争压力在一定程度上有所缓解。     

古尔班通古特沙漠固定沙丘上白梭梭和梭梭的空间分布及种间关联性

为了探讨沙漠中固沙灌木种群共存和演替机制, 本文基于古尔班通古特沙漠东南缘固定沙丘上白梭梭(Haloxylon persicum)和梭梭(H. ammodendron)种群的地理位置和生长发育阶段信息(幼株、营养株、生殖株和死株), 采用点格局分析方法(g(r)函数)及Monte-Carlo随机模拟检验和零模型选取的方法, 分析了固沙灌木白梭梭和梭梭种群不同生长发育阶段在0-20 m尺度内的空间分布格局及种间关联性。结果表明: (1)两个种群在研究尺度范围内呈聚集分布, 随着尺度的增大, 其聚集强度逐渐减弱; (2)两个种群整体上呈负关联关系, 尺度越大负关联关系越显著; (3)白梭梭种群生长发育阶段相差越大, 个体间正关联关系越显著; 梭梭种群生长发育阶段越接近, 个体间正关联关系越显著; (4)两个种群中龄级较大的个体(如营养株、生殖株和死株)会对对方种群中龄级较小的幼株产生一定的抑制作用; 同时, 随着两个种群中个体的成长, 双方受到的抑制作用逐渐减弱, 主要表现为正关联和无关联。总体而言, 古尔班通古特沙漠固定沙丘白梭梭和梭梭种群的分布格局整体上为聚集分布, 随龄级增加聚集性减弱, 受生境异质性和扩散限制的影响明显。种间关系多为负相关, 种内不同生长发育阶段之间均为正关联关系。     

Identification of novel loci influencing refractive error in East Asian populations using an extreme phenotype design

The global “myopia boom” has raised significant international concerns. Despite a higher myopia prevalence in Asia, previous large-scale genome-wide association studies (GWASs) were mostly based on European descendants. Here, we report a GWAS of spherical equivalent (SE) in 1852 Chinese Han individuals with extreme SE from Guangzhou (631 < ?6.00D and 574 > 0.00D) and Wenzhou (593 < ?6.00D and 54 > ?1.75D), followed by a replication study in two independent cohorts with totaling 3538 East Asian individuals. The discovery GWAS and meta-analysis identify three novel loci, which show genome-wide significant associations with SE, including 1q25.2 FAM163A, 10p11.22 NRP1/PRAD3, and 10p11.21 ANKRD30A/MTRNR2L7, together explaining 3.34% of SE variance. 10p11.21 is successfully replicated. The allele frequencies of all three loci show significant differences between major continental groups (P < 0.001). The SE reducing (more myopic) allele of rs10913877 (1q25.2 FAM163A) demonstrates the highest frequency in East Asians and much lower frequencies in Europeans and Africans (EAS = 0.60, EUR = 0.20, and AFR = 0.18). The gene-based analysis additionally identifies three novel genes associated with SE, including EI24, LHX5, and ARPP19. These results provide new insights into myopia pathogenesis and indicate the role of genetic heterogeneity in myopia epidemiology among different ethnicities.     

A single lycaenid caterpillar gets an ant‐constructed shelter and uninterrupted ant attendance

Ant‐lycaenid associations range from mutualism to parasitism and the caterpillars of some species of lycaenids are reported to enter ant nests for shelter, diapause, or pupation. The present study aimed to examine the nature of the association between Euchrysops cnejus (Fabricius) (Lepidoptera: Lycaenidae) and Camponotus compressus (Fabricius) (Hymenoptera: Formicidae) worker ants on the extrafloral nectary‐bearing cowpea plant, Vigna unguiculata (L.) Walp. (Fabaceae). The abundance patterns of the ants and the lycaenid caterpillars together with the spatial patrolling patterns of the ants on the plants revealed that ant abundance increased with the occurrence of the lycaenid caterpillars and the ants preferred the lycaenids over the extrafloral nectar. Camponotus compressus worker ants constructed a shelter at the cowpea plant base after interaction with one or more lycaenid caterpillar(s) and tended the caterpillars and pupae till the emergence of the butterfly. The ant‐constructed shelters (ACSs) inhabited by the minor caste workers (13 ± 1.3 ants per ACS), were utilized by the caterpillars to undergo pupation. The ants confined their activities predominantly to tending the pod‐feeding caterpillars and the solitary pupa within each ACS. It appears that the behavior of the tending worker ants is modulated by the lycaenid vulnerable stages.     

Stable deep-sea macrobenthic trace maker associations in disturbed environments from the Eocene Lefkara Formation,Cyprus

Ichnological analysis of Eocene deep-pelagic whitish chalky calcilutites interstratified with high-energy calcarenite beds in the lower part of the Petra Tou Romiou section (southern Cyprus) was conducted to interpret the development and evolution of the trace maker associations during calcilutite deposition after high-energy episodes. The trace fossil assemblage from the chalky calcilutites consists of Chondrites isp. (Chondrites intricatus and Chondrites targionii), Planolites isp., Taenidium isp., Thalassinoides isp., and Zoophycos isp., typical of the Zoophycos ichnofacies. A composite chalky ichnofabric reveals a multi-tiered association of burrowing animals: the uppermost tier determines a mottled background, the upper tier shows the highest trace fossil abundance and diversity (Planolites, Taenidium and Thalassinoides), the middle tier features Zoophycos and large Chondrites, and the deepest tier consists mainly/exclusively of small Chondrites. This ichnofabric has an autocomposite character, associated with bioturbation by a single ichnocoenosis and gradual upward migration of the tiered macrobenthic community as the pelagic calcilutite sedimentation slowly progresses. There are no changes in the trace fossil assemblage between or within calcilutite intervals, regardless of the associated calcarenite beds. This supports a stable, mature, background calcilutite trace maker association, which recovers shortly after the deposition of high-energy calcarenites. In turn, there would have been a rapid re-establishment of paleoenvironmental conditions during pelagic calcilutite accumulation after episodic deposition of any calcarenitic material.     

The PDZ-GEF Gef26 regulates synapse development and function via FasII and Rap1 at the Drosophila neuromuscular junction

Guanine nucleotide exchange factors (GEFs) are essential for small G proteins to activate their downstream signaling pathways, which are involved in morphogenesis, cell adhesion, and migration. Mutants of Gef26, a PDZ-GEF (PDZ domain-containing guanine nucleotide exchange factor) in Drosophila, exhibit strong defects in wings, eyes, and the reproductive and nervous systems. However, the precise roles of Gef26 in development remain unclear. In the present study, we analyzed the role of Gef26 in synaptic development and function. We identified significant decreases in bouton number and branch length at larval neuromuscular junctions (NMJs) in Gef26 mutants, and these defects were fully rescued by restoring Gef26 expression, indicating that Gef26 plays an important role in NMJ morphogenesis. In addition to the observed defects in NMJ morphology, electrophysiological analyses revealed functional defects at NMJs, and locomotor deficiency appeared in Gef26 mutant larvae. Furthermore, Gef26 regulated NMJ morphogenesis by regulating the level of synaptic Fasciclin II (FasII), a well-studied cell adhesion molecule that functions in NMJ development and remodeling. Finally, our data demonstrate that Gef26-specific small G protein Rap1 worked downstream of Gef26 to regulate the level of FasII at NMJs, possibly through a βPS integrin-mediated signaling pathway. Taken together, our findings define a novel role of Gef26 in regulating NMJ development and function.     

Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project

The Alzheimer's Disease Sequencing Project (ADSP) performed whole genome sequencing (WGS) of 584 subjects from 111 multiplex families at three sequencing centers. Genotype calling of single nucleotide variants (SNVs) and insertion-deletion variants (indels) was performed centrally using GATK-HaplotypeCaller and Atlas V2. The ADSP Quality Control (QC) Working Group applied QC protocols to project-level variant call format files (VCFs) from each pipeline, and developed and implemented a novel protocol, termed “consensus calling,” to combine genotype calls from both pipelines into a single high-quality set. QC was applied to autosomal bi-allelic SNVs and indels, and included pipeline-recommended QC filters, variant-level QC, and sample-level QC. Low-quality variants or genotypes were excluded, and sample outliers were noted. Quality was assessed by examining Mendelian inconsistencies (MIs) among 67 parent-offspring pairs, and MIs were used to establish additional genotype-specific filters for GATK calls. After QC, 578 subjects remained. Pipeline-specific QC excluded ~12.0% of GATK and 14.5% of Atlas SNVs. Between pipelines, ~91% of SNV genotypes across all QCed variants were concordant; 4.23% and 4.56% of genotypes were exclusive to Atlas or GATK, respectively; the remaining ~0.01% of discordant genotypes were excluded. For indels, variant-level QC excluded ~36.8% of GATK and 35.3% of Atlas indels. Between pipelines, ~55.6% of indel genotypes were concordant; while 10.3% and 28.3% were exclusive to Atlas or GATK, respectively; and ~0.29% of discordant genotypes were. The final WGS consensus dataset contains 27,896,774 SNVs and 3,133,926 indels and is publicly available.