Electron acceptors for anaerobic oxidation of methane drive microbial community structure and diversity in mud volcanoes

Mud volcanoes (MVs) emit globally significant quantities of methane into the atmosphere, however, methane cycling in such environments is not yet fully understood, as the roles of microbes and their associated biogeochemical processes have been largely overlooked. Here, we used data from high‐throughput sequencing of microbial 16S rRNA gene amplicons from six MVs in the Junggar Basin in northwest China to quantify patterns of diversity and characterize the community structure of archaea and bacteria. We found anaerobic methanotrophs and diverse sulfate‐ and iron‐reducing microbes in all of the samples, and the diversity of both archaeal and bacterial communities was strongly linked to the concentrations of sulfate, iron and nitrate, which could act as electron acceptors in anaerobic oxidation of methane (AOM). The impacts of sulfate/iron/nitrate on AOM in the MVs were verified by microcosm experiments. Further, two representative MVs were selected to explore the microbial interactions based on phylogenetic molecular ecological networks. The sites showed distinct network structures, key species and microbial interactions, with more complex and numerous linkages between methane‐cycling microbes and their partners being observed in the iron/sulfate‐rich MV. These findings suggest that electron acceptors are important factors driving the structure of microbial communities in these methane‐rich environments.     

Maturation and germination of walnut somatic embryos

Walnut somatic embryos were multiplied by repetitive embryogenesis on a solid basal DKW medium at 25°C in the dark. When the embryos were isolated at early cotyledonary stage (1–2 mm long) from the primary embryos and cultured on the medium for 3 weeks, they developed into mature embryos showing white, enlarged cotyledons and shoot and root apex. After transfer to light on solid germination medium, however, few mature embryos (0–5%) germinated. Germination percentage increased to about 10% when the mature embryos were pretreated by a storage at 4°C in the dark for 2 months, or by desiccation at 25°C in the dark for 3 or 5 days under an air-humidity conditioned by saturated salt solutions (Mg(NO₃)₂.6H₂O, or ZnSO₄.7H₂O). Similar results were obtained by the addition of gibberellic acid (GA₃) to the germination medium. When mature embryos were desiccated and then placed on medical cotton compresses in liquid germination medium, 45% of the embryos germinated into complete plantlets. These plantlets continued their growth after transplanting to a mixture of peat and vermiculite in pots.Abbreviations GA₃ gibberellic acid - DKW medium Driver & Kuniyuki Walnut medium     

Noggin and bFGF cooperate to maintain the pluripotency of human embryonic stem cells in the absence of feeder layers

Human embryonic stem (hES) cells are typically maintained on mouse embryonic fibroblast (MEF) feeders or with MEF-conditioned medium. However, these xenosupport systems greatly limit the therapeutic applications of hES cells because of the risk of cross-transfer of animal pathogens. Here we showed that the bone morphogenetic protein antagonist noggin is critical in preventing differentiation of hES cells in culture. Furthermore, we found that the combination of noggin and basic fibroblast growth factor (bFGF) was sufficient to maintain the prolonged growth of hES cells while retaining all hES cell features. Since both noggin and bFGF are expressed in MEF, our findings suggest that they may be important factors secreted by MEF for maintaining undifferentiated pluripotent hES cells. Our data provide new insight into the mechanism how hES cell self-renewal is regulated. The newly developed feeder-free culture system will provide a more reliable alternative for future therapeutic applications of hES cells.     

Toward a theory for diversity gradients: the abundance–adaptation hypothesis

The abundance–adaptation hypothesis argues that taxa with more individuals and faster generation times will have more evolutionary ‘experiments’ allowing expansion into, and diversification within, novel habitats. Thus, as older taxa have produced more individuals over time, and smaller taxa have higher population sizes and faster generation times, the Latitudinal Diversity Gradients (LDGs) of these clades should show shallower slopes. We describe the LDGs for archaea, bacteria, fungi, invertebrates and trees from six North American forests. For three focal groups – bacteria, ants, and trees – older taxa had shallower LDG slopes than the more recent, terminal taxa. Across 12 orders of magnitude of body mass, LDG slopes were steeper in larger taxa. The slopes of LDGs vary systematically with body size and clade age, underscoring the non‐canonical nature of LDGs. The steepest LDG slopes were found for the largest organisms while the smallest, from bacteria to small litter‐soil invertebrates, have shallower‐ to zero‐slope LDGs. If tropical niche conservatism is the failure of clades to adapt to, and diversify in temperate habitats, then the steep LDGs of chordates and plants likely arise from the decreased ability of clades with large individuals to adapt to the multiple challenges of extra‐tropical life.     

Optimal stimulation frequency for vibrational optical coherence elastography

Vibrational optical coherence elastography (OCE) is a promising tool for extracting the mechanical property of soft tissue. Purpose of this study is focusing on settling the optimal frequency range for vibrational OCE with evenly distributed stress filed. A finite element model of 2% agar phantom was built by ANSYS with a vibration stimulation frequency range from 200 to 3000 Hz. Practical experiments were carried out for cross‐validation with the same frequencies and sample. Lateral and horizontal stress filed distributions under different frequencies were mathematically evaluated by coefficient of variance and degree of linearity. Results from simulation and practical experiment cross‐validated each other and 1000 Hz was set as the maximum ideal frequency for vibrational OCE, while the minimum frequency is set by theoretical calculation with a result of 250 Hz. An ex vivo biological sample was utilised to testify performance of vibrational OCE with excitation frequencies in and out of concluded optimal range, which showed that stiffness was better mapped out in optimal frequency range.     

买麻藤根的异常次生生长

买麻藤(Cnetum montanum)根的异常次生生长与茎的异常次生生长相似,位于维管束外围的薄壁组织细胞可以形成维管束,以这种方式使根加粗。并且在生长过程中以同样的方式,在维管束的外围不断形成新的维管束。这些新的维管束成环状排列,因此,在老根中呈多圈的维管束。与茎唯一不同的是根的异常次生生长为不均等的,在两个宽大的射线区外侧,没有异常的维管束形成,因此,根主要向着与两条宽大射线相垂直的方向扩展,故外形呈扁圆形。     

水稻叶绿素合成缺陷突变体及其生物学研究进展

叶绿素是植物叶绿体内参与光合作用的重要色素,叶绿素合成缺陷突变是一类明显的性状突变,其在理论研究和实际应用方面均具有重要的意义。本文介绍了国内外在水稻叶绿素合成缺陷突变体的发掘、作用机理及其基因定位等方面的研究进展。     

Confounding from cryptic relatedness in haplotype-based association studies

Cryptic relatedness was suggested to be an important source of confounding in population-based association studies (PBAS). The impact of cryptic relatedness on the performance of haplotype phase inference and haplotype-based association tests is not clear. In this study, we used the Hapmap genetic data to simulate a set of related samples. We evaluated the accuracy of haplotype phase inferred by PHASE 2.1 and calculated the power, type I error rates, accuracy and positive prediction value (PPV) of haplotype frequency-based association tests (HFAT) and haplotype similarity-based association tests (HSAT) under various scenarios, considering relatedness levels, disease models and sample sizes. Cryptic relatedness appeared to slightly increase the accuracy of haplotype phase inference. We observed significant negative effect of cryptic relatedness on the performance of HFAT and HSAT. Ignoring cryptic relatedness may increase spurious association results in haplotype-based PBAS.     

CO2浓度升高对不同品种水稻镉吸收和根形态的影响

为了探讨CO2浓度升高下不同水稻品种荣优398 (RY)和粤杂889(YZ)吸收重金属Cd差异性的原因,利用水培试验研究了不同浓度Cd处理下两种水稻吸收Cd的差异及根形态的变化特征.结果表明:低Cd处理(5、10、20 μmol·L-1)显著增加水稻生物量;当Cd浓度高于50 μmol·L-1时,Cd胁迫效果开始显现,水稻生物量减少.CO2浓度升高显著增加了水稻的生物量,增加了YZ茎Cd含量而降低了RY茎Cd含量.在5～200 μmol·L-1的Cd浓度下,CO2浓度升高增加了YZ活性根在总根长中的比例,降低了RY活性根的比例.CO2浓度升高下不同水稻品种根形态的变化是导致其对Cd吸收差异性的原因之一.     

OsGRF4 controls grain shape,panicle length and seed shattering in rice

Traits such as grain shape, panicle length and seed shattering, play important roles in grain yield and harvest. In this study, the cloning and functional analysis of PANICLE TRAITS 2 (PT2), a novel gene from the Indica rice Chuandali (CDL), is reported. PT2 is synonymous with Growth‐Regulating Factor 4 (OsGRF4), which encodes a growth‐regulating factor that positively regulates grain shape and panicle length and negatively regulates seed shattering. Higher expression of OsGRF4 is correlated with larger grain, longer panicle and lower seed shattering. A unique OsGRF4 mutation, which occurs at the OsmiRNA396 target site of OsGRF4, seems to be associated with high levels of OsGRF4 expression, and results in phenotypic difference. Further research showed that OsGRF4 regulated two cytokinin dehydrogenase precursor genes (CKX5 and CKX1) resulting in increased cytokinin levels, which might affect the panicle traits. High storage capacity and moderate seed shattering of OsGRF4 may be useful in high‐yield breeding and mechanized harvesting of rice. Our findings provide additional insight into the molecular basis of panicle growth.