The distribution of coastal fish eDNA sequences in the Anthropocene

Aim

Coastal fishes have a fundamental role in marine ecosystem functioning and contributions to people, but face increasing threats due to climate change, habitat degradation and overexploitation. The extent to which human pressures are impacting coastal fish biodiversity in comparison with geographic and environmental factors at large spatial scale is still under scrutiny. Here, we took advantage of environmental DNA (eDNA) metabarcoding to investigate the relationship between fish biodiversity, including taxonomic and genetic components, and environmental but also socio-economic factors.

Location

Tropical, temperate and polar coastal areas.

Time period

Present day.

Major taxa studied

Marine fishes.

Methods

We analysed fish eDNA in 263 stations (samples) in 68 sites distributed across polar, temperate and tropical regions. We modelled the effect of environmental, geographic and socio-economic factors on α- and β-diversity. We then computed the partial effect of each factor on several fish biodiversity components using taxonomic molecular units (MOTU) and genetic sequences. We also investigated the relationship between fish genetic α- and β-diversity measured from our barcodes, and phylogenetic but also functional diversity.

Results

We show that fish eDNA MOTU and sequence α- and β-diversity have the strongest correlation with environmental factors on coastal ecosystems worldwide. However, our models also reveal a negative correlation between biodiversity and human dependence on marine ecosystems. In areas with high dependence, diversity of all fish, cryptobenthic fish and large fish MOTUs declined steeply. Finally, we show that a sequence diversity index, accounting for genetic distance between pairs of MOTUs, within and between communities, is a reliable proxy of phylogenetic and functional diversity.

Main conclusions

Together, our results demonstrate that short eDNA sequences can be used to assess climate and direct human impacts on marine biodiversity at large scale in the Anthropocene and can further be extended to investigate biodiversity in its phylogenetic and functional dimensions.     

Differential induction of regulatory genes during mesoderm formation in Xenopus laevis embryos

Mesoderm development in Xenopus laevis depends on inductive cell interactions mediated by diffusible molecules. The mesoderm inducer activin is capable of redirecting the development of animal explants both morphologically and biochemically. We have studied the induction of four regulatory genes, Mix. 1, goosecoid (gsc), Xlim-1 and Xbra in such explants by activin, and the influence of other factors on this induction. Activin induction of gsc is strongly enhanced by dorsalization of the embryo by LiCl, while expression of the other genes is only slightly enhanced. The protein synthesis inhibitor cycloheximide (CHX) inhibits the activin-dependent induction of Xbra partially, while induction of Mix. 1 and Xlim- 1 is essentially unaffected. In contrast, gsc shows strong superinduction in the presence of activin and CHX, and can be induced in animal explants by CHX alone. Induction and superinduction by CHX have previously been observed for immediate early genes in a variety of systems, notably for the activation of c-fos expression by serum stimulation, but have not been reported in early amphibian embryos. © 1993Wiley-Liss, Inc.     

Identification of tyrosines 154 and 307 in the extracellular domain and 653 and 766 in the intracellular domain as phosphorylation sites in the heparin-binding fibroblast growth factor receptor tyrosine kinase (flg).

Four tyrosine residues have been identified as phosphorylation sites in the tyrosine kinase isoform of the heparin-binding fibroblast growth factor receptor flg (FGF-R1). Baculoviral-insect cell-derived recombinant FGF-R1 was phosphorylated and fragmented with trypsin while immobilized on heparin-agarose beads. Phosphotyrosine peptides were purified by chromatography on immobilized anti-phosphotyrosine antibody and analyzed by Edman degradation and electrospray tandem mass spectrometry. Tyrosine residue 653, which is in a homologous spatial position to major autophosphorylation sites in the catalytic domain of the src and insulin receptor kinases, is the major intracellular FGF-R1 phosphorylation site. Residue 766 in the COOH-terminus outside the kinase domain is a secondary site. Tyrosine residues 154 and 307, which are in the extracellular domain of transmembrane receptor isoforms and are in an unusual sequence context for tyrosine phosphorylation, were also phosphorylated.     

大陈岛海域浮游动物群落季节变化及其影响因素

为探究大陈岛海域浮游动物群落的季节变化,于2020年9月（夏季）、11月（秋季）和2021年1月（冬季）、4月（春季）分别对大陈岛海域的浮游动物及环境因子进行了4个航次的调查。结果共鉴定浮游动物90种,包括浮游幼体15类,其中夏季种类数最多（68种）,冬季最少（20种）,常见的优势种有：百陶箭虫（Sagitta bedoti）、微刺哲水蚤（Canthocalanus pauper）、中华哲水蚤（Calanus sinicus）等12种（Y>0.02）。浮游动物的年平均丰度和生物量分别为（153.40±214.73）个/m³、（411.93±561.76） mg/m³,二者存在明显的季节变化,平均丰度为春季（380.17±296.14）个/m³>夏季（135.30±112.59）个/m³>秋季（67.88±90.52）个/m³>冬季（25.30±19.11）个/m³;平均生物量为夏季（895.01±802.54） mg/m³>春季（623.39±358.73） mg/m³>秋季（91.08±82.36） mg/m³>冬季（45.96±84.95） mg/m³。多样性指数（H''）和均匀度指数（J''）的年平均值分别为1.71±0.96和0.53±0.20,均表现出夏秋季较高、冬春季较低的特征。聚类分析结果表明调查海域的浮游动物可划分为夏季类群、秋季类群、冬季类群和春季类群4组类群。Pearson相关性分析和冗余分析（RDA）结果表明,海水温度、盐度、叶绿素a浓度是影响大陈岛海域浮游动物群落特征的重要环境因素。此外,夏季大陈岛海域水母类浮游动物暴发的现象值得关注。研究结果将为大陈岛海域的生物多样性保护及渔业资源可持续开发利用提供可参考的数据资料。     

组织器官通讯对骨骼肌发育的作用及调控机制研究进展

骨骼肌是动物机体最重要的器官之一,研究骨骼肌发育调控机制对于肌肉相关疾病的诊断以及家畜肉质的改善都有着重要意义。骨骼肌发育调控是一个复杂的过程,受到大量肌肉分泌因子和信号通路的调节。此外,为了维持体内代谢稳态并最大限度地利用能量,机体协调多个组织器官形成了复杂而又精密的代谢调控网络,对于调控骨骼肌发育也发挥着重要的作用。随着组学技术的发展,人们对于组织器官通讯的潜在机制进行了深入研究。本文综述了脂肪组织、神经组织、肠道等组织器官通讯对于骨骼肌发育的影响,以期为靶向调控骨骼肌发育提供理论基础。     

Studies on Prolonged Storage of Beauveria bassiana Conidia: Effects of Temperature and Relative Humidity on Conidial Viability and Virulence against Chickpea Borer,Helicoverpa armigera

Unformulated conidia of Beauveria bassiana were stored at five different temperatures (0°, 10°, 20°, 30° and 40°C) at six different relative humidities (RH) (0, 33, 53, 75, 85 and 98%). Conidial viabilities and virulence against third instar larvae of Helicoverpa armigera were determined over a 24‐month period. Conidia survived longest at lower temperatures (0–20°C) and lower RH levels (0–53% RH). At higher temperatures (30–40°C) conidia did not survive. When the temperature was decreased from 30°C to 0°C, at nearly all RH levels the longevity of conidia increased. Conidia remained virulent for third instar larvae of H. armigera under favourable storage conditions for 24 months.     

基于DNA分子标记的潘氏闭壳龟遗传多样性分析

潘氏闭壳龟（Cuora pani）是中国特有种,国家二级重点保护野生动物。由于非法贸易加之栖息地破坏等,其野外种群数量十分稀少。本研究旨在利用线粒体基因与核基因标记揭示潘氏闭壳龟的遗传多样性和遗传结构,以期为中国潘氏闭壳龟的种群保护和管理提供科学依据。本次共研究14只潘氏闭壳龟个体,其中,6只原产地为四川广元,8只产地未知。结果表明,在14只潘氏闭壳龟样本中鉴定出Cyt b单倍型、ND4单倍型和R35单倍型各2个,且均有1个新单倍型;Cyt b、ND4和R35基因单倍型多样性分别为0.440、0.143和0.154,核苷酸多样性分别为0.000 41、0.000 19和0.000 63;各单倍型的平均遗传距离（p）均小于0.01。基于三个基因联合数据集的系统发育分析表明,潘氏闭壳龟与金头闭壳龟（C.aurocapitata）互为单系进化支,且中性检测和核苷酸错配分析显示,潘氏闭壳龟群体近期历史上可能未经历群体扩张事件。潘氏闭壳龟群体遗传多样性低,种内变异小,群体应对环境变化的能力低,建议应加强对中国潘氏闭壳龟野外种群的基础研究和保护力度,同时规范人工繁殖,以避免近亲繁殖和种群衰退。     

A carbon-13 nuclear magnetic resonance investigation of the metabolic fluxes associated withy glucose metabolism in human erythrocytes

We have used [2-¹³C]d-glucose and carbon-13 nuclear magnetic resonance (NMR) spectroscopy to investigate metabolic fluxes through the major pathways of glucose metabolism in intact human erythrocytes and to determine the interactions among these pathways under conditions that perturb metabolism. Using the method described, we have been able to measure fluxes through the pentose phosphate pathway, phosphofructokinase, the 2,3-diphosphoglycerate bypass, and phosphoglycerate kinase, as well as glucose uptake, concurrently and in a single experiment. We have measured these fluxes in normal human erythrocytes under the following conditions: (1) fully oxygenated; (2) treated with methylene blue; and (3) deoxygenated. This method makes it possible to monitor various metabolic effects of stresses in normal and pathological states. Not only has ¹³C-NMR spectroscopy proved to be a useful method for measuring in vivo flux through the pentose phosphate pathway, but it has also provided additional information about the cycling of metabolites through the non-oxidative portion of the pentose phosphate pathway. Our evidence from experiments with [1-¹³C]-, [2-¹³C]-, and [3-¹³C]d-glucoses indicates that there is an observable reverse flux of fructose 6-phosphate through the reactions catalyzed by transketolase and transaldolase, even in the presence of a net flux through the pentose phosphate pathway.     

Localisation of acidic and basic fibroblast growth factors during mouse palate development and their effects on mouse palate mesenchyme cells in vitro

Summary The distribution of acidic and basic fibroblast growth factors (aFGF, bFGF) was mapped during mouse embryonic palate development. Generally, they localised most intensely in the basement membrane and epithelia rather than the mesenchyme. Localisation was predominantly restricted to the palatal nasal, and medial edge epithelia. Staining was particularly intense in the medial edge epithelia at the time of mid-line epithelial seam formation. Intense staining persisted in the epithelia of the degenerating seam and later in the oral and nasal epithelial triangles. Mouse embryonic palate mesenchyme (MEPM) cells cultured in vitro on a variety of substrata (on plastic, on the surface of a collagen gel and within a collagen gel) responded to treatment with aFGF or bFGF. These responses were modulated by the culture substratum. The FGFs stimulated MEPM cell proliferation on plastic and on collagen, but inhibited cell growth in collagen. The FGFs had little effect on protein production when cells were cultured on plastic, but caused a large reduction in on-collagen and incollagen cultures. This reduction was greater in collagenous than non-collagenous proteins. Generally, treatment with FGFs stimulated the production of glycosaminoglycans (GAGs), particularly hyaluronan (HA) and dermatan sulphate (DS). In addition, the size class of HA was shifted to a higher molecular weight form. These data indicate that aFGF and bFGF may play a role in modulating mesenchymal cell matrix biosynthesis, so facilitating palatal epithelial seam degeneration. Correspondence to: M.W.J. Ferguson