A three-dimensional model of the U1 small nuclear ribonucleoprotein particle

Most of the pre-mRNAs in the eukaryotic cell are comprised of protein-coding exons and non-protein-coding introns. The introns are removed and the exons are ligated together, or spliced, by a large, macromolecular complex known as the spliceosome. This RNA-protein assembly is made up of five uridine-rich small nuclear RNAs (U1-, U2-, U4-, U5- and U6-snRNA) as well over 300 proteins, which form small nuclear ribonucleoprotein particles (snRNPs). Initial recognition of the 5′ exon/intron splice site is mediated by the U1 snRNP, which is composed of the U1 snRNA as well as at least ten proteins. By combining structural informatics tools with the available biochemical and crystallographic data, we attempted to simulate a complete, three dimensional U1 snRNP from the silk moth, Bombyx mori. Comparison of our model with empirically derived crystal structures and electron micrographs pinpoints both the strengths and weaknesses in the in silico determination of macromolecular complexes. One of the most striking differences between our model and experimentally generated structures is in the positioning of the U1 snRNA stem-loops. This highlights the continuing difficulties in generating reliable, complex RNA structures; however, three-dimensional modeling of individual protein subunits by threading provided models of biological significance and the use of both automated and manual docking strategies generated a complex that closely reflects the assembly found in nature. Yet, without utilizing experimentally-derived contacts to select the most likely docking scenario, ab initio docking would fall short of providing a reliable model. Our work shows that the combination of experimental data with structural informatics tools can result in generation of near-native macromolecular complexes.     

Using diffusion distances for flexible molecular shape comparison

Background  

Many molecules are flexible and undergo significant shape deformation as part of their function, and yet most existing molecular shape comparison (MSC) methods treat them as rigid bodies, which may lead to incorrect shape recognition.     

Size-dependent mortality in a Neotropical savanna tree: the role of height-related adjustments in hydraulic architecture and carbon allocation

Size-related changes in hydraulic architecture, carbon allocation and gas exchange of Sclerolobium paniculatum (Leguminosae), a dominant tree species in Neotropical savannas of central Brazil (Cerrado), were investigated to assess their potential role in the dieback of tall individuals. Trees greater than ∼6-m-tall exhibited more branch damage, larger numbers of dead individuals, higher wood density, greater leaf mass per area, lower leaf area to sapwood area ratio (LA/SA), lower stomatal conductance and lower net CO₂ assimilation than small trees. Stem-specific hydraulic conductivity decreased, while leaf-specific hydraulic conductivity remained nearly constant, with increasing tree size because of lower LA/SA in larger trees. Leaves were substantially more vulnerable to embolism than stems. Large trees had lower maximum leaf hydraulic conductance ( K _leaf) than small trees and all tree sizes exhibited lower K _leaf at midday than at dawn. These size-related adjustments in hydraulic architecture and carbon allocation apparently incurred a large physiological cost: large trees received a lower return in carbon gain from their investment in stem and leaf biomass compared with small trees. Additionally, large trees may experience more severe water deficits in dry years due to lower capacity for buffering the effects of hydraulic path-length and soil water deficits.     

Microbial Symbionts Accelerate Wound Healing via the Neuropeptide Hormone Oxytocin

Wound healing capability is inextricably linked with diverse aspects of physical fitness ranging from recovery after minor injuries and surgery to diabetes and some types of cancer. Impact of the microbiome upon the mammalian wound healing process is poorly understood. We discover that supplementing the gut microbiome with lactic acid microbes in drinking water accelerates the wound-healing process to occur in half the time required for matched control animals. Further, we find that Lactobacillus reuteri enhances wound-healing properties through up-regulation of the neuropeptide hormone oxytocin, a factor integral in social bonding and reproduction, by a vagus nerve-mediated pathway. Bacteria-triggered oxytocin serves to activate host CD4+Foxp3+CD25+ immune T regulatory cells conveying transplantable wound healing capacity to naive Rag2-deficient animals. This study determined oxytocin to be a novel component of a multi-directional gut microbe-brain-immune axis, with wound-healing capability as a previously unrecognized output of this axis. We also provide experimental evidence to support long-standing medical traditions associating diet, social practices, and the immune system with efficient recovery after injury, sustained good health, and longevity.     

The impact of special issues

With support from many authors from many different scientific fields,Zoological Research(ZR)successfully released eight special issues from 2011 to 2014 on various topics,including Animal Ecology and Resources,Animal Genetic Diversity,Development and Evolution,Fish Diversity and Primates and Animal Models of Human Diseases.These special issues strongly align with our aims and scope,which have been     

Tooth Eruption Results from Bone Remodelling Driven by Bite Forces Sensed by Soft Tissue Dental Follicles: A Finite Element Analysis

Intermittent tongue, lip and cheek forces influence precise tooth position, so we here examine the possibility that tissue remodelling driven by functional bite-force-induced jaw-strain accounts for tooth eruption. Notably, although a separate true ‘eruptive force’ is widely assumed, there is little direct evidence for such a force. We constructed a three dimensional finite element model from axial computerized tomography of an 8 year old child mandible containing 12 erupted and 8 unerupted teeth. Tissues modelled included: cortical bone, cancellous bone, soft tissue dental follicle, periodontal ligament, enamel, dentine, pulp and articular cartilage. Strain and hydrostatic stress during incisive and unilateral molar bite force were modelled, with force applied via medial and lateral pterygoid, temporalis, masseter and digastric muscles. Strain was maximal in the soft tissue follicle as opposed to surrounding bone, consistent with follicle as an effective mechanosensor. Initial numerical analysis of dental follicle soft tissue overlying crowns and beneath the roots of unerupted teeth was of volume and hydrostatic stress. To numerically evaluate biological significance of differing hydrostatic stress levels normalized for variable finite element volume, ‘biological response units’ in Nmm were defined and calculated by multiplication of hydrostatic stress and volume for each finite element. Graphical representations revealed similar overall responses for individual teeth regardless if incisive or right molar bite force was studied. There was general compression in the soft tissues over crowns of most unerupted teeth, and general tension in the soft tissues beneath roots. Not conforming to this pattern were the unerupted second molars, which do not erupt at this developmental stage. Data support a new hypothesis for tooth eruption, in which the follicular soft tissues detect bite-force-induced bone-strain, and direct bone remodelling at the inner surface of the surrounding bony crypt, with the effect of enabling tooth eruption into the mouth.     

斑纹小贻贝(Mytella strigata)基础生物学与生物入侵

生物入侵是继栖息地破坏之后，全球生物多样性丧失的第二大驱动因素。近年来，原产于南美洲地区的斑纹小贻贝（Mytella strigata）在印度-西太平洋海区被陆续报道，而我国台湾、广东、海南、福建、广西等省份同样发现斑纹小贻贝，且其已经建立可自我维持的种群。但是，作为一种新型入侵生物，斑纹小贻贝尚未引起国内海洋管理部门和科研人员足够重视，亟待查明其在我国沿海的分布现状、扩散趋势和生态影响等，为斑纹小贻贝的检测、监测、防控和管理提供科学依据。综述了斑纹小贻贝的基础生物学特征和全球生物入侵现状，发现国内的斑纹小贻贝源于南美洲加勒比海地区，于2014年左右通过船舶压舱水或船体生物污损的形式侵入我国南方沿海并迅速扩散。此外，斑纹小贻贝在我国的生物入侵处于"引进-传播"阶段，即将大规模扩繁，因此亟需开展应急清除行动。     

县域城镇空间形态与居住建筑能耗关联性的连续尺度研究——以浙江长兴、福建连江为例

居住建筑能耗受建筑周边空间形态的直接影响，确定空间形态低碳效应及其最佳尺度将有助于实现县域城镇低碳转型。以浙江省长兴县、福建省连江县为例，共计选取49个具有代表性的居住建筑样本，采用GIS分析与数理统计相结合的方式，在居住建筑1800m半径范围内，以200m为间隔建立缓冲区，开展全年、最冷月份能耗期及最热月份能耗期建筑能耗与周边空间形态关联性的连续尺度研究。结果表明：(1)道路密度、开发密度、容积率均与建筑能耗呈正相关，但各指标对应的能耗时期、尺度范围有较大差异。(2)水面率、土地利用混合度是与建筑能耗相关的共性指标，但在不同地区的正负效应及尺度范围不同；(3)影响浙闽地区县域城镇最热月份能耗期能耗的关键形态因子为1000m-道路密度、800m-水面率、1600m-开放空间率；影响连江最冷月份能耗期能耗的关键形态因子为800m-水面率。(4)就控碳单元设置而言，长兴县可重点关注1000—1200m半径范围，连江县可重点关注800—1000m、1400m半径范围。(5)浙闽地区县域城镇特性指标为开放空间率，与最热月份能耗期建筑能呈负相关；长兴县特性指标为容积率、水岸密度，分别与全年、最冷...     

基于MODIS NDVI的长江中游区域植被动态及与气候因子的关系

基于1999-2015年的MODIS NDVI时间序列遥感数据，应用趋势分析、变异系数、重标极差分析和偏相关分析等方法，分析了长江中游的植被时空变化特征及其与气象因子的关系。结果表明，长江中游地区NDVI均值总体上呈上升趋势（从0.72增加到0.80）。从空间分布来看，NDVI低值区域（0.1-0.5）占1.40%，高值区域（>0.7）占87.15%；NDVI空间格局呈"西高东低、北高南低"的分布特征，低值区域表现为以三省省会城市为中心向外辐射。Hurst指数显示，研究区大部分区域（60.54%）的NDVI变化趋势具有不确定性，持续性改善区域（34.78%）主要分布在西部山地区，持续性退化区域（3.26%）主要分布在人类活动频繁的较发达城市区域。在年际尺度上，研究区NDVI与各气象因子关系均不显著；月际尺度上，NDVI与降水、相对湿度和日照时数显著相关，降水和日照时数有明显的时滞性。区域内NDVI动态趋势以不确定性发展为主，城市群周边NDVI呈现持续退化的区域应该引起关注。