The role of olfactory cues in mother–pup,groupmate, and sex recognition of lesser flat‐headed bats,Tylonycteris pachypus

Tylonycteris pachypus is a gregarious bat species with tens of individuals in a colony. The mechanisms by which mother bats recognize their pups and adult bats recognize each other are not clear. We hypothesized that such recognition is achieved by chemical discrimination and performed experiments to test the hypothesis. Results showed that mother bats were much more attracted to the scent from their own pups. For adult bats, females were attracted to the scent from both male and female groupmates but had a higher preference to the scent from female than from male groupmates. Male bats were much more attracted to the scent from male groupmates while showed no preference to the scent from female groupmates. Within a group, both female and male bats had no difference in preference to the scent from the same or opposite sex. These results suggest that mother–pup and groupmate recognition of T. pachypus can be achieved by olfactory cues.     

SIDD: A Semantically Integrated Database towards a Global View of Human Disease

Background

A number of databases have been developed to collect disease-related molecular, phenotypic and environmental features (DR-MPEs), such as genes, non-coding RNAs, genetic variations, drugs, phenotypes and environmental factors. However, each of current databases focused on only one or two DR-MPEs. There is an urgent demand to develop an integrated database, which can establish semantic associations among disease-related databases and link them to provide a global view of human disease at the biological level. This database, once developed, will facilitate researchers to query various DR-MPEs through disease, and investigate disease mechanisms from different types of data.

Methodology

To establish an integrated disease-associated database, disease vocabularies used in different databases are mapped to Disease Ontology (DO) through semantic match. 4,284 and 4,186 disease terms from Medical Subject Headings (MeSH) and Online Mendelian Inheritance in Man (OMIM) respectively are mapped to DO. Then, the relationships between DR-MPEs and diseases are extracted and merged from different source databases for reducing the data redundancy.

Conclusions

A semantically integrated disease-associated database (SIDD) is developed, which integrates 18 disease-associated databases, for researchers to browse multiple types of DR-MPEs in a view. A web interface allows easy navigation for querying information through browsing a disease ontology tree or searching a disease term. Furthermore, a network visualization tool using Cytoscape Web plugin has been implemented in SIDD. It enhances the SIDD usage when viewing the relationships between diseases and DR-MPEs. The current version of SIDD (Jul 2013) documents 4,465,131 entries relating to 139,365 DR-MPEs, and to 3,824 human diseases. The database can be freely accessed from: http://mlg.hit.edu.cn/SIDD.     

西双版纳热带季节雨林的粗死木质残体及其养分元素

对西双版纳热带季节雨林的粗死木质残体及养分元素贮量进行了研究。结果表明,西双版纳热带季节雨林粗死木质残体的贮量为16.2 t·hm^-2,约占地上活体生物量的4%左右。其中枯立木占32.5%,倒木占33.2%,倒木残体占12.6%,大枝占21.7%。本研究的粗死木质残体贮量低于巴西和东南亚的热带雨林,处于全球热带雨林的下限。粗死木质残体的氮、磷、钾、钙、镁5种元素的贮量分别为61.8、3.4、30.4、118.3和16.5 kg·hm^-2。其中倒木所占比例最大,为31.9%～44.8%;枯立木次之（21.5%～28.7%）;倒木残体占10.3%～25.5%;3个径级的大枝占14.4%～28.9%。枯立木的C/N、C/P和N/P要高于倒木、倒木残体和大枝。     

Epitranscriptomic technologies and analyses

RNA can interact with RNA-binding proteins(RBPs), mRNA, or other non-coding RNAs(ncRNAs) to form complex regulatory networks. High-throughput CLIP-seq, degradome-seq, and RNA-RNA interactome sequencing methods represent powerful approaches to identify biologically relevant ncRNA-target and protein-ncRNA interactions. However, assigning ncRNAs to their regulatory target genes or interacting RNA-binding proteins(RBPs) remains technically challenging. Chemical modifications to mRNA also play important roles in regulating gene expression. Investigation of the functional roles of these modifications relies highly on the detection methods used. RNA structure is also critical at nearly every step of the RNA life cycle. In this review, we summarize recent advances and limitations in CLIP technologies and discuss the computational challenges of and bioinformatics tools used for decoding the functions and regulatory networks of ncRNAs. We also summarize methods used to detect RNA modifications and to probe RNA structure.     

Temporal properties of dual-peak responses of mouse retinal ganglion cells and effects of inhibitory pathways

Dual-peak responses of retinal ganglion cells (RGCs) are observed in various species, previous researches suggested that both response peaks were involved in retinal information coding. In the present study, we investigated the temporal properties of the dual-peak responses recorded in mouse RGCs elicited by spatially homogeneous light flashes and the effect of the inhibitory inputs mediated by GABAergic and/or glycinergic pathways. We found that the two peaks in the dual-peak responses exhibited distinct temporal dynamics, similar to that of short-latency and long-latency single-peak responses respectively. Pharmacological studies demonstrated that the application of exogenous GABA or glycine greatly suppressed or even eliminated the second peak of the cells’ firing activities, while little change was induced in the first peak. Co-application of glycine and GABA led to complete elimination of the second peak. Moreover, application of picrotoxin or strychnine induced dual-peak responses in some cells with transient responses by unmasking a second response phase. These results suggest that both GABAergic and glycinergic pathways are involved in the dual-peak responses of the mouse RGCs, and the two response peaks may arise from distinct pathways that would converge on the ganglion cells.     

Growth characteristics of Protoheliolites norvegicus (Tabulata; Upper Ordovician; Estonia)

Protoheliolites is an early heliolitine coral characterized by closely spaced corallites separated in places by sparse coenenchyme. Growth characteristics in the type species, P. norvegicus, are revealed by detailed analysis based on serial peels and thin sections of coralla from the uppermost Katian of north‐western Estonia. Colonies of this species had a strong ability to recover from damage and partial mortality, resulting in various forms of rejuvenation, regeneration, fusion and reorganization of corallites; in some cases, this involved relatively large areas of undifferentiated soft parts. The shells of commensal cornulitids became enclosed in host coralla during colony growth. Coralla of P. norvegicus exhibit distinctive growth cycles due to responses to seasonal changes. The production of new corallites by coenenchymal increase usually occurred in low‐density bands, in which corallites generally display round to subrounded transverse outlines. In high‐density bands, the corallites became crenulated, their wall thickness increased, septal development was more pronounced, and the amount of coenenchyme increased. In addition to these cyclomorphic changes, there were significant astogenetic changes during growth. Compared with the early stage of colony development, distinctive characteristics in the late astogenetic stage include a decrease in the growth rate of the colony, better coordination among corallites, maximum development of corallite crenulations and septa in high‐density bands, more numerous coenenchymal tubules and a greater proportion of corallum area occupied by coenenchyme. In general, the role of polyps in determining morphological characteristics of individual corallites, such as tabularium area, corallite crenulations and wall thickness, was subordinate to the astogeny of the colony. Growth characteristics including colony‐wide coordination of polyp behaviour and subjugation of individuals to restore the colony following damage suggest a strong astogenetic control and high level of colony integration. Protoheliolites probably arose from a heliolitine genus rather than from a nonheliolitine group as some authors have proposed.     

急性缺血性脑卒中患者血清GAL3、CXCL12水平与病情严重程度和预后的关系研究

目的:探讨急性缺血性脑卒中(AIS)患者血清半乳糖凝集素3(GAL3)、血清趋化因子12(CXCL12)水平与病情严重程度和预后的关系。方法:选取成都市第五人民医院于2016年2月～2018年9月期间接收的AIS患者138例为观察组,另选取同期来该院行健康体检的志愿者60例为对照组。其中观察组根据美国国立卫生研究所中风量表(NIHSS)评分分为轻症组(n=42,4分),中症组(n=61,4～15分),重症组(n=35,15分),根据改良RABKIN量表(m RS)评分分为预后良好组(n=82)和预后不良组(n=56)。比较对照组、观察组的血清GAL3、CXCL12水平,分析不同NIHSS得分、不同预后的血清GAL3、CXCL12水平,采用Pearson相关性分析血清GAL3、CXCL12水平与NIHSS评分、m RS评分的相关性。结果:观察组血清GAL3、CXCL12水平均显著高于对照组,差异有统计学意义(P0.05)。重症组、中症组AIS患者血清GAL3、CXCL12水平高于轻症组,且重症组高于中症组,差异有统计学意义(P0.05)。预后不良组的AIS患者血清GAL3、CXCL12水平均高于预后良好组,差异有统计学意义(P0.05)。Pearson相关性分析结果可知,血清GAL3、CXCL12水平与NIHSS评分、m RS评分均呈正相关(P0.05)。结论:AIS患者的血清GAL3、CXCL12水平均异常升高,且其升高程度与AIS患者病情严重程度及预后息息相关。     

The pKa of the protonated Schiff bases of gecko cone and octopus visual pigments.

A visual pigment is composed of retinal bound to its apoprotein by a protonated Schiff base linkage. Light isomerizes the chromophore and eventually causes the deprotonation of this Schiff base linkage at the meta II stage of the bleaching cycle. The meta II intermediate of the visual pigment is the active form of the pigment that binds to and activates the G protein transducin, starting the visual cascade. The deprotonation of the Schiff base is mandatory for the formation of meta II intermediate. We studied the proton binding affinity, pKa, of the Schiff base of both octopus rhodopsin and the gecko cone pigment P521 by spectral titration. Several fluorinated retinal analogs have strong electron withdrawing character around the Schiff base region and lower the Schiff base pKa in model compounds. We regenerated octopus and gecko visual pigments with these fluorinated and other retinal analogs. Experiments on these artificial pigments showed that the spectral changes seen upon raising the pH indeed reflected the pKa of the Schiff base and not the denaturation of the pigment or the deprotonation of some other group in the pigment. The Schiff base pKa is 10.4 for octopus rhodopsin and 9.9 for the gecko cone pigment. We also showed that although the removal of Cl- ions causes considerable blue-shift in the gecko cone pigment P521, it affects the Schiff base pKa very little, indicating that the lambda max of visual pigment and its Schiff base pKa are not tightly coupled.     

Insights into the fluoride-resistant regulation mechanism of <Emphasis Type="Italic">Acidithiobacillus ferrooxidans</Emphasis> ATCC 23270 based on whole genome microarrays

Acidophilic microorganisms involved in uranium bioleaching are usually suppressed by dissolved fluoride ions, eventually leading to reduced leaching efficiency. However, little is known about the regulation mechanisms of microbial resistance to fluoride. In this study, the resistance of Acidithiobacillus ferrooxidans ATCC 23270 to fluoride was investigated by detecting bacterial growth fluctuations and ferrous or sulfur oxidation. To explore the regulation mechanism, a whole genome microarray was used to profile the genome-wide expression. The fluoride tolerance of A. ferrooxidans cultured in the presence of FeSO₄ was better than that cultured with the S⁰ substrate. The differentially expressed gene categories closely related to fluoride tolerance included those involved in energy metabolism, cellular processes, protein synthesis, transport, the cell envelope, and binding proteins. This study highlights that the cellular ferrous oxidation ability was enhanced at the lower fluoride concentrations. An overview of the cellular regulation mechanisms of extremophiles to fluoride resistance is discussed.