湖南鱼类新记录4种

2004年8月～2005年7月,在湖南安化进行鱼类资源调查期间,发现湖南鱼类新记录4种：漓江副沙鳅、盎堂拟鲿、越南鲇和司氏（鱼央）.     

Morphological Alteration of Golgi Apparatus and Subcellular Compartmentalization of TGF-β1 in Golgi Apparatus in Gerbils Following Transient Forebrain Ischemia

Golgi apparatus (GA) is a very important organelle involved in the metabolism of numerous proteins. TGF-β1 plays an important role in supporting neuronal survival after ischemic insults. Little is known, however, about the morphological alteration of GA and subcellular compartmentalization of TGF-β1 in brain after ischemia. Therefore, our present study was designed to check for GA morphological alterations and TGF-β1 subcellular localization. GA immunoreactivities were examined in the somatosensory cortex of gerbils after 10 min transient forebrain ischemia. Confocal Immunofluorographs of TGF-β1 and TGN38 were also taken. Results indicated that no fragmentation of GA was found in gerbils of norm, shams and 6, 24 and 72 h postocclusion, but some of the cortical cells showed fragmentation of GA in gerbils 7 days postocclusion. TGF-β1 was colocalized with TGN38, a marker molecule for the GA. We conclude that there was morphological alterations of GA and TGF-β1 was present in GA in the somatosensory cortex after 10 min ischemia.     

iGibbs: improving Gibbs motif sampler for proteins by sequence clustering and iterative pattern sampling

The motif prediction problem is to predict short, conserved subsequences that are part of a family of sequences, and it is a very important biological problem. Gibbs is one of the first successful motif algorithms and it runs very fast compared with other algorithms, and its search behavior is based on the well-studied Gibbs random sampling. However, motif prediction is a very difficult problem and Gibbs may not predict true motifs in some cases. Thus, the authors explored a possibility of improving the prediction accuracy of Gibbs while retaining its fast runtime performance. In this paper, the authors considered Gibbs only for proteins, not for DNA binding sites. The authors have developed iGibbs, an integrated motif search framework for proteins that employs two previous techniques of their own: one for guiding motif search by clustering sequences and another by pattern refinement. These two techniques are combined to a new double clustering approach to guiding motif search. The unique feature of their framework is that users do not have to specify the number of motifs to be predicted when motifs occur in different subsets of the input sequences since it automatically clusters input sequences into clusters and predict motifs from the clusters. Tests on the PROSITE database show that their framework improved the prediction accuracy of Gibbs significantly. Compared with more exhaustive search methods like MEME, iGibbs predicted motifs more accurately and runs one order of magnitude faster.     

Synthesis of alginic acid-poly[2-(diethylamino)ethyl methacrylate] monodispersed nanoparticles by a polymer-monomer pair reaction system

In this paper, alginic acid-poly(2-(diethylamino)ethyl methacrylate) (ALG-PDEA) nanoparticles were successfully prepared in aqueous medium using a polymer-monomer pair reaction system consisting of the anionic alginic acid (ALG) and the cationic 2-(diethylamino)ethyl methacrylate (DEA), without any aid of surfactants or organic solvents. The ALG-PDEA nanoparticles were monodispersed and stable in aqueous solution. Nanoparticles with desired size could be obtained by varying the amount of initiator or changing the concentration of reactants in solution, which renders this system highly controllable. After the ALG moiety was gelled by Ca(2+), the stability of the nanoparticles in basic or high salt concentration solutions could be notably enhanced. A pH-sensitive anticancer agent, hydroxycamptothecin (HCPT), was encapsulated in ALG-PDEA nanoparticles, and preliminary in vitro release as well as cytotoxicity experiments were carried out. It is found that this system seems to be a very promising carrier for the loading and delivery of labile drugs, taking into account that the preparation procedure is simple, mild, and organic solvent- and surfactant-free. Moreover, the abundant functional groups on the particle surface, such as carboxyls and hydroxyls, allow subsequent chemical modification, which may further unleash the potential of such a system in either biomedical applications or in the construction of other functional mesoscopic architectures.     

近20年来京津冀地区土壤风蚀扬尘颗粒物排放变化

京津冀地区是我国大气污染严重区域,土壤扬尘颗粒物排放变化研究对于改善京津冀地区空气质量具有重要意义。收集2000-2019年京津冀地区气候、土壤、植被覆盖数据,分析近20年来京津冀地区土壤扬尘颗粒物排放变化,揭示其变化的影响因素。结果显示2000-2019年京津冀地区土壤扬尘源总悬浮颗粒物（TSP）排放系数均值为1.79 t km^-2 a^-1,其中PM10占8.99%,PM2.5占0.25%。近20年土壤扬尘源TSP排放系数具有下降趋势,PM10和PM2.5排放系数变化过程与TSP一致。上述变化主要受气候因子变化影响,其次受植被覆盖度影响。分析发现近20年来京津冀地区土壤扬尘源TSP排放系数变化主要受年降水量影响。沧州市、天津市和石家庄市土壤扬尘源TSP、PM10和PM2.5排放系数均值较高,张家口市、保定市和沧州市土壤扬尘源TSP排放量占京津冀地区总量的19.18%、12.98%和11.63%。耕地土壤扬尘排放量最大占京津冀地区总量的59.83%,是抑制土壤扬尘源颗粒物排放的重点关注对象,其次为草地占15.66%。2019年邢台市土壤扬尘源PM10排放占观测值比例最高为12.66%,石家庄市和天津市占比也较高分别为11.09%和10.30%,沧州市和邯郸市占比分别为8.63%和8.02%。上述地区环境管理部门均应关注土壤扬尘源颗粒物排放对空气质量的影响。     

Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs

Small silencing RNAs, including microRNAs, endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), have been shown to play important roles in fine-tuning gene expression, defending virus and controlling transposons. Loss of small silencing RNAs or components in their pathways often leads to severe developmental defects, including lethality and sterility. Recently, non-templated addition of nucleotides to the 3′ end, namely tailing, was found to associate with the processing and stability of small silencing RNAs. Next Generation Sequencing has made it possible to detect such modifications at nucleotide resolution in an unprecedented throughput. Unfortunately, detecting such events from millions of short reads confounded by sequencing errors and RNA editing is still a tricky problem. Here, we developed a computational framework, Tailor, driven by an efficient and accurate aligner specifically designed for capturing the tailing events directly from the alignments without extensive post-processing. The performance of Tailor was fully tested and compared favorably with other general-purpose aligners using both simulated and real datasets for tailing analysis. Moreover, to show the broad utility of Tailor, we used Tailor to reanalyze published datasets and revealed novel findings worth further experimental validation. The source code and the executable binaries are freely available at https://github.com/jhhung/Tailor.     

A comprehensive analysis of root morphological changes and nitrogen allocation in maize in response to low nitrogen stress

The plasticity of root architecture is crucial for plants to acclimate to unfavourable environments including low nitrogen (LN) stress. How maize roots coordinate the growth of axile roots and lateral roots (LRs), as well as longitudinal and radial cell behaviours in response to LN stress, remains unclear. Maize plants were cultivated hydroponically under control (4 mm nitrate) and LN (40 μm ) conditions. Temporal and spatial samples were taken to analyse changes in the morphology, anatomical structure and carbon/nitrogen (C/N) ratio in the axile root and LRs. LN stress increased axile root elongation, reduced the number of crown roots and decreased LR density and length. LN stress extended cell elongation zones and increased the mature cell length in the roots. LN stress reduced the cell diameter and total area of vessels and increased the amount of aerenchyma, but the number of cell layers in the crown root cortex was unchanged. The C/N ratio was higher in the axile roots than in the LRs. Maize roots acclimate to LN stress by optimizing the anatomical structure and N allocation. As a result, axile root elongation is favoured to efficiently find available N in the soil.     

Structural Features of Membrane-bound Glucocerebrosidase and α-Synuclein Probed by Neutron Reflectometry and Fluorescence Spectroscopy

Mutations in glucocerebrosidase (GCase), the enzyme deficient in Gaucher disease, are a common genetic risk factor for the development of Parkinson disease and related disorders, implicating the role of this lysosomal hydrolase in the disease etiology. A specific physical interaction exists between the Parkinson disease-related protein α-synuclein (α-syn) and GCase both in solution and on the lipid membrane, resulting in efficient enzyme inhibition. Here, neutron reflectometry was employed as a first direct structural characterization of GCase and α-syn·GCase complex on a sparsely-tethered lipid bilayer, revealing the orientation of the membrane-bound GCase. GCase binds to and partially inserts into the bilayer with its active site most likely lying just above the membrane-water interface. The interaction was further characterized by intrinsic Trp fluorescence, circular dichroism, and surface plasmon resonance spectroscopy. Both Trp fluorescence and neutron reflectometry results suggest a rearrangement of loops surrounding the catalytic site, where they extend into the hydrocarbon chain region of the outer leaflet. Taking advantage of contrasting neutron scattering length densities, the use of deuterated α-syn versus protiated GCase showed a large change in the membrane-bound structure of α-syn in the complex. We propose a model of α-syn·GCase on the membrane, providing structural insights into inhibition of GCase by α-syn. The interaction displaces GCase away from the membrane, possibly impeding substrate access and perturbing the active site. GCase greatly alters membrane-bound α-syn, moving helical residues away from the bilayer, which could impact the degradation of α-syn in the lysosome where these two proteins interact.     

Neuropeptide Receptors NPR-1 and NPR-2 Regulate Caenorhabditis elegans Avoidance Response to the Plant Stress Hormone Methyl Salicylate

Alternative splicing is prevalent in plants, but little is known about its regulation in the context of developmental and signaling pathways. We describe here a new factor that influences pre-messengerRNA (mRNA) splicing and is essential for embryonic development in Arabidopsis thaliana. This factor was retrieved in a genetic screen that identified mutants impaired in expression of an alternatively spliced GFP reporter gene. In addition to the known spliceosomal component PRP8, the screen recovered Arabidopsis RTF2 (AtRTF2), a previously uncharacterized, evolutionarily conserved protein containing a replication termination factor 2 (Rtf2) domain. A homozygous null mutation in AtRTF2 is embryo lethal, indicating that AtRTF2 is an essential protein. Quantitative RT-PCR demonstrated that impaired expression of GFP in atrtf2 and prp8 mutants is due to inefficient splicing of the GFP pre-mRNA. A genome-wide analysis using RNA sequencing indicated that 13–16% of total introns are retained to a significant degree in atrtf2 mutants. Considering these results and previous suggestions that Rtf2 represents an ubiquitin-related domain, we discuss the possible role of AtRTF2 in ubiquitin-based regulation of pre-mRNA splicing.