Raman spectroscopy of liver alcohol dehydrogenase

We report the Raman spectrum of liver alcohol dehydrogenase in solution. The enzyme's secondary structure as determined from an examination of the Raman bands is slightly different than that found in crystals by X-ray diffraction.     

Comparative analysis of zygospore transcripts during early germination in Chlamydomonas reinhardtii

The unicellular green alga Chlamydomonas reinhardtii has a haplontic life cycle, and forms diploid zygotes for reproduction. The zygospore, a sporulating zygote, begins germination in response to light signals, generating haploid progenies and inducing several cell-biological events; e.g., DNA synthesis and meiotic division, successively. Their regulatory mechanisms remain largely unknown, so we focused on the early stages of germination and analyzed the dynamics of gene expression associated with the germination process. The gene expression levels of zygospores at 1 and 6 h after light exposure were analyzed by a next-generation sequencing platform, the 454 GS Junior. At 6 h, the photosynthesis pathway, including its antenna proteins and two methionine metabolism-related genes (methionine synthase and sulfite reductase), were up-regulated compared to 1 h after light exposure. Meanwhile, three uncharacterized genes that contained an antibiotic biosynthesis monooxygenase domain and an HSP20/alpha crystallin family protein were specifically expressed at 1 h after light exposure. These gene expressions were also verified by quantitative real-time PCR analysis. These results suggest that the photosynthesis and methionine synthesis pathways, both of which occur in the chloroplast, are activated in zygospores at around 6 h after light exposure, and that some polyketides and/or a small heat shock protein may be related to the initiation of zygospore germination.     

Bovine TWINKLE and mitochondrial ribosomal protein L43 genes are regulated by an evolutionary conserved bidirectional promoter

TWINKLE is a mitochondrial DNA helicase playing an important role in mitochondrial DNA replication. In human, mutations in this gene cause progressive external ophtalmoplegia and mitochondrial DNA depletion syndrome-7. TWINKLE is well conserved among multicellular eukaryotes and is believed to be a key regulator of mitochondrial DNA copy number in mammals.     

Proliferation and copy number variation of BEL-like long terminal repeat retrotransposons within the Diabrotica virgifera virgifera genome

The proliferation of retrotransposons within a genome can contribute to increased size and affect the function of eukaryotic genes. BEL/Pao-like long-terminal repeat (LTR) retrotransposons were annotated from the highly adaptable insect species Diabrotica virgifera virgifera, the Western corn rootworm, using survey sequences from bacterial artificial chromosome (BAC) inserts and contigs derived from a low coverage next-generation genome sequence assembly. Eleven unique D. v. virgifera BEL elements were identified that contained full-length gag–pol coding sequences, whereas 88 different partial coding regions were characterized from partially assembled elements. Estimated genome copy number for full and partial BEL-like elements ranged from ~ 8 to 1582 among individual contigs using a normalized depth of coverage (DOC) among Illumina HiSeq reads (total genome copy number ~ 8821). BEL element copy number was correlated among different D. v. virgifera populations (R² = 0.9846), but individual element numbers varied ≤ 1.68-fold and the total number varied by ~ 527 copies. These data indicate that BEL element proliferation likely contributed to a large genome size, and suggest that differences in copy number are a source of genetic variability among D. v. virgifera.     

Digital gene expression analysis of the pathogenesis and therapeutic mechanisms of ligustrazine and puerarin in rat atherosclerosis

Atherosclerosis (AS) is the leading cause of death in modern societies. Active substance from Traditional Chinese Medicine has been used for the treatment of AS, such as ligustrazine and puerarin. However, the pathogenesis of AS and the curative mechanisms of ligustrazine and puerarin stay unclear. In this work, we attempted to figure out these questions using a rat AS model and digital gene expression (DGE) system. Our results showed that DGE sequencing outcomes were high quality and reproductively. Differentially expressed genes were obtained from different comparisons. The Gene Ontology (GO) analysis revealed that mainly enriched GO terms due to the drug treatment were the same as those obtained from the control group vs. the AS model group. Pathway analysis indicated that metabolic pathways, oxidative phosphorylation, and PPAR single pathways were enriched in all comparisons. Our work provided a comprehensive basis for a better understanding of the pathogenesis of AS and the curative mechanisms of ligustrazine and puerarin.     

Structure of a Double Transmembrane Fragment of a G-Protein-Coupled Receptor in Micelles

The structure and dynamic properties of an 80-residue fragment of Ste2p, the G-protein-coupled receptor for α-factor of Saccharomyces cerevisiae, was studied in LPPG micelles with the use of solution NMR spectroscopy. The fragment Ste2p(G31-T110) (TM1-TM2) consisted of 19 residues from the N-terminal domain, the first TM helix (TM1), the first cytoplasmic loop, the second TM helix (TM2), and seven residues from the first extracellular loop. Multidimensional NMR experiments on [¹⁵N], [¹⁵N, ¹³C], [¹⁵N, ¹³C, ²H]-labeled TM1-TM2 and on protein fragments selectively labeled at specific amino acid residues or protonated at selected methyl groups resulted in >95% assignment of backbone and side-chain nuclei. The NMR investigation revealed the secondary structure of specific residues of TM1-TM2. TALOS constraints and NOE connectivities were used to calculate a structure for TM1-TM2 that was highlighted by the presence of three α-helices encompassing residues 39-47, 49-72, and 80-103, with higher flexibility around the internal Arg⁵⁸ site of TM1. RMSD values of individually superimposed helical segments 39-47, 49-72, and 80-103 were 0.25 ± 0.10 Å, 0.40 ± 0.13 Å, and 0.57 ± 0.19 Å, respectively. Several long-range interhelical connectivities supported the folding of TM1-TM2 into a tertiary structure typified by a crossed helix that splays apart toward the extracellular regions and contains considerable flexibility in the G⁵⁶VRSG⁶⁰ region. ¹⁵N-relaxation and hydrogen-deuterium exchange data support a stable fold for the TM parts of TM1-TM2, whereas the solvent-exposed segments are more flexible. The NMR structure is consistent with the results of biochemical experiments that identified the ligand-binding site within this region of the receptor.     

西藏普若岗日冰帽15世纪以来植被与生态环境变化的孢粉记录

本文提供西藏普若岗日冰芯高分辨率的孢粉记录,证实普若岗日冰帽15世纪以来植被主要经历由寒冷干旱荒漠草原向寒冷潮湿的草甸草原和温暖干旱草原发展的演替过程.在大约550年来植被与生态环境变化中,明显出现AD1500-1515年(7 500-7 300cm)、ADl565-1575年(7 200-7 000cm)以及AD1635-1640年(6 300-6 200cm)期间是当地土壤和空气较为湿润的时期,发育草甸草原植被.在AD1770-1800年(4 700-4 200cm)、AD1815-1825年(4 000-3 800cm)、AD1850-1865(3 400-3 200cm)以及ADl 980年(500cm)以后是气温升高时期,气候温暖干燥,干旱草原植被逐渐扩大.冰芯记录的草原和草甸植被中主要植物花粉的百分含量与高原中部历年夏季温度呈正相关,推算最近150年内在19世纪70、90年代和20世纪90年代曾出现高于现今当地气温约1.9℃的高温期,而在19世纪60、80年代和20世纪初,20世纪50和60-70年代是相对寒冷的时期.过去100年中20世纪晚期的渐暖现象尤其明显,与整个青藏高原年平均温度显著相关,也与青藏高原记录的冰川缩小较一致.     

A comparison of ring-width and event-year chronologies derived from white oak (Quercus alba) and northern red oak (Quercus rubra), southwestern Quebec, Canada

In dendrochronology, ring width has been a variable of choice when assessing the radial growth–climate association of tree species. We compared ring-width and event-year chronologies from a dendroclimatic perspective using both white oak (Quercus alba L.) and northern red oak (Quercus rubra L.). The study was conducted in three regions of the Ottawa valley in southern Québec. Twelve mixed red and white oak stands were selected and for each oak species, 12 chronologies were developed from tree-ring measurement and 12 others were derived using visual assessment of narrow or wide rings (event years). Ring-width and event-year chronologies gave almost identical results and revealed the prevalence of drought in the early growing season as the most influential factor in both species. This study emphasizes the utility of event-year chronologies in tree-ring studies and their comparativeness with ring width. Establishing event-year chronologies has the advantage of being faster than measuring ring width, it does not necessitate complex equipment and depending on the purpose of the study may prove to be at least comparable. The choice of species, their mean sensitivity, the ability to recognize narrow or large rings as well as the number of trees and sites to analyze may, however, be factors to consider when choosing to use event-year chronologies over the more commonly used ring-width ones.