The Crystal Structure of the Yeast Hsp40 Ydj1 Complexed with Its Peptide Substrate

AbstractThe mechanisms by which Hsp40 functions as a molecular chaperone to recognize and bind nonnative polypeptides is not understood. We have identified a peptide substrate for Ydj1, a member of the type I Hsp40 from yeast. The structure of the Ydj1 peptide binding fragment and its peptide substrate complex was determined to 2.7 Å resolution. The complex structure reveals that Ydj1 peptide binding fragment forms an L-shaped molecule constituted by three domains. The domain I exhibits a similar protein folds as domain III while the domain II contains two Zinc finger motifs. The peptide substrate binds Ydj1 by forming an extra β strand with domain I of Ydj1. The Leucine residue in the middle of the peptide substrate GWLYEIS inserts its side chain into a hydrophobic pocket formed on the molecular surface of Ydj1 domain I. The Zinc finger motifs located in the Ydj1 domain II are not in the vicinity of peptide substrate binding site

Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants

<p>Abstract</p> <p>Background</p> <p>Wood is a valuable natural resource and a major carbon sink. Wood formation is an important developmental process in vascular plants which played a crucial role in plant evolution. Although genes involved in xylem formation have been investigated, the molecular mechanisms of xylem evolution are not well understood. We use comparative genomics to examine evolution of the xylem transcriptome to gain insights into xylem evolution.</p> <p>Results</p> <p>The xylem transcriptome is highly conserved in conifers, but considerably divergent in angiosperms. The functional domains of genes in the xylem transcriptome are moderately to highly conserved in vascular plants, suggesting the existence of a common ancestral xylem transcriptome. Compared to the total transcriptome derived from a range of tissues, the xylem transcriptome is relatively conserved in vascular plants. Of the xylem transcriptome, cell wall genes, ancestral xylem genes, known proteins and transcription factors are relatively more conserved in vascular plants. A total of 527 putative xylem orthologs were identified, which are unevenly distributed across the <it>Arabidopsis </it>chromosomes with eight hot spots observed. Phylogenetic analysis revealed that evolution of the xylem transcriptome has paralleled plant evolution. We also identified 274 conifer-specific xylem unigenes, all of which are of unknown function. These xylem orthologs and conifer-specific unigenes are likely to have played a crucial role in xylem evolution.</p> <p>Conclusions</p> <p>Conifers have highly conserved xylem transcriptomes, while angiosperm xylem transcriptomes are relatively diversified. Vascular plants share a common ancestral xylem transcriptome. The xylem transcriptomes of vascular plants are more conserved than the total transcriptomes. Evolution of the xylem transcriptome has largely followed the trend of plant evolution.</p

A Real-time Faint Space Debris Detector With Learning-based LCM

With the development of aerospace technology, the increasing population of space debris has posed a great threat to the safety of spacecraft. However, the low intensity of reflected light and high angular velocity of space debris impede the extraction. Besides, due to the limitations of the ground observation methods, small space debris can hardly be detected, making it necessary to enhance the spacecraft's capacity for space situational awareness (SSA). Considering that traditional methods have some defects in low-SNR target detection, such as low effectiveness and large time consumption, this paper proposes a method for low-SNR streak extraction based on local contrast and maximum likelihood estimation (MLE), which can detect space objects with SNR 2.0 efficiently. In the proposed algorithm, local contrast will be applied for crude classifications, which will return connected components as preliminary results, and then MLE will be performed to reconstruct the connected components of targets via orientated growth, further improving the precision. The algorithm has been verified with both simulated streaks and real star tracker images, and the average centroid error of the proposed algorithm is close to the state-of-the-art method like ODCC. At the same time, the algorithm in this paper has significant advantages in efficiency compared with ODCC. In conclusion, the algorithm in this paper is of high speed and precision, which guarantees its promising applications in the extraction of high dynamic targets.Comment: 13 pages, 28 figures, normal articl

Anoxia Treatment for Delaying Skin Browning, Inhibiting Disease Development and Maintaining the Quality of Litchi Fruit

Litchi fruit has a very short shelf life after harvest, so marketers and consumers alike desire longer periods of storage, transportation and distribution. To extend shelf life, anoxia treatments were used for the fruit. Litchi fruit were exposed to pure N2 for 0, 3, 6, 12 or 24 h. They were then kept individually in closed but vented containers for 6 days in the dark at 20 °C and 95–100 % relative humidity. Exposure of litchi fruit to N2 for 3 or 6 h markedly delayed skin browning, reduced rot development and maintained higher concentrations of total soluble solids, titratable acidity and ascorbic acid after 6 days of storage. Anoxia treatment for 24 h reduced browning index, but it accelerated disease development, compared to the control. Thus, a pre-storage pure N2 treatment for 3 or 6 h can be an effective means of reducing rotting while maintaining the physical quality of the fruit

Mineralogy and Geochemistry of Late Permian Coals within the Tongzi Coalfield in Guizhou Province, Southwest China

first_pagesettings Open AccessArticle Mineralogy and Geochemistry of Late Permian Coals within the Tongzi Coalfield in Guizhou Province, Southwest China by Baoqing Li 1,*,Xinguo Zhuang 1,Xavier Querol 1,2,Natalia Moreno 2OrcID,Linjian Yang 3,Yunfei Shangguan 1 andJing Li 1 1 Key Laboratory of Tectonics and Petroleum Resources (China University of Geosciences), Ministry of Education, Wuhan 430074, China 2 Institute of Environmental Assessment and Water Research, CSIC, C/Jordi Girona 18–26, 08034 Barcelona, Spain 3 No. 106 Geological Team of Guizhou Province Geology and Mineral Bureau, Zunyi 563000, China * Author to whom correspondence should be addressed. Minerals 2020, 10(1), 44; https://doi.org/10.3390/min10010044 Received: 18 December 2019 / Revised: 29 December 2019 / Accepted: 30 December 2019 / Published: 31 December 2019 (This article belongs to the Collection Minerals in Coal and Coal Combustion Products) Download PDF Browse Figures Abstract The lowermost Late Permian coal seam (C4 Coal) in the Tongzi Coalfield offers an opportunity to investigate the influence of terrigenous detrital materials from the Qianbei Upland on the mineralogical and geochemical patterns of the C4 Coal. The minerals are mainly dominated by pyrite and, to a lesser extent, tobelite, kaolinite, and calcite, along with traces of Al-oxyhydroxide minerals. The various degrees of marine influence may have resulted in the variation in the amount of Fe-sulfides (e.g., pyrite) and elements having Fe-sulfides affinity. Furthermore, the abundant Fe ions involved in the formation of Fe-sulfides were most likely derived from the claystone on the Qianbei Upland. The tobelite identified in the C4 Coal probably originated from the interaction between pre-existing kaolinite and NH4+ from NH3 released from the thermally affected organic matter at least shortly after the highly volatile bituminous stage under NH4+-rich and K+-poor conditions. The terrigenous detrital materials were derived from two possible sediment-region sources—the Qianbei Upland and Kangdian Upland—which is different from Late Permian coals in Western Guizhou Province. The claystone on the Qianbei Upland may have served as parent rock, as indicated by the presence of the Al-oxyhydroxide minerals as well as low SiO2/Al2O3 ratio (0.66 on average) and low quartz content. Meanwhile, the detrital materials from the Kangdian Upland most likely originated from the erosion of the felsic rocks at the uppermost part of the Kangdian Upland, as evidenced by the high Al2O3/TiO2 ratio (36.0 on average) and the strongly negative Eu anomaly (0.61 on average).The authors would like to give their sincere thanks to No. 106 Geological Team of Guizhou Province Geology for assistance during sampling and Institute of Environmental Assessment and Water Research, CSIC, Spain for assistance during the sample analysis. Also, many thanks are given to academic editor and two anonymous reviewers for their valuable comments on the manuscript.Peer reviewe

Generation and analysis of expressed sequence tags from six developing xylem libraries in Pinus radiata D. Don

<p>Abstract</p> <p>Background</p> <p>Wood is a major renewable natural resource for the timber, fibre and bioenergy industry. <it>Pinus radiata </it>D. Don is the most important commercial plantation tree species in Australia and several other countries; however, genomic resources for this species are very limited in public databases. Our primary objective was to sequence a large number of expressed sequence tags (ESTs) from genes involved in wood formation in radiata pine.</p> <p>Results</p> <p>Six developing xylem cDNA libraries were constructed from earlywood and latewood tissues sampled at juvenile (7 yrs), transition (11 yrs) and mature (30 yrs) ages, respectively. These xylem tissues represent six typical development stages in a rotation period of radiata pine. A total of 6,389 high quality ESTs were collected from 5,952 cDNA clones. Assembly of 5,952 ESTs from 5' end sequences generated 3,304 unigenes including 952 contigs and 2,352 singletons. About 97.0% of the 5,952 ESTs and 96.1% of the unigenes have matches in the UniProt and TIGR databases. Of the 3,174 unigenes with matches, 42.9% were not assigned GO (Gene Ontology) terms and their functions are unknown or unclassified. More than half (52.1%) of the 5,952 ESTs have matches in the Pfam database and represent 772 known protein families. About 18.0% of the 5,952 ESTs matched cell wall related genes in the MAIZEWALL database, representing all 18 categories, 91 of all 174 families and possibly 557 genes. Fifteen cell wall-related genes are ranked in the 30 most abundant genes, including <it>CesA</it>, <it>tubulin</it>, <it>AGP</it>, <it>SAMS</it>, <it>actin</it>, <it>laccase, CCoAMT, MetE</it>, <it>phytocyanin, pectate lyase</it>, <it>cellulase, SuSy</it>, <it>expansin</it>, <it>chitinase </it>and <it>UDP-glucose dehydrogenase</it>. Based on the PlantTFDB database 41 of the 64 transcription factor families in the poplar genome were identified as being involved in radiata pine wood formation. Comparative analysis of GO term abundance revealed a distinct transcriptome in juvenile earlywood formation compared to other stages of wood development.</p> <p>Conclusion</p> <p>The first large scale genomic resource in radiata pine was generated from six developing xylem cDNA libraries. Cell wall-related genes and transcription factors were identified. Juvenile earlywood has a distinct transcriptome, which is likely to contribute to the undesirable properties of juvenile wood in radiata pine. The publicly available resource of radiata pine will also be valuable for gene function studies and comparative genomics in forest trees.</p