Nonlinearities in protein space limit the utility of informatics in protein biophysics

We examine the utility of informatic‐based methods in computational protein biophysics. To do so, we use newly developed metric functions to define completely independent sequence and structure spaces for a large database of proteins. By investigating the relationship between these spaces, we demonstrate quantitatively the limits of knowledge‐based correlation between the sequences and structures of proteins. It is shown that there are well‐defined, nonlinear regions of protein space in which dissimilar structures map onto similar sequences (the conformational switch), and dissimilar sequences map onto similar structures (remote homology). These nonlinearities are shown to be quite common—almost half the proteins in our database fall into one or the other of these two regions. They are not anomalies, but rather intrinsic properties of structural encoding in amino acid sequences. It follows that extreme care must be exercised in using bioinformatic data as a basis for computational structure prediction. The implications of these results for protein evolution are examined. Proteins 2015; 83:1923–1928. © 2015 Wiley Periodicals, Inc.     

Molecular Detection and Characterization of Chinese Yam Mild Mosaic Virus Isolates

An improved RT‐PCR was developed and validated for the detection of Yam mild mosaic virus (YMMV). Sequences of the coat protein core region of 19 Chinese isolates were obtained, and analysis indicated the presence of different genetic variants. Phylogenetic analyses showed that the Chinese isolates were divided into two distinct clusters. Complete genomic sequences of two distinct Chinese variants were determined to be 9527 and 9529 nucleotides long, excluding the 3′ poly (A) tail. Their genomic structure and organization were virtually identical to that of a Brazilian isolate. The two variants shared identity of 87.3% to one another and 83.9–84.6% to the Brazilian variant at the genomic sequence level. Phylogenetic analyses supported that they represented two distinct YMMV lineages.     

Integrated genome sequence and linkage map of physic nut (Jatropha curcas L.), a biodiesel plant

The family Euphorbiaceae includes some of the most efficient biomass accumulators. Whole genome sequencing and the development of genetic maps of these species are important components in molecular breeding and genetic improvement. Here we report the draft genome of physic nut (Jatropha curcas L.), a biodiesel plant. The assembled genome has a total length of 320.5 Mbp and contains 27 172 putative protein‐coding genes. We established a linkage map containing 1208 markers and anchored the genome assembly (81.7%) to this map to produce 11 pseudochromosomes. After gene family clustering, 15 268 families were identified, of which 13 887 existed in the castor bean genome. Analysis of the genome highlighted specific expansion and contraction of a number of gene families during the evolution of this species, including the ribosome‐inactivating proteins and oil biosynthesis pathway enzymes. The genomic sequence and linkage map provide a valuable resource not only for fundamental and applied research on physic nut but also for evolutionary and comparative genomics analysis, particularly in the Euphorbiaceae.     

微流控芯片电泳及其法医学应用

在光学性能良好的Brofloat玻璃电泳芯片上,利用自行搭建的共聚焦激光诱导荧光检测系统,通过对芯片管道表面修饰、筛分介质、分离电场强度、进样方式、电泳温度、进样时间等条件的优化,对含15个STR基因座的法医DNA样品进行电泳分离测试实验.通过对芯片电泳条件优化获得了本电泳系统的最佳条件,成功实现8 min内完成DNA样品片段的分离,表明该微流控芯片电泳系统在法医DNA快速分析方面具有良好的应用前景.     

A long downstream probe-based platform for multiplex target capture

A simple and rapid detection platform was established for multiplex target capture through generating single-strand long downstream probe (ssLDP), which was integrated with the ligase detection reaction (LDR) method for the purpose of multiplicity and high specificity. To increase sensitivity, the ladder-like polymerase chain reaction (PCR) amplicons were generated by using universal primers that complement ligated products. Each of the amplicons contained a stuffer sequence with a defined yet variable length. Thus, the length of the amplicon is an index of the specific suppressor, allowing its identification via electrophoresis. The multiplexed diagnostic platform was optimized using standard plasmids and validated by using potato virus suppressors as a detection model. This technique can detect down to 1.2 × 10³ copies for single or two mixed target plasmids. When compared with microarray results, the electrophoresis showed 98.73–100% concordance rates for the seven suppressors in the 79 field samples. This strategy could be applied to detect a large number of targets in field and clinical surveillance.     

Understanding the epidemiological factors that intensify the incidence of maize rough dwarf disease in Spain

Currently the dominant limiting factor to maize production in Spain is caused by Maize rough dwarf virus (MRDV). This study aimed to evaluate the epidemiology factors involved in the increased incidence of MRD disease in Spain. We examined the maize planthopper dynamics and MRDV incidence throughout two maize growing seasons in six locations using a set of eight maize varieties: four Bt‐varieties (BT‐var) and their isogenic counterparts (NBT‐var). Our results indicate that MRDV incidence is greatly influenced by the first colonisation of maize by Laodelphax striatellus but not by Metadelphax propinqua and by the susceptibility of the maize varieties. No significant differences were observed between the BT‐var and NBT‐var, although BT‐var exhibited 1% less MRDV infection than NBT‐var. Cultivated wheat and Lolium perenne were found for the first time to be natural hosts of MRDV. However, wheat does not seem to be a preferred host for the development of L. striatellus. Partial sequencing of genome segments S1–S9 and full sequencing of segment S10 revealed that the Spanish MRDV isolate shares nucleotide identities ranging from 93% to 97% with the available sequences of segments S7–S10 of the Italian MRDV isolate. The highest nucleotide identities with other fijiviruses were observed with Rice black‐streaked dwarf virus. Molecular variability analysis of MRDV isolates collected over a ten years period showed high nucleotide (>97%) and amino sequence identities (>99%) on segment S10, suggesting a low temporal variability.     

Isolation and characterization of tri‐ and tetra‐repeat microsatellite loci in the white‐spotted charr Salvelinus leucomaenis (Salmonidae)

Tri‐ and tetra‐motif repeat microsatellite marker loci were developed for the white‐spotted charr Salvelinus leucomaenis. The 454 pyrosequencing was used to discover repeat arrays, and eight microsatellite‐primer sets, available for the estimation of polymorphisms, were identified. The number of alleles in a wild population ranged from two to four and the observed and expected heterozygosities were 0·180–0·600 and 0·188–0·599, respectively.     

Population genetic diversity of the clonal self‐incompatible herbaceous plant Linaria vulgaris along an urbanization gradient

How increasing urbanization affects biodiversity is one of the most understudied aspects of global change biology. It is, however, known that it may negatively affect plant population genetic diversity in numerous ways, for example through its negative effects on plant population size, between‐population connectivity, and reproductive success. Therefore, it is important to investigate to what extent different levels of urbanization result in these negative phenomena. Here we used microsatellite markers to investigate urbanization effects on the population genetic structure of 23 populations of the self‐incompatible, partially clonal herb Linaria vulgaris which were sampled across a gradient of urbanization. Clonal diversity as measured by the Pareto‐parameter varied between 1.11 and 2.97 and was negatively correlated to both the degree of urbanization and to population size. Urbanization and population size were not interrelated. The least clonally rich populations also experienced significantly reduced seed set. Irrespective of the degree of urbanization, L. vulgaris populations exhibited strong genetic differentiation (F_ST = 0.33) and there was no significant correlation between genetic and geographic distances, suggesting low gene flow among populations. In conclusion, we showed that urbanization negatively affected fitness of L. vulgaris populations through decreasing their clonal diversity and reproductive success, an effect that may be exacerbated by the low gene flow between populations. Although the effect was modest, the results could probably be extrapolated to bigger cities where it would be considerably more pronounced.     

Herbivory-induced glucose transporter gene expression in the brown planthopper,Nilaparvata lugens

Nilaparvata lugens, the brown planthopper (BPH) feeds on rice phloem sap, containing high amounts of sucrose as a carbon source. Nutrients such as sugars in the digestive tract are incorporated into the body cavity via transporters with substrate selectivity. Eighteen sugar transporter genes of BPH (Nlst) were reported and three transporters have been functionally characterized. However, individual characteristics of NlST members associated with sugar transport remain poorly understood. Comparative gene expression analyses using oligo-microarray and quantitative RT-PCR revealed that the sugar transporter gene Nlst16 was markedly up-regulated during BPH feeding. Expression of Nlst16 was induced 2 h after BPH feeding on rice plants. Nlst16, mainly expressed in the midgut, appears to be involved in carbohydrate incorporation from the gut cavity into the hemolymph. Nlst1 (NlHT1), the most highly expressed sugar transporter gene in the midgut was not up-regulated during BPH feeding. The biochemical function of NlST16 was shown as facilitative glucose transport along gradients. Glucose uptake activity by NlST16 was higher than that of NlST1 in the Xenopus oocyte expression system. At least two NlST members are responsible for glucose uptake in the BPH midgut, suggesting that the midgut of BPH is equipped with various types of transporters having diversified manner for sugar uptake.