“Closer‐to‐home” strategy benefits juvenile survival in a long‐distance migratory bird

Human‐induced changes in the climate and environment that occur at an unprecedented speed are challenging the existence of migratory species. Faced with these new challenges, species with diverse and flexible migratory behaviors may suffer less from population decline, as they may be better at responding to these changes by altering their migratory behavior. At the individual level, variations in migratory behavior may lead to differences in fitness and subsequently influence the population's demographic dynamics. Using lifetime GPS bio‐logging data from 169 white storks (Ciconia ciconia), we explore whether the recently shortened migration distance of storks affects their survival during different stages of their juvenile life. We also explore how other variations in migratory decisions (i.e., time, destination), movement activity (measured using overall body dynamic acceleration), and early life conditions influence juvenile survival. We observed that their first autumn migration was the riskiest period for juvenile white storks. Individuals that migrated shorter distances and fledged earlier experienced lower mortality risks. In addition, higher movement activity and overwintering “closer‐to‐home” (with 84.21% of the tracked individuals stayed Europe or North Africa) were associated with higher survival. Our study shows how avian migrants can change life history decisions over only a few decades, and thus it helps us to understand and predict how migrants respond to the rapidly changing world.     

梅与山桃远缘杂交亲和性初步研究

为培育早花抗寒梅花新品种,以梅(Prunus mume)品种‘江梅’(P.mume‘Jiangmei’)、‘淡丰后’(P.mume‘Dan Fenghou’)与山桃(P.davidiana)、‘白花’山桃(P.davidiana‘Alba’)为亲本进行杂交试验,记录种间杂交结实率,观察花粉管生长,对未成熟胚进行培养。结果表明:(1)梅与山桃、‘白花’山桃杂交结实率很低,‘江梅’ב白花’山桃未结果,结实率最高的组合为‘淡丰后’×山桃,也仅有7.4%,且杂交果实的果核内部分胚干瘪、败育。(2)山桃和‘白花’山桃的花粉在梅柱头上都能正常萌发,但花粉管生长受抑制,多数花粉管到达花柱中部即弯曲、缠绕、断裂,花粉管生长过程中有大量的胼胝质产生,表现较低的杂交亲和性,但不同种间杂交亲和程度又有所不同。(3)通过未成熟胚培养获得了杂种苗。研究表明,梅与同属种杂交存在不亲和性,幼胚拯救是获得梅与李属其他种远缘杂交杂种苗的有效途径。     

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.     

A prognostic eight-gene expression signature for patients with breast cancer receiving adjuvant chemotherapy

Breast cancer is a popularly diagnosed malignant tumor. Genomic profiling studies suggest that breast cancer is a disease with heterogeneity. Chemotherapy is one of the chief means to treat breast cancer, while its responses and clinical outcomes vary largely due to the conventional clinicopathological factors and inherent chemosensitivity of breast cancer. Using the least absolute shrinkage and selection operator (LASSO) Cox regression model, our study established a multi-mRNA-based signature model and constructed a relative nomogram in predicting distant-recurrence-free survival for patients receiving surgery and following chemotherapy. We constructed a signature of eight mRNAs (IPCEF1, SYNDIG1, TIGIT, SPESP1, C2CD4A, CLCA2, RLN2, and CCL19) with the LASSO model, which was employed to separate subjects into groups with high- and low-risk scores. Obvious differences of distant-recurrence-free survival were found between these two groups. This eight-mRNA-based signature was independently associated with the prognosis and had better prognostic value than classical clinicopathologic factors according to multivariate Cox regression results. Receiver operating characteristic results demonstrated excellent performance in diagnosing 3-year distant-recurrence by the eight-mRNA signature. A nomogram that combined both the eight-mRNA-based signature and clinicopathological risk factors was constructed. Comparing with an ideal model, the nomograms worked well both in the training and validation sets. Through the results that the eight-mRNA signature effectively classified patients into low- and high-risk of distant recurrence, we concluded that this eight-mRNA-based signature played a promising predictive role in prognosis and could be clinically applied in breast cancer patients receiving adjuvant chemotherapy.     

Characterization of the Trypanosoma cruzi ortholog of the SBDS protein reveals an intrinsically disordered extended C-terminal region showing RNA-interacting activity

The human SBDS gene and its yeast ortholog SDO1 encode essential proteins that are involved in ribosome biosynthesis. SDO1 has been implicated in recycling of the ribosomal biogenesis factor Tif6p from pre-66S particles as well as in translation activation of 60S ribosomes. The SBDS protein is highly conserved, containing approximately 250 amino acid residues in animals, fungi and Archaea, while SBDS orthologs of plants and a group of protists contain an extended C-terminal region. In this work, we describe the characterization of the Trypanosoma cruzi SBDS ortholog (TcSBDS). TcSBDS co-fractionates with polysomes in sucrose density gradients, which is consistent with a role in ribosome biosynthesis. We show that TcSBDS contains a C-terminal extension of 200 amino acids that displays the features of intrinsically disordered proteins as determined by proteolytic, circular dichroism and NMR analyses. Interestingly, the C-terminal extension is responsible for TcSBDS–RNA interaction activity in electrophoretic mobility shift assays. This finding suggests that Trypanosomatidae and possibly also other organisms containing SBDS with extended C-terminal regions have evolved an additional function for SBDS in ribosome biogenesis.     

More constraint on ParaHox than Hox gene families in early metazoan evolution

Hox and ParaHox (H/P) genes belong to evolutionary-sister clusters that arose through duplication of a ProtoHOX cluster early in animal evolution. In contrast to bilaterians, cnidarians express, beside PG1, PG2 and Gsx orthologs, numerous Hox-related genes with unclear origin. We characterized from marine hydrozoans three novel Hox-related genes expressed at medusa and polyp stages, which include a Pdx/Xlox ParaHox ortholog induced 1 day later than Gsx during embryonic development. To reconstruct H/P genes' early evolution, we performed multiple systematic comparative phylogenetic analyses, which identified derived sequences that blur the phylogenetic picture, recorded dramatically different evolutionary rates between ParaHox and Hox in cnidarians and showed the unexpected grouping of [Gsx-Pdx/Xlox-PG2-PG3] families in a single metagroup distinct from PG1. We propose a novel more parsimonious evolutionary scenario whereby H/P genes originated from a [Gsx-Pdx/Xlox-PG2-PG3]-related ProtoHox gene, the «posterior» and «anterior» H/P genes appearing secondarily. The ProtoHOX cluster would have contained the three Gsx/PG2, Pdx/PG3, Cdx/PG9 paralogs and produced through tandem duplication the primordial HOX and ParaHOX clusters in the Cnidaria-Bilateria ancestor. The stronger constraint on cnidarian ParaHox genes suggests that the primary function of pre-bilaterian H/P genes was to drive cellular evolutionary novelties such as neurogenesis rather than axis specification.     

系统发育谱构建方法研究

随着后基因组时代的到来,系统发育谱方法作为一种非同源性的功能注释方法,已经被成功的应用到基因组功能预测、蛋白质相互作用预测等一些重要领域的研究中去。本文阐述了系统发育谱法的基本原理,详细地介绍了现有的几种系统发育谱的构建方法,并提出了利用ortholog来构建基因的系统发育谱的思想。     

中国春及其ph2b突变体与秦岭黑麦杂种胚胎发育的比较研究

对普通小麦中国春(CS)及其突变体(CSph2b)与秦岭黑麦远缘杂交的受精过程及其杂种早期胚胎发育进行了研究.结果显示,大部分秦岭黑麦花粉能在CS及CSph2b小麦柱头上萌发,花粉管可顺利伸入花柱和胚囊;CS和CSph2b已授粉子房中,分别有80.12%和84.80%完成双受精过程而形成正常胚及胚乳,也有小部分仅有卵核受精或极核受精而只形成胚或胚乳,两者总受精率分别为86.74%和88.89%,成胚率分别为83.73%和87.14%.表明中国春及其突变体CSph2b与秦岭黑麦的可杂交性都很高,并且CSph2b略高于CS.     

Sequence and hydropathy profile analysis of two classes of secondary transporters

A structural class in the MemGen classification of membrane proteins is a set of evolutionary related proteins sharing a similar global fold. A structural class contains both closely related pairs of proteins for which homology is clear from sequence comparison and very distantly related pairs, for which it is not possible to establish homology based on sequence similarity alone. In the latter case the evolutionary link is based on hydropathy profile analysis. Here, we use these evolutionary related sets of proteins to analyze the relationship between E-values in BLAST searches, sequence similarities in multiple sequence alignments and structural similarities in hydropathy profile analyses. Two structural classes of secondary transporters termed ST[3], which includes the Ion Transporter (IT) superfamily and ST[4], which includes the DAACS family (TC# 2.A.23) were extracted from the NCBI protein database. ST[3] contains 2051 unique sequences distributed over 32 families and 59 subfamilies. ST[4] is a smaller class containing 399 unique sequences distributed over 2 families and 7 subfamilies. One subfamily in ST[4] contains a new class of binding protein dependent secondary transporters. Comparison of the averaged hydropathy profiles of the subfamilies in ST[3] and ST[4] revealed that the two classes represent different folds. Divergence of the sequences in ST[4] is much smaller than observed in ST[3], suggesting different constraints on the proteins during evolution. Analysis of the correlation between the evolutionary relationship of pairs of proteins in a class and the BLAST E-value revealed that: (i) the BLAST algorithm is unable to pick up the majority of the links between proteins in structural class ST[3], (ii) ‘low complexity filtering’ and ‘composition based statistics’ improve the specificity, but strongly reduce the sensitivity of BLAST searches for distantly related proteins, indicating that these filters are too stringent for the proteins analyzed, and (iii) the E-value cut-off, which may be used to evaluate evolutionary significance of a hit in a BLAST search is very different for the two structural classes of membrane proteins.