In‐depth proteomic analysis of whole testis tissue from the adult rhesus macaque

The rhesus macaque is similar to humans both anatomically and physiologically as a primate, and has therefore been used extensively in medical and biological research, including reproductive physiology. Despite sequencing of the macaque genome, limited postgenomic studies have been performed to date. In studies aimed at characterizing spermatogenesis, we successfully identified 9078 macaque testis proteins corresponding to 8662 genes, using advanced MS and an optimized proteomics platform, indicative of complex protein compositions during macaque spermatogenesis. Immunohistochemistry analysis further revealed the presence of proteins from different types of testicular cells, including Sertoli cells, Leydig cells, and various stages of germ cells. Our data provide expression evidence at protein level of 3010 protein‐coding genes in 8662 identified testis genes for the first time. We further identified 421 homologous genes from the proteome already known to be essential for male infertility in mouse. Comparative analysis of the proteome showed high similarity with the published human testis proteome, implying that macaque and human may use similar proteins to regulate spermatogenesis. Our in‐depth analysis of macaque spermatogenesis provides a rich resource for further studies, and supports the utility of macaque as a suitable model for the study of human reproduction.     

我国设施黄瓜新育成品种芽期耐盐性评价

用100 mmol/L Mg(NO3)2盐溶液对不同生态类型的143个设施黄瓜新品种进行4 d芽期胁迫处理,调查各种质的发芽势、发芽指数、相对伤害率、发芽率、相对发芽率、第2天和第4天胚根伸长长度、后2 d胚根伸长速度等8个指标,利用各指标隶属函数值对其耐盐性进行聚类分析,并对耐盐强的种质进行恢复出苗初步筛选。研究结果表明,黄瓜萌发期的耐盐性强弱评价结果受多个指标的影响。8个发芽指标的变异系数为10.5%~81.0%,除了发芽率和相对发芽率的变异较小外,其他性状的变异幅度均较大(32.0%~81.0%);各性状指标变异系数在不同生态类型种质中表现不同,华北型和欧洲温室型种质以相对伤害率变异系数为最大,华南型和欧美加工型种质以后2 d胚根伸长速度变异系数最大。从种质总体抗盐结果看,欧美加工型和欧洲温室型>华南型>华北型。各指标隶属函数值聚类分析结果表明,将所有种质划为耐盐强、中、弱3类,其中耐盐强的品种共有54个,占37.8%。54个耐盐品种胁迫后经出苗试验初步筛选出12个恢复能力强的品种,即:J31-1>绿精灵>DRT5>YT24>东农02号>上海农科4号>冬灵102>IVF8>津优35>HGS-2>扬大13>J30-1。     

MiR-29a/b/c regulate human circadian gene hPER1 expression by targeting its 3/UTR

Several essential biological progresses in mammals are regulated by circadian rhythms. Though the molecular mechanisms of oscillating these circadian rhythms have been uncovered, the specific functions of the circadian genes are not very clear. It has been reported that knocking down circadian genes by microRNA is a useful strategy to explore the function of the circadian rhythms. In this study, through a forward bioinformatics screening ap- proach, we identified miR-29a/b/c as potent inhibitors for the human circadian gene hPER1. We further found that miR-29a/b/c could directly target hPER1 3/untranslated region （UTR） and down-regulate hPER1 at both mRNA and protein expression levels in human A549 cells. Thus, our findings suggested that the expression of hPER1 is regulated by miR-29a/b/c, which may also provide a new clue for the function ofhPER1.     

High-throughput sequencing exclusively identified a novel Torque teno virus genotype in serum of a patient with fatal fever

Torque teno virus (TTV) has been found to be prevalent world-wide in healthy populations and in patients with various diseases, but its etiological role has not yet been determined. Using high-throughput unbiased sequencing to screen for viruses in the serum of a patient with persistent high fever who died of suspected viral infection and prolonged weakness, we identified the complete genome sequence of a TTV (isolate Hebei-1). The genome of TTV-Hebei-1 is 3649 bp in length, encoding four putative open reading frames, and it has a G+C content of 49%. Genomic comparison and a BLASTN search revealed that the assembled genome of TTV-Hebei-1 represented a novel isolate, with a genome sequence that was highly heterologous to the sequences of other reported TTV strains. A phylogenetic tree constructed using the complete genome sequence showed that TTV-Hebei-1 and an uncharacterized Taiwanese strain, TW53A37, constitute a new TTV genotype. The patient was strongly suspected of carrying a viral infection and died eventually without any other possible causes being apparent. No virus other than the novel TTV was identified in his serum sample. Although a direct causal link between the novel TTV genotype infection and the patient’s disease could not be confirmed, the findings suggest that surveillance of this novel TTV genotype is necessary and that its role in disease deserves to be explored.     

French broom (Teline monspessulana) invasion in south-central Chile depends on factors operating at different spatial scales

The interaction between plant attributes, environmental factors and the history of human intervention determines which species show a more invasive behavior and which areas are more likely to be invaded. Identifying which factors favor the invasion and which constraint it, remains an essential goal for understanding the process of invasion and to provide a stronger scientific basis for designing management actions to reduce susceptibility to invasion. In this paper we analyze the relative role of different environmental factors in plant invasion, in particular the comparison between human versus climatic and biotic variables at different spatial scales. Furthermore, we show how these factors interact to influence the distribution and abundance of an invasive plant. We have built mixed models to explain the presence and abundance of a renowned invasive species in the south-central area of Chile, Teline monspessulana (French broom, Fabaceae). We recorded the presence and cover of this invasive shrub in a series of transects along the main roads of the study area. For each transect we recorded variables at different spatial scales related to climate and land use. We found that the presence and cover of T. monspessulana are strongly related to proximity to roads, urban areas and locations with higher rainfall. Although this shrub is present in most of the landscape, it is most abundant in shrublands and forest plantations. In a complex human-dominated landscape matrix, shrublands and forest plantations act as a source of propagules from which new areas can be invaded. Interestingly, the presence of this species can be better predicted by combining predictors taken at two hierarchical levels, the so-called transect and plot scales, whereas the species abundance only depends on factors at the plot level. The presence and abundance of this species is highly dependent on human disturbance, and the occurrence of certain landscape elements closely linked to land management is critical to the performance of this species. Maintaining a dense tree canopy cover and reducing the use of fire could help reduce the rate of expansion of this species across the landscape.     

The potato amylase inhibitor gene SbAI regulates cold‐induced sweetening in potato tubers by modulating amylase activity

Potato cold‐induced sweetening (CIS) is critical for the postharvest quality of potato tubers. Starch degradation is considered to be one of the key pathways in the CIS process. However, the functions of the genes that encode enzymes related to starch degradation in CIS and the activity regulation of these enzymes have received less attention. A potato amylase inhibitor gene known as SbAI was cloned from the wild potato species Solanum berthaultii. This genetic transformation confirmed that in contrast to the SbAI suppression in CIS‐resistant potatoes, overexpressing SbAI in CIS‐sensitive potatoes resulted in less amylase activity and a lower rate of starch degradation accompanied by a lower reducing sugar (RS) content in cold‐stored tubers. This finding suggested that the SbAI gene may play crucial roles in potato CIS by modulating the amylase activity. Further investigations indicated that pairwise protein–protein interactions occurred between SbAI and α‐amylase StAmy23, β‐amylases StBAM1 and StBAM9. SbAI could inhibit the activities of both α‐amylase and β‐amylase in potato tubers primarily by repressing StAmy23 and StBAM1, respectively. These findings provide the first evidence that SbAI is a key regulator of the amylases that confer starch degradation and RS accumulation in cold‐stored potato tubers.     

Accurate genome relative abundance estimation for closely related species in a metagenomic sample

Background

Metagenomics has a great potential to discover previously unattainable information about microbial communities. An important prerequisite for such discoveries is to accurately estimate the composition of microbial communities. Most of prevalent homology-based approaches utilize solely the results of an alignment tool such as BLAST, limiting their estimation accuracy to high ranks of the taxonomy tree.

Results

We developed a new homology-based approach called Taxonomic Analysis by Elimination and Correction (TAEC), which utilizes the similarity in the genomic sequence in addition to the result of an alignment tool. The proposed method is comprehensively tested on various simulated benchmark datasets of diverse complexity of microbial structure. Compared with other available methods designed for estimating taxonomic composition at a relatively low taxonomic rank, TAEC demonstrates greater accuracy in quantification of genomes in a given microbial sample. We also applied TAEC on two real metagenomic datasets, oral cavity dataset and Crohn’s disease dataset. Our results, while agreeing with previous findings at higher ranks of the taxonomy tree, provide accurate estimation of taxonomic compositions at the species/strain level, narrowing down which species/strains need more attention in the study of oral cavity and the Crohn’s disease.

Conclusions

By taking account of the similarity in the genomic sequence TAEC outperforms other available tools in estimating taxonomic composition at a very low rank, especially when closely related species/strains exist in a metagenomic sample.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-242) contains supplementary material, which is available to authorized users.     

Genetic assessment of safflower (Carthamus tinctorius L.) collection with microsatellite markers acquired via pyrosequencing method

A genetic evaluation of safflower germplasm collections derived from different geographical regions and countries will provide useful information for sustainable conservation and the utilization of genetic diversity. However, the molecular marker information is limited for evaluation of genetic diversity of safflower germplasm. In this study, we acquired 509 putative genomic SSR markers for sufficient genome coverage using next‐generation sequencing methods and characterized thirty polymorphic SSRs in safflower collection composed of 100 diverse accessions. The average allele number and expected heterozygosity were 2.8 and 0.386, respectively. Analysis of population structure and phylogeny based on thirty SSR profiles revealed genetic admixture between geographical regions contrary to genetic clustering. However, the accessions from Korea were genetically conserved in distinctive groups in contrast to other safflower gene pool. In conclusion, these new genomic SSRs will facilitate valuable studies to clarify genetic relationships as well as conduct population structure analyses, genetic map construction and association analysis for safflower.     

Whole-genome sequencing of matched primary and metastatic hepatocellular carcinomas

Background

To gain biological insights into lung metastases from hepatocellular carcinoma (HCC), we compared the whole-genome sequencing profiles of primary HCC and paired lung metastases.

Methods

We used whole-genome sequencing at 33X-43X coverage to profile somatic mutations in primary HCC (HBV+) and metachronous lung metastases (> 2 years interval).

Results

In total, 5,027-13,961 and 5,275-12,624 somatic single-nucleotide variants (SNVs) were detected in primary HCC and lung metastases, respectively. Generally, 38.88-78.49% of SNVs detected in metastases were present in primary tumors. We identified 65–221 structural variations (SVs) in primary tumors and 60–232 SVs in metastases. Comparison of these SVs shows very similar and largely overlapped mutated segments between primary and metastatic tumors. Copy number alterations between primary and metastatic pairs were also found to be closely related. Together, these preservations in genomic profiles from liver primary tumors to metachronous lung metastases indicate that the genomic features during tumorigenesis may be retained during metastasis.

Conclusions

We found very similar genomic alterations between primary and metastatic tumors, with a few mutations found specifically in lung metastases, which may explain the clinical observation that both primary and metastatic tumors are usually sensitive or resistant to the same systemic treatments.     

Developing a quantitative landscape regionalization framework integrating driving factors and response attributes of landscapes

Regionalization plays an important role in delineating landscape heterogeneity and providing spatial frameworks for environmental management. In this study, we developed a comprehensive regionalization approach that integrated multiple quantitative techniques and differentiated two distinct types of landscape variables, i.e., response attributes and driving factors. This approach was applied to the regionalization of surface-water resource in the Huai River Basin (HRB), China. In the regionalization scheme, the 25 subwatersheds of the HRB were adopted as the basic spatial unit; surface-water capacity, runoff depth, and drainage system density were used to characterize surface-water distribution (i.e., response attributes). The HRB subwatersheds were classified into a certain number of groups using the k-means cluster analysis based on the three response attributes. A goodness-of-fit index, calculated as the ratio of between-group/within-group variation, was employed as a quantitative criterion to assess the statistical performance of the classification results. Ultimately, the 25 subwatersheds were partitioned into five distinct regions. Results from redundancy analysis suggested that such regional pattern of surface-water resource was primarily correlated with driving factors representing climate conditions; soil and geological properties also had significant influences. Overall, our approach presents two advantages over previous regionalization frameworks: (1) It improves objectivity of landscape regionalization and reveals underlying mechanisms, generating landscape patterns by integrating response attributes and driving factors; (2) Goodness-of-fit evaluation can substantially reduce subjectivity in determining regionalization results.