Lower leaf gas‐exchange and higher photorespiration of treated wastewater irrigated Citrus trees is modulated by soil type and climate

Water quality, soil and climate can interact to limit photosynthesis and to increase photooxidative damage in sensitive plants. This research compared diffusive and non‐diffusive limitations to photosynthesis as well as photorespiration of leaves of grapefruit trees in heavy clay and sandy soils having a previous history of treated wastewater (TWW) irrigation for >10 years, with different water qualities [fresh water (FW) vs TWW and sodium amended treated wastewater (TWW + Na)] in two arid climates (summer vs winter) and in orchard and lysimeter experiments. TWW irrigation increased salts (Na⁺ and Cl⁻), membrane leakage, proline and soluble sugar content, and decreased osmotic potentials in leaves of all experiments. Reduced leaf growth and higher stomatal and non‐stomatal (i.e. mesophyll) limitations were found in summer and on clay soil for TWW and TWW + Na treatments in comparison to winter, sandy soil and FW irrigation, respectively. Stomatal closure, lower chlorophyll content and altered Rubisco activity are probable causes of higher limitations. On the other hand, non‐photochemical quenching, an alternative energy dissipation pathway, was only influenced by water quality, independent of soil type and season. Furthermore, light and CO₂ response curves were investigated for other possible causes of higher non‐stomatal limitation. A higher proportion of non‐cyclic electrons were directed to the O₂ dependent pathway, and a higher proportion of electrons were diverted to photorespiration in summer than in winter. In conclusion, both diffusive and non‐diffusive limitations contribute to the lower photosynthetic performance of leaves following TWW irrigation, and the response depends on soil type and environmental factors.     

Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins

Background  

Many structural properties such as solvent accessibility, dihedral angles and helix-helix contacts can be assigned to each residue in a membrane protein. Independent studies exist on the analysis and sequence-based prediction of some of these so-called one-dimensional features. However, there is little explanation of why certain residues are predicted in a wrong structural class or with large errors in the absolute values of these features. On the other hand, membrane proteins undergo conformational changes to allow transport as well as ligand binding. These conformational changes often occur via residues that are inherently flexible and hence, predicting fluctuations in residue positions is of great significance.     

The PluriNetWork: an electronic representation of the network underlying pluripotency in mouse, and its applications

Background

Analysis of the mechanisms underlying pluripotency and reprogramming would benefit substantially from easy access to an electronic network of genes, proteins and mechanisms. Moreover, interpreting gene expression data needs to move beyond just the identification of the up-/downregulation of key genes and of overrepresented processes and pathways, towards clarifying the essential effects of the experiment in molecular terms.

Methodology/Principal Findings

We have assembled a network of 574 molecular interactions, stimulations and inhibitions, based on a collection of research data from 177 publications until June 2010, involving 274 mouse genes/proteins, all in a standard electronic format, enabling analyses by readily available software such as Cytoscape and its plugins. The network includes the core circuit of Oct4 (Pou5f1), Sox2 and Nanog, its periphery (such as Stat3, Klf4, Esrrb, and c-Myc), connections to upstream signaling pathways (such as Activin, WNT, FGF, BMP, Insulin, Notch and LIF), and epigenetic regulators as well as some other relevant genes/proteins, such as proteins involved in nuclear import/export. We describe the general properties of the network, as well as a Gene Ontology analysis of the genes included. We use several expression data sets to condense the network to a set of network links that are affected in the course of an experiment, yielding hypotheses about the underlying mechanisms.

Conclusions/Significance

We have initiated an electronic data repository that will be useful to understand pluripotency and to facilitate the interpretation of high-throughput data. To keep up with the growth of knowledge on the fundamental processes of pluripotency and reprogramming, we suggest to combine Wiki and social networking software towards a community curation system that is easy to use and flexible, and tailored to provide a benefit for the scientist, and to improve communication and exchange of research results. A PluriNetWork tutorial is available at http://www.ibima.med.uni-rostock.de/IBIMA/PluriNetWork/.     

Urinary miR-29 Correlates with Albuminuria and Carotid Intima-Media Thickness in Type 2 Diabetes Patients

Background

Cell-free microRNAs stably and abundantly exist in body fluids and emerging evidence suggests cell-free microRNAs as novel and non-invasive disease biomarker. Deregulation of miR-29 is involved in the pathogenesis of diabetic nephropathy and insulin resistance thus may be implicated in diabetic vascular complication. Therefore, we investigated the possibility of urinary miR-29 as biomarker for diabetic nephropathy and atherosclerosis in patients with type 2 diabetes.

Methods

83 patients with type 2 diabetes were enrolled in this study, miR-29a, miR-29b and miR-29c levels in urine supernatant was determined by TaqMan qRT-PCR, and a synthetic cel-miR-39 was added to the urine as a spike-in control before miRNAs extraction. Urinary albumin excretion rate and urine albumin/creatinine ratio, funduscopy and carotid ultrasound were used for evaluation of diabetic vascular complication. The laboratory parameters indicating blood glucose level, renal function and serum lipids were also collected.

Results

Patients with albuminuria (n = 42, age 60.62±12.00yrs) showed significantly higher comorbidity of diabetic retinopathy (p = 0.015) and higher levels of urinary miR-29a (p = 0.035) compared with those with normoalbuminuria (n = 41, age 58.54±14.40yrs). There was no significant difference in urinary miR-29b (p = 0.148) or miR-29c level (p = 0.321) between groups. Urinary albumin excretion rate significantly correlated with urinary miR-29a level (r = 0.286, p = 0.016), while urinary miR-29b significantly correlated with carotid intima-media thickness (cIMT) (r = 0.286, p = 0.046).

Conclusion

Urinary miR-29a correlated with albuminuria while urinary miR-29b correlated with carotid intima-media thickness (cIMT) in patients with type 2 diabetes. Therefore, they may have the potential to serve as alternative biomarker for diabetic nephropathy and atherosclerosis in type 2 diabetes.     

C19orf12 mutation leads to a pallido-pyramidal syndrome

Pallido-pyramidal syndromes combine dystonia with or without parkinsonism and spasticity as part of a mixed neurodegenerative disorder. Several causative genes have been shown to lead to pallido-pyramidal syndromes, including FBXO7, ATP13A2, PLA2G6, PRKN and SPG11. Among these, ATP13A2 and PLA2G6 are inconsistently associated with brain iron deposition. Using homozygosity mapping and direct sequencing in a multiplex consanguineous Saudi Arabian family with a pallido-pyramidal syndrome, iron deposition and cerebellar atrophy, we identified a homozygous p.G53R mutation in C19orf12. Our findings add to the phenotypic spectrum associated with C19orf12 mutations.     

Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations

The merging of populations after an extended period of isolation and divergence is a common phenomenon, in natural settings as well as due to human interference. Individuals with such hybrid origins contain genomes that essentially form a mosaic of different histories and demographies. Pigs are an excellent model species to study hybridization because European and Asian wild boars diverged ~1.2 Mya, and pigs were domesticated independently in Europe and Asia. During the Industrial Revolution in England, pigs were imported from China to improve the local pigs. This study utilizes the latest genomics tools to identify the origin of haplotypes in European domesticated pigs that are descendant from Asian and European populations. Our results reveal fine‐scale haplotype structure representing different ancient demographic events, as well as a mosaic composition of those distinct histories due to recently introgressed haplotypes in the pig genome. As a consequence, nucleotide diversity in the genome of European domesticated pigs is higher when at least one haplotype of Asian origin is present, and haplotype length correlates negatively with recombination frequency and nucleotide diversity. Another consequence is that the inference of past effective population size is influenced by the background of the haplotypes in an individual, but we demonstrate that by careful sorting based on the origin of haplotypes, both distinct demographic histories can be reconstructed. Future detailed mapping of the genomic distribution of variation will enable a targeted approach to increase genetic diversity of captive and wild populations, thus facilitating conservation efforts in the near future.     

西双版纳布龙自然保护区勐宋片区附生维管植物多样性与分布特征

利用地面观测和单绳上树法初次对布龙自然保护区勐宋片区开展的附生维管植物调查表明:1)在6个样地77株宿主上(共调查96株乔木,占地约0.2ha),共有1 756株、丛个体,隶属14科47属103种;相比世界其他区域,物种丰富度处于旧世界热带水平区间,高于温带,但明显低于新世界热带水平;2)兰科植物为最丰富的类群(60％),其次为蕨类植物(24％),其他类群占16％;3)垂直分布特征研究表明,距地面10～ 15 m的中等高度带为物种最丰富的区间,约有51％的物种;0～5m高度带为个体数量最多的区间,共有约24％个体,揭示了除中等高度带以外的另一个重要附生生境;4)常见的绞杀型榕属植物未见,而半附生植物密脉鹅掌柴(Schefflera elliptica)和多蕊木(Tupidanthus calyptratus)数量较多.     

Phylogenetic clustering increases with succession for lianas in a Chinese tropical montane rain forest

Previous research found that phylogenetic clustering increased with disturbance for tropical trees, suggesting that community assembly is mainly influenced by abiotic factors during early succession. Lianas are an important additional component of tropical forests, but their phylogenetic community structure has never been investigated. Unlike tropical trees, liana abundance is often high in disturbed forests and diversity can peak in old secondary forest. Therefore, phylogenetic structure along a disturbance gradient might also differ from tropical tree communities. Here we determined phylogenetic community structure of lianas along a disturbance gradient in a tropical montane forest in China, using the net relatedness index (NRI) from 100 equivalent phylogenies with varying branch length that were constructed using DNA‐barcode sequences. Three additional phylogenetic indices were also considered for comparison. When NRI was used as index phylogenetic clustering of liana communities decreased with decreasing tree basal area, suggesting that liana competitive interactions dominate during early succession, which is in contrast to the pattern reported for trees. Liana communities in mature forests, on the other hand, were phylogenetic clustered, which could be caused by dispersal limitation and/or environmental filtering. The three additional phylogenetic indices identified different, sometimes contradicting predictors of phylogenetic community structure, indicating that caution is needed when generalizing interpretations of studies based on a single phylogenetic community structure index. Our study provides a more nuanced picture of non‐random assembly along disturbance gradients by focusing on a non‐tree forest component.     

SV-AUTOPILOT: optimized,automated construction of structural variation discovery and benchmarking pipelines

Background

Many tools exist to predict structural variants (SVs), utilizing a variety of algorithms. However, they have largely been developed and tested on human germline or somatic (e.g. cancer) variation. It seems appropriate to exploit this wealth of technology available for humans also for other species. Objectives of this work included:

1. Creating an automated, standardized pipeline for SV prediction.
2. Identifying the best tool(s) for SV prediction through benchmarking.
3. Providing a statistically sound method for merging SV calls.

Results

The SV-AUTOPILOT meta-tool platform is an automated pipeline for standardization of SV prediction and SV tool development in paired-end next-generation sequencing (NGS) analysis. SV-AUTOPILOT comes in the form of a virtual machine, which includes all datasets, tools and algorithms presented here. The virtual machine easily allows one to add, replace and update genomes, SV callers and post-processing routines and therefore provides an easy, out-of-the-box environment for complex SV discovery tasks. SV-AUTOPILOT was used to make a direct comparison between 7 popular SV tools on the Arabidopsis thaliana genome using the Landsberg (Ler) ecotype as a standardized dataset. Recall and precision measurements suggest that Pindel and Clever were the most adaptable to this dataset across all size ranges while Delly performed well for SVs larger than 250 nucleotides. A novel, statistically-sound merging process, which can control the false discovery rate, reduced the false positive rate on the Arabidopsis benchmark dataset used here by >60%.

Conclusion

SV-AUTOPILOT provides a meta-tool platform for future SV tool development and the benchmarking of tools on other genomes using a standardized pipeline. It optimizes detection of SVs in non-human genomes using statistically robust merging. The benchmarking in this study has demonstrated the power of 7 different SV tools for analyzing different size classes and types of structural variants. The optional merge feature enriches the call set and reduces false positives providing added benefit to researchers planning to validate SVs. SV-AUTOPILOT is a powerful, new meta-tool for biologists as well as SV tool developers.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1376-9) contains supplementary material, which is available to authorized users.