Establishment of compatibility in the Ustilago maydis/maize pathosystem

The fungus Ustilago maydis is a biotrophic pathogen parasitizing on maize. The most prominent symptoms of the disease are large tumors in which fungal proliferation and spore differentiation occur. In this study, we have analyzed early and late tumor stages by confocal microscopy. We show that fungal differentiation occurs both within plant cells as well as in cavities where huge aggregates of fungal mycelium develop. U. maydis is poorly equipped with plant CWDEs and we demonstrate by array analysis that the respective genes follow distinct expression profiles at early and late stages of tumor development. For the set of three genes coding for pectinolytic enzymes, deletion mutants were generated by gene replacement. Neither single nor triple mutants were affected in pathogenic development. Based on our studies, we consider it unlikely that U. maydis feeds on carbohydrates derived from the digestion of plant cell wall material, but uses its set of plant CWDEs for softening the cell wall structure as a prerequisite for in planta growth.     

Economically and ecologically important plant communities in high altitude coniferous forest of Malam Jabba,Swat, Pakistan

A study on the economically important plant communities was carried out during summer 2008 in various parts of Malam Jabba valley, Swat. The principal aim of the study was phytosociological evaluation with special reference to the occurrence of commercially important medicinal plant species in coniferous forest of the study area. Secondly to prepare ethnobotanical inventory of the plant resources of the area, as well as to evaluate the conservation status of important medicinal and aromatic plants (MAPs) through rapid vulnerable assessment (RVA) procedure. The study documented 90 species of ethnobotanical importance, out of these 71 spp used as medicinal plant, 20 spp fodder plant, 10 spp vegetables, 14 spp wild fruit, 18 spp fuel wood, 9 spp furniture and agricultural tools, 9 spp thatching, fencing and hedges, 4 spp honey bee, 2 spp evil eyes, 2 spp religious and 3 spp as poison. Phytosociologically six plant communities were found, comprising five herbs-shrubs-trees communities and one meadow community. Further study is, therefore, required to quantify the availability of species and to suggest suitable method for their production and conservation. Recommendations are also given in the spheres of training in identification, sustainable collection, value addition, trade monitoring and cooperative system of marketing.     

Differential susceptibility epidemic models

We formulate compartmental differential susceptibility (DS) susceptible-infective-removed (SIR) models by dividing the susceptible population into multiple subgroups according to the susceptibility of individuals in each group. We analyze the impact of disease-induced mortality in the situations where the number of contacts per individual is either constant or proportional to the total population. We derive an explicit formula for the reproductive number of infection for each model by investigating the local stability of the infection-free equilibrium. We further prove that the infection-free equilibrium of each model is globally asymptotically stable by qualitative analysis of the dynamics of the model system and by utilizing an appropriately chosen Liapunov function. We show that if the reproductive number is greater than one, then there exists a unique endemic equilibrium for all of the DS models studied in this paper. We prove that the endemic equilibrium is locally asymptotically stable for the models with no disease-induced mortality and the models with contact numbers proportional to the total population. We also provide sufficient conditions for the stability of the endemic equilibrium for other situations. We briefly discuss applications of the DS models to optimal vaccine strategies and the connections between the DS models and predator-prey models with multiple prey populations or host-parasitic interaction models with multiple hosts are also given.This research was partially supported by the Department of Energy under contracts W-7405-ENG-36 and the Applied Mathematical Sciences Program KC-07-01-01.     

Data standards, sense and stability: Scratchpads, the ICZN and ZooBank

The International Commission of Zoological Nomenclature has used the Scratchpads platform (currently being developed and maintained by ViBRANT) as the foundation for its redesigned website and as a platform for engaging with its users. The existing Scratchpad tools, with extensions to provide additional functions, have allowed for a major transformation in presentation of linked nomenclatural tools. Continued development of the new website will act as a springboard for the ICZN to participate more fully in the wider community of biodiversity informatics.     

Proteomic analysis of Medicago truncatula root plastids

Despite the recognized importance of non‐photosynthetic plastids in a wide array of plant processes, the root plastid proteome of soil‐grown plants still remains to be explored. In this study, we used a protocol allowing the isolation of Medicago truncatula root plastids with sufficient protein recovery and purity for their subsequent in‐depth analysis by nanoscale capillary LC‐MS/MS. Besides providing the first picture of a root plastid proteome, the results obtained highlighted the identification of 266 protein candidates whose functional distribution mainly resembled that of wheat endosperm amyloplasts and tobacco proplastids together with displaying major differences to those reported for chloroplasts. Most of the identified proteins have a role in nucleic acid‐related processes (16%), carbohydrate (15%) and nitrogen/sulphur (12%) metabolisms together with stress response mechanisms (10%). It is noteworthy that BLAST searches performed against the proteins reported in different plastidomes allowed detecting 30 putative root plastid proteins for which homologues were previously unsuspected as plastid‐located, most of them displaying a common putative role in participating in the plant cell responses against abiotic and/or biotic stresses. Taken together, the data obtained provide new insights into the functioning of root plastids and reinforce the emerging idea for an important role of these organelles in sustaining plant defence reactions.     

A novel approach for multi-domain and multi-gene family identification provides insights into evolutionary dynamics of disease resistance genes in core eudicot plants

Background

Recent advances in DNA sequencing techniques resulted in more than forty sequenced plant genomes representing a diverse set of taxa of agricultural, energy, medicinal and ecological importance. However, gene family curation is often only inferred from DNA sequence homology and lacks insights into evolutionary processes contributing to gene family dynamics. In a comparative genomics framework, we integrated multiple lines of evidence provided by gene synteny, sequence homology and protein-based Hidden Markov Modelling to extract homologous super-clusters composed of multi-domain resistance (R)-proteins of the NB-LRR type (for NUCLEOTIDE BINDING/LEUCINE-RICH REPEATS), that are involved in plant innate immunity.

Results

To assess the diversity of R-proteins within and between species, we screened twelve eudicot plant genomes including six major crops and found a total of 2,363 NB-LRR genes. Our curated R-proteins set shows a 50% average for tandem duplicates and a 22% fraction of gene copies retained from ancient polyploidy events (ohnologs). We provide evidence for strong positive selection and show significant differences in molecular evolution rates (Ka/Ks-ratio) among tandem- (mean = 1.59), ohnolog (mean = 1.36) and singleton (mean = 1.22) R-gene duplicates. To foster the process of gene-edited plant breeding, we report species-specific presence/absence of all 140 NB-LRR genes present in the model plant Arabidopsis and describe four distinct clusters of NB-LRR “gatekeeper” loci sharing syntenic orthologs across all analyzed genomes.

Conclusion

By curating a near-complete set of multi-domain R-protein clusters in an eudicot-wide scale, our analysis offers significant insight into evolutionary dynamics underlying diversification of the plant innate immune system. Furthermore, our methods provide a blueprint for future efforts to identify and more rapidly clone functional NB-LRR genes from any plant species.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-966) contains supplementary material, which is available to authorized users.     

西双版纳野象谷景区亚洲象取食作用对五种植物的影响

摘要：本研究在西双版纳利用样线调查法调查亚洲象的取食作用对野象谷景区常见分布的5种植物即酸苔树、象鼻藤、粗糠柴、翅果麻和黄牛木的影响,调查中记录样线上每一目标植株的基径、高度、影响类型、影响程度等信息。结果表明：1）植物受影响的数量与其植株总数之间的相关性不大（Pearson correlation, r=0.608, P=0.277）;2）亚洲象对5种植物的偏爱程度不一样,酸苔树、象鼻藤、粗糠柴和翅果麻都是大象喜爱的食物,尤其是象鼻藤（偏爱指数=1.4855）,而黄牛木不受大象喜爱（偏爱指数=0.5855）;3）亚洲象对5种植物有不同的影响方式和影响程度,酸苔树以主干折断和枝叶损失为主,受大象的取食影响最严重,象鼻藤虽然是大象最喜爱的食物,但受到的取食影响最小,粗糠柴以枝叶损失和主干折断为主,翅果麻以枝叶损失为主,同时也是唯一被亚洲象剥皮的植物,黄牛木以枝叶损失为主,被推倒的情况最普遍。树干基部直径为3-8cm的植株最受大象偏爱。亚洲象对植物的选择性以及植株自身的特性是导致上述差异的主要原因。建议后续开展长期的调查以了解亚洲象对这些植物种群数量及群落结构的影响,同时应采取有效保护措施以避免象群在当地过于集中的现象。     

Cis- and trans-splicing and RNA editing are required for the expression of nad2 in wheat mitochondria

In wheat mitochondria, the gene coding for subunit 2 of the NADH-ubiquinone oxidoreductase (nad2) is divided into five exons located in two distant genomic regions. The first two exons of the gene, a and b, lie 22 kb downstream of exons c, d, and e, on the same DNA strand. All introns of nad2 are group II introns. A trans-splicing event is required to join exons b and c. It involves base pairing of the two precursor RNAs in the stem of domain IV of the intron. A gene coding for tRNA^Tyr is located upstream of exon c. In addition to splicing processes, mRNA editing is also required for the correct expression of nad2. The mature mRNA is edited at 36 positions, distributed over its five exons, resulting in 28 codon modifications. Editing increases protein hydrophobicity and conservation. Received: 11 August 1997 / Accepted: 2 February 1998     

Vegetation control effects on untreated wood,crude cellulose and holocellulose δ<Superscript>13</Superscript>C of early and latewood in 3- to 5-year-old rings of Douglas-fir

The stable carbon (C) composition of tree rings expressed as δ¹³C, is a measure of intrinsic water-use efficiency and can indicate the occurrence of past water shortages for tree growth. We examined δ¹³C in 3- to 5-year-old rings of Douglas-fir (Pseudotsuga menziesii (Mirb) Franco) trees to elucidate if decreased water supply or uptake was a critical factor in the observed growth reduction of trees competing with understory herb and shrub vegetation compared to those growing without competition. We hypothesized that there would be no differences in δ¹³C of earlywood in trees growing in plots with competing vegetation and those in plots receiving complete vegetation control during 5 years because earlywood formed early in the growing season when soil water was ample. We also hypothesized that δ¹³C in latewood which was formed during the later half of the growing season when precipitation was low, would be greater (less negative) in trees in plots without vegetation control. We then separated early and latewood from rings for three consecutive years and analyzed their δ¹³C composition. No significant differences in earlywood δ¹³C in years 3–5 were observed for trees in the two vegetation control treatments. δ¹³C of untreated latewood separated from wood cores was greater in 4- and 5-year-old rings of trees growing with competing vegetation compared to trees growing without vegetation competition (i.e., −25.5 vs. −26.3‰ for year 4, and −26.1 vs. −26.8‰ for year 5). Results suggest that water shortages occurred in Douglas-fir trees on this coastal Washington site in the latewood-forming portion of the growing season of years 4 and 5 in the no-vegetation control treatment. We also compared δ¹³C from untreated wood, crude cellulose extracted with the Diglyme–HCl method, and holocellulose extracted with toluene–ethanol to see if the extraction method would increase the sensitivity of the analysis. δ¹³C values from the two extraction methods were highly correlated with those from untreated samples (r ² = 0.97, 0.98, respectively). Therefore, using untreated wood would be as effective as using crude cellulose or holocellulose to investigate δ¹³C patterns in young Douglas-fir.