AXL and AXR1 have redundant functions in RUB conjugation and growth and development in Arabidopsis

Cullin-RING ubiquitin-protein ligases such as the Skp1, cullin, F-box protein (SCF) have been implicated in many growth and developmental processes in plants. Normal SCF function requires that the CUL1 subunit be post-translationally modified by related to ubiquitin (RUB), a protein related to ubiquitin. This process is mediated by two enzymes: the RUB-activating and RUB-conjugating enzymes. In Arabidopsis, the RUB-activating enzyme is a heterodimer consisting of AXR1 and ECR1. Mutations in the AXR1 gene result in a pleiotropic phenotype that includes resistance to the plant hormone auxin. Here we report that the AXL (AXR1-like) gene also functions in the RUB conjugation pathway. Overexpression of AXL in the axr1-3 background complements the axr1-3 phenotype. Biochemical analysis indicates that AXL overexpression restores CUL1 modification to the wild-type level, indicating that AXR1 and AXL have the same biochemical activity. Although the axl mutant resembles wild-type plants, the majority of axr1 axl-1 double mutants are embryo or seedling lethal. Furthermore, the axl-1 mutation reveals novel RUB-dependent processes in embryo development. We conclude that AXR1 and AXL function redundantly in the RUB conjugating pathway.     

Three new species of Lentinus from northern Thailand

There have been few studies on the taxonomy and biodiversity of the genus Lentinus in Thailand, which is a genus of edible mushrooms. Recently, collections from 17 sites in northern Thailand yielded 47 specimens of Lentinus sensu lato. Three were shown to be new species of Lentinus sensu stricto and Lentinus roseus, L. concentricus and L. megacystidiatus are introduced in this paper. The new species are described and illustrated with line drawings and are justified and compared with similar taxa. Furthermore, ITS sequence data do not match closely with any species presently lodged in GenBank.     

The importance of plot size and the number of sampling seasons on capturing macrofungal species richness

The species-area relationship is an important factor in the study of species diversity, conservation biology, and landscape ecology. A deeper understanding of this relationship is necessary, in order to provide recommendations on how to improve the quality of data collection on macrofungal diversity in different land use systems in future studies, a systematic assessment of methodological parameters, in particular optimal plot sizes. The species-area relationship of macrofungi in tropical and temperate climatic zones and four different land use systems were investigated by determining the macrofungal species richness in plot sizes ranging from 100 m² to 10 000 m² over two sampling seasons. We found that the effect of plot size on recorded species richness significantly differed between land use systems with the exception of monoculture systems. For both climate zones, land use system needs to be considered when determining optimal plot size. Using an optimal plot size was more important than temporal replication (over two sampling seasons) in accurately recording species richness.     

Agaricus subrufescens: A review

Medicinal mushrooms have currently become a hot issue due to their various therapeutic properties. Of these, Agaricus subrufescens, also known as the “almond mushroom”, has long been valued by many societies (i.e., Brazil, China, France, and USA). Since its discovery in 1893, this mushroom has been cultivated throughout the world, especially in Brazil where several strains of A. subrufescens have been developed and used as health food and alternative medicine. This article presents up-to-date information on this mushroom including its taxonomy and health promoting benefits. Medicinal properties of A. subrufescens are emphasized in several studies which are reviewed here. In addition, safety issues concerning the use of this fungus will be discussed.     

Biogeography of the world: a case study from cyphophthalmid Opiliones, a globally distributed group of arachnids

Aim To test the hypothesis that continental drift drives diversification of organisms through vicariance, we selected a group of primitive arachnids which originated before the break‐up of Pangaea and currently inhabits all major landmasses with the exception of Antarctica, but lacks the ability to disperse across oceanic barriers. Location Major continental temperate to tropical landmasses (North America, South America, Eurasia, Africa, Australia) and continental islands (Bioko, Borneo, Japan, Java, New Caledonia, New Guinea, New Zealand, Sri Lanka, Sulawesi, Sumatra). Methods Five kb of sequence data from five gene regions for more than 100 cyphophthalmid exemplars were analysed phylogenetically using different methods, including direct optimization under parsimony and maximum likelihood under a broad set of analytical parameters. We also used geological calibration points to estimate gross phylogenetic time divergences. Results Our analyses show that all families except the Laurasian Sironidae are monophyletic and adhere to clear biogeographical patterns. Pettalidae is restricted to temperate Gondwana, Neogoveidae to tropical Gondwana, Stylocellidae to Southeast Asia, and Troglosironidae to New Caledonia. Relationships between the families inhabiting these landmasses indicate that New Caledonia is related to tropical Gondwana instead of to the Australian portion of temperate Gondwana. The results also concur with a Gondwanan origin of Florida, as supported by modern geological data. Main conclusions By studying a group of organisms with not only an ancient origin, low vagility and restricted habitats, but also a present global distribution, we have been able to test biogeographical hypotheses at a scale rarely attempted. Our results strongly support the presence of a circum‐Antarctic clade of formerly temperate Gondwanan species, a clade restricted to tropical Gondwana and a Southeast Asian clade that originated from a series of early Gondwanan terranes that rifted off northwards from the Devonian to the Triassic and accreted to tropical Laurasia. The relationships among the Laurasian species remain more obscure.     

A Novel Cryptochrome-Dependent Oscillator in Neurospora crassa

Several lines of evidence suggest that the circadian clock is constructed of multiple molecular feedback oscillators that function to generate robust rhythms in organisms. However, while core oscillator mechanisms driving specific behaviors are well described in several model systems, the nature of other potential circadian oscillators is not understood. Using genetic approaches in the fungus Neurospora crassa, we uncovered an oscillator mechanism that drives rhythmic spore development in the absence of the well-characterized FRQ/WCC oscillator (FWO) and in constant light, conditions under which the FWO is not functional. While this novel oscillator does not require the FWO for activity, it does require the blue-light photoreceptor CRYPTOCHROME (CRY); thus, we call it the CRY-dependent oscillator (CDO). The CDO was uncovered in a strain carrying a mutation in cog-1 (cry-dependent oscillator gate-1), has a period of ∼1 day in constant light, and is temperature-compensated. In addition, cog-1 cells lacking the circadian blue-light photoreceptor WC-1 respond to blue light, suggesting that alternate light inputs function in cog-1 mutant cells. We show that the blue-light photoreceptors VIVID and CRY compensate for each other and for WC-1 in CRY-dependent oscillator light responses, but that WC-1 is necessary for circadian light entrainment.     

Morphology,Phylogeny and Culture Characteristics of <i>Ganoderma gibbosum</i> Collected from Kunming,Yunnan Province,China

Ganoderma is a genus of medicinally and economically important mushrooms in the family Ganodermataceae. Ganoderma species are popular medicinal mushrooms and their health benefits are well-documented. Ganoderma is a cosmopolitan genus that is widely distributed in both tropical and temperate regions. This genus is characterized by its unique laccate or non-laccate species with double-walled basidiospores. Here, we report on eight collections of G. gibbosum collected during surveys in Kunming, Yunnan Province, China. The specimens are described and illustrated based on macro- and micro-morphological characteristics. Total DNA of the eight G. gibbosum strains were extracted using the Biospin Fungal Extraction Kit following manufacturer protocol. Amplification of the Internal Transcribed Spacer (nrITS) region was carried out using ITS5/ITS4 primers and LROR/LR5 for the nuclear ribosomal large subunit 28S rDNA gene (LSU). Phylogenetic analysis with closely related species to G. gibbosum showed that all eight collections grouped with G. gibbosum with 100% bootstrap support. Phylogenetic similarity and morphological variations within the eight collections of G. gibbosum are discussed.     

An APETALA1 ortholog affects plant architecture and seed yield component in oilseed rape (Brassica napus L.)

Exploring the natural occurring genetic variation of the wild barley genepool has become a major target of barley crop breeding programmes aiming to increase crop productivity and sustainability in global climate change scenarios. However this diversity remains unexploited and effective approaches are required to investigate the benefits that unadapted genomes could bring to crop improved resilience. In the present study, a set of Recombinant Chromosome Substitution Lines (RCSLs) derived from an elite barley cultivar ‘Harrington’ as the recurrent parent, and a wild barley accession from the Fertile Crescent ‘Caesarea 26–24’, as the donor parent (Matus et al. Genome 46:1010–23, 2003) have been utilised in field and controlled conditions to examine the contribution of wild barley genome as a source of novel allelic variation for the cultivated barley genepool. Twenty-eight RCSLs which were selected to represent the entire genome of the wild barley accession, were genotyped using the 9 K iSelect SNP markers (Comadran et al. Nat Genet 44:1388–92, 2012) and phenotyped for a range of morphological, developmental and agronomic traits in 2 years using a rain-out shelter with four replicates and three water treatments. Data were analysed for marker traits associations using a mixed model approach. We identified lines that differ significantly from the elite parent for both qualitative and quantitative traits across growing seasons and water regimes. The detailed genotypic characterisation of the lines for over 1800 polymorphic SNP markers and the design of a mixed model analysis identified chromosomal regions associated with yield related traits where the wild barley allele had a positive response increasing grain weight and size. In addition, variation for qualitative characters, such as the presence of cuticle waxes on the developing spikes, was associated with the wild barley introgressions. Despite the coarse location of the QTLs, interesting candidate genes for the major marker-trait associations were identified using the recently released barley genome assembly. This study has highlighted the role of exotic germplasm to contribute novel allelic variation by using an optimised experimental approach focused on an exotic genetic library. The results obtained constitute a step forward to the development of more tolerant and resilient varieties.     

Personalized treatment plans with multivariate outcomes

In this work, we propose a novel method for individualized treatment selection when the treatment response is multivariate. Our method covers any number of treatments and it can be applied for a broad set of models. The proposed method uses a Mahalanobis-type distance measure to establish an ordering of treatments based on treatment performance measures. Our investigation in this work deals with means of responses conditional on lower dimensional composite scores based on covariates where these scores are built using single index models to approximate mean responses against patient covariates. Smoothed estimates of such conditional means are combined to construct an estimate of the aforementioned distance measure, which is then used to estimate the optimal treatment. An empirical study demonstrates the performance of the proposed method in finite samples. We also present a data analysis using an HIV clinical trial data to show the applicability of the proposed procedure for real data.