The UBAP1 subunit of ESCRT-I interacts with ubiquitin via a SOUBA domain

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Highlights? ESCRT-I subunit UBAP1 is essential for degradation of antiviral protein tetherin ? UBAP1 has a domain consisting of a solenoid of overlapping UBAs (SOUBA) ? Each of the three UBAs in the SOUBA binds monoubiquitin     

Genomic dissection of pod shattering in common bean: mutations at non‐orthologous loci at the basis of convergent phenotypic evolution under domestication of leguminous species

The complete or partial loss of shattering ability occurred independently during the domestication of several crops. Therefore, the study of this trait can provide an understanding of the link between phenotypic and molecular convergent evolution. The genetic dissection of ‘pod shattering’ in Phaseolus vulgaris is achieved here using a population of introgression lines and next‐generation sequencing techniques. The ‘occurrence’ of the indehiscent phenotype (indehiscent versus dehiscent) depends on a major locus on chromosome 5. Furthermore, at least two additional genes are associated with the ‘level’ of shattering (number of shattering pods per plant: low versus high) and the ‘mode’ of shattering (non‐twisting versus twisting pods), with all of these loci contributing to the phenotype by epistatic interactions. Comparative mapping indicates that the major gene identified on common bean chromosome 5 corresponds to one of the four quantitative trait loci for pod shattering in Vigna unguiculata. None of the loci identified comprised genes that are homologs of the known shattering genes in Glycine max. Therefore, although convergent domestication can be determined by mutations at orthologous loci, this was only partially true for P. vulgaris and V. unguiculata, which are two phylogenetically closely related crop species, and this was not the case for the more distant P. vulgaris and G. max. Conversely, comparative mapping suggests that the convergent evolution of the indehiscent phenotype arose through mutations in different genes from the same underlying gene networks that are involved in secondary cell‐wall biosynthesis and lignin deposition patterning at the pod level.     

A short note on predicted motifs in the Thaparocleidus wallagonius genome

Thaparocleidus wallagonius is a monogenean parasite and a fish-borne pathogen with a worldwide distribution. The genome for Thaparocleidus wallagonius is known. Therefore, it is of interest to report the DNA motif analysis data in the 18S rDNA of Thaparocleidus wallagonius collected from the fish Wallago attu in India. This data forms a framework for an in-depth analysis of the parasite biology and development, immune evasion strategies, virulence and long-term survival within the definitive host.     

Mechanistically distinct roles for Sgs1p in checkpoint activation and replication fork maintenance

The RecQ helicase Sgs1p forms a complex with the type 1 DNA topoisomerase Top3p that resolves double Holliday junctions resulting from Rad51-mediated exchange. We find, however, that Sgs1p functions independently of both Top3p and Rad51p to stimulate the checkpoint kinase Rad53p when replication forks stall due to dNTP depletion on hydroxyurea. Checkpoint activation does not require Sgs1p function as a helicase, and correlates with its ability to bind the Rad53p kinase FHA1 motif directly. On the other hand, Sgs1p's helicase activity is required together with Top3p and the strand-exchange factor Rad51p, to help stabilise DNA polymerase epsilon at stalled replication forks. In this function, the Sgs1p/Top3p complex acts in parallel to the Claspin-related adaptor, Mrc1p, although the sgs1 and mrc1 mutations are epistatic for Rad53p activation. We thus identify two distinct pathways through which Sgs1p contributes to genomic integrity: checkpoint kinase activation requires Sgs1p as a noncatalytic Rad53p-binding site, while the combined Top3p/Sgs1p resolvase activity contributes to replisome stability and recovery from arrested replication forks.     

Variation in Aboveground Cover Influences Soil Nitrogen Availability at Fine Spatial Scales Following Severe Fire in Subalpine Conifer Forests

Following fire, fine-scale variation in early successional vegetation and soil nutrients may influence development of ecosystem structure and function. We studied conifer forests burned by stand-replacing wildfire in Greater Yellowstone (Wyoming, USA) to address two questions: (1) How do the variability and spatial structure of aboveground cover and soil nitrogen availability change during the first 4 years following stand-replacing fire? (2) At fine scales (2–20 m), are postfire soil inorganic N pools and fluxes related to aboveground cover? Aboveground cover, soil N pools, and annual net N transformations were measured from 2001 to 2004 using a spatially explicit sampling design in four 0.25-ha plots that burned during summer 2000. Within-stand variability (coefficient of variation) in postfire live vegetative cover declined with time since fire, whereas variability in bare mineral soil, charred litter and fresh litter was greatest 2-3 years postfire. The soil nitrate pool was more variable than the soil ammonium pool, but annual net nitrification was less variable than annual net N mineralization. Spatial structure (quantified by semivariograms) was observed in some aboveground cover variables (for example, graminoids and fresh litter), but there was little spatial structure in soil N variables and no obvious congruence in spatial scales of autocorrelation for soil N and aboveground cover. Significant Spearman correlations (at the sample point) indicated that aboveground cover and soil N were coupled following severe fire, and the dominant influence was from aboveground cover to soil N, rather than from soil N to vegetation. Initial patterns of fire severity and re-vegetation contributed to fine-scale heterogeneity in soil N availability for at least 4 years after severe fire.     

Beta-adenosine, a bioactive compound in grass chaff stimulating mushroom production

Fructification and yield of the edible mushrooms Pleurotus pulmonarius and Stropharia rugosoannulata are clearly enhanced when wheat straw is supplemented with 30% Lolium perenne grass chaff. The bioactive compound in the methanol extract of grass chaff was identified as beta-adenosine. In vitro biological activity tests showed that 0.012 mg of beta-adenosine per ml of medium stimulated earlier fructification of Pleurotus pulmonarius. Mushroom fruiting trials showed that when 12 mg beta-adenosine was added to 1 kg wet wheat straw, primordia of Pleurotus pulmonarius appeared two days earlier and primordia of Stropharia rugosoannulata appeared 18 days earlier when compared to pure wheat straw substrate. This concentration of beta-adenosine had no impact on the mushroom yield of Pleurotus, but resulted in a 2.2 fold increase in yield for Stropharia. beta-Adenosine at 25 mg per kg wet wheat straw increased the yield of Pleurotus with 52% and the yield of Stropharia with 258%, but this concentration delayed primordial formation in Pleurotus.