Structural and biochemical analysis of Cellvibrio japonicus xylanase 10C: how variation in substrate-binding cleft influences the catalytic profile of family GH-10 xylanases

Microbial degradation of the plant cell wall is the primary mechanism by which carbon is utilized in the biosphere. The hydrolysis of xylan, by endo-beta-1,4-xylanases (xylanases), is one of the key reactions in this process. Although amino acid sequence variations are evident in the substrate binding cleft of "family GH10" xylanases (see afmb.cnrs-mrs.fr/CAZY/), their biochemical significance is unclear. The Cellvibrio japonicus GH10 xylanase CjXyn10C is a bi-modular enzyme comprising a GH10 catalytic module and a family 15 carbohydrate-binding module. The three-dimensional structure at 1.85 A, presented here, shows that the sequence joining the two modules is disordered, confirming that linker sequences in modular glycoside hydrolases are highly flexible. CjXyn10C hydrolyzes xylan at a rate similar to other previously described GH10 enzymes but displays very low activity against xylooligosaccharides. The poor activity on short substrates reflects weak binding at the -2 subsite of the enzyme. Comparison of CjXyn10C with other family GH10 enzymes reveals "polymorphisms" in the substrate binding cleft including a glutamate/glycine substitution at the -2 subsite and a tyrosine insertion in the -2/-3 glycone region of the substrate binding cleft, both of which contribute to the unusual properties of the enzyme. The CjXyn10C-substrate complex shows that Tyr-340 stacks against the xylose residue located at the -3 subsite, and the properties of Y340A support the view that this tyrosine plays a pivotal role in substrate binding at this location. The generic importance of using CjXyn10C as a template in predicting the biochemical properties of GH10 xylanases is discussed.     

The use of free groin flaps in children

The free groin flap is a well-established method of skin coverage. Although its use in children has been reported, there have been no published series specifically in such cases. The authors report 33 consecutive cases of free groin flaps in children in their unit over a period of 9 years (1992 to 2001). Tissue transfer was performed to provide soft-tissue coverage during reconstruction of congenital defects and tumor resection and following trauma. Twenty-six cases (79 percent) involved the upper limb, six cases (18 percent) involved the lower limb, and one case involved the head. The complication rate compares favorably with similar series published for adults, with only two complete failures (6 percent), three (9 percent) minor donor-site complications (superficial wound infection, hypertrophic scarring, and dog-ears), and nine flaps requiring debulking. The reexploration rate was 24 percent, with seven of the eight flaps undergoing reexploration surviving. The groin flap is a reliable flap that can be used safely in children, with minimal morbidity.     

Fibrillar beta-lactoglobulin gels: Part 3. Dynamic mechanical characterization of solvent-induced systems

Oscillatory shear rheometry has been used to study the gelation of beta-lactoglobulin at ambient in 50% v/v trifluoroethanol (TFE)/pH 7 aqueous buffer and in 50% v/v ethanol (EtOH)/water at pH 2. In contrast to what was found on heating aqueous solutions at pH 2 (Part 2 of this series), a more expected "chemical gelation"-like profile was found with modulus components G' and G' ' crossing over as the gels formed and then with G' ' passing through a maximum. In addition, for the EtOH system, there was a significant modulus increase at long time, suggestive of a more complex two-step aggregation scheme. Modulus-concentration relationships were obtained for both systems by extrapolating cure data to infinite time. For the TFE gels, this data was accurately described by classical branching theory, although it could also be approximated by a constant power--law relationship. Only the latter described the modulus--concentration data for the gels in ethanol, but there were problems here of greater frequency dependence of the modulus values and much less certain extrapolation. Gel times for the TFE systems showed higher power laws in the concentration than could be explained by the branching theory in its simplest form being similar, in this respect, to the heat-set systems at pH 2. Such power laws were harder to establish for the EtOH gels as for these there was evidence of gel time divergence close to a critical concentration. Reduced G'/G'inf versus t/tgel data were difficult to interpret for the gels in ethanol, but for the TFE system they were consistent with previous results for the heat-set gels and approximated master curve superposition. The frequency and temperature dependences of the final gel moduli were also studied. In general, the networks induced by alcohols appeared more flexible than those obtained by heating.     

Genotyping over 100,000 SNPs on a pair of oligonucleotide arrays

We present a genotyping method for simultaneously scoring 116,204 SNPs using oligonucleotide arrays. At call rates >99%, reproducibility is >99.97% and accuracy, as measured by inheritance in trios and concordance with the HapMap Project, is >99.7%. Average intermarker distance is 23.6 kb, and 92% of the genome is within 100 kb of a SNP marker. Average heterozygosity is 0.30, with 105,511 SNPs having minor allele frequencies >5%.     

Progression of mycotoxin and nutrient concentrations in wheat after inoculation with Fusarium culmorum

The objective of this study was to follow the mycotoxin formation and changes in nutrient composition of wheat (cv. Ritmo) artificially inoculated with Fusarium culmorum. From anthesis until harvest, samples were taken once a week from the inoculated and control plots. The investigations were focused on monitoring the progression of the contamination of the wheat kernels with deoxynivalenol (DON) and zearalenone (ZON). Both the uncontaminated control kernels and the contaminated kernels were examined also for the presence of zearalenone-4-beta-D-glucopyranoside and several trichothecenes at harvest. Furthermore, the impact of the Fusarium inoculation on some nutrients as starch, crude protein, amino acid composition, crude ash, non starch polysaccharides (NSP) as well as viscosity and thousand seed weight (TSW) was examined. Also proteolytic and amylolytic activity as well as the NSP-degrading enzyme activities of inoculated and control samples were analysed at the time of harvest. DON was detected in higher concentrations and in earlier stages, while ZON was found later and in smaller amounts. On average 7.79?mg/kg DM of DON and 100?μg/kg DM of ZON were found in the inoculated kernels at the time of harvest. Neither in the contaminated nor in the control samples glucose conjugates of ZON (Zearalenone-4-beta-D-glucopyranoside) were detected. Moreover, the infection with Fusarium culmorum had pronounced effects on some quality parameters. The crude protein content of the inoculated kernels showed significantly higher values over the whole period compared to the control kernels. The protein content of the inoculated kernels amounted 13.9% DM at harvest, while only a concentration of 12.5% DM was detected in the control samples. Similarly, in almost all stages of development the crude ash content of inoculated samples was higher than in control samples. These distinct differences in kernel composition resulted possibly from the changes of the thousand seed weight. In the present work the grain harvested from the control plots showed a significantly higher TSW (24.2?g) as compared to their inoculated counterparts (15.5?g). Despite lower extract viscosity of inoculated samples at time of harvest, the content of soluble NSP of inoculated plots was higher than in control samples at the same time. Moreover, inoculation resulted in markedly increased activities of protease, amylase and several NSP-degrading enzyme activities. This would suggest that the cell wall penetrating properties of the fungus itself and/or that the fungus induced alterations of the metabolic activity of the embryo or other constituents of the wheat kernel could be responsible.     

Solution Structure of Rnase T1 and Its Complexes with Nucleotides

Abstract

The solution structure of RNase T₁ and its complexes with 2′-GMP and. 3′-GMP have been investigated by combined use of 2D-NMR spectroscopy and restrained molecular dynamics calculations (MD). An analysis of the nuclear Overhauser effects (NOEs) observed indicates the presence of one a helix as well as of two antiparallel β sheets. Interaction of the nucleotides with the active site leads to changes of the backbone conformation of the amino acids involved. However, the interaction between the protein and 3′-GMP is not as strong as the interaction with 2′-GMP, possibly because of weaker binding.     

Annotated expressed sequence tags for studies of the regulation of reproductive modes in aphids

The damaging effect of aphids to crops is largely determined by the spectacular rate of increase of populational expansion due to their parthenogenetic generations. Despite this, the molecular processes triggering the transition between the parthenogenetic and sexual phases between their annual life cycle have received little attention. Here, we describe a collection of genes from the cereal aphid Rhopalosiphum padi expressed during the switch from parthenogenetic to sexual reproduction. After cDNA cloning and sequencing, 726 expressed sequence tags (EST) were annotated. The R. padi EST collection contained a substantial number (139) of bacterial endosymbiont sequences. The majority of R. padi cDNAs encoded either unknown proteins (56%) or housekeeping polypeptides (38%). The large proportion of sequences without similarities in the databases is related to both their small size and their high GC content, corresponding probably to the presence of 5'-unstranslated regions. Fifteen genes involved in developmental and differentiation events were identified by similarity to known genes. Some of these may be useful candidates for markers of the early steps of sexual differentiation.     

Co-occurrence patterns of Bornean vertebrates suggest competitive exclusion is strongest among distantly related species

Assessing the importance of deterministic processes in structuring ecological communities is a central focus of community ecology. Typically, community ecologists study a single taxonomic group, which precludes detection of potentially important biotic interactions between distantly related species, and inherently assumes competition is strongest between closely related species. We examined distribution patterns of vertebrate species across the island of Borneo in Southeast Asia to assess the extent to which inter-specific competition may have shaped ecological communities on the island and whether the intensity of inter-specific competition in present-day communities varies as a function of evolutionary relatedness. We investigated the relative extent of competition within and between species of primates, birds, bats and squirrels using species presence–absence and attribute data compiled for 21 forested sites across Borneo. We calculated for each species pair the checkerboard unit value (CU), a statistic that is often interpreted as indicating the importance of interspecific competition. The percentage of species pairs with significant CUs was lowest in within-taxon comparisons. Moreover, for invertebrate-eating species the percentage of significantly checkerboarded species pairs was highest in comparisons between primates and other taxa, particularly birds and squirrels. Our results are consistent with the interpretation that competitive interactions between distantly related species may have shaped the distribution of species and thus the composition of Bornean vertebrate communities. This research highlights the importance of taking into account the broad mammalian and avian communities in which species occur for understanding the factors that structure biodiversity.     

Temporal and spatial dispersal of cladobotryum conidia in the controlled environment of a mushroom growing room

Cladobotryum spp. are responsible for cobweb disease of mushrooms. In two commercial and one experimental mushroom-growing room, Cladobotryum conidia were released into the air in direct response to physical disturbance of disease colonies during either crop watering or treatment by covering with salt to 10 mm. Conidia were detected using a Burkard spore trap or agar-based trap plates. A maximum concentration of approximately 25,000 conidia m(-3) was recorded in a small (75-m(3)) experimental growing room in the hour following the salting of 16 cobweb patches (0.55 m(2)). Concentrations of 100 and 40 conidia m(-3) were recorded in the two larger commercial growing rooms in the hour following the salting of 18 and 11 patches of cobweb (diameter, approximately 50 to 200 mm), respectively. In controlled experiments, disturbed conidia were dispersed rapidly throughout a small growing room, with 91 to 97% of conidia settling out within 15 min. Eighty-five percent of conidia settled out within a 0.5-m radius when air-conditioning fans were switched off, consistent with airborne spore dispersal. Alternative methods for treating diseased areas to minimize conidial release and distribution were investigated and included covering disease colonies with damp paper tissue prior to salt application (tissue salting) and holding a dust extractor above disease colonies during salt application. Both methods resulted in no detectable airborne conidia, but the tissue paper salting technique was more convenient. Prevention of airborne conidial release and distribution is essential to avoid mushroom spotting symptoms, secondary colonies, and early crop termination.     

Hypoxia-induced energy stress regulates mRNA translation and cell growth

Oxygen (O2) deprivation, or hypoxia, has profound effects on cell metabolism and growth. Cells can adapt to low O2 in part through activation of hypoxia-inducible factor (HIF). We report here that hypoxia inhibits mRNA translation by suppressing multiple key regulators, including eIF2alpha, eEF2, and the mammalian target of rapamycin (mTOR) effectors 4EBP1, p70S6K, and rpS6, independent of HIF. Hypoxia results in energy starvation and activation of the AMPK/TSC2/Rheb/mTOR pathway. Hypoxic AMP-activated protein kinase (AMPK) activation also leads to eEF2 inhibition. Moreover, hypoxic effects on cellular bioenergetics and mTOR inhibition increase over time. Mutation of the TSC2 tumor suppressor gene confers a growth advantage to cells by repressing hypoxic mTOR inhibition and hypoxia-induced G1 arrest. Together, eIF2alpha, eEF2, and mTOR inhibition represent important HIF-independent mechanisms of energy conservation that promote survival under low O2 conditions.