bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stoichiometry and perturbation studies of the LiaFSR system of Bacillus subtilis
Authors: Schrecke Karen , Jordan Sina , Mascher Thorsten 
Published: December 2012

SummaryThe response regulator/histidine kinase pair LiaRS of Bacillus subtilis, together with its membrane‐bound inhibitor protein LiaF, constitutes an envelope stress‐sensing module that is conserved in Firmicutes bacteria. LiaR positively autoregulates the expression of the liaIH‐liaGFSR operon from a strictly LiaR‐dependent promoter (PliaI). A comprehensive perturbation analysis revealed that the functionality of the LiaFSR system is very susceptible to alterations of its protein composition and amounts. A genetic analysis indicates a LiaF:LiaS:LiaR ratio of 18:4:1. An excess of LiaS over LiaR was subsequently verified by quantitative Western analysis. This stoichiometry, which is crucial to maintain a functional Lia system, differs from any other two‐component system studied to date, in which the response regulator is present in excess over the histidine kinase. Moreover, we demonstrate that LiaS is a bifunctional histidine kinase that acts as a phosphatase on LiaR in the absence of a suitable stimulus. An increased amount of LiaR – both in the presence and in the absence of LiaS – leads to a strong induction of PliaI activity due to phosphorylation of the response regulator by acetyl phosphate. Our data demonstrate that LiaRS, in contrast to other two‐component systems, is non‐robust with regard to perturbations of its stoichiometry.
Membrane sequestration by the EIIB domain of the mannitol permease MtlA activates the Bacillus subtilismtl operon regulator MtlR
Authors: Bouraoui Houda , Ventroux Magali , Noirot‐Gros Marie‐Françoise , Deutscher Josef , Joyet Philippe 
Published: December 2012

SummaryIn most firmicutes expression of the mannitol operon is regulated by MtlR. This transcription activator is controlled via phosphorylation of its regulatory domains by components of the phosphoenolpyruvate : carbohydrate phosphotransferase system (PTS). We found that activation of Bacillus subtilis MtlR also requires an interaction with the EIIBMtl domain of the mannitol permease MtlA (EIICBMtl). The constitutive expression of the mtlAFD operon in an mtlF mutant was prevented when entire mtlA or only its 3′ part (EIIBMtl) were deleted. Yeast two‐hybrid experiments revealed a direct interaction of the EIIBMtl domain with the two C‐terminal domains of MtlR. Complementation of the Δ3′‐mtlA ΔmtlF or ΔmtlAFD mutants with mtlA restored constitutive MtlR activity, whereas complementation with only 3′‐mtlA had no effect. Moreover, synthesis of EIIBMtl in strains producing constitutively active MtlR caused MtlR inactivation. Interestingly, EIIBMtl fused to the trans‐membrane protein YwqC restored constitutive MtlR activity in the above mutants. Replacing the phosphorylatable Cys with Asp in MtlA or soluble EIIBMtl lowered MtlR activation, indicating that MtlR does not interact with phosphorylatyed EIIBMtl. Induction of the B. subtilis mtl operon therefore follows a novel regulation mechanism where the transcription activator needs to be sequestered to the membrane by unphosphorylated EIICBMtl in order to be functional.
The C‐terminal portion of the cleaved HT motif is necessary and sufficient to mediate export of proteins from the malaria parasite into its host cell
Authors: Tarr Sarah J. , Cryar Adam , Thalassinos Konstantinos , Haldar Kasturi , Osborne Andrew R. 
Published: December 2012

SummaryThe malaria parasite exports proteins across its plasma membrane and a surrounding parasitophorous vacuole membrane, into its host erythrocyte. Most exported proteins contain a Host Targeting motif (HT motif) that targets them for export. In the parasite secretory pathway, the HT motif is cleaved by the protease plasmepsin V, but the role of the newly generated N‐terminal sequence in protein export is unclear. Using a model protein that is cleaved by an exogenous viral protease, we show that the new N‐terminal sequence, normally generated by plasmepsin V cleavage, is sufficient to target a protein for export, and that cleavage by plasmepsin V is not coupled directly to the transfer of a protein to the next component in the export pathway. Mutation of the fourth and fifth positions of the HT motif, as well as amino acids further downstream, block or affect the efficiency of protein export indicating that this region is necessary for efficient export. We also show that the fifth position of the HT motif is important for plasmepsin V cleavage. Our results indicate that plasmepsin V cleavage is required to generate a new N‐terminal sequence that is necessary and sufficient to mediate protein export by the malaria parasite.
Obesity and its relation to chronic kidney disease: A population‐based, cross‐sectional study of a Thai army population and relatives
Authors: Satirapoj Bancha , Supasyndh Ouppatham , Mayteedol Natee , Punpanich Dollapas , Chaiprasert Amnart , Nata Naowanit , Ruangkanchanasetr Prajej , Kanjanakul Inseey , Choovichian Panbubpa 
Published: December 2012

AbstractAimObesity represents a significant problem in patients with cardiovascular disease and chronic kidney disease (CKD). The aim of the present study was to investigate the association between body mass index (BMI) and CKD in Thai individuals.MethodsParticipants underwent general health screening. Overweight, weight at risk, obese I and obese II were defined as having a BMI ≥23 kg/m2, 23–24.9 kg/m2, 25–29.9 kg/m2 and ≥30 kg/m2, respectively. Waist circumference ≥ 90 cm for men and > 80 cm for women were represented by abdominal obesity. CKD was defined as a glomerular filtration rate (GFR) < 60 mL/min per 1.73 m2. An estimate of the GFR was obtained by the four‐variable Modification of Diet in Renal Disease (MDRD) equation.ResultsThe study population had 12 348 males and 3009 females. The survey population had a 7.5% prevalence of CKD. There was also a significant graded relationship between the degrees of overweight with the prevalence of CKD. Mean BMI were 25.36 ± 3.29 kg/m2 for CKD subjects and 24.04 ± 3.13 kg/m2 for non‐CKD subjects (P < 0.001). Prevalence of overweight and abdominal obesity in the participants with CKD were found to be higher than in those without CKD (overweight, 77.6% vs. 61.6%, P < 0.001; abdominal obesity, 35.7% vs. 25.3%, P < 0.001). In a multivariate logistic regression analysis, weight at risk (adjusted odds ratio 1.29; 95% CI 1.07–1.54), obese I (adjusted odds ratio 1.58; 95% CI 1.33–1.87) and obese II (adjusted odds ratio 1.65; 95% CI 1.24–2.19) were associated with CKD.ConclusionOur data showed that overweight and obesity were associated with CKD in Thai members of the army population and their relatives undergoing a general health screening, independently of age, gender, blood pressure, serum lipid, uric acid and glucose levels.
Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control and genetic correlations
Authors: Porth Ilga , Klápště Jaroslav , Skyba Oleksandr , Lai Ben S. K. , Geraldes Armando , Muchero Wellington , Tuskan Gerald A. , Douglas Carl J. , El‐Kassaby Yousry A. , Mansfield Shawn D. 
Published: December 2012

Summary

The increasing ecological and economical importance of Populus species and hybrids has stimulated research into the investigation of the natural variation of the species and the estimation of the extent of genetic control over its wood quality traits for traditional forestry activities as well as the emerging bioenergy sector. A realized kinship matrix based on informative, high‐density, biallelic single nucleotide polymorphism (SNP) genetic markers was constructed to estimate trait variance components, heritabilities, and genetic and phenotypic correlations.

Seventeen traits related to wood chemistry and ultrastructure were examined in 334 9‐yr‐old Populus trichocarpa grown in a common‐garden plot representing populations spanning the latitudinal range 44° to 58.6°. In these individuals, 9342 SNPs that conformed to Hardy–Weinberg expectations were employed to assess the genomic pair‐wise kinship to estimate narrow‐sense heritabilities and genetic correlations among traits.

The range‐wide phenotypic variation in all traits was substantial and several trait heritabilities were > 0.6. In total, 61 significant genetic and phenotypic correlations and a network of highly interrelated traits were identified.

The high trait variation, the evidence for moderate to high heritabilities and the identification of advantageous trait combinations of industrially important characteristics should aid in providing the foundation for the enhancement of poplar tree breeding strategies for modern industrial use.
Polymorphic simple sequence repeat (SSR) loci within cellulose synthase (PtoCesA) genes are associated with growth and wood properties in Populus tomentosa
Authors: Du Qingzhang , Pan Wei , Xu Baohua , Li Bailian , Zhang Deqiang 
Published: December 2012

Summary

Chinese white poplar (Populus tomentosa), an important commercial tree species for timber and pulp production in northern China, has been used to examine the individual genes and allelic diversity responsible for complex traits controlling growth and lignocellulosic biosynthesis. Taking advantage of the low degree of linkage disequilibrium (LD) within P. tomentosa association populations, we examined associations between 15 cellulose synthase (PtoCesA) genes and traits including growth and wood properties.

Thirty‐six novel simple sequence repeat (SSR) markers within PtoCesA genes were detected by re‐sequencing and genotyped in an association population (460 individuals). Single‐marker and haplotype‐based LD approaches were used to identify significant marker–trait associations. Family‐based linkage studies and real‐time PCR testing were conducted to validate the functional significance of SSR variation.

Fifteen single‐marker associations from seven PtoCesA genes and nine haplotype‐based associations within six genes were identified in the association population (false discovery rate Q < 0.05). Next, five SSR marker–trait associations (Q < 0.05) from four PtoCesA genes were successfully validated in a linkage mapping population (1200 individuals).

The results imply a functional role for these genes in mediating wood properties, demonstrating the potential of combining single‐marker and haplotype‐based LD approaches to detect functional allelic variation underlying quantitative traits in a low‐LD population.
Root stress and nitrogen deposition: consequences and research priorities
Authors: Smithwick Erica A. H. , Eissenstat David M. , Lovett Gary M. , Bowden Richard D. , Rustad Lindsey E. , Driscoll Charles T. 
Published: December 2012

SummaryStress within tree roots may influence whole‐tree responses to nutrient deficiencies or toxic ion accumulation, but the mechanisms that govern root responses to the belowground chemical environment are poorly quantified. Currently, root production is modeled using rates of forest production and stoichiometry, but this approach alone may be insufficient to forecast variability in forest responses when physical and chemical stressors alter root lifespan, rooting depth or mycorrhizal colonization directly. Here, we review key research priorities for improving predictions of tree responses to changes in the belowground biogeochemical environment resulting from nitrogen deposition, including: limits of the optimum allocation paradigm, root physiological stress and lifespan, contingency effects that determine threshold responses across broad gradients, coupled water‐biogeochemical interactions on roots, mycorrhizal dynamics that mediate root resilience and model frameworks to better simulate root feedbacks to aboveground function. We conclude that models incorporating physiological feedbacks, dynamic responses to coupled stressors, mycorrhizal interactions, and which challenge widely‐accepted notions of optimum allocation, can elucidate potential thresholds of tree responses to biogeochemical stressors. Emphasis on comparative studies across species and environmental gradients, and which incorporates insights at the cellular and ecosystem level, is critical for forecasting whole‐tree responses to altered biogeochemical landscapes.
Vessel diameter–stem diameter scaling across woody angiosperms and the ecological causes of xylem vessel diameter variation
Authors: Olson Mark E. , Rosell Julieta A. 
Published: December 2012

Summary

Variation in angiosperm vessel diameter is of major functional significance. In the light of recent models predicting optimal vessel taper given resistance imposed by conductive path length, we tested the prediction that plant size should predict vessel diameter, with dryland plants having narrower vessels for their stem sizes.

We assembled a comparative dataset including vessel and stem diameter measurements from 237 species from over 40 angiosperm orders across a wide range of habits and habitats.

Stem diameter predicted vessel diameter across self‐supporting plants (slope 0.36, 95% CI 0.32–0.39). Samples from 142 species from five communities of differing water availability showed no tendency for dryland plants to have narrower vessels. Predictable relationships between vessel diameter and stem diameter mirrored predictable relationships between stem length and diameter across self‐supporting species.

That vessels are proportional to stem diameter and stem diameter is proportional to stem length suggests that taper in relation to conductive path length gives rise to the vessel diameter–stem diameter relationship. In turn, plant size is related to climate, leading indirectly to the vessel–climate relationship: vessels are likely narrower in drier communities because dryland plants are on average smaller, not because they have narrow vessels for their stem sizes.
Elevated night‐time temperatures increase growth in seedlings of two tropical pioneer tree species
Authors: Cheesman Alexander W. , Winter Klaus 
Published: December 2012

Summary

Increased night‐time temperatures, through their influence on dark respiration, have been implicated as a reason behind decreasing growth rates in tropical trees in the face of contemporary climate change.

Seedlings of two neo‐tropical tree species (Ficus insipida and Ochroma pyramidale) were grown in controlled‐environment chambers at a constant daytime temperature (33°C) and a range of increasing night‐time temperatures (22, 25, 28, 31°C) for between 39 d and 54 d. Temperature regimes were selected to represent a realistic baseline condition for lowland Panama, and a rise in night‐time temperatures far in excess of those predicted for Central America in the coming decades. Experiments were complemented by an outdoor open‐top chamber study in which night‐time temperatures were elevated by 2.4°C above ambient.

Increasing night‐time temperatures resulted in > 2‐fold increase in biomass accumulation in growth‐chamber studies despite an increase in leaf‐level dark respiration. Similar trends were seen in open‐top chambers, in which elevated night‐time temperatures resulted in stimulation of growth.

These findings challenge simplistic considerations of photosynthesis‐directed growth, highlighting the role of temperature‐dependent night‐time processes, including respiration and leaf development as drivers of plant performance in the tropics.
Prevalence of gene expression additivity in genetically stable wheat allohexaploids
Authors: Chelaifa Houda , Chagué Véronique , Chalabi Smahane , Mestiri Imen , Arnaud Dominique , Deffains Denise , Lu Yunhai , Belcram Harry , Huteau Virginie , Chiquet Julien , Coriton Olivier , Just Jérémy , Jahier Joseph , Chalhoub Boulos 
Published: December 2012

Summary

The reprogramming of gene expression appears as the major trend in synthetic and natural allopolyploids where expression of an important proportion of genes was shown to deviate from that of the parents or the average of the parents.

In this study, we analyzed gene expression changes in previously reported, highly stable synthetic wheat allohexaploids that combine the D genome of Aegilops tauschii and the AB genome extracted from the natural hexaploid wheat Triticum aestivum. A comprehensive genome‐wide analysis of transcriptional changes using the Affymetrix GeneChip Wheat Genome Array was conducted.

Prevalence of gene expression additivity was observed where expression does not deviate from the average of the parents for 99.3% of 34 820 expressed transcripts. Moreover, nearly similar expression was observed (for 99.5% of genes) when comparing these synthetic and natural wheat allohexaploids. Such near‐complete additivity has never been reported for other allopolyploids and, more interestingly, for other synthetic wheat allohexaploids that differ from the ones studied here by having the natural tetraploid Triticum turgidum as the AB genome progenitor.

Our study gave insights into the dynamics of additive gene expression in the highly stable wheat allohexaploids.
Dynamic Factor Models with Jagged Edge Panel Data: Taking on Board the Dynamics of the Idiosyncratic Components
Authors: Pinheiro Maximiano , Rua António , Dias Francisco 
Published: December 2012

AbstractAs macroeconomic data are released with different delays, one has to handle unbalanced panel data sets with missing values at the end of the sample period when estimating dynamic factor models. We propose an EM algorithm which copes with such data sets while accounting for autoregressive common factors and allowing for serial correlation in the idiosyncratic components. Based on Monte Carlo simulations, we find that taking on board the dynamics of the idiosyncratic components improves significantly the accuracy of the estimation of both the missing values and the common factors at the end of the sample period.
Differential interactions of Streptococcus gordonii and Staphylococcus aureus with cultured osteoblasts
Authors: Jauregui C.E. , Mansell J.P. , Jepson M.A. , Jenkinson H.F. 
Published: December 2012

SummaryThe impedance of normal osteoblast function by microorganisms is at least in part responsible for the failure of dental or orthopedic implants. Staphylococcus aureus is a major pathogen of bone, and exhibits high levels of adhesion and invasion of osteoblasts. In this article we show that the commensal oral bacterium Streptococcus gordonii also adheres to and is internalized by osteoblasts. Entry of S. gordonii cells had typical features of phagocytosis, similar to S. aureus, with membrane protrusions characterizing initial uptake, and closure of the osteoblast membrane leading to engulfment. The sensitivities of S. gordonii internalization to inhibitors cytochalasin D, colchicine and monensin indicated uptake through endocytosis, with requirement for actin accumulation. Internalization levels of S. gordonii were enhanced by expression of S. aureus fibronectin‐binding protein A (FnBPA) on the S. gordonii cell surface. Lysosomal‐associated membrane protein‐1 phagosomal membrane marker accumulated with intracellular S. aureus and S. gordonii FnBPA, indicating trafficking of bacteria into the late endosomal/lysosomal compartment. Streptococcus gordonii cells did not survive intracellularly for more than 12 h, unless expressing FnBPA, whereas S. aureus showed extended survival times (>48 h). Both S. aureus and S. gordonii DL‐1 elicited a rapid interleukin‐8 response by osteoblasts, whereas S. gordonii FnBPA was slower. Only S. aureus elicited an interleukin‐6 response. Hence, S. gordonii invades osteoblasts by a mechanism similar to that exhibited by S. aureus, and elicits a proinflammatory response that may promote bone resorption.
Sustainable plant breeding
Authors: Cowling Wallace A. 
Published: December 2012

AbstractPlant breeders disrupt Hardy–Weinberg equilibrium through selection, non‐random mating, drift, migration and mutation. Sustainable plant breeding can be defined as productive and competitive breeding that is achieved without loss of genetic diversity in the elite breeding population during the professional career of the breeder. Breeding is often productive but not sustainable. From 1974 to 2000, the animal breeding programme Meatlinc in the United Kingdom had effective population size of 95, population inbreeding of 0.19% per year and generation interval of 2.15 years. Genetic progress in Meatlinc tripled in the 8 years following introduction of best linear unbiased prediction (BLUP) selection (based on the information from relatives) in 1992. Canola breeding in Australia from 1970 to 2000 had longer generation interval (6 years), smaller effective population size (<11) and higher rates of inbreeding (>0.7% per year). BLUP selection in canola was first reported in 2010. Neither programme replaced genetic diversity lost through selection and drift. Most breeding programmes violate conditions of the infinitesimal model, thereby reducing predictability of selection, but breeders can minimize these limitations to sustainable plant breeding.
Genetic identity of free‐living Symbiodinium obtained over a broad latitudinal range in the Japanese coast
Authors: Yamashita Hiroshi , Koike Kazuhiko 
Published: December 2012

SummaryThe dinoflagellate Symbiodinium is well known to engage symbiosis with various marine animals, including corals. Recent records of environmental Symbiodinium (occurring in the environment and separately from host animals; usually referred to as ‘free‐living’ Symbiodinium) are of special interest, since these environmental populations are essential as symbiont sources for many host animals. In the present study, we carried out a phylogenetic analysis of environmental Symbiodinium isolates (culture strains) from sand, tide pools, or macroalgal surfaces, and environmental DNA clones extracted from the water‐column, at numerous sites around Japan. Our phylogenetic analysis based on the nuclear rRNA gene (internal transcribed spacers ‐1, ‐2, and 5.8S), indicated that most of the environmental isolates form monophyletic subclades within the Clade‐A lineage, and separate from a host‐associated Clade‐A population with high bootstrap values. Results of the partial nuclear 28S rDNA phylogeny and thecal‐plate observations revealed that these environmental isolates were closely related to a previously‐described ‘planktonic species’, Symbiodinium natans Gert Hansen et Daugbjerg, which was isolated from a plankton‐net sample from the Northeast‐Atlantic Ocean. On the other hand, the environmental DNA clones were also noted to be mostly nested within host‐associated Symbiodinium groups scattered in various clades. These results led to the assumption that the environmental Symbiodinium can be divided into two groups. One group, as typified by environmental isolates in the present study and previous reports, may be exclusively free‐living; the other group exists transiently in free‐living forms, possibly having been expelled from animal hosts. The populations within the latter group probably represent environmental sources of viable symbionts, because these are normally host‐associated. However, the Symbiodinium in the former group are not expected to engage in stable symbioses with host cnidarians.