bluuebunny/crossref_metadata_2025 huggingface dataset:
AMP-activated protein kinase adapts rRNA synthesis to cellular energy supply
Authors: Hoppe Sven , Bierhoff Holger , Cado Ivana , Weber Andrea , Tiebe Marcel , Grummt Ingrid , Voit Renate
Published: October 2009

AMP-activated protein kinase (AMPK) senses changes in the intracellular AMP/ATP ratio, switching off energy-consuming processes and switching on catabolic pathways in response to energy depletion. Here, we show that AMPK down-regulates rRNA synthesis under glucose restriction by phosphorylating the RNA polymerase I (Pol I)-associated transcription factor TIF-IA at a single serine residue (Ser-635). Phosphorylation by AMPK impairs the interaction of TIF-IA with the TBP-containing promoter selectivity factor SL1, thereby precluding the assembly of functional transcription initiation complexes. Mutation of Ser-635 compromises down-regulation of Pol I transcription in response to low energy supply, supporting that activation of AMPK adapts rRNA synthesis to nutrient availability and the cellular energy status.
Effect of gestational zinc deficiency on pregnancy outcomes: summary of observation studies and zinc supplementation trials
Authors: Shah Dheeraj , Sachdev H. P. S
Published: October 2009

The lack of a valid indicator precludes a true estimate of zinc deficiency in pregnancy in various populations. However, it is possible that mild to moderate deficiency (as assessed by available indicators) may be common in the developing world. Animal experiments indicate that zinc deficiency can result in adverse maternal and fetal consequences. Human data, particularly from prenatal zinc supplementation trials, has failed to document a consistent maternal or infant benefit on evaluated outcome measures including pregnancy induced hypertension, preterm/post-term labour, premature rupture of membranes, maternal infection, postpartum haemorrhage, perinatal mortality, congenital malformations and fetal growth and gestation. Preliminary data suggest a beneficial effect of prenatal zinc supplementation on infants’ neurobehavioural development and immune function (evaluated by diarrhoeal and ARI morbidity incidence in the first year of life). Future research should focus on these functional consequences and congenital malformations (with adequate sample sizes), and simultaneously address the safety issue, particularly in relation to micronutrient interactions. In the light of the currently available information, routine zinc supplementation can not be advocated to improve pregnancy outcome.
Micronutrients in pregnancy
Authors: Black Robert E.
Published: October 2009

Vitamins and minerals, referred to collectively as micronutrients, have important influences on the health of pregnant women and the growing fetus. Iron deficiency results in anemia which may increase the risk of death from hemorrhage during delivery, but its effects on fetal development and birth outcomes is still unclear. Folic acid deficiency can lead to hematological consequences, pregnancy complications and congenital malformations, but again the association with other birth outcomes is equivocal. Zinc deficiency has been associated in some, but not all studies with complications of pregnancy and delivery, as well as with growth retardation, congenital abnormalities and retarded neurobehavioral and immunological development in the fetus. Iodine deficiency during pregnancy results in cretinism and possible fetal wastage and preterm delivery. Deficiency of other minerals such as magnesium, selenium, copper, and calcium have also been associated with complications of pregnancy, childbirth or fetal development. Deficiencies of vitamins other than folate may likewise be related to such complications; and vitamin A or β-carotene supplements in pregnancy reduced maternal mortality by 50 % in a controlled trial in Nepal. Additional research is need on the prevalence of such deficiencies and their consequences and on cost-effective public health interventions for their control.
Dietary diversification/modification strategies to enhance micronutrient content and bioavailability of diets in developing countries
Authors: Gibson Rosalind S. , Hotz Christine
Published: October 2009

Both cereal staples and household diets can be manipulated to enhance the content of micronutrients and/or alter the levels of absorption modifiers to improve micronutrient bioavailability. Strategies described range from plant breeding, use of fertilizers and genetic engineering to changes in food preparation and processing methods at the household level involving soaking, fermentation and germination. The impact of five household strategies designed to enhance the content and bioavailability of iron, zinc and calcium in a representative daily menu for rural Malawian preschool children has been calculated using food composition data. In the five strategies, relishes based on small dried fish replaced plant-based relishes, maize-based porridges prepared with maize flour soaked to reduce its hexa (IP-6)- and penta (IP-5)-inositol phosphate content replaced conventional porridges; and a pumpkin-leaf relish replaced sweet potato to increase the retinol content of the daily menu. Comparison of the calculated energy, nutrient, and phytate content, and [phytate]:[zinc] molar ratios of the five modified menus compared with the unmodified menu emphasizes that to ensure that the estimated requirements for iron and zinc are met, the optimal strategy includes dried fish relish twice daily together with porridges prepared using soaked (or fermented) maize flour to reduce their hexa- and penta-inositol phosphate content. Implementation of these household strategies has the potential to increase the bioavailability of iron and zinc in rural Malawian diets from low to high.
POVERTY TRAJECTORIES AFTER RISKY LIFE COURSE EVENTS IN DIFFERENT EUROPEAN WELFARE REGIMES
Authors: Vandecasteele Leen
Published: October 2009

This article complements existing life course research on poverty by looking at the typical income poverty trajectories during the first five years after experiencing a risky life event such as partnership dissolution and leaving the parental home. By broadening the time frame of research into poverty transitions, a more complete picture can be drawn of the poverty patterns related to these life events. Latent class analyses of the European Community Household Panel show that the poverty risk after experiencing a life course event is not equally large and long-lasting for everyone. Broadly, four comparable latent classes can be found across Germany, Spain, Denmark and the United Kingdom: persistent non-poor, persons with a transient – or transient-recurrent – poverty risk, persons with longer-term poverty risk and late poverty entrants. Yet, the size and occurrence of the latent classes differs between countries according to welfare regime. The article discusses country differences and social determinants of the different poverty trajectories.
T-bet–dependent S1P5 expression in NK cells promotes egress from lymph nodes and bone marrow
Authors: Jenne Craig N. , Enders Anselm , Rivera Richard , Watson Susan R. , Bankovich Alexander J. , Pereira Joao P. , Xu Ying , Roots Carla M. , Beilke Joshua N. , Banerjee Arnob , Reiner Steven L. , Miller Sara A. , Weinmann Amy S. , Goodnow Chris C. , Lanier Lewis L. , Cyster Jason G. , Chun Jerold
Published: October 2009

During a screen for ethylnitrosourea-induced mutations in mice affecting blood natural killer (NK) cells, we identified a strain, designated Duane, in which NK cells were reduced in blood and spleen but increased in lymph nodes (LNs) and bone marrow (BM). The accumulation of NK cells in LNs reflected a decreased ability to exit into lymph. This strain carries a point mutation within Tbx21 (T-bet), which generates a defective protein. Duane NK cells have a 30-fold deficiency in sphingosine-1-phosphate receptor 5 (S1P5) transcript levels, and S1P5-deficient mice exhibit an egress defect similar to Duane. Chromatin immunoprecipitation confirms binding of T-bet to the S1pr5 locus. S1P-deficient mice exhibit a more severe NK cell egress block, and the FTY720-sensitive S1P1 also plays a role in NK cell egress from LNs. S1P5 is not inhibited by CD69, a property that may facilitate trafficking of activated NK cells to effector sites. Finally, the accumulation of NK cells within BM of S1P-deficient mice was associated with reduced numbers in BM sinusoids, suggesting a role for S1P in BM egress. In summary, these findings identify S1P5 as a T-bet–induced gene that is required for NK cell egress from LNs and BM.
Evidence that Electrostatic Interactions between Vesicle-associated Membrane Protein 2 and Acidic Phospholipids May Modulate the Fusion of Transport Vesicles with the Plasma Membrane
Authors: Williams Dumaine , Vicôgne Jérome , Zaitseva Irina , McLaughlin Stuart , Pessin Jeffrey E.
Published: October 2009

The juxtamembrane domain of vesicle-associated membrane protein (VAMP) 2 (also known as synaptobrevin2) contains a conserved cluster of basic/hydrophobic residues that may play an important role in membrane fusion. Our measurements on peptides corresponding to this domain determine the electrostatic and hydrophobic energies by which this domain of VAMP2 could bind to the adjacent lipid bilayer in an insulin granule or other transport vesicle. Mutation of residues within the juxtamembrane domain that reduce the VAMP2 net positive charge, and thus its interaction with membranes, inhibits secretion of insulin granules in β cells. Increasing salt concentration in permeabilized cells, which reduces electrostatic interactions, also results in an inhibition of insulin secretion. Similarly, amphipathic weak bases (e.g., sphingosine) that reverse the negative electrostatic surface potential of a bilayer reverse membrane binding of the positively charged juxtamembrane domain of a reconstituted VAMP2 protein and inhibit membrane fusion. We propose a model in which the positively charged VAMP and syntaxin juxtamembrane regions facilitate fusion by bridging the negatively charged vesicle and plasma membrane leaflets.
Adaptive multi-agent architecture for functional sequence motifs recognition
Authors: Zeng Jia , Alhajj Reda , Demetrick Douglas
Published: October 2009

Motivation: Accurate genome annotation or protein function prediction requires precise recognition of functional sequence motifs. Many computational motif prediction models have been proposed. Due to the complexity of the biological data, it may be desirable to apply an integrated approach that uses multiple models for analysis.

Results: In this article, we propose a novel multi-agent architecture for the general purpose of functional sequence motif recognition. The approach takes advantage of the synergy provided by multiple agents through the employment of different agents equipped with distinctive problem solving skills and promotes the collaborations among them through decision maker (DM) agents that work as classifier ensembles. A genetic algorithm-based fusion strategy is applied which offers evolutionary property to the DM agents. The consistency and robustness of the system are maintained by an evolvable agent that mediates the team of the ensemble agents. The combined effort of a recommendation system (Seer) and the self-learning mediator agent yields a successful identification of the most efficient agent deployment scheme at an early stage of the experimentation process, which has the potential of greatly reducing the computational cost of the system. Two concrete systems are constructed that aim at predicting two important sequence motifs—the translational initiation sites (TISs) and the core promoters. With the incorporation of three distinctive problem solver agents, the TIS predictor consistently outperforms most of the state-of-the-art approaches under investigation. Integrating three existing promoter predictors, our system is able to yield consistently good performance.

Availability: The program (MotifMAS) and the datasets are available upon request.

Contact:  jzeng@ucalgary.ca
ncRNAppi—a tool for identifying disease-related miRNA and siRNA targeting pathways
Authors: Ng Ka-Lok , Liu Hsueh-Chuan , Lee Shan-Chih
Published: October 2009

Summary: Currently, there are a number of databases which store microRNA (miRNA) information, and tools available which provide miRNA target prediction. In this article, we describe a novel web-based tool that integrate the miRNA-targeted mRNA data, protein–protein interactions (PPI) records, tissues, biochemical pathways, human disease and gene function information to establish a disease-related miRNA target pathway database. This database is unique in the sense that it links miRNA target genes with their PPI partners according to being tissue- and diseases-specific or both. The same approach is also applied to siRNA data. This database provides two types of searches: (i) tissue- and (ii) disease-specific miRNA (or siRNA) targeting pathways. The search allows one to identify tissue- or disease-specific miRNA (or siRNA) target gene's PPI partners two levels beyond.

Availability: The release version 1.0 is a freely accessible database available at http://ncrnappi.cs.nthu.edu.tw and http://ncRNAppi.bioinfo.asia.edu.tw/

Contact:  ppiddi@gmail.com; o2snow@gmail.com
HTqPCR: high-throughput analysis and visualization of quantitative real-time PCR data in R
Authors: Dvinge Heidi , Bertone Paul
Published: October 2009

Motivation: Quantitative real-time polymerase chain reaction (qPCR) is routinely used for RNA expression profiling, validation of microarray hybridization data and clinical diagnostic assays. Although numerous statistical tools are available in the public domain for the analysis of microarray experiments, this is not the case for qPCR. Proprietary software is typically provided by instrument manufacturers, but these solutions are not amenable to the tandem analysis of multiple assays. This is problematic when an experiment involves more than a simple comparison between a control and treatment sample, or when many qPCR datasets are to be analyzed in a high-throughput facility.

Results: We have developed HTqPCR, a package for the R statistical computing environment, to enable the processing and analysis of qPCR data across multiple conditions and replicates.

Availability:  HTqPCR and user documentation can be obtained through Bioconductor or at http://www.ebi.ac.uk/bertone/software.

Contact:  bertone@ebi.ac.uk
Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data
Authors: Degner Jacob F. , Marioni John C. , Pai Athma A. , Pickrell Joseph K. , Nkadori Everlyne , Gilad Yoav , Pritchard Jonathan K.
Published: October 2009

Motivation: Next-generation sequencing has become an important tool for genome-wide quantification of DNA and RNA. However, a major technical hurdle lies in the need to map short sequence reads back to their correct locations in a reference genome. Here, we investigate the impact of SNP variation on the reliability of read-mapping in the context of detecting allele-specific expression (ASE).

Results: We generated 16 million 35 bp reads from mRNA of each of two HapMap Yoruba individuals. When we mapped these reads to the human genome we found that, at heterozygous SNPs, there was a significant bias toward higher mapping rates of the allele in the reference sequence, compared with the alternative allele. Masking known SNP positions in the genome sequence eliminated the reference bias but, surprisingly, did not lead to more reliable results overall. We find that even after masking, ∼5–10% of SNPs still have an inherent bias toward more effective mapping of one allele. Filtering out inherently biased SNPs removes 40% of the top signals of ASE. The remaining SNPs showing ASE are enriched in genes previously known to harbor cis-regulatory variation or known to show uniparental imprinting. Our results have implications for a variety of applications involving detection of alternate alleles from short-read sequence data.

Availability: Scripts, written in Perl and R, for simulating short reads, masking SNP variation in a reference genome and analyzing the simulation output are available upon request from JFD. Raw short read data were deposited in GEO (http://www.ncbi.nlm.nih.gov/geo/) under accession number GSE18156.

Contact:  jdegner@uchicago.edu; marioni@uchicago.edu; gilad@uchicago.edu; pritch@uchicago.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Schwann Cell Migration Induced by Earthworm Extract via Activation of PAs and MMP2/9 Mediated through ERK1/2 and p38
Authors: Chang Yung-Ming , Shih Ying-Ting , Chen Yueh-Sheng , Liu Chien-Liang , Fang Wen-Kuei , Tsai Chang-Hai , Tsai Fuu-Jen , Kuo Wei-Wen , Lai Tung-Yuan , Huang Chih-Yang
Published: October 2009

The earthworm, which has stasis removal and wound‐healing functions, is a widely used Chinese herbal medicine in China. Schwann cell migration is critical for the regeneration of injured nerves. Schwann cells provide an essentially supportive activity for neuron regeneration. However, the molecular migration mechanisms induced by earthworms in Schwann cells remain unclear. Here, we investigate the roles of MAPK (ERK1/2, JNK and p38) pathways for earthworm‐induced matrix‐degrading proteolytic enzyme (PAs and MMP2/9) production in Schwann cells. Moreover, earthworm induced phosphorylation of ERK1/2 and p38, but not JNK, activate the downstream signaling expression of PAs and MMPs in a time‐dependent manner. Earthworm‐stimulated ERK1/2 and p38 phosphorylation was attenuated by pretreatment with U0126 and SB203580, resulting in migration and uPA‐related signal pathway inhibition. The results were confirmed using small interfering ERK1/2 and p38 RNA. These results demonstrated that earthworms can stimulate Schwann cell migration and up‐regulate PAs and MMP2/9 expression mediated through the MAPK pathways, ERK1/2 and p38. Taken together, our data suggests the MAPKs (ERK1/2, p38)‐, PAs (uPA, tPA)‐, MMP (MMP2, MMP9) signaling pathway of Schwann cells regulated by earthworms might play a major role in Schwann cell migration and nerve regeneration.
AGB1 and PMR5 Contribute to PEN2-Mediated Preinvasion Resistance to Magnaporthe oryzae in Arabidopsis thaliana
Authors: Maeda Kana , Houjyou Yasunari , Komatsu Takuma , Hori Hiroki , Kodaira Takahiro , Ishikawa Atsushi
Published: October 2009

Rice blast, caused by Magnaporthe oryzae, is a devastating disease of rice (Oryza sativa). The mechanisms involved in resistance of rice to blast have been studied extensively and the rice–M. oryzae pathosystem has become a model for plant–microbe interaction studies. However, the mechanisms involved in nonhost resistance (NHR) of other plants to rice blast are still poorly understood. Here, we investigated interactions between Arabidopsis thaliana and M. oryzae to identify the genetic basis of NHR. In A. thaliana accessions, preinvasion resistance to M. oryzae in Col-0 was stronger than that of Ler. To examine the genetic basis underlying the natural variation in the responses, we used a well-established set of recombinant inbred lines (RIL) derived from a Col × Ler cross and identified three quantitative trait loci that govern the expression of NHR in A. thaliana against M. oryzae. Among the penetration (pen) mutants, only the pen2 mutant allowed increased penetration into epidermal cells by M. oryzae. Double mutant analysis indicated that AGB1 and PMR5 contribute to PEN2-mediated preinvasion resistance to M. oryzae in A. thaliana, suggesting a complex genetic network regulating the resistance. Our results demonstrate that A. thaliana can be used to study mechanisms of NHR to M. oryzae.
Pseudomonas syringae pv. tomato DC3000 Type III Effector HopAA1-1 Functions Redundantly with Chlorosis-Promoting Factor PSPTO4723 to Produce Bacterial Speck Lesions in Host Tomato
Authors: Munkvold Kathy R. , Russell Alistair B. , Kvitko Brian H. , Collmer Alan
Published: October 2009

The ability of Pseudomonas syringae pv. tomato DC3000 to cause bacterial speck disease in tomato is dependent on the injection, via the type III secretion system, of approximately 28 Avr/Hop effector proteins. HopAA1-1 is encoded in the conserved effector locus (CEL) of the P. syringae Hrp pathogenicity island. Transiently expressed HopAA1-1 acts inside Saccharomyces cerevisiae and plant cells to elicit cell death. hopAA1 homologs were cloned and sequenced from the CEL of seven P. syringae strains representing diverse pathovars. Analysis of the sequences revealed that HopAA1-1 carries a potential GTPase-activating protein (GAP) domain, GALRA, which is polymorphic (FEN instead of LRA) in HopAA1-2, a paralogous DC3000 effector. Deleting hopAA1-1 from DC3000 reduces the formation of necrotic speck lesions in dip-inoculated tomato leaves if effector-gene cluster IX or just PSPTO4723 within this region has been deleted. A HopAA1-1 mutant in which the putative catalytic arginine in the GAP-like domain has been replaced with alanine retains its ability to kill yeast and promote the formation of speck lesions by the ΔhopAA1-1ΔIX mutant, but a HopAA1-1 mutant carrying the FEN polymorphism loses both of these abilities. Unexpectedly, PSPTO4723 does not appear to encode an effector and its deletion also reduces disease-associated chlorosis.
Agrobacterium-Mediated T-DNA Transfer and Integration by Minimal VirD2 Consisting of the Relaxase Domain and a Type IV Secretion System Translocation Signal
Authors: van Kregten Maartje , Lindhout Beatrice I. , Hooykaas Paul J. J. , van der Zaal Bert J.
Published: October 2009

The VirD2 protein of Agrobacterium tumefaciens is essential for processing and transport of the T-DNA. It has at least three functional domains: a relaxase domain at the N terminus, a bipartite nuclear localization signal (NLS), and a sequence called ω at the C terminus. We confirm here that deletions of the C-terminal part of VirD2 led to lack of transfer of T-DNA but, for the first time, we report that virulence is restored when these truncations are supplemented at the C terminus by a short translocation signal from the VirF protein. The lack of virulence of C-terminal deletions suggests that the C-terminal part contains all or part of the translocation signal of VirD2. Using a novel series of mutant VirD2 proteins, the C-terminal half of VirD2 was further investigated. We demonstrate that the C-terminal 40 amino acids of VirD2, which include the NLS and ω, contain all or part of the translocation domain necessary for transport of VirD2 into plant cells, while another element is present in the middle of the protein. The finding that a type IV secretion system transport signal at the C terminus of VirD2 is necessary for virulence provides evidence for the role of VirD2 as a pilot protein driving translocation of the T-strand.
Transcriptome Analysis of a Wheat Near-Isogenic Line Pair Carrying Fusarium Head Blight–Resistant and –Susceptible Alleles
Authors: Jia Haiyan , Cho Seungho , Muehlbauer Gary J.
Published: October 2009

Fusarium head blight (FHB), caused primarily by Fusarium graminearum, decreases grain yield and quality in wheat and barley. Disease severity, deoxynivalenol (DON), fungal biomass, and transcript accumulation were examined in a wheat near-isogenic line pair carrying either the resistant or susceptible allele for the chromosome 3BS FHB-resistance quantitative trait locus (Fhb1). Fhb1 restricts spread of disease symptoms but does not provide resistance to initial infection or initial DON accumulation. Wheat exhibits both induction and repression of large sets of gene transcripts during F. graminearum infection. In addition, a difference in the general timing of transcript accumulation in plants carrying either the resistant or susceptible allele at the Fhb1 locus was detected, and 14 wheat gene transcripts were detected that exhibited accumulation differences between the resistant and susceptible alleles. These results indicate that these may be host responses that differentiate the resistant from the susceptible interaction. Comparative analysis of the wheat–F. graminearum and the barley–F. graminearum interactions revealed a large set of conserved transcript accumulation patterns. However, we also detected gene transcripts that were repressed in wheat but not in barley. Based on the disease symptoms, transcript accumulation data, and comparative analysis of the barley and wheat host response to F. graminearum infection, we developed an integrated model for the interactions of wheat and barley with F. graminearum.
Identification of Six Type III Effector Genes with the PIP Box in Xanthomonas campestris pv. campestris and Five of Them Contribute Individually to Full Pathogenicity
Authors: Jiang Wei , Jiang Bo-Le , Xu Rong-Qi , Huang Jun-Ding , Wei Hong-Yu , Jiang Guo-Feng , Cen Wei-Jian , Liu Jiao , Ge Ying-Ying , Li Guang-Hua , Su Li-Li , Hang Xiao-Hong , Tang Dong-Jie , Lu Guang-Tao , Feng Jia-Xun , He Yong-Qiang , Tang Ji-Liang
Published: October 2009

Xanthomonas campestris pv. campestris is the pathogen of black rot of cruciferous plants. The pathogenicity of the pathogen depends on the type III secretion system (T3SS) that translocates directly effector proteins into plant cells, where they play important roles in the molecular interaction between the pathogen and its hosts. The T3SS of Xanthomonas spp. is encoded by a cluster of hypersensitive response and pathogenicity (hrp) genes. It has been demonstrated that the expression of hrp genes and some type III secreted (T3S)-effector genes is coactivated by the key hrp regulatory protein HrpX. The regulation by HrpX can be mediated by the binding of HrpX protein to a cis-regulatory element named the plant-inducible promoter (PIP) box present in the promoter region of HrpX-regulated genes. A genome screen revealed that X. campestris pv. campestris 8004 possesses 56 predicted genes with the PIP box. Nine of these genes have been shown to encode T3S effectors, Hrp, and Hrp-associated proteins. In this study, we employed an established T3S effector translocation assay with the hypersensitive-reaction-inducing domain of X. campestris pv. campestris AvrBs1 as a reporter to characterize the remaining 47 genes with the PIP box and showed that 6 of them, designated as XopXccE1, XopXccP, XopXccQ, XopXccR1, XopXccLR, and AvrXccB, harbor a functional translocation signal in their N-terminal regions, indicating that they are T3S effectors of X. campestris pv. campestris. We provided evidence to demonstrate that all these effectors are expressed in an HrpX-dependent manner and their translocation into plant cells relies on the translocon protein HrpF and the chaperone HpaB. Mutational analyses demonstrated that all these effectors, except AvrXccB, are individually required for full virulence and growth of X. campestris pv. campestris in the host plant Chinese radish.
Genetic Analysis of the rkp-3 Gene Region in Sinorhizobium meliloti 41: rkpY Directs Capsular Polysaccharide Synthesis to KR5 Antigen Production
Authors: Pálvölgyi Adrienn , Deák Veronika , Poinsot Véréna , Nagy Tibor , Nagy Enik , Kerepesi Ildikó , Putnoky Péter
Published: October 2009

Rhizobial surface polysaccharides, including capsular polysaccharides (KPS), are involved in symbiotic infection. The rkp-3 locus of Sinorhizobium meliloti 41 is responsible for the production of pseudaminic acid, one of the components of the KR5 antigen, a strain-specific KPS. We have extended the sequence determination and genetic dissection of the rkp-3 region to clarify the structure and function of the rkpY gene and to identify additional rkp genes. Except for rkpY, no other genes were found where mutation affected the KPS structure and symbiosis. These mutants show a unique phenotype producing a low molecular weight polysaccharide (LMW PS). Creating double mutants, we have shown that biosynthesis genes of the KR5 antigen except rkpZ are not necessary for the production of this LMW PS. Polysaccharide analysis of genetically modified strains suggests that rkpY has pleiotropic effects on polysaccharide production. It directs KPS synthesis to the KR5 antigen and influences lipo-oligo 3-deoxy-d-manno-2 octulosonic acid (Kdo) production in S. meliloti 41. In addition, rkpY suppresses the lipo-oligoKdo production when it is introduced into S. meliloti 1021.
Hexanoic Acid-Induced Resistance Against Botrytis cinerea in Tomato Plants
Authors: Vicedo Begonya , Flors Víctor , de la O Leyva María , Finiti Ivan , Kravchuk Zhana , Real María Dolores , García-Agustín Pilar , González-Bosch Carmen
Published: October 2009

We have demonstrated that root treatment with hexanoic acid protects tomato plants against Botrytis cinerea. Hexanoic acid-induced resistance (Hx-IR) was blocked in the jasmonic acid (JA)-insensitive mutant jai1 (a coi1 homolog) and in the abscisic acid (ABA)-deficient mutant flacca (flc). Upon infection, the LoxD gene as well as the oxylipin 12-oxo-phytodienoic acid and the bioactive molecule JA-Ile were clearly induced in treated plants. However, the basal ABA levels were not altered. Hexanoic acid primed callose deposition against B. cinerea in a cultivar-dependent manner. Treated plants from Ailsa Craig, Moneymaker, and Rheinlands Ruhm showed increased callose deposition but not from Castlemart. Hexanoic acid did not prime callose accumulation in flc plants upon B. cinerea infection; therefore, ABA could act as a positive regulator of Hx-IR by enhancing callose deposition. Furthermore, although hexanoic acid protected the JA-deficient mutant defensless1 (def1), the priming for callose was higher than in the wild type. This suggests a link between JA and callose deposition in tomato. Hence, the obtained results support the idea that callose, oxylipins, and the JA-signaling pathway are involved in Hx-IR against B. cinerea. Moreover our data support the relevance of JA-signaling for basal defense against this necrotroph in tomato. Hexanoic acid also protected against Pseudomonas syringae, indicating a broad-spectrum effect for this new inducer.
RNA Interference Highlights the Role of CCaMK in Dissemination of Endosymbionts in the Aeschynomeneae Legume Arachis
Authors: Sinharoy Senjuti , DasGupta Maitrayee
Published: October 2009

In legume–rhizobia symbiosis, Ca2+/calmodulin-dependent protein kinase (CCaMK) is essential for rhizobial invasion through infection threads in the epidermis and nodule organogenesis in the cortex. Though CCaMK is actively transcribed in the infected zone of nodules, its role in the later stages of nodule development remain elusive because of the epidermal arrest of “loss-of-function” mutants. In Aeschynomeneae legumes such as Arachis hypogea, rhizobia directly access the cortex, where nodule organogenesis as well as endosymbiont dissemination take place by multiplication of infected cortical cells. We characterized CCaMK (GI:195542474) from A. hypogea and downregulated the kinase through RNA interference (RNAi) to understand its role during organogenesis of its characteristic aeschynomenoid nodules. In CCaMK downregulated plants, the inception of nodules was delayed by approximately 4 weeks and nodulation capacity was decreased (>90%). The infected zones of the RNA interference nodules were scattered with uninfected or binucleated cells as opposed to the homogeneous infection zone in empty-vector-transformed nodules. Symbiosomes in RNAi nodules were pleomorphic with diverse geometrical shapes or arrested during division in the final stages of their fission as opposed to uniform-sized, spherical symbiosomes in empty-vector-transformed nodules. Together, our results reveal CCaMK to be essential for development of functional aeschynomenoid nodules, with a critical role in rhizobial dissemination during nodule organogenesis.
Phylogenomics of primates and their ancestral populations
Authors: Siepel Adam
Published: October 2009

Genome assemblies are now available for nine primate species, and large-scale sequencing projects are underway or approved for six others. An explicitly evolutionary and phylogenetic approach to comparative genomics, called phylogenomics, will be essential in unlocking the valuable information about evolutionary history and genomic function that is contained within these genomes. However, most phylogenomic analyses so far have ignored the effects of variation in ancestral populations on patterns of sequence divergence. These effects can be pronounced in the primates, owing to large ancestral effective population sizes relative to the intervals between speciation events. In particular, local genealogies can vary considerably across loci, which can produce biases and diminished power in many phylogenomic analyses of interest, including phylogeny reconstruction, the identification of functional elements, and the detection of natural selection. At the same time, this variation in genealogies can be exploited to gain insight into the nature of ancestral populations. In this Perspective, I explore this area of intersection between phylogenetics and population genetics, and its implications for primate phylogenomics. I begin by “lifting the hood” on the conventional tree-like representation of the phylogenetic relationships between species, to expose the population-genetic processes that operate along its branches. Next, I briefly review an emerging literature that makes use of the complex relationships among coalescence, recombination, and speciation to produce inferences about evolutionary histories, ancestral populations, and natural selection. Finally, I discuss remaining challenges and future prospects at this nexus of phylogenetics, population genetics, and genomics.
Energy-Resolving Neutron Transmission Radiography at the ISIS Pulsed Spallation Source With a High-Resolution Neutron Counting Detector
Authors: Tremsin Anton S. , McPhate Jason B. , Kockelmann Winfried A. , Vallerga John V. , Siegmund Oswald H. W. , Feller W. Bruce
Published: October 2009

Neutron transmission radiography can be strongly enhanced by adding spectroscopic data spatially correlated with the attenuation coefficient. This can now be achieved at pulsed neutron sources, utilizing a neutron detector with high spatial and temporal resolution. The energy of transmitted neutrons can be recovered from their time-of-flight, simultaneously with the acquisition of the transmission radiographic image by a pixelated detector. From this, the positions of Bragg edges can be obtained for each pixel of the radiographic image. The combination of both spectroscopic and transmission information enables high spatial resolution studies to be carried out on material composition, phase transitions, texture variations, as well as strain analysis, as long as the resolution and statistics are favorable. This paper presents initial results from proof-of-principle experiments on energy-resolved neutron transmission radiography, using a neutron counting detector consisting of neutron-sensitive microchannel plates (MCPs) and a Medipix2 electronic readout. These experiments demonstrate that the position of Bragg edges are measurable with a few mAring resolution in each 55-mum pixel of the detector, corresponding to DeltaE/E~0.1%. However, the limited intensity of most current neutron sources requires a compromise between the energy resolution and the area over which it was integrated. Still, the latter limitation can be overcome by combining energy information for several neighboring pixels, while transmission radiography can still be done at the limit of the detector spatial resolution.
Prediction of Prosopis species invasion in Kenya using geographical information system techniques
Authors: Muturi Gabriel M. , Mohren Godefridus M. J. , Kimani Jacob N.
Published: October 2009

Tree species from Prosopis genus were widely planted for rehabilitation of degraded drylands of Kenya. However, they have invaded riverine ecosystems where they cause negative socio‐economic and ecological impacts. GIS was used to estimate the reverine area threatened by Prosopis invasion in Kenya. Landsat satellite images, field surveys and past studies were also used to assess the resulting potential ecological impacts in the Turkwel ecosystem in Kenya. The study revealed that 3.0 to 27.7 million hectares are threatened by invasion, based on documented riverine forests width of 0.5–3 km. Image analysis showed that 34% of the sites under positive change were invaded, with most invasions occurring in natural forests and abandoned farms. Prosopis had overall occurrence of 39% in all the sampled sites in 2007, in contrast to 0% in 1990 that was reported in an earlier study. In these areas, Acacia tortilis occurrence dropped from 81% in 1990 to 43% in 2007, suggesting that Prosopis could be displacing it. Utilization of Prosopis for fodder, fuel wood and pods for animal feeds is recommended as a management tool to reverse the trend. The methods used in this study are also recommended for invasion prediction and management in other similar ecosystems.
Indications of higher diversity and abundance of small rodents in human‐influenced Sudanian savannah than in the Niokolo Koba National Park (Senegal)
Authors: Konečný Adam , Koubek Petr , Bryja Josef
Published: October 2009

Expansion of human activities in the Sudanian savannah is changing natural habitats together with their animal communities. The abundance and diversity of small mammal communities were investigated in human‐influenced savannahs in close proximity to Niokolo Koba National Park (NKNP) in south‐eastern Senegal and compared with those from NKNP. Two localities were sampled in natural and two in human‐influenced areas during two dry and two rainy seasons. Total sampling effort was 5400 trap‐nights. Ninety‐eight individuals of eleven species were captured outside NKNP, while only 28 individuals of five rodent species were caught inside the park (all of which were found also outside NKNP). The most abundant species outside NKNP was Mastomys erythroleucus, while inside NKNP it was Praomys daltoni. Both relative abundance and diversity were significantly higher in human‐influenced landscape than in natural savannahs of NKNP. The difference in species richness may be linked with lower population densities of certain species in NKNP and the effect of traditional agriculture, which may support the presence of species typical for deforested landscape. Furthermore, food availability, and predator abundances are discussed as possible reasons for the higher rodent abundances outside NKNP.
Range expansion of the globally Vulnerable Karamoja apalis Apalis karamojae in the Serengeti ecosystem
Authors: Shaw Philip , Sinclair A.R.E. , Metzger Kristine , Nkwabi Ally , Mduma Simon A.R. , Baker Neil
Published: October 2009

The underlying causes of change in geographic range size are less well understood in African birds than in north temperate species. Here, we examine factors associated with range expansion in the Karamoja apalis (Apalis karamojae), a globally Vulnerable warbler confined to north‐east Uganda, north‐central Tanzania and southern Kenya. In Tanzania, it was originally known only from the Wembere Steppe, but since 1993 (and possibly as early as 1983) has extended its range into the Serengeti ecosystem, c. 140 km to the north, reaching southern Kenya by 2004. Changes in the warbler’s range within the Serengeti have broadly reflected a cyclical change in the density of its main habitat, Acacia drepanolobium woodland, which was low in the 1970s, high during the 1980s and 1990s, and declined in the early 2000s. Karamoja apalis records in the Serengeti showed a 5 year time lag behind A. drepanolobium density, which was in turn negatively correlated with the area of grassland burnt 10 years earlier. Previous studies in the Serengeti have also linked Acacia regeneration to changes in grazing pressure, as increasing wildebeest (Connochaetes taurinus) numbers have reduced the volume of combustible material present, and hence the frequency of damaging ‘hot burns’. We conclude that this globally threatened warbler appears to have benefited from changes in ungulate populations in the Serengeti, which have influenced burning intensity and hence tree regeneration. The warbler’s range now appears to be declining, however, following a recent reduction in the density and annual survival of A. drepanolobium in the northern Serengeti.
Density dependence and population dynamics of black rhinos (Diceros bicornis michaeli) in Kenya’s rhino sanctuaries
Authors: Okita‐Ouma Benson , Amin Rajan , Van Langevelde Frank , Leader‐Williams Nigel
Published: October 2009

Density‐dependent feedback mechanisms provide insights into the population dynamics and interactions of large herbivores with their ecosystem. Sex ratio also has particularly important implications for growth rates of many large mammal populations through its influence on reproductive potential. Therefore, the interrelationships between density‐dependent factors, comprising density, sex ratio and underlying growth rates (r) were examined for the Eastern black rhino (Diceros bicornis michaeli) living in three rhino sanctuaries in Kenya using four population models. The exponential and logistic models gave similar results and the former were accepted because they better portrayed the actual situation on the ground. Sex ratios in all sanctuary populations were positively correlated withrbut interpreted with realization of other factors also affectingr. We caution that the results of population models should be interpreted alongside ground‐truthed observations. We recommend that future translocation strategies should take into account sex and age structures of the donor population, while future studies of density dependence should take into account both biotic and abiotic factors.
Habitat selection by blue swallowsHirundo atrocaerulea Sundevall, 1850 breeding in South Africa and its implications for conservation
Authors: Evans Steven W. , Bouwman Henk
Published: October 2009

This study investigated the utilization of mist‐belt grassland habitat by the threatened blue swallow and was conducted over three successive breeding seasons in the Blue Swallow Natural Heritage Site at Kaapsehoop, Mpumalanga, South Africa. Blue swallows significantly preferred wetlands over grasslands for foraging. Sufficient foraging habitat must be within a 1.5 km radius from an active nest site. The minimum size of a pair of blue swallows home range should be 333 ha, consisting at a minimum of grasslands (243 ha or 73%) and wetlands (90 ha or 27%). In order to conserve this threatened species, habitat transformation should not take place within a minimum radius of 1.5 km of any blue swallow nest. Due to the critical dependence of the blue swallow on wetland habitat for foraging, any development outside the 1.5 km radius that would affect hydrology and water quality within this range would need to be considered, and any adverse effect mitigated. Rehabilitation of areas to a grassland/wetland mosaic would rather quickly support foraging, and eventually breeding. Although a better understanding of the dynamics between wetlands and adjacent grasslands regarding blue swallow habitat requirements is needed, action can already be taken, based on our results.
The concordance between serum anti‐Mullerian hormone and testosterone concentrations depends on duration of hCG stimulation in boys undergoing investigation of gonadal function
Authors: Ahmed S. F. , Keir L. , McNeilly J. , Galloway P. , O’Toole S. , Wallace A. M.
Published: October 2009

Background  In boys undergoing investigation of gonadal function, the relationship between a single measurement of serum anti‐Mullerian hormone (AMH) and hCG stimulated serum testosterone is unclear.

Aim  The aim of the study was to assess concordance between serum AMH and testosterone concentrations following hCG stimulation of two different durations.

Methods  Samples from 284 children (M : F, 154 : 130) with a median age of 8 years (10th, 90th centiles, 0·25, 14) were used to establish an AMH reference range. Clinical data were reviewed in boys undergoing investigation of gonadal function and who had an AMH measurement and a hCG stimulated (3‐day or 3‐week) (n = 26) testosterone. Of these 26 boys, 11 had combined genital anomalies, whereas the rest had conditions such as isolated hypospadias, undescended testes or microphallus. Normal testosterone response to hCG stimulation was defined as a level greater than 3·5 nmol at day 4 and 9·5 nmol/l at day 22.

Results  In the reference group, the 5th centile AMH for boys below 1 year was 215 pmol/l and between 1 and 8 years 180 pmol/l. The 95th centile for girls for these respective age groups was 30 pmol/l and 25 pmol/l. In those cases where serum testosterone concentrations were available at day 1, day 4 and day 22 of the 3 week‐hCG test, five cases had a normal serum testosterone at day 4 and three cases only showed such a response by day 22. In those where serum AMH was less than 180 pmol/l, a poor testosterone response of less than 3·5 nmol was observed in approximately seven of eight (88%) cases with a 3‐day hCG stimulation test or the 3‐week test. An AMH of greater than 180 pmol/l was associated with a normal testosterone response at day 4 in 10 out of 15 (67%) cases and at day 22 in eight of 11 (73%) cases. However, a low serum testosterone concentration of less than 3·5 nmol after the 3‐day hCG test was only associated with a likelihood of a low AMH in three of eight (37%) cases. With the 3‐week hCG test, a low day 22 testosterone of 9·5 mmol/l or less was associated with a low AMH of 180 pmol/l or less in four of seven (57%) cases.

Conclusion  In boys undergoing investigation of gonadal function, the concordance between AMH and testosterone is better at day 22 than day 4. A normal AMH may provide useful information on overall testicular function but does not exclude the need for an hCG stimulation test.
MMP/ TIMP balance is modulated in vitro by 15dPGJ2 in fetuses and placentas from diabetic rats
Authors: Pustovrh M. C. , Capobianco E. , Martínez N. , Higa R. , White V. , Jawerbaum A.
Published: October 2009

Background  Maternal diabetes is associated with morphological placental abnormalities and foeto‐placental impairments. These alterations are linked with a dysregulation of the activity of matrix metalloproteinases (MMPs). We investigated the action of 15deoxyΔ12,14 prostaglandin J2 (15dPGJ2), a natural ligand of the peroxisome proliferator activated receptor (PPAR) γ, on MMP‐2 and MMP‐9 activities and tissue inhibitors of matrix metalloproteinases (TIMP) levels in foetuses and placentas from diabetic rats.

Materials and methods  Diabetes was induced in rat neonates by a single streptozotocin administration (90 mg kg−1 s.c.). At 13·5 days of gestation, foetal and placental homogenates were prepared for the determination of PPARγ levels (western blot) and 15dPGJ2 concentration (enzyme‐immunoassay), whereas the in vitro effect of 15dPGJ2 (2 μM) was evaluated on placental and foetal MMPs and TIMP activities (zymography and reverse zymography), nitrate/nitrite concentrations (Griess method) and thiobarbituric acid reactive substances (TBARS).

Results  PPARγ was increased while 15dPGJ2 was decreased in placentas and foetuses from diabetic rats. 15dPGJ2 additions were able to reduce the high activities of MMP‐2 and MMP‐9 present in diabetic placental tissues. 15dPGJ2 additions reduced MMP‐2 activity in control and diabetic foetuses. TIMP‐3 levels were decreased in diabetic placentas and 15dPGJ2 was able to enhance them to control values. Nitrates/nitrites and TBARS, metabolites of MMPs activators, were increased in the diabetic placenta and reduced by 15dPGJ2.

Conclusions  This study demonstrates that 15dPGJ2 is a potent modulator of the balance between MMP activities and TIMP levels, which is needed in the correct formation and function of the placenta and foetal organs.