bluuebunny/crossref_metadata_2025_split huggingface dataset:
Recombination and genetic differentiation among natural populations of the ectomycorrhizal mushroom Tricholoma matsutake from southwestern China
Authors: XU JIANPING , SHA TAO , LI YAN‐CHUN , ZHAO ZHI‐WEI , YANG ZHU L. 
Published: February 2008

AbstractEffective conservation and utilization strategies for natural biological resources require a clear understanding of the natural populations of the target organisms. Tricholoma matsutake is an ectomycorrhizal mushroom that forms symbiotic associations with plants and plays an important ecological role in natural forest ecosystems in many parts of the world. It is also an economically very important gourmet mushroom. Because no artificial cultivation is available, natural populations of this species are under increasing threats, primarily from habitat disturbance and destruction. Despite its economical and ecological importance, little is known about its genetics and population biology. Here, using 14 polymerase chain reaction–restriction fragment length polymorphism markers, we analysed 154 strains from 17 geographical locations in southwestern China, a region where over 25% of the global T. matsutake harvest comes from. Our results revealed abundant genetic variation within individual populations. The analyses of gene and genotype frequencies within populations indicated that most loci did not deviate from Hardy–Weinberg equilibrium in most populations and that alleles among loci were in linkage equilibrium in the majority of the local populations. These results are consistent with the hypothesis that sexual reproduction and recombination play an important role in natural populations of this species. Our analyses indicated low but significant genetic differentiation among the geographical populations, with a significant positive correlation between genetic distance and geographical distance. We discuss the implications of our results to the ecology and resource management of this species.
Biliprotein maturation: the chromophore attachment
Authors: Scheer H. , Zhao K.‐H. 
Published: February 2008

SummaryBiliproteins are a widespread group of brilliantly coloured photoreceptors characterized by linear tetrapyrrolic chromophores, bilins, which are covalently bound to the apoproteins via relatively stable thioether bonds. Covalent binding stabilizes the chromoproteins and is mandatory for phycobilisome assembly; and, it is also important in biliprotein applications such as fluorescence labelling. Covalent binding has, on the other hand, also considerably hindered biliprotein research because autocatalytic chromophore additions are rare, and information on enzymatic addition by lyases was limited to a single example, an EF‐type lyase attaching phycocyanobilin to cysteine‐α84 of C‐phycocyanin. The discovery of new activities for the latter lyases, and of new types of lyases, have reinvigorated research activities in the subject. So far, work has mainly concentrated on cyanobacterial phycobiliproteins. Methodological advances in the process, however, as well as the finding of often large numbers of homologues, opens new possibilities for research on the subsequent assembly/disassembly of the phycobilisome in cyanobacteria and red algae, on the assembly and organization of the cryptophyte light‐harvesting system, on applications in basic research such as protein folding, and on the use of phycobiliproteins for labelling.
Negative regulation of pPS10 plasmid replication: origin pairing by zipping‐up DNA‐bound RepA monomers
Authors: Gasset‐Rosa Fátima , Díaz‐López Teresa , Lurz Rudi , Prieto Alicia , Fernández‐Tresguerres M. Elena , Giraldo Rafael 
Published: February 2008

SummaryIn many plasmid replicons of Gram‐negative bacteria, Rep protein dimers are transcriptional self‐repressors of their genes, whereas monomers are initiators of DNA replication. Switching between both functions implies conformational remodelling of Rep, and is promoted by Rep binding to the origin DNA repeats (iterons) or chaperones. Rep proteins play another key role: they bridge together two iteron DNA stretches, found either on the same or on different plasmid molecules. These so‐called, respectively, ‘looped’ and ‘handcuffed’ complexes are thought to be negative regulators of plasmid replication. Although evidence for Rep‐dependent plasmid handcuffing has been found in a number of replicons, the structure of these Rep–DNA assemblies is still unknown. Here, by a combination of proteomics, electron microscopy, genetic analysis and modelling, we provide insight on a possible three‐dimensional structure for two handcuffed arrays of the iterons found at the origin of pPS10 replicon. These are brought together in parallel register by zipping‐up DNA‐bound RepA monomers. We also present evidence for a distinct role of RepA dimers in DNA looping. This work defines a new regulatory interface in Rep proteins.
Peptide inhibitor of cytokinesis during sporulation in Bacillus subtilis
Authors: Handler Aaron A. , Lim Joo Eun , Losick Richard 
Published: February 2008

SummaryCytokinesis in bacteria is mediated by the tubulin‐like protein FtsZ, which forms a Z‐ring at the division site. Using FtsZ as bait in a two‐hybrid screen, we discovered a 40‐amino‐acid peptide, termed MciZ, from Bacillus subtilis that appeared to interact with FtsZ. Cells engineered to produce MciZ during growth formed aseptate filaments that lacked Z‐rings. A mutant resistant to the toxic effects of MciZ during growth harboured an amino acid substitution near the GTP binding pocket of FtsZ. Synthetic MciZ inhibited the GTPase activity of FtsZ and its ability to polymerize. MciZ was produced during sporulation under the control of the transcription factor σE. In the absence of MciZ, the mother‐cell compartment of the sporangium aberrantly formed a Z‐ring at a time in development when cytokinetic events normally have ceased. We conclude that MciZ is a previously unrecognized inhibitor of FtsZ that prevents inappropriate Z‐ring formation during sporulation. MciZ showed little sequence similarity to other peptides in the databases, except the mouse antimicrobial peptide CRAMP, which we speculate works in part by inhibiting cytokinesis.
Significance of terpenoids in induced indirect plant defence against herbivorous arthropods
Authors: MUMM ROLAND , POSTHUMUS MAARTEN A. , DICKE MARCEL 
Published: February 2008

ABSTRACTMany plants respond to herbivory by arthropods with an induced emission of volatiles such as green leaf volatiles and terpenoids. These herbivore‐induced plant volatiles (HIPVs) can attract carnivores, for example, predators and parasitoids. We investigated the significance of terpenoids in attracting herbivores and carnivores in two tritrophic systems where we manipulated the terpenoid emission by treating the plants with fosmidomycin, which inhibits one of the terpenoid biosynthetic pathways and consequently terpenoid emission.In the ‘lima bean’ system, volatiles from spider‐mite‐infested fosmidomycin‐treated plants were less attractive to the predatory mite Phytoseiulus persimilis than from infested control plants. In the ‘cabbage’ system, fosmidomycin treatment did not alter the attractiveness of Brussels sprouts to two Pieris butterflies for oviposition. The parasitoid Cotesia glomerata did not discriminate between the volatiles of fosmidomycin‐treated and water‐treated caterpillar‐infested cabbage. Both P. persimilis and C. glomerata preferred volatiles from infested plants to uninfested ones when both were treated with fosmidomycin.Chemical analysis showed that terpenoid emission was inhibited more strongly in infested lima bean plants than in Brussels sprouts plants after fosmidomycin treatment.This study shows an important role of terpenoids in the indirect defence of lima bean, which is discussed relative to the role of other HIPVs.
The Adjuvant Effect of CpG Oligodeoxynucleotide Linked to the Non‐Toxic B Subunit of Cholera Toxin for Induction of Immunity Against H. pylori in Mice
Authors: Nyström‐Asklin J. , Adamsson J. , Harandi A. M. 
Published: February 2008

AbstractThe present study was carried out to test the immunostimulatory and adjuvant effects of the non‐toxic B subunit of cholera toxin (CTB), CpG oligodeoxynucleotide (ODN) and CpG ODN linked to CTB (CTB–CpG) for generation of immunity against H. pylori in mice. Herein, we showed that CTB–CpG induces more potent proinflammatory cytokine and chemokine responses in the cervical and the mesenteric lymph nodes (CLN and MLN, respectively) cells in vitro compared with those of CTB and CpG ODN. The adjuvant effects of these agents were examined following intranasal immunization of C57Bl/6 mice with H. pylori lysate in combination with CpG ODN, CTB or CTB–CpG. All three immunization regimes resulted in high H. pylori‐specific IgG antibody responses; however, only the CTB–CpG and, to some extent, the CpG ODN immunized mice mounted a sustainable IgG2c antibody response. Importantly, mice immunized with H. pylori antigen and CTB–CpG or CpG ODN, but not CTB, developed strong H. pylori‐specific proliferative and IFN‐γ responses in their MLN CD4+ T cells upon recall antigen stimulation in vitro. These mice also had significantly lower bacterial load compared with the control‐infected mice. Furthermore, the CTB–CpG and the CpG ODN immunized mice developed increased specific IgA antibody responses in their gastrointestinal tracts following H. pylori challenge. These results imply that CTB–CpG and CpG ODN, but not CTB, could serve as nasal adjuvants for induction of a H. pylori‐specific Th1 type immunity in MLN and also a specific mucosal IgA antibody response in the gastrointestinal tract upon H. pylori challenge.
Gene trap lines identify Arabidopsis genes expressed in stomatal guard cells
Authors: Galbiati Massimo , Simoni Laura , Pavesi Giulio , Cominelli Eleonora , Francia Priscilla , Vavasseur Alain , Nelson Timothy , Bevan Michael , Tonelli Chiara 
Published: February 2008

SummaryWe employed a gene trap approach to identify genes expressed in stomatal guard cells of Arabidopsis thaliana. We examined patterns of reporter gene expression in approximately 20 000 gene trap lines, and recovered five lines with exclusive or preferential expression in stomata. The screen yielded two insertions in annotated genes, encoding the CYTOCHROME P450 86A2 (CYP86A2) mono‐oxygenase, and the PLEIOTROPIC DRUG RESISTANCE 3 (AtPDR3) transporter. Expression of the trapped genes in guard cells was confirmed by RT‐PCR experiments in purified stomata. Examination of homozygous mutant lines revealed that abscisic acid (ABA)‐induced stomatal closure was impaired in the atpdr3 mutant. In three lines, insertions occurred outside transcribed units. Expression analysis of the genes surrounding the trapping inserts identified two genes selectively expressed in guard cells, corresponding to a PP2C PROTEIN PHOSPHATASE and an unknown expressed protein gene. Statistical analyses of the chromosomal regions tagged by the gene trap insertions revealed an over‐represented [A/T]AAAG motif, previously described as an essential cis‐active element for gene expression in stomata. The lines described in this work identify novel genes involved in the modulation of stomatal activity, provide useful markers for the study of developmental pathways in guard cells, and are a valuable source of guard cell‐specific promoters.
Chlamydomonas chloroplasts can use short dispersed repeats and multiple pathways to repair a double‐strand break in the genome
Authors: Odom Obed W. , Baek Kwang‐Hyun , Dani Radhika N. , Herrin David L. 
Published: February 2008

SummaryCertain group I introns insert into intronless DNA via an endonuclease that creates a double‐strand break (DSB). There are two models for intron homing in phage: synthesis‐dependent strand annealing (SDSA) and double‐strand break repair (DSBR). The Cr.psbA4 intron homes efficiently from a plasmid into the chloroplast psbA gene in Chlamydomonas, but little is known about the mechanism. Analysis of co‐transformants selected using a spectinomycin‐resistant 16S gene (16Sspec) provided evidence for both pathways. We also examined the consequences of the donor DNA having only one‐sided or no homology with the psbA gene. When there was no homology with the donor DNA, deletions of up to 5 kb involving direct repeats that flank the psbA gene were obtained. Remarkably, repeats as short as 15 bp were used for this repair, which is consistent with the single‐strand annealing (SSA) pathway. When the donor had one‐sided homology, the DSB in most co‐transformants was repaired using two DNAs, the donor and the 16Sspec plasmid, which, coincidentally, contained a region that is repeated upstream of psbA. DSB repair using two separate DNAs provides further evidence for the SDSA pathway. These data show that the chloroplast can repair a DSB using short dispersed repeats located proximally, distally, or even on separate molecules relative to the DSB. They also provide a rationale for the extensive repertoire of repeated sequences in this genome.
LZF1, a HY5‐regulated transcriptional factor, functions in Arabidopsis de‐etiolation
Authors: Chang Chiung‐swey Joanne , Li Yi‐Hang , Chen Li‐Teh , Chen Wan‐Chieh , Hsieh Wen‐Ping , Shin Jieun , Jane Wann‐Neng , Chou Shu‐Jen , Choi Giltsu , Hu Jer‐Ming , Somerville Shauna , Wu Shu‐Hsing 
Published: February 2008

SummaryWe surveyed differential gene expression patterns during early photomorphogenesis in both wild‐type and mutant Arabidopsis defective in HY5, an influential positive regulator of the responses of gene expression to a light stimulus, to identify light‐responsive genes whose expression was HY5 dependent. These gene‐expression data identified light‐regulated zinc finger protein 1 (LZF1), a gene encoding a previously uncharacterized C2C2‐CO B‐box transcriptional regulator. HY5 has positive trans‐activating activity toward LZF1 and binding affinity to LZF1 promoter in vivo. HY5 is needed but not sufficient for the induction of LZF1 expression. Anthocyanin content is significantly diminished in lzf1 under far red, which is the most efficient light for the induction of LZF1. The expression of PAP1/MYB75 is elevated in plants overexpressing LZF1, which leads to the hyperaccumulation of anthocyanin in transgenic Arabidopsis. The transition from etioplast to chloroplast and the accumulation of chlorophyll were notably compromised in the lzf1 mutant. We provide molecular evidence that LZF1 influences chloroplast biogenesis and function via regulating genes encoding chloroplast proteins. In the absence of HY5, mutation of LZF1 leads to further reduced light sensitivity for light‐regulated inhibition of hypocotyl elongation and anthocyanin and chlorophyll accumulation. Our data indicate that LZF1 is a positive regulator functioning in Arabidopsis de‐etiolation.
Enzymatic, but not non‐enzymatic, 1O2‐mediated peroxidation of polyunsaturated fatty acids forms part of the EXECUTER1‐dependent stress response program in the flu mutant of Arabidopsis thaliana
Authors: Przybyla Dominika , Göbel Cornelia , Imboden André , Hamberg Mats , Feussner Ivo , Apel Klaus 
Published: February 2008

SummaryThe conditional flu mutant of Arabidopsis accumulates excess amounts of protochlorophyllide within plastid membranes in the dark and generates singlet oxygen upon light exposure. By varying the length of the dark period, the level of the photosensitizer protochlorophyllide may be modulated, and conditions have been established that either endorse the cytotoxicity of 1O2 or reveal its signaling role. Two criteria have been used to distinguish between these two modes of activity of 1O2: the impact of the EXECUTER1 mutation and the prevalence of either non‐enzymatic or enzymatic lipid peroxidation. During illumination of etiolated flu seedlings, toxic effects of 1O2 prevail and non‐enzymatic lipid peroxidation proceeds rapidly. In contrast, in light‐grown flu plants that were subjected to an 8 h dark/light shift, lipid peroxidation occurred almost exclusively enzymatically. The resulting oxidation product, 13‐hydroperoxy octadecatrienoic acid (13‐HPOT), serves as a substrate for synthesis of 12‐oxo phytodienoic acid (OPDA) and jasmonic acid (JA), both of which are known to control various metabolic and developmental processes in plants. Inactivation of the EXECUTER1 protein abrogates not only 1O2‐mediated cell death and growth inhibition of flu plants, but also enzymatic lipid peroxidation. However, inactivation of jasmonate biosynthesis in the aos/flu double mutant does not affect 1O2‐mediated growth inhibition and cell death. Hence, JA and OPDA do not act as second messengers during 1O2 signaling, but form an integral part of a stress‐related signaling cascade activated by 1O2 that encompasses several signaling pathways known to be activated by abiotic and biotic stressors.
Engines of speciation: a comparative study in birds of prey
Authors: KRÜGER O. 
Published: February 2008

AbstractSexual selection as a promoter of speciation has received much attention in recent years, but has produced highly equivocal evidence. Here, I test whether sexual conflict is related to species richness among genera in accipitrid birds of prey using phylogenetically controlled comparative analyses. Increased species richness was associated with both ‘male‐win’ as well as ‘female‐win’ situations, i.e. males being able to promote gene flow through mating or females being able to restrict gene flow through female choice. Species richness was higher when plumage differed between males and females and in polygynous breeding systems compared with monogamous ones. To assess the relative importance of sexual conflict and natural selection as correlates of species richness simultaneously, I also performed a multivariate analysis of correlates of species richness. Population density, plumage polymorphism, geographic range size and breeding latitude were predictors of species richness for birds of prey. These results stress the importance of both sexual and natural selection in determining species richness but with a clear overall emphasis on natural selection in birds of prey.
Structure of the Lipopolysaccharide Side‐chain of Pseudomonas syringae pv. syringae Strain S29
Authors: Smith A. R. W. 
Published: February 2008

AbstractUsing 1H‐ and 13C‐nuclear magnetic resonance spectroscopy, the repeat unit of the lipopolysaccharide side‐chain from Pseudomonas syringae pv. syringae strain S29 was shown to have the following structure:
image

This structure is identical with that of the side‐chain of Pseudomonas syringae pv. mori CFPB 1656.a
Familial scleroderma: nature, nurture or both?
Authors: Englert H. , Roberts‐Thomson P. J. , Byth K. , Manolios N. 
Published: February 2008

AbstractBackground:  The aim of the study was to investigate: (i) familial scleroderma (FS) risk factors, (ii) subtype concordance and (iii) relationship between dates (DSO) and ages (ASO) at scleroderma onset.Methods:  Forty‐seven cases (23 families; 25 FS pairs) were identified. Scleroderma disease onset was defined by (i) Raynaud’s onset, (ii) first symptom onset (1SxO), (iii) second symptom onset (2SxO) and (iv) scleroderma diagnosis (SDx).Results:  Female : male and limited : diffuse (L : D) ratios were 8.4:1 and 3.3:1. The Raynaud’s onset – SDx interval was longer in limited disease (L : D = 14.6:3.1 years; P = 0.01). Raynaud’s first occurred in 36% women ≥50 years. The median differences in ASO between affected family members were 10–12 years. Disease subtype concordance exceeded discordance (16:9 clusters; (P = 0.32) 16:7 families; (P = 0.17)). The observed/expected LL : LD : DD ratios were 14: 8:1/11:7:1 (P = 0.66). FS affected 34% (95% confidence interval 19–50) sister–sister and 44% (95% confidence interval 27–75) mother–daughter pairs. The second family member’s SDx was made at the same (9%) or a younger age (80%) than the first family member. In 14 LL disease families ASO was closer between sisters than mothers–daughters (P = 0.07). There was a trend towards closer ages – than dates – at Raynaud’s and 1SxO in scleroderma‐affected family members (P = 0.054) and closer dates – than ages – at 2SxO (P = 0.02) and SDx.Conclusion:  FS showed female predominance, relatively late onset Raynaud’s, subtype ratios similar to idiopathic scleroderma and earlier SDx in younger family members. Familial L scleroderma has a longer prediagnostic latency than familial D scleroderma. FS is likely under‐ascertained. In LL scleroderma, Raynaud’s/1SxO is possibly more genetically determined and 2SxO/SDx more environmentally determined.
Marine methylotrophs revealed by stable‐isotope probing, multiple displacement amplification and metagenomics
Authors: Neufeld Josh D. , Chen Yin , Dumont Marc G. , Murrell J. Colin 
Published: February 2008

SummaryThe concentrations of one‐carbon substrates that fuel methylotrophic microbial communities in the ocean are limited and the specialized guilds of bacteria that use these molecules may exist at low relative abundance. As a result, these organisms are difficult to identify and are often missed with existing cultivation and gene retrieval methods. Here, we demonstrate a novel proof of concept: using environmentally‐relevant substrate concentrations in stable‐isotope probing (SIP) incubations to yield sufficient DNA for large‐insert metagenomic analysis through multiple displacement amplification (MDA). A marine surface‐water sample was labelled sufficiently by incubation with near in situ concentrations of methanol. Picogram quantities of labelled 13C‐DNA were purified from caesium chloride gradients, amplified with MDA to produce microgram amounts of high‐molecular‐weight DNA (≤ 40 kb) and cloned to produce a fosmid library of > 10 000 clones. Denaturing gradient gel electrophoresis (DGGE) demonstrated minimal bias associated with the MDA step and implicated Methylophaga‐like phylotypes with the marine metabolism of methanol. Polymerase chain reaction screening of 1500 clones revealed a methanol dehydrogenase (MDH) containing insert and shotgun sequencing of this insert resulted in the assembly of a 9‐kb fragment of DNA encoding a cluster of enzymes involved in MDH biosynthesis, regulation and assembly. This novel combination of methodology enables future structure–function studies of microbial communities to achieve the long‐desired goal of identifying active microbial populations using in situ conditions and performing a directed metagenomic analysis for these ecologically relevant microorganisms.