bluuebunny/crossref_metadata_2025 huggingface dataset:
Parameters Affecting Ethyl Ester Production bySaccharomyces cerevisiaeduring Fermentation
Authors: Saerens S. M. G. , Delvaux F. , Verstrepen K. J. , Van Dijck P. , Thevelein J. M. , Delvaux F. R.
Published: November 2007

Volatile esters are responsible for the fruity character of fermented beverages and thus constitute a vital group of aromatic compounds in beer and wine. Many fermentation parameters are known to affect volatile ester production. In order to obtain insight into the production of ethyl esters during fermentation, we investigated the influence of several fermentation variables. A higher level of unsaturated fatty acids in the fermentation medium resulted in a general decrease in ethyl ester production. On the other hand, a higher fermentation temperature resulted in greater ethyl octanoate and decanoate production, while a higher carbon or nitrogen content of the fermentation medium resulted in only moderate changes in ethyl ester production. Analysis of the expression of the ethyl ester biosynthesis genesEEB1andEHT1after addition of medium-chain fatty acid precursors suggested that the expression level is not the limiting factor for ethyl ester production, as opposed to acetate ester production. Together with the previous demonstration that provision of medium-chain fatty acids, which are the substrates for ethyl ester formation, to the fermentation medium causes a strong increase in the formation of the corresponding ethyl esters, this result further supports the hypothesis that precursor availability has an important role in ethyl ester production. We concluded that, at least in our fermentation conditions and with our yeast strain, the fatty acid precursor level rather than the activity of the biosynthetic enzymes is the major limiting factor for ethyl ester production. The expression level and activity of the fatty acid biosynthetic enzymes therefore appear to be prime targets for flavor modification by alteration of process parameters or through strain selection.
Characterization of Two New Genes,
amoR
and
amoD
, in the
amo
Operon of the Marine Ammonia Oxidizer
Nitrosococcus oceani
ATCC 19707
Authors: El Sheikh Amal F. , Poret-Peterson Amisha T. , Klotz Martin G.
Published: November 2007

Molecular analysis of the
amo
gene cluster in
Nitrosococcus oceani
revealed that it consists of five genes, instead of the three known genes,
amoCAB
. The two additional genes,
orf1
and
orf5
, were introduced as
amoR
and
amoD
, respectively. Putative functions of the AmoR and AmoD proteins are discussed.
Conjugative Transfer between
Escherichia coli
and
Leptospira
spp. as a New Genetic Tool
Authors: Picardeau Mathieu
Published: November 2007

Our understanding of leptospiral pathogenesis, which remains poorly understood, depends on reliable genetic tools for functional analysis of genes in pathogenic strains. In this study, we report the first demonstration of conjugation between
Escherichia coli
and
Leptospira
spp. by using RP4 derivative conjugative plasmids. The DNA transfer described here was due to authentic conjugation, as shown by the requirement for cell-to-cell contact and the resistance of DNA transfers to the addition of DNase I. Transposition via conjugation of a plasmid delivering
Himar1
yielded frequencies ranging from 1 × 10
−6
to 8.5 × 10
−8
transconjugants/recipient cell in the saprophyte
L. biflexa
and the pathogen
L. interrogans
, respectively. Analysis of mutants indicated that transposition occurs randomly, and at single sites in the genome of these strains, allowing the utilization of this system to generate libraries of transposon mutants.
Survival of and In Situ Gene Expression by
Vibrio vulnificus
at Varying Salinities in Estuarine Environments
Authors: Jones Melissa K. , Warner Elizabeth , Oliver James D.
Published: November 2007

The opportunistic human pathogen
Vibrio vulnificus
survives in a wide range of ecological environments, which demonstrates its ability to adapt to highly variable conditions. Survival and gene expression under various conditions have been extensively studied in vitro; however, little work has been done to evaluate this bacterium in its natural habitat. Therefore, this study monitored the long-term survival of
V. vulnificus
in situ and simultaneously evaluated the expression of stress (
rpoS
,
relA
,
hfq
, and
groEL
) and putative virulence (
vvpE
,
smcR
,
viuB
, and
trkA
) genes at estuarine sites of varying salinity. Additionally, the survival and gene expression of an
rpoS
and an
oxyR
mutant were examined under the same conditions. Differences between the sampling sites in the long-term survival of any strain were not seen. However, differences were seen in the expression of
viuB
,
trkA
, and
relA
but our findings differed from what has been previously shown in vitro. These results also routinely demonstrated that genes required for survival under in vitro stress or host conditions are not necessarily required for survival in the water column. Overall, this study highlights the need for further in situ evaluation of this bacterium in order to gain a true understanding of its ecology and how it relates to its natural habitat.
Basic-Zipper-Type Transcription Factor FlbB Controls Asexual Development in
Aspergillus nidulans
Authors: Etxebeste Oier , Ni Min , Garzia Aitor , Kwon Nak-Jung , Fischer Reinhard , Yu Jae-Hyuk , Espeso Eduardo A. , Ugalde Unai
Published: November 2007

The fungal colony is a complex multicellular unit consisting of various cell types and functions. Asexual spore formation (conidiation) is integrated through sensory and regulatory elements into the general morphogenetic plan, in which the activation of the transcription factor BrlA is the first determining step. A number of early regulatory elements acting upstream of BrlA (
fluG
and
flbA-E
) have been identified, but their functional relations remain to be further investigated. In this report we describe FlbB as a putative basic-zipper-type transcription factor restricted to filamentous fungi. FlbB accumulates at the hyphal apex during early vegetative growth but is later found in apical nuclei, suggesting that an activating modification triggers nuclear import. Moreover, proper temporal and quantitative expression of FlbB is a prerequisite for
brlA
transcription, and misscheduled overexpression inhibits conidiation. We also present evidence that FlbB activation results in the production of a second diffusible signal, acting downstream from the FluG factor, to induce conidiation.
Responses of Pathogenic and Nonpathogenic Yeast Species to Steroids Reveal the Functioning and Evolution of Multidrug Resistance Transcriptional Networks
Authors: Banerjee Dibyendu , Lelandais Gaelle , Shukla Sudhanshu , Mukhopadhyay Gauranga , Jacq Claude , Devaux Frederic , Prasad Rajendra
Published: November 2007

Steroids are known to induce pleiotropic drug resistance states in hemiascomycetes, with tremendous potential consequences for human fungal infections. Our analysis of gene expression in
Saccharomyces cerevisiae
and
Candida albicans
cells subjected to three different concentrations of progesterone revealed that their pleiotropic drug resistance (PDR) networks were strikingly sensitive to steroids. In
S. cerevisiae
, 20 of the Pdr1p/Pdr3p target genes, including
PDR3
itself, were rapidly induced by progesterone, which mimics the effects of
PDR1
gain-of-function alleles. This unique property allowed us to decipher the respective roles of Pdr1p and Pdr3p in PDR induction and to define functional modules among their target genes. Although the expression profiles of the major PDR transporters encoding genes Sc
PDR5
and Ca
CDR1
were similar, the
S. cerevisiae
global PDR response to progesterone was only partly conserved in
C. albicans
. In particular, the role of Tac1p, the main
C. albicans
PDR regulator, in the progesterone response was apparently restricted to five genes. These results suggest that the
C. albicans
and
S. cerevisiae
PDR networks, although sharing a conserved core regarding the regulation of membrane properties, have different structures and properties. Additionally, our data indicate that other as yet undiscovered regulators may second Tac1p in the
C. albicans
drug response.
Exit from Host Cells by the Pathogenic Parasite
Toxoplasma gondii
Does Not Require Motility
Authors: Lavine Mark D. , Arrizabalaga Gustavo
Published: November 2007

The process by which the intracellular parasite
Toxoplasma gondii
exits its host cell is central to its propagation and pathogenesis. Experimental induction of motility in intracellular parasites results in parasite egress, leading to the hypothesis that egress depends on the parasite's actin-dependent motility. Using a novel assay to monitor egress without experimental induction, we have established that inhibiting parasite motility does not block this process, although treatment with actin-disrupting drugs does delay egress. However, using an irreversible actin inhibitor, we show that this delay is due to the disruption of host cell actin alone, apparently resulting from the consequent loss of membrane tension. Accordingly, by manipulating osmotic pressure, we show that parasite egress is delayed by releasing membrane tension and promoted by increasing it. Therefore, without artificial induction, egress does not depend on parasite motility and can proceed by mechanical rupture of the host membrane.
Functional Characterization of
Pneumocystis carinii brl1
by Transspecies Complementation Analysis
Authors: Lo Presti Libera , Cockell Moira , Cerutti Lorenzo , Simanis Viesturs , Hauser Philippe M.
Published: November 2007

Pneumocystis jirovecii
is a fungus which causes severe opportunistic infections in immunocompromised humans. The
brl1
gene of
P. carinii
infecting rats was identified and characterized by using bioinformatics in conjunction with functional complementation in
Saccharomyces cerevisiae
and
Schizosaccharomyces pombe
. The ectopic expression of this gene rescues null alleles of essential nuclear membrane proteins of the Brr6/Brl1 family in both yeasts.
ChsVb, a Class VII Chitin Synthase Involved in Septation, Is Critical for Pathogenicity in
Fusarium oxysporum
Authors: Martín-Urdíroz Magdalena , Roncero M. Isabel G. , González-Reyes José Antonio , Ruiz-Roldán Carmen
Published: November 2007

A new myosin motor-like chitin synthase gene,
chsVb
, has been identified in the vascular wilt fungus
Fusarium oxysporum
f. sp.
lycopersici
. Phylogenetic analysis of the deduced amino acid sequence of the
chsVb
chitin synthase 2 domain (CS2) revealed that ChsVb belongs to class VII chitin synthases. The ChsVb myosin motor-like domain (MMD) is shorter than the MMD of class V chitin synthases and does not contain typical ATP-binding motifs. Targeted disrupted single (Δ
chsVb
) and double (Δ
chsV
Δ
chsVb
) mutants were unable to infect and colonize tomato plants or grow invasively on tomato fruit tissue. These strains were hypersensitive to compounds that interfere with fungal cell wall assembly, produced lemon-like shaped conidia, and showed swollen balloon-like structures in hyphal subapical regions, thickened walls, aberrant septa, and intrahyphal hyphae. Our results suggest that the
chsVb
gene is likely to function in polarized growth and confirm the critical importance of cell wall integrity in the complex infection process of this fungus.
Three Pathogenicity Islands of
Vibrio cholerae
Can Excise from the Chromosome and Form Circular Intermediates
Authors: Murphy Ronan A. , Boyd E. Fidelma
Published: November 2007

Vibrio
pathogenicity island-2 (VPI-2) is a 57-kb region integrated at a transfer RNA (tRNA)-serine locus that encompasses VC1758 to VC1809 on the
V. cholerae
N16961 genome and is present in pandemic isolates. VPI-2 encodes a P4-like integrase, a restriction modification system, a Mu phage-like region, and a sialic acid metabolism region, as well as neuraminidase (VC1784), which is a glycosylhydrolase known to release sialic acid from sialoglycoconjugates to unmask GM1 gangliosides, the receptor for cholera toxin. We examined the tRNA-serine locus among the sequenced
V. cholerae
genomes and identified five variant VPI-2 regions, four of which retained the sialometabolism region. Three variant VPI-2 regions contained a type three secretion system. By using an inverse nested PCR approach, we found that the VPI-2 region can form an extrachromosomal circular intermediate (CI) molecule after precise excision from its tRNA-serine attachment site. We constructed a knockout mutant of VC1758 (
int
) with
V. cholerae
strain N16961 and found that no excision PCR product was produced, indicating that a functional cognate, VPI-2 integrase, is required for excision. The
Vibrio
seventh pandemic island-I (VSP-I) and VSP-II regions are present in
V. cholerae
O1 El Tor and O139 serogroup isolates. Novel regions are present at the VSP-I insertion site in strain MZO-3 and at the VSP-II insertion site in strain 623-39. VSP-II is a 27-kb region that integrates at a tRNA-methionine locus, is flanked by direct repeats, and encodes a P4-like integrase. We show that VSP-II can excise and form a CI and that the cognate VSP-II integrase is required for excision. Interestingly, VSP-I is not inserted at a tRNA locus and does encode a XerDC-like recombinase, but similar to VPI-2 and VSP-II, VSP-I does excise from the genome to form a CI. These results show that all three pathogenicity islands can excise from the chromosome, which is likely a first step in their horizontal transfer.
Global Genomic Analysis of
Pseudomonas savastanoi
pv. savastanoi Plasmids
Authors: Pérez-Martínez Isabel , Zhao Youfu , Murillo Jesús , Sundin George W. , Ramos Cayo
Published: November 2007

Pseudomonas savastanoi
pv. savastanoi strains harbor native plasmids belonging to the pPT23A plasmid family (PFPs) which are detected in all pathovars of the related species
Pseudomonas syringae
examined and contribute to the ecological and pathogenic fitness of their host. However, there is a general lack of information about the gene content of
P. savastanoi
pv. savastanoi plasmids and their role in the interaction of this pathogen with olive plants. We designed a DNA macroarray containing 135 plasmid-borne
P. syringae
genes to conduct a global genetic analysis of 32 plasmids obtained from 10
P. savastanoi
pv. savastanoi strains. Hybridization results revealed that the number of PFPs per strain varied from one to four. Additionally, most strains contained at least one plasmid (designated non-PFP) that did not hybridize to the
repA
gene of pPT23A. Only three PFPs contained genes involved in the biosynthesis of the virulence factor indole-3-acetic acid (
iaaM
,
iaaH
, and
iaaL
). In contrast,
ptz
, a gene involved in the biosynthesis of cytokinins, was found in five PFPs and one non-PFP. Genes encoding a type IV secretion system (T4SS), type IVA, were found in both PFPs and non-PFPs; however, type IVB genes were found only on PFPs. Nine plasmids encoded both T4SSs, whereas seven other plasmids carried none of these genes. Most PFPs and non-PFPs hybridized to at least one putative type III secretion system effector gene and to a variety of additional genes encoding known
P. syringae
virulence factors and one or more insertion sequence transposase genes. These results indicate that non-PFPs may contribute to the virulence and fitness of the
P. savastanoi
pv. savastanoi host. The overall gene content of
P. savastanoi
pv. savastanoi plasmids, with their repeated information, mosaic arrangement, and insertion sequences, suggests a possible role in adaptation to a changing environment.
Interaction ofBacillus subtilisCodY with GTP
Authors: Handke Luke D. , Shivers Robert P. , Sonenshein Abraham L.
Published: November 2007

Many of the adaptive mechanisms that allowBacillus subtilisto adjust to changes in nutrient availability are controlled by CodY. Binding of CodY to its target genes is stimulated by interaction with its effectors, GTP and the branched-chain amino acids (BCAAs). Upon nutrient limitation, intracellular pools of these effectors are depleted and CodY can no longer repress genes required for adaptation. In vitro studies reported here explored in more detail the interaction of CodY with GTP. DNase I footprinting experiments indicated that CodY has an affinity for GTP in the millimolar range. Further, CodY was shown to interact specifically with GTP and dGTP; no other naturally occurring nucleotides that were tested, including ppGpp and pppGpp, resulted in DNA protection. Two nonhydrolyzable analogs of GTP were fully able to activate CodY binding to target DNA, demonstrating that GTP hydrolysis is not necessary for CodY-dependent regulation. GTP and the BCAAs were shown to act additively to increase the affinity of CodY for DNA; increased protection was observed in DNase I footprinting experiments when both effectors were present, compared to either effector alone, and in in vitro transcription reactions, transcriptional repression by CodY was stronger in the presence of both GTP and BCAAs than of BCAAs alone. Thus, interaction of CodY with GTP is specific and results in increased affinity for its target genes. This increase in affinity is independent of GTP hydrolysis and is augmented in the presence of BCAAs.
LmrR Is a Transcriptional Repressor of Expression of the Multidrug ABC Transporter LmrCD in
Lactococcus lactis
Authors: Agustiandari Herfita , Lubelski Jacek , van den Berg van Saparoea H. Bart , Kuipers Oscar P. , Driessen Arnold J. M.
Published: November 2007

LmrCD is an ABC-type multidrug transporter in
Lactococcus lactis
. LmrR encodes a putative transcriptional regulator. In a Δ
lmrR
strain,
lmrCD
is up-regulated. LmrR binds the promoter region of
lmrCD
and interacts with drugs that cause
lmrCD
up-regulation. This suggests that LmrR is a drug-dependent transcriptional regulator of
lmrCD
expression.
Crystal Structure of PhnH: an Essential Component of Carbon-Phosphorus Lyase in
Escherichia coli
Authors: Adams Melanie A. , Luo Yan , Hove-Jensen Bjarne , He Shu-Mei , van Staalduinen Laura M. , Zechel David L. , Jia Zongchao
Published: November 2007

Organophosphonates are reduced forms of phosphorous that are characterized by the presence of a stable carbon-phosphorus (C-P) bond, which resists chemical hydrolysis, thermal decomposition, and photolysis. The chemically inert nature of the C-P bond has raised environmental concerns as toxic phosphonates accumulate in a number of ecosystems. Carbon-phosphorous lyase (CP lyase) is a multienzyme pathway encoded by the
phn
operon in gram-negative bacteria. In
Escherichia coli
14 cistrons comprise the operon (
phnCDEFGHIJKLMNOP
) and collectively allow the internalization and degradation of phosphonates. Here we report the X-ray crystal structure of the PhnH component at 1.77 Å resolution. The protein exhibits a novel fold, although local similarities with the pyridoxal 5′-phosphate-dependent transferase family of proteins are apparent. PhnH forms a dimer in solution and in the crystal structure, the interface of which is implicated in creating a potential ligand binding pocket. Our studies further suggest that PhnH may be capable of binding negatively charged cyclic compounds through interaction with strictly conserved residues. Finally, we show that PhnH is essential for C-P bond cleavage in the CP lyase pathway.
Genome Sequence of
Lactobacillus helveticus
, an Organism Distinguished by Selective Gene Loss and Insertion Sequence Element Expansion
Authors: Callanan Michael , Kaleta Pawel , O'Callaghan John , O'Sullivan Orla , Jordan Kieran , McAuliffe Olivia , Sangrador-Vegas Amaia , Slattery Lydia , Fitzgerald Gerald F. , Beresford Tom , Ross R. Paul
Published: November 2007

Mobile genetic elements are major contributing factors to the generation of genetic diversity in prokaryotic organisms. For example, insertion sequence (IS) elements have been shown to specifically contribute to niche adaptation by promoting a variety of genetic rearrangements. The complete genome sequence of the cheese culture
Lactobacillus helveticus
DPC 4571 was determined and revealed significant conservation compared to three nondairy gut lactobacilli. Despite originating from significantly different environments, 65 to 75% of the genes were conserved between the commensal and dairy lactobacilli, which allowed key niche-specific gene sets to be described. However, the primary distinguishing feature was 213 IS elements in the DPC 4571 genome, 10 times more than for the other lactobacilli. Moreover, genome alignments revealed an unprecedented level of genome stability between these four
Lactobacillus
species, considering the number of IS elements in the
L. helveticus
genome. Comparative analysis also indicated that the IS elements were not the primary agents of niche adaptation for the
L. helveticus
genome. A clear bias toward the loss of genes reported to be important for gut colonization was observed for the cheese culture, but there was no clear evidence of IS-associated gene deletion and decay for the majority of genes lost. Furthermore, an extraordinary level of sequence diversity exists between copies of certain IS elements in the DPC 4571 genome, indicating they may represent an ancient component of the
L. helveticus
genome. These data suggest a special unobtrusive relationship between the DPC 4571 genome and its mobile DNA complement.
Novel Protein Antigen (JHP940) from the Genomic Plasticity Region ofHelicobacter pyloriInduces Tumor Necrosis Factor Alpha and Interleukin-8 Secretion by Human Macrophages
Authors: Rizwan Mohammed , Alvi Ayesha , Ahmed Niyaz
Published: November 2007

The plasticity region of theHelicobacter pylorigenome comprises strain-specific gene loci. We performed genotyping and functional biology analysis of one such locus (jhp940) that was previously found to be functionally unknown but present in gastric cancer-associated strains from many different countries. We found its geographic prevalence to be independent ofcagApresence and disease status. Cloning, expression, and purification of JHP940 revealed a novel, ∼36-kDa protein in a biologically active form which elicited strong and significant levels of tumor necrosis factor alpha and interleukin-8 in human macrophages. Also, JHP940 was able to induce enhanced translocation of the transcription factor NF-κB complex in cultured macrophages. The induction of the proinflammatory cytokines by JHP940, therefore, points to its putative role in chronic gastric inflammation and, possibly, the various other outcomes ofH. pyloriinfection, including gastric cancer.
Conditional Lethality, Division Defects, Membrane Involution, and Endocytosis inmreandmrdShape Mutants ofEscherichia coli
Authors: Bendezú Felipe O. , de Boer Piet A. J.
Published: November 2007

Maintenance of rod shape inEscherichia colirequires the shape proteins MreB, MreC, MreD, MrdA (PBP2), and MrdB (RodA). How loss of the Mre proteins affectsE. coliviability has been unclear. We generated Mre and Mrd depletion strains under conditions that minimize selective pressure for undefined suppressors and found their phenotypes to be very similar. Cells lacking one or more of the five proteins were fully viable and propagated as small spheres under conditions of slow mass increase but formed large nondividing spheroids with noncanonical FtsZ assembly patterns at higher mass doubling rates. Extra FtsZ was sufficient to suppress lethality in each case, allowing cells to propagate as small spheres under any condition. The failure of each unsuppressed mutant to divide under nonpermissive conditions correlated with the presence of elaborate intracytoplasmic membrane-bound compartments, including vesicles/vacuoles and more-complex systems. Many, if not all, of these compartments formed by FtsZ-independent involution of the cytoplasmic membrane (CM) rather than de novo. Remarkably, while some of the compartments were still continuous with the CM and the periplasm, many were topologically separate, indicating they had been released into the cytoplasm by an endocytic-like membrane fission event. Notably, cells failed to adjust the rate of phospholipid synthesis to their new surface requirements upon depletion of MreBCD, providing a rationale for the “excess” membrane in the resulting spheroids. Both FtsZ and MinD readily assembled on intracytoplasmic membrane surfaces, and we propose that this contributes significantly to the lethal division block seen in all shape mutants under nonpermissive conditions.
DNA Polymerase I Is Not Required for Replication of Linear Chromosomes in
Streptomyces
Authors: Huang Tzu-Wen , Chen Carton W.
Published: November 2007

Both
polA
(encoding DNA polymerase I; Pol I) and a paralog were deleted from
Streptomyces
strains. Despite the UV sensitivity and slow growth caused by the Δ
polA
mutation, the double mutant was viable. Thus, in contrast to a previous postulate, Pol I and its paralog are not essential for replication of
Streptomyces
chromosomes.
Transcriptome Analysis of a Phenol-Producing
Pseudomonas putida
S12 Construct: Genetic and Physiological Basis for Improved Production
Authors: Wierckx Nick J. P. , Ballerstedt Hendrik , de Bont Jan A. M. , de Winde Johannes H. , Ruijssenaars Harald J. , Wery Jan
Published: November 2007

The unknown genetic basis for improved phenol production by a recombinant
Pseudomonas putida
S12 derivative bearing the
tpl
(tyrosine-phenol lyase) gene was investigated via comparative transcriptomics, nucleotide sequence analysis, and targeted gene disruption. We show upregulation of tyrosine biosynthetic genes and possibly decreased biosynthesis of tryptophan caused by a mutation in the
trpE
gene as the genetic basis for the enhanced phenol production. In addition, several genes in degradation routes connected to the tyrosine biosynthetic pathway were upregulated. This either may be a side effect that negatively affects phenol production or may point to intracellular accumulation of tyrosine or its intermediates. A number of genes identified by the transcriptome analysis were selected for targeted disruption in
P. putida
S12TPL3. Physiological and biochemical examination of
P. putida
S12TPL3 and these mutants led to the conclusion that the metabolic flux toward tyrosine in
P. putida
S12TPL3 was improved to such an extent that the heterologous tyrosine-phenol lyase enzyme had become the rate-limiting step in phenol biosynthesis.
Coupled Ferredoxin and Crotonyl Coenzyme A (CoA) Reduction with NADH Catalyzed by the Butyryl-CoA Dehydrogenase/Etf Complex from
Clostridium kluyveri
Authors: Li Fuli , Hinderberger Julia , Seedorf Henning , Zhang Jin , Buckel Wolfgang , Thauer Rudolf K.
Published: November 2007

Cell extracts of butyrate-forming clostridia have been shown to catalyze acetyl-coenzyme A (acetyl-CoA)- and ferredoxin-dependent formation of H
2
from NADH. It has been proposed that these bacteria contain an NADH:ferredoxin oxidoreductase which is allosterically regulated by acetyl-CoA. We report here that ferredoxin reduction with NADH in cell extracts from
Clostridium kluyveri
is catalyzed by the butyryl-CoA dehydrogenase/Etf complex and that the acetyl-CoA dependence previously observed is due to the fact that the cell extracts catalyze the reduction of acetyl-CoA with NADH via crotonyl-CoA to butyryl-CoA. The cytoplasmic butyryl-CoA dehydrogenase complex was purified and is shown to couple the endergonic reduction of ferredoxin (E
0
′ = −410 mV) with NADH (E
0
′ = −320 mV) to the exergonic reduction of crotonyl-CoA to butyryl-CoA (E
0
′ = −10 mV) with NADH. The stoichiometry of the fully coupled reaction is extrapolated to be as follows: 2 NADH + 1 oxidized ferredoxin + 1 crotonyl-CoA = 2 NAD
+
+ 1 ferredoxin reduced by two electrons + 1 butyryl-CoA. The implications of this finding for the energy metabolism of butyrate-forming anaerobes are discussed in the accompanying paper.
Linking Ultrastructure and Function in Four Genera of Anaerobic Ammonium-Oxidizing Bacteria: Cell Plan, Glycogen Storage, and Localization of Cytochrome
c
Proteins
Authors: van Niftrik Laura , Geerts Willie J. C. , van Donselaar Elly G. , Humbel Bruno M. , Webb Richard I. , Fuerst John A. , Verkleij Arie J. , Jetten Mike S. M. , Strous Marc
Published: November 2007

Anaerobic ammonium oxidation (anammox) is an ecologically and industrially important process and is performed by a clade of deeply branching
Planctomycetes
. Anammox bacteria possess an intracytoplasmic membrane-bounded organelle, the anammoxosome. In the present study, the ultrastructures of four different genera of anammox bacteria were compared with transmission electron microscopy and electron tomography. The four anammox genera shared a common cell plan and contained glycogen granules. Differences between the four genera included cell size (from 800 to 1,100 nm in diameter), presence or absence of cytoplasmic particles, and presence or absence of pilus-like appendages. Furthermore, cytochrome
c
proteins were detected exclusively inside the anammoxosome. This detection provides further support for the hypothesis that this organelle is the locus of anammox catabolism.
Role of Hypermutability in the Evolution of the GenusOenococcus
Authors: Marcobal Angela M. , Sela David A. , Wolf Yuri I. , Makarova Kira S. , Mills David A.
Published: November 2007

Oenococcus oeniis an alcohol-tolerant, acidophilic lactic acid bacterium primarily responsible for malolactic fermentation in wine. A recent comparative genomic analysis ofO. oeniPSU-1 with other sequenced lactic acid bacteria indicates that PSU-1 lacks the mismatch repair (MMR) genesmutSandmutL. Consistent with the lack of MMR, mutation rates forO. oeniPSU-1 and a second oenococcal species,O. kitaharae, were higher than those observed for neighboring taxa,Pediococcus pentosaceusandLeuconostoc mesenteroides. Sequence analysis of therpoBmutations in rifampin-resistant strains from both oenococcal species revealed a high percentage of transition mutations, a result indicative of the lack of MMR. An analysis of common alleles in the two sequencedO. oenistrains, PSU-1 and BAA-1163, also revealed a significantly higher level of transition substitutions than were observed in otherLactobacillalesspecies. These results suggest that the genusOenococcusis hypermutable due to the loss ofmutSandmutL, which occurred with the divergence away from the neighboringLeuconostocbranch. The hypermutable status of the genusOenococcusexplains the observed high level of allelic polymorphism among knownO. oeniisolates and likely contributed to the unique adaptation of this genus to acidic and alcoholic environments.
Vibrio parahaemolyticusScrC Modulates Cyclic Dimeric GMP Regulation of Gene Expression Relevant to Growth on Surfaces
Authors: Ferreira Rosana B. R. , Antunes Luis Caetano M. , Greenberg E. Peter , McCarter Linda L.
Published: November 2007

InVibrio parahaemolyticus,scrCparticipates in controlling the decision to be a highly mobile swarmer cell or a more adhesive, biofilm-proficient cell type.scrCmutants display decreased swarming motility over surfaces and enhanced capsular polysaccharide production. ScrC is a cytoplasmic membrane protein that contains both GGDEF and EAL conserved protein domains. These domains have been shown in many organisms to respectively control the formation and degradation of the small signaling nucleotide cyclic dimeric GMP (c-di-GMP). ThescrCgene is part of the three-genescrABCoperon. Here we report that this operon influences the cellular nucleotide pool and that c-di-GMP levels inversely modulate lateral flagellar and capsular polysaccharide gene expression. High concentrations of this nucleotide prevent swarming and promote adhesiveness. Further, we demonstrate that ScrC has intrinsic diguanylate cyclase and phosphodiesterase activities, and these activities are controlled by ScrAB. Specifically, ScrC acts to form c-di-GMP in the absence of ScrA and ScrB; whereas ScrC acts to degrade c-di-GMP in the presence of ScrA and ScrB. ThescrABCoperon is specifically induced by growth on a surface, and the analysis of mutant phenotypes supports a model in which the phosphodiesterase activity of ScrC plays a dominant role during surface translocation and in biofilms.
Characterization of the CopR Regulon ofLactococcus lactisIL1403
Authors: Magnani David , Barré Olivier , Gerber Simon D. , Solioz Marc
Published: November 2007

To identify components of the copper homeostatic mechanism ofLactococcus lactis, we employed two-dimensional gel electrophoresis to detect changes in the proteome in response to copper. Three proteins upregulated by copper were identified: glyoxylase I (YaiA), a nitroreductase (YtjD), and lactate oxidase (LctO). The promoter regions of these genes featurecopboxes of consensus TACAnnTGTA, which are the binding site of CopY-type copper-responsive repressors. A genome-wide search forcopboxes revealed 28 such sequence motifs. They were tested by electrophoretic mobility shift assays for the interaction with purified CopR, the CopY-type repressor ofL. lactis. Seven of thecopboxes interacted with CopR in a copper-sensitive manner. They were present in the promoter region of five genes,lctO, ytjD, copB, ydiD, andyahC; and two polycistronic operons,yahCD-yaiABandcopRZA. Induction of these genes by copper was confirmed by real-time quantitative PCR. ThecopRZAoperon encodes the CopR repressor of the regulon; a copper chaperone, CopZ; and a putative copper ATPase, CopA. When expressed inEscherichia coli, thecopRZAoperon conferred copper resistance, suggesting that it functions in copper export from the cytoplasm. Other member genes of the CopR regulon may similarly be involved in copper metabolism.
Bioinformatics and Experimental Analysis of Proteins of Two-Component Systems in
Myxococcus xanthus
Authors: Shi Xingqi , Wegener-Feldbrügge Sigrun , Huntley Stuart , Hamann Nils , Hedderich Reiner , Søgaard-Andersen Lotte
Published: November 2007

Proteins of two-component systems (TCS) have essential functions in the sensing of external and self-generated signals in bacteria and in the generation of appropriate output responses. Accordingly, in
Myxococcus xanthus
, TCS are important for normal motility and fruiting body formation and sporulation. Here we analyzed the
M. xanthus
genome for the presence and genetic organization of genes encoding TCS. Two hundred seventy-two TCS genes were identified, 251 of which are not part of
che
gene clusters. We report that the TCS genes are unusually organized, with 55% being orphan and 16% in complex gene clusters whereas only 29% display the standard paired gene organization. Hybrid histidine protein kinases and histidine protein kinases predicted to be localized to the cytoplasm are overrepresented among proteins encoded by orphan genes or in complex gene clusters. Similarly, response regulators without output domains are overrepresented among proteins encoded by orphan genes or in complex gene clusters. The most frequently occurring output domains in response regulators are involved in DNA binding and cyclic-di-GMP metabolism. Our analyses suggest that TCS encoded by orphan genes and complex gene clusters are functionally distinct from TCS encoded by paired genes and that the connectivity of the pathways made up of TCS encoded by orphan genes and complex gene clusters is different from that of pathways involving TCS encoded by paired genes. Experimentally, we observed that orphan TCS genes are overrepresented among genes that display altered transcription during fruiting body formation. The systematic analysis of the 25 orphan genes encoding histidine protein kinases that are transcriptionally up-regulated during development showed that 2 such genes are likely essential for viability and identified 7 histidine protein kinases, including 4 not previously characterized that have important function in fruiting body formation or spore germination.
Niche-Specific Features of the Intestinal
Bacteroidales
Authors: Coyne Michael J. , Comstock Laurie E.
Published: November 2007

By analyzing the genomic sequences of 12
Bacteroidales
species, we found that all intestinal species have numerous polysaccharide biosynthesis loci, many with promoters that we demonstrate undergo DNA inversion. This feature is not conserved in the
Bacteroidales
order as a whole, as oral species do not share these genetic features.
Massetolide A Biosynthesis inPseudomonas fluorescens
Authors: de Bruijn I. , de Kock M. J. D. , de Waard P. , van Beek T. A. , Raaijmakers J. M.
Published: November 2007

Massetolide A is a cyclic lipopeptide (CLP) antibiotic produced by variousPseudomonasstrains from diverse environments. Cloning, sequencing, site-directed mutagenesis, and complementation showed that massetolide A biosynthesis inP. fluorescensSS101 is governed by three nonribosomal peptide synthetase (NRPS) genes, designatedmassA,massB, andmassC, spanning approximately 30 kb. Prediction of the nature and configuration of the amino acids by in silico analysis of adenylation and condensation domains of the NRPSs was consistent with the chemically determined structure of the peptide moiety of massetolide A. Structural analysis of massetolide A derivatives produced by SS101 indicated that most of the variations in the peptide moiety occur at amino acid positions 4 and 9. Regions flanking themassgenes contained several genes found in otherPseudomonasCLP biosynthesis clusters, which encode LuxR-type transcriptional regulators, ABC transporters, and an RND-like outer membrane protein. In contrast to mostPseudomonasCLP gene clusters known to date, themassgenes are not physically linked but are organized in two separate clusters, withmassAdisconnected frommassBandmassC. Quantitative real-time PCR analysis indicated that transcription ofmassCis strongly reduced whenmassBis mutated, suggesting that these two genes function in an operon, whereas transcription ofmassAis independent ofmassBCand vice versa. Massetolide A is produced in the early exponential growth phase, and biosynthesis appears not to be regulated byN-acylhomoserine lactone-based quorum sensing. Massetolide A production is essential in swarming motility ofP. fluorescensSS101 and plays an important role in biofilm formation.
Do female frogs exploit inadvertent social information to locate breeding aggregations?
Authors: Swanson E.M. , Tekmen S.M. , Bee M.A.
Published: November 2007

The advertisement calls of male anurans (frogs and toads) are loud and conspicuous signals, and the sound generated by breeding aggregations of males propagates over long distances. As a by-product of communication within an aggregation, the sounds of a frog chorus constitute a form of inadvertent social information that provides potential long-distance cues about the location and timing of breeding. We investigated whether female American toads ( Bufo americanus Holbrook, 1836) and Cope’s gray treefrogs ( Hyla chrysoscelis Cope, 1880) use the sounds of a chorus to locate breeding aggregations in the absence of other sensory cues. Females of both species approached speakers broadcasting recordings of a chorus made from distances of 0, 20, and 40 m, but not from distances of 80 and 160 m. Female toads also exhibited phonotaxis to a completely artificial chorus sound, but female gray treefrogs did not. We found little evidence to suggest that female American toads and Cope’s gray treefrogs differed substantially in their responses to natural chorus sounds despite potential differences in the predictability and duration of breeding seasons in these two species. Our results suggest that the inadvertent social information of a chorus could be used over short distances to locate breeding aggregations.
Age and food hardness affect food handling by insectivorous bats
Authors: Fraser E.E. , Fenton M.B.
Published: November 2007

Eating behaviour can vary with age, experience, and gender, as well as food hardness. This variation can contribute to intraspecific dietary differences and may result in variable definitions of optimal foraging and decreased intraspecific competition. We quantified feeding behaviour of insectivorous bats eating hard and soft mealworm-based food items based on the bats’ ability to consume and manipulate food items, consumption time, chew frequency, and total chews to consume. Adult Myotis lucifugus (LeConte, 1831) were more successful at both consuming and manipulating mealworms and consumed mealworms more quickly, with greater chew frequency and in fewer chews, than did subadults. Adults chewed mealworm viscera more frequently than did subadults but showed no differences in the other variables. Adult Eptesicus fuscus (Beauvois, 1796) consumed mealworms more quickly and with fewer chews than did subadults but showed no differences in the other variables. There were no differences between adult and subadult E. fuscus when consuming mealworm viscera. Male and female M. lucifugus did not differ significantly when eating either mealworms or mealworm viscera. There was no change in subadult consumption time of mealworms over the summer. Age-based differences in eating abilities may play a role in defining optimal foraging and dietary composition in insectivorous bats.
How to find a metapopulationThis review is one of a series dealing with some aspects of the impact of habitat fragmentation on animals and plants. This series is one of several virtual symposia focussing on ecological topics that will be published in the Journal from time to time.
Authors: Driscoll D.A.
Published: November 2007

Where habitat loss and fragmentation is severe, many native species are likely to have reduced levels of dispersal between remnant populations. For those species to avoid regional extinction in fragmented landscapes, they must undergo some kind of metapopulation dynamics so that local extinctions are countered by recolonisation. The importance of spatial dynamics for regional survival means that research into metapopulation dynamics is essential. In this review I explore the approaches taken to examine metapopulation dynamics, highlight the analytical methods used to get the most information out of field data, and discover some of the major research gaps. Statistical models, including Hanski’s incidence function model (IFM) are frequently applied to presence–absence data, an approach that is often strengthened using long-term data sets that document extinctions and colonisations. Recent developments are making the IFM more biologically realistic and expanding the range of situations for which the model is relevant. Although accurate predictions using the IFM seem unlikely, it may be useful for ranking management decisions. A key weakness of presence–absence modelling is that the mechanisms underlying spatial dynamics remain inferential, so combining modelling approaches with detailed demographic research is warranted. For species where very large data sets cannot be obtained to facilitate statistical modelling, a demographic approach alone or with stochastic modelling may be the only viable research angle to take. Dispersal is a central process in metapopulation dynamics. Research combining mark–recapture or telemetry methods with model-selection procedures demonstrate that dispersal is frequently oversimplified in conceptual and statistical metapopulation models. Dispersal models like the island model that underlies classic metapopulation theory do not approximate the behaviour of real species in fragmented landscapes. Nevertheless, it remains uncertain if additional biological realism will improve predictions of statistical metapopulation models. Genetic methods can give better estimates of dispersal than direct methods and take less effort, so they should be routinely explored alongside direct ecological methods. Recent development of metacommunity theory (communities connected by dispersal) emphasises a range of mechanisms that complement metapopulation theory. Taking both theories into account will enhance interpretation of field data. The extent of metapopulation dynamics in human modified landscapes remains uncertain, but we have a powerful array of field and analytical approaches for reducing this knowledge gap. The most informative way forward requires that many species are studied in the same fragmented landscape by applying a selection of approaches that reveal complementary aspects of spatial dynamics.
THREE NUCLEON FORCES AND NUCLEAR STRUCTURE
Authors: BARRETT B. R.
Published: November 2007

The author's earlier research with Professor Bruce McKellar, some 30 years ago, led to the Tucson-Melbourne three-nucleon interaction, which is still relevant today. The new significance of three-nucleon forces in determining the structure of atomic nuclei will be discussed. This has led to increased efforts to learn more about the nature of these three-nucleon interactions, both experimentally and theoretically. The recently developed no-core shell model (NCSM) has the ability to test different theoretical models for three-nucleon forces by making direct comparisons of results produced by these forces with experimental data.
INTERACTING BOSE GAS CONFINED BY AN EXTERNAL POTENTIAL
Authors: GNANAPRAGASAM G. , DAS M. P.
Published: November 2007

Interacting Bose gas confined by an external potential is studied using Green functions in spectral representation. The calculation is presented transparently using the equation of motion method. With this, the interplay between the condensed and the non-condensed atoms is inevitably seen. An expression for the condensate number at finite temperature is obtained in the lowest and first orders, from which depletion of bosons from the ground state is qualitatively analyzed. Finally, we discuss the behaviour of the specific heat of a trapped interacting Bose gas in the quasi-continuum limit.
VARIATION OF THE FUNDAMENTAL CONSTANTS: THEORY AND OBSERVATIONS
Authors: FLAMBAUM V. V.
Published: November 2007

Review of recent works devoted to the variation of the fine structure constant α, strong interaction and fundamental masses (Higgs vacuum) is presented. The results from Big Bang nucleosynthesis, quasar absorption spectra, and Oklo natural nuclear reactor data give us the space-time variation on the Universe lifetime scale. Comparison of different atomic clocks gives us the present time variation. Assuming linear variation with time we can compare different results. The best limit on the variation of the electron-to-proton mass ratio μ = me/Mp and Xe = me/ΛQCD follows from the quasar absorption spectra:1[Formula: see text]. A combination of this result and the atomic clock results2,3 gives the best limt on variation of [Formula: see text]. The Oklo natural reactor gives the best limit on the variation of Xs = ms/ΛQCD where ms is the strange quark mass:4,5[Formula: see text]. Note that the Oklo data can not give us any limit on the variation of α since the effect of α there is much smaller than the effect of Xs and should be neglected.

Huge enhancement of the relative variation effects happens in transitions between close atomic, molecular and nuclear energy levels. We suggest several new cases where the levels are very narrow. Large enhancement of the variation effects is also possible in cold atomic and molecular collisions near Feshbach resonance.

How changing physical constants and violation of local position invariance may occur? Light scalar fields very naturally appear in modern cosmological models, affecting parameters of the Standard Model (e.g. α). Cosmological variations of these scalar fields should occur because of drastic changes of matter composition in Universe: the latest such event is rather recent (about 5 billion years ago), from matter to dark energy domination. Massive bodies (stars or galaxies) can also affect physical constants. They have large scalar charge S proportional to number of particles which produces a Coulomb-like scalar field U = S/r. This leads to a variation of the fundamental constants proportional to the gravitational potential, e.g. δα/α = kαδ(GM/rc2). We compare different manifestations of this effect. The strongest limits6kα + 0.17ke = (-3.5 ±6) × 10-7 and kα + 0.13kq = (-1 ± 17) × 10-7 are obtained from the measurements of dependence of atomic frequencies on the distance from Sun2,7 (the distance varies due to the ellipticity of the Earth's orbit).