bluuebunny/crossref_metadata_2025_split huggingface dataset:
Direct Image-Based Correlative Microscopy Technique for Coupling Identification and Structural Investigation of Bacterial Symbionts Associated with Metazoans
Authors: Halary Sébastien , Duperron Sébastien , Boudier Thomas 
Published: April 2011

ABSTRACTCoupling prokaryote identification with ultrastructural investigation of bacterial communities has proven difficult in environmental samples. Prokaryotes can be identified by using specific probes and fluorescencein situhybridization (FISH), but resolution achieved by light microscopes does not allow ultrastructural investigation. In the case of symbioses involving bacteria associated with metazoan tissues, FISH-based studies often indicate the co-occurrence of several bacterial types within a single host species. The ultrastructure is then relevant to address host and bacterial morphology and the intra- or extracellular localization of symbionts. A simple protocol for correlative light and electron microscopy (CLEM) is presented here which allows FISH-based identification of specific 16S rRNA phylotypes and transmission electron microscopy to be performed on a same sample. Image analysis tools are provided to superimpose images obtained and generate overlays. This procedure has been applied to two symbiont-bearing metazoans, namely, aphids and deep-sea mussels. The FISH protocol was modified to take into account constraints associated with the use of electron microscopy grids, and intense and specific signals were obtained. FISH signals were successfully overlaid with bacterial morphotypes in aphids. We thus used the method to address the question of symbiont morphology and localization in a deep-sea mussel. Signals from a type I methanotroph-related phylotype were associated with morphotypes displaying the stacked internal membranes typical for this group and three-dimensional electron tomography was performed, confirming for the first time the correspondence between morphology and phylotype. CLEM is thus feasible and reliable and could emerge as a potent tool for the study of prokaryotic communities.
Development of an Effective Method for Recovery of Viral Genomic RNA from Environmental Silty Sediments for Quantitative Molecular Detection
Authors: Miura Takayuki , Masago Yoshifumi , Sano Daisuke , Omura Tatsuo 
Published: April 2011

ABSTRACT

Nine approaches to recover viral RNA from environmental silty sediments were newly developed and compared to quantify RNA viruses in sediments using molecular methods. Four of the nine approaches employed direct procedures for extracting RNA from sediments (direct methods), and the remaining five approaches used indirect methods wherein viral particles were recovered before RNA extraction. A direct method using an SDS buffer with EDTA to lyse viral capsids in sediments, phenol-chloroform-isoamyl alcohol to extract RNA, isopropanol to concentrate RNA, and magnetic beads to purify RNA resulted in the highest rate of recovery (geometric mean of 11%, with a geometric standard deviation of 0.02;
n
= 7) of poliovirus 1 (PV1) inoculated in an environmental sediment sample. The direct method exhibiting the highest rate of PV1 recovery was applied to environmental sediment samples. One hundred eight sediment samples were collected from the Takagi River, Miyagi, Japan, and its estuary from November 2007 to April 2009, and the genomic RNAs of enterovirus and human norovirus in these samples were quantified by reverse transcription (RT)-quantitative PCR (qPCR). The human norovirus genome was detected in one sample collected at the bay, although its concentration was below the quantification limit. Meanwhile, the enterovirus genome was detected in two samples at the river mouth and river at concentrations of 8.6 × 10
2
and 2.4 × 10
2
copies/g (wet weight), respectively. This is the first report to obtain quantitative data for a human pathogenic virus in a river and in estuarine sediments using RT-qPCR.
Acetate Repression of Methane Oxidation by Supplemental Methylocella silvestris in a Peat Soil Microcosm
Authors: Rahman M. Tanvir , Crombie Andrew , Moussard Hélène , Chen Yin , Murrell J. Colin 
Published: April 2011

ABSTRACTMethylocellaspp. are facultative methanotrophs that grow on methane and multicarbon substrates, such as acetate. Acetate represses transcription of methane monooxygenase ofMethylocella silvestrisin laboratory culture. DNA stable-isotope probing (DNA-SIP) using13C-methane and12C-acetate, carried out withMethylocella-spiked peat soil, showed that acetate also repressed methane oxidation byMethylocellain environmental samples.
Engineering Trehalose Synthesis in Lactococcus lactis for Improved Stress Tolerance
Authors: Carvalho Ana Lúcia , Cardoso Filipa S. , Bohn Andreas , Neves Ana Rute , Santos Helena 
Published: April 2011

ABSTRACTTrehalose accumulation is a common cell defense strategy against a variety of stressful conditions. In particular, our team detected high levels of trehalose inPropionibacterium freudenreichiiin response to acid stress, a result that led to the idea that endowingLactococcus lactiswith the capacity to synthesize trehalose could improve the acid tolerance of this organism. To this end, we took advantage of the endogenous genes involved in the trehalose catabolic pathway ofL. lactis, i.e.,trePPandpgmB, encoding trehalose 6-phosphate phosphorylase and β-phosphoglucomutase, respectively, which enabled the synthesis of trehalose 6-phosphate. Given thatL. lactislacks trehalose 6-phosphate phosphatase, the respective gene,otsB, from the food-grade organismP. freudenreichiiwas used to provide the required activity. The trehalose yield was approximately 15% in resting cells and in mid-exponential-phase cells grown without pH control. The intracellular concentration of trehalose reached maximal values of approximately 170 mM, but at least 67% of the trehalose produced was found in the growth medium. The viability of mutant and control strains was examined after exposure to heat, cold or acid shock, and freeze-drying. The trehalose-producing strains showed improved tolerance (5- to 10-fold-higher survivability) to acid (pH 3) and cold shock (4°C); there was also a strong improvement in cell survival in response to heat shock (45°C), and no protection was rendered against dehydration. The insight provided by this work may help the design of food-grade strains optimized for the dairy industry as well as for oral drug delivery.
An Orphan Histidine Kinase, OhkA, Regulates Both Secondary Metabolism and Morphological Differentiation in Streptomyces coelicolor
Authors: Lu Yinhua , He Juanmei , Zhu Hong , Yu Zhenyu , Wang Rui , Chen Yunliang , Dang Fujun , Zhang Weiwen , Yang Sheng , Jiang Weihong 
Published: April 2011

ABSTRACT

We report here the physiological and genetic characterization of an orphan histidine kinase (HK) (OhkA,
SCO1596
) in
Streptomyces coelicolor
and its homolog (OhkAsav,
SAV_6741
) in
Streptomyces avermitilis
. The physiological analysis showed that the
ohkA
mutant of
S. coelicolor
exhibits impaired aerial mycelium formation and sporulation and overproduction of multiple antibiotics on mannitol-soy flour (MS) medium, especially actinorhodin (ACT) and calcium-dependent antibiotic (CDA), and disruption of
ohkAsav
in
S. avermitilis
also led to the similar phenotypes of impaired morphological differentiation and significantly increased oligomycin A production. DNA microarray analysis combined with real-time reverse transcription-PCR (RT-PCR) and RNA dot blot assay in the
S. coelicolor ohkA
deletion mutant confirmed the physiological results by showing the upregulation of genes involved in the biosynthesis of ACT, CDA, undecylprodigiosin (RED), a yellow type I polyketide (CPK,
SCO6273-6289
), and a sesquiterpene antibiotic, albaflavenone (
SCO5222-5223
). The results also suggested that the increased production of ACT and RED in the mutant could be partly ascribed to the enhanced precursor malonyl coenzyme A (malonyl-CoA) supply through increased transcription of genes encoding acetyl-CoA carboxylase (ACCase). Interestingly, DNA microarray analysis also showed that deletion of
ohkA
greatly downregulated the transcription of
chpABCDEFGH
genes essential for aerial mycelium formation by
S. coelicolor
on MS medium but significantly increased transcription of
ramS
/
C
/
R
, which is responsible for SapB formation and regulation and is normally absent on MS medium. Moreover, many other genes involved in development, such as
bldM
/
N
,
whiG
/
H
/
I
,
ssgA
/
B
/
E
/
G
/
R
, and
whiE
, were also significantly downregulated upon
ohkA
deletion. The results clearly demonstrated that OhkA is an important global regulator for both morphological differentiation and secondary metabolism in
S. coelicolor
and
S. avermitilis
.
Novel Reaction of Succinyl Coenzyme A (Succinyl-CoA) Synthetase: Activation of 3-Sulfinopropionate to 3-Sulfinopropionyl-CoA in Advenella mimigardefordensis Strain DPN7
T
during Degradation of 3,3′-Dithiodipropionic Acid
Authors: Schürmann Marc , Wübbeler Jan Hendrik , Grote Jessica , Steinbüchel Alexander 
Published: April 2011

ABSTRACT

The
sucCD
gene of
Advenella mimigardefordensis
strain DPN7
T
encodes a succinyl coenzyme A (succinyl-CoA) synthetase homologue (EC 6.2.1.4 or EC 6.2.1.5) that recognizes, in addition to succinate, the structural analogues 3-sulfinopropionate (3SP) and itaconate as substrates. Accumulation of 3SP during 3,3′-dithiodipropionic acid (DTDP) degradation was observed in Tn
5
::
mob-
induced mutants of
A. mimigardefordensis
strain DPN7
T
disrupted in
sucCD
and in the defined deletion mutant
A. mimigardefordensis
Δ
sucCD
. These mutants were impaired in growth with DTDP and 3SP as the sole carbon source. Hence, it was proposed that the succinyl-CoA synthetase homologue in
A. mimigardefordensis
strain DPN7
T
activates 3SP to the corresponding CoA-thioester (3SP-CoA). The putative genes coding for
A. mimigardefordensis
succinyl-CoA synthetase (SucCD

Am

) were cloned and heterologously expressed in
Escherichia coli
BL21(DE3)/pLysS. Purification and characterization of the enzyme confirmed its involvement during degradation of DTDP. 3SP, the cleavage product of DTDP, was converted into 3SP-CoA by the purified enzyme, as demonstrated by
in vitro
enzyme assays. The structure of 3SP-CoA was verified by using liquid chromatography-electrospray ionization-mass spectrometry. SucCD

Am

is Mg
2+
or Mn
2+
dependent and unspecific regarding ATP or GTP. In kinetic studies the enzyme showed highest enzyme activity and substrate affinity with succinate (
V
max
= 9.85 ± 0.14 μmol min
−1
mg
−1
,

K
m

= 0.143 ± 0.001 mM). In comparison to succinate, activity with 3SP was only ca. 1.2% (
V
max
= 0.12 ± 0.01 μmol min
−1
mg
−1
) and the affinity was 6-fold lower (

K
m

= 0.818 ± 0.046 mM). Based on the present results, we conclude that SucCD

Am

is physiologically associated with the citric acid cycle but is mandatory for the catabolic pathway of DTDP and its degradation intermediate 3SP.
Transcription Factor GreA Contributes to Resolving Promoter-Proximal Pausing of RNA Polymerase in Bacillus subtilis Cells
Authors: Kusuya Yoko , Kurokawa Ken , Ishikawa Shu , Ogasawara Naotake , Oshima Taku 
Published: April 2011

ABSTRACT

Bacterial Gre factors associate with RNA polymerase (RNAP) and stimulate intrinsic cleavage of the nascent transcript at the active site of RNAP. Biochemical and genetic studies to date have shown that
Escherichia coli
Gre factors prevent transcriptional arrest during elongation and enhance transcription fidelity. Furthermore, Gre factors participate in the stimulation of promoter escape and the suppression of promoter-proximal pausing during the beginning of RNA synthesis in
E. coli
. Although Gre factors are conserved in general bacteria, limited functional studies have been performed in bacteria other than
E. coli
. In this investigation, ChAP-chip analysis (chromatin affinity precipitation coupled with DNA microarray) was conducted to visualize the distribution of
Bacillus subtilis
GreA on the chromosome and to determine the effects of GreA inactivation on core RNAP trafficking. Our data show that GreA is uniformly distributed in the transcribed region from the promoter to coding region with core RNAP, and its inactivation induces RNAP accumulation at many promoter or promoter-proximal regions. Based on these findings, we propose that GreA would constantly associate with core RNAP during transcriptional initiation and elongation and resolves its stalling at promoter or promoter-proximal regions, thus contributing to the even distribution of RNAP along the promoter and coding regions in
B. subtilis
cells.
Under-estimation of self-reported occupational exposure by questionnaire in hospital workers
Authors: Donnay C , Denis M-A , Magis R , Fevotte J , Massin N , Dumas O , Pin I , Choudat D , Kauffmann F , Le Moual N 
Published: April 2011

ObjectivesThe aim of the study was to determine whether self-reported occupational exposure to cleaning/disinfecting agents in hospital workers is accurate, in comparison to expert assessment, taken to be the gold standard.MethodsIn the Epidemiological Study of the Genetics and Environment of Asthma (EGEA), participants were interviewed on occupation with a specific questionnaire for hospital workers regarding tasks and cleaning/disinfecting agents. Two estimates of exposure were available: self-report and expert assessment. The expert assessment involved a standardised procedure to estimate intensity, frequency and probability of exposure for each job. The present analysis focused on eight exposures: formaldehyde, glutaraldehyde, bleach/chlorine, alcohol, quaternary ammonium components, ammonia, sprays and latex gloves. Agreement and differences between self-reported and expert estimates were studied by kappa and phi coefficients and McNemar tests, respectively.ResultsIn the survey of 1571 adults, 176 ever hospital workers (327 occupations) with both self-reported and expert exposure assessments were studied. An underestimation of self-reported exposure was observed especially for formaldehyde (26.5% vs 32.7%, p=0.01), ammonia (7.4% vs 18.8%, p<0.0001), alcohol (64.9% vs 93.0%, p<0.0001) and quaternary ammonium components (16.6% vs 70.9%, p<0.0001), compared to expert assessment.ConclusionOccupational exposure to disinfecting/cleaning agents is common and high in hospitals. A large underestimation of self-reported exposure and a lack of knowledge of product components was observed. Our results show the relevance of expert assessment in epidemiological studies to limit measurement bias. This work underlines the need for health education programmes on the occupational risks induced by these types of products.
A Shell Disease in Lobsters (Homarus americanus) Caused by Chitinovorous Bacteria
Authors: Hess Ernest 
Published: April 2011

Chitinovorous bacteria have been isolated from lobsters (Homarus americanus) showing a peculiar shell disease. Cases are reported (1936) from ten widely separated localities in Cape Breton, Prince Edward Island and Magdalen islands. A regular epidemic occurred in a lobster pound at Yarmouth, N.S. All isolated strains attack strips of purified chitin in Benecke's saline medium in a characteristic manner.
Physical and Chemical Characteristics of Cultus Lake, British Columbia.
Authors: Ricker William E. 
Published: April 2011

Cultus lake is a rather small, fairly deep, clear lake of the western Cascade mountains, and is the home of one of the populations of Fraser river sockeye. The equable climate of the region is reflected in the low annual heat budget of the lake and its normal lack of an ice cover in winter, with continued complete or partial circulation of its water throughout that season. Judged by the low degree of hypolimnial oxygen consumption in summer, the lake is to be classed as distinctly oligotrophic. The oxygen content at all depths and seasons is sufficient for the respiration of salmonoid fishes. The water is moderately hard and slightly alkaline. Quantities of dissolved nitrates and phosphates in the water appear to be of the order characteristic of oligotrophic lakes. Silicates are present much in excess of the requirements of the lake's diatom populations. The number of adult sockeye returning to the lake in normal years is insufficient to add to its supply of nutritive salts in significant amount. Temperature observations and oxygen determinations, taken at frequent intervals for several years, have contributed to the knowledge of certain questions of general limnological interest. Such include (1) the manner in which the hypolimnion of a lake is warmed in summer; (2) the classification of the seasonal circulation periods in temperate lakes; and (3) the oxygen content of a lake at the close of vernal circulation, and its use as a standard from which to measure oxygen consumption throughout the summer.
Cytological identification of telotrisomic and double ditelosomic lines in Secale cereale cv. Heines Hellkorn by means of Giemsa C-banding patterns and crosses with wheat–rye addition lines
Authors: Zeller Friedrich J. , Cermeño Mari-Carmen , Friebe Bernd 
Published: April 2011

Seven telotrisomic lines (1RS, 1RL, 2RS, 2RL, 3RS acro, 5RS, and 6RS), two double monotelosomic, and two double ditelosomic lines of Secale cereale cv. Heines Hellkorn were analyzed by means of Giemsa C-banding techniques. In crosses with several wheat–rye chromosome addition lines, the telosomic chromosomes in double ditelosomic lines 1/23 and 3/23 were found to be homologous to chromosomes 1R and 2RL of cv. Imperial rye. The C-banding pattern observed for the telosomes in these lines was similar to that detected in the 1R and 2R telosomics of the corresponding telotrisomic lines. Key words: Secale cereale, telotrisomics, double ditelosomics, C-banding pattern.
Relationships between three measures of genetic distance and breeding behaviour in oats (Avena sativa L.)
Authors: Cowen N. M. , Frey K. J. 
Published: April 2011

Nine oat cultivars and experimental lines from four diverse germ plasm sources were crossed in a diallel mating design, without reciprocals. Heterosis for grain yield was evaluated in two experiments and 48 F2-derived lines from each of the 36 matings were evaluated for bundle weight, grain yield, straw yield, harvest index, and heading date in two experiments. The number of transgressive segregates per trait and generalized genetic variances were calculated for each mating. Euclidean distance between parents was calculated by using the first five principal components of the parental correlation matrix. The distance measures of W. D. Hanson and E. Casas (1968. Biometrics, 24: 867–880) and T. S. Cervantes, M. M. Goodman, E. Casas, and J. O. Rawlings (1978. Genetics, 90: 339–348) were calculated for each of two experiments. The relationships between the three distance measures and the three types of breeding behavior were examined via correlation and regression. Euclidean distance was negatively correlated with transgressive segregation and generalized genetic variances. Hanson and Casas' distance measure was positively correlated with transgressive segregation and generalized genetic variances. The distance measure of Cervantes et al. was negatively correlated with heterosis in one experiment. Regressions on the three distances measures, when significant, were linear. The single exception was the regression of heterosis on Euclidean distance, which had significant linear and quadratic coefficients and high R2. No distance measure was closely associated with all three types of breeding behavior. Using information from more than one measure improved the R2 value for polynomial regressions. Key words: oats, genetic distance, heterosis, generalized variances.
Metaphase I chiasmata in silver-stained cores of bivalents in grasshopper spermatocytes
Authors: Santos J. L. , Ciprés G. , Lacadena J. R. 
Published: April 2011

Chiasmata can clearly be observed in proteinaceous scaffold-like structures in condensed metaphase I bivalents of grasshopper spermatocytes by using a highly reproducible silver-staining procedure. Origin and significance of these structures are discussed and the possibility of analyzing several topics related with chiasma formation such as distribution, interference, terminalization, or terminal associations is pointed out. Key words: scaffold, chiasma, silver staining, terminalization, Chorthippus.
Host–parasite genome relationships in Acridid grasshoppers. I. Variation in the isoenzymes of the Caledia captiva species complex and in the gut bacterium Enterobacter cloacae
Authors: Colgan D. J. 
Published: April 2011

Isoenzymic variation was investigated in populations of the four recognized taxa of the Australian acridine Caledia captiva and in 110 isolates of the bacterium Enterobacter cloacae present in their guts. Four types of colony morphology, of which two were common, were discernible in these bacteria. All representatives of each type appeared to be very close to typical members of E. cloacae. The genetic diversity of the eight bacterial enzymes scored was very high, both overall and in respect of the two common morphological types. This diversity is consistent with selective neutrality and is too great to be explained by selective discrimination between genotypes. There was no compelling evidence for any interaction between the host and bacterial genotypes. The results thus argue against the possibility that the parasites are involved in a system of frequency dependent selection. There was also no evidence of an association of bacterial type with divergence between the taxa of the C. captiva complex. Key words: host–parasite, isoenzymes, grasshoppers, bacteria.
Highly repeated DNA and allozyme variation between sibling species: evidence for introgression
Authors: Arnold M. L. , Wilkinson P. , Shaw D. D. , Marchant A. D. , Contreras N. 
Published: April 2011

The Caledia captiva complex of grasshoppers includes two sibling species along with two subspecies. Two populations (Papuan Torresian and Daintree) representing the two sibling species were found to share six allozyme characters and a highly repeated DNA family not found in any of the other Caledia taxa. These two populations showed genic divergence that was equivalent to comparisons between the two subspecies from the complex. Sequenced, cloned repeats from the Papuan Torresian and Daintree taxa showed equivalent variation for both intra- and inter-specific comparisons. A phenetic clustering analysis did not separate the repeats from these two taxa into different clades. Furthermore, the overall genomic organization of the sequence family in the two species is very similar, although the repeats are cytologically dispersed in one form (Papuan Torresian) and clustered in the other form (Daintree). It is argued that the most likely evolutionary explanation for the observed pattern of variation in the allozymes and highly repeated DNA sequences between these types is introgressive hybridization. The possible consequences of such an event are discussed in light of the population genetics and distribution of the present day Caledia taxa. Key words: highly repeated DNA, Caledia, grasshopper, allozymes.