bluuebunny/crossref_metadata_2025_split huggingface dataset:
MicroFilament Analyzer, an image analysis tool for quantifying fibrillar orientation, reveals changes in microtubule organization during gravitropism
Authors: Jacques Eveline , Buytaert Jan , Wells Darren M. , Lewandowski Michal , Bennett Malcolm J. , Dirckx Joris , Verbelen Jean‐Pierre , Vissenberg Kris 
Published: March 2013

SummaryImage acquisition is an important step in the study of cytoskeleton organization. As visual interpretations and manual measurements of digital images are prone to errors and require a great amount of time, a freely available software package named MicroFilament Analyzer (MFA) was developed. The goal was to provide a tool that facilitates high‐throughput analysis to determine the orientation of filamentous structures on digital images in a more standardized, objective and repeatable way. Here, the rationale and applicability of the program is demonstrated by analyzing the microtubule patterns in epidermal cells of control and gravi‐stimulated Arabidopsis thaliana roots. Differential expansion of cells on either side of the root results in downward bending of the root tip. As cell expansion depends on the properties of the cell wall, this may imply a differential orientation of cellulose microfibrils. As cellulose deposition is orchestrated by cortical microtubules, the microtubule patterns were analyzed. The MFA program detects the filamentous structures on the image and identifies the main orientation(s) within individual cells. This revealed four distinguishable microtubule patterns in root epidermal cells. The analysis indicated that gravitropic stimulation and developmental age are both significant factors that determine microtubule orientation. Moreover, the data show that an altered microtubule pattern does not precede differential expansion. Other possible applications are also illustrated, including field emission scanning electron micrographs of cellulose microfibrils in plant cell walls and images of fluorescent actin.
Estimating the viscoelastic modulus of a thrombus using an ultrasonic shear‐wave approach
Authors: Huang Chih‐Chung , Chen Pay‐Yu , Shih Cho‐Chiang 
Published: March 2013

Purpose:Measurements of the viscoelastic properties of a thrombus can be used to assess whether blood clots are likely to become occlusive or to break apart and leak into the blood circulation and block smaller vessels. An accurate method for estimating both the shear elasticity and viscosity of a blood clotin vivo is still lacking, which prompted us to use a novel shear‐wave approach to measure the viscoelastic modulus of blood clots.Methods:The shear‐wave dispersion ultrasound vibrometry was used to measure both the elasticity and viscosity of blood clots. The experimental system was verified by measuring the viscoelastic modulus of phantoms containing gelatin at different concentrations. Blood‐clot experiments were carried out using porcine whole blood with hematocrits ranging from 3% to 40%. The measured values for both clots and gelatin phantoms were compared to those obtained using an embedded‐sphere method in order to validate the accuracy of the viscoelastic modulus estimations.Results:The shear elastic modulus increased from 406.9 ± 15.8 (mean ± SD) Pa for 3% gelatin to 1587.2 ± 28.9 Pa for 7% gelatin, while the viscosity increased from 0.12 ± 0.02 Pa s to 0.86 ± 0.05 Pa s, respectively. The shear modulus increased from 196.8 ± 58.4 Pa for 40%‐hematocrit clots to 641.4 ± 76.3 Pa for 3%‐hematocrit clots, while the viscosity increased from 0.29 ± 0.02 Pa s to 0.42 ± 0.01 Pa s, respectively.Conclusions:The results from the statistical analysis indicated that both the embedded‐sphere and shear‐wave approaches can provide accurate estimations of the shear elasticity for clots and gelatin phantoms. In contrast, the shear‐wave approach as well as other methods of rheological measurements does not provide accurate viscosity estimations for blood clots. However, the measured viscosity range of 0.29–0.42 Pa s is reasonable for blood clots.
First study of on‐treatment volumetric imaging during respiratory gated VMAT
Authors: Choi Kihwan , Xing Lei , Koong Albert , Li Ruijiang 
Published: March 2013

Purpose:To obtain on‐treatment volumetric patient anatomy during respiratory gated volumetric modulated arc therapy (VMAT).Methods:On‐board imaging device integrated with Linacs offers a viable tool for obtaining patient anatomy during radiation treatment delivery. In this study, the authors acquired beam‐level kV images during gated VMAT treatments using a Varian TrueBeam™STx Linac. These kV projection images are triggered by a respiratory gating signal and can be acquired immediately before treatment MV beam on at every breathing cycle during delivery. Because the kV images are acquired with an on‐board imaging device during a rotational arc therapy, they provide the patient anatomical information from many different angles or projection views (typically 20–40). To reconstruct the volumetric image representing patient anatomy during the VMAT treatment, the authors used a compressed sensing method with a fast first‐order optimization algorithm. The conventional FDK reconstruction was also used for comparison purposes. The method was tested on a dynamic anthropomorphic physical phantom as well as a lung patient.Results:The reconstructed volumetric images for a dynamic anthropomorphic physical phantom and a lung patient showed clearly visible soft‐tissue target as well as other anatomical structures, with the proposed compressed sensing‐based image reconstruction method. Compared with FDK, the compressed sensing method leads to a ∼two and threefold increase in contrast‐to‐noise ratio around the target area in the phantom and patient case, respectively.Conclusions:The proposed technique provides on‐treatment volumetric patient anatomy, with only a fraction (<10%) of the imaging dose used in conventional CBCT procedures. This anatomical information may be valuable for geometric verification and treatment guidance, and useful for verification of treatment dose delivery, accumulation, and adaptation in the future.
Identification of the Receptor-Binding Protein in Lytic Leuconostoc pseudomesenteroides Bacteriophages
Authors: Kot Witold , Hammer Karin , Neve Horst , Vogensen Finn K. 
Published: March 2013

ABSTRACT

Two phages, P793 and ΦLN04, sharing 80.1% nucleotide sequence identity but having different strains of
Leuconostoc pseudomesenteroides
as hosts, were selected for identification of the host determinant gene. Construction of chimeric phages leading to the expected switch in host range identified the host determinant genes as ORF21
P793
/ORF23
ΦLN04
. The genes are located in the tail structural module and have low sequence similarity at the distal end.
Loss of Culturability of Salmonella enterica subsp. enterica Serovar Typhimurium upon Cell-Cell Contact with Human Fecal Bacteria
Authors: Avendaño-Pérez Gaspar , Pin Carmen 
Published: March 2013

ABSTRACT

Loss of culturability of
Salmonella enterica
subsp.
enterica
serovar Typhimurium has been observed in mixed cultures with anaerobic fecal bacteria under conditions that allow local interaction between cells, such as cell contact. A reduction of a population of culturable
S.
Typhimurium on the order of ∼10
4
to 10
5
CFU/ml was observed in batch anaerobic mixed cultures with fecal samples from different human donors. Culturability was not affected either in supernatants collected at several times from fecal cultures, when separated from fecal bacteria by a membrane of 0.45-μm pore size, or when in contact with inactivated fecal bacterial cells. Loss of culturability kinetics was characterized by a sharp reduction of several logarithmic units followed by a pronounced tail. A mathematical model was developed to describe the rate of loss of culturability as a function of the frequency of encounters between populations and the probability of inactivation after encounter. The model term
F
(
S
·
F
)
1/2
quantifies the effect of the concentration of both populations, fecal bacteria (
F
) and
S.
Typhimurium (
S
), on the loss of culturability of
S.
Typhimurium by cell contact with fecal bacteria. When the value of
F
(
S
·
F
)
1/2
decreased below ca. 10
15
(CFU/ml)
2
, the frequency of encounters sharply decreased, leading to the deceleration of the inactivation rate and to the tailing off of the
S.
Typhimurium population. The probability of inactivation after encounter,
P
, was constant, with an estimated value of ∼10
−5
for all data sets.
P
might be characteristic of the mechanism of growth inhibition after a cell encounter.
3′ Truncation of the
GPD1
Promoter in Saccharomyces cerevisiae for Improved Ethanol Yield and Productivity
Authors: Ding Wen-Tao , Zhang Guo-Chang , Liu Jing-Jing 
Published: March 2013

ABSTRACT

Glycerol is a major by-product in bioethanol fermentation by the yeast
Saccharomyces cerevisiae
, and decreasing glycerol formation for increased ethanol yield has been a major research effort in the bioethanol field. A new strategy has been used in the present study for reduced glycerol formation and improved ethanol fermentation performance by finely modulating the expression of
GPD1
in the KAM15 strain (
fps1
Δ
pPGK1-GLT1 gpd2
Δ). The
GPD1
promoter was serially truncated from the 3′ end by 20 bp to result in a different expression strength of
GPD1
. The two engineered promoters carrying 60- and 80-bp truncations exhibited reduced promoter strength but unaffected osmostress response. These two promoters were integrated into the KAM15 strain, generating strains LE34U and LE35U, respectively. The transcription levels of LE34U and LE35U were 37.77 to 45.12% and 21.34 to 24.15% of that of KAM15U, respectively, depending on osmotic stress imposed by various glucose concentrations. In very high gravity (VHG) fermentation, the levels of glycerol for LE34U and LE35U were reduced by 15.81% and 30.66%, respectively, compared to KAM15U. The yield and final concentration of ethanol for LE35U were 3.46% and 0.33% higher, respectively, than those of KAM15U. However, fermentation rate and ethanol productivity for LE35U were reduced. On the other hand, the ethanol yield and final concentration for LE34U were enhanced by 2.28% and 2.32%, respectively, compared to those of KAM15U. In addition, a 2.31% increase in ethanol productivity was observed for LE34U compared to KAM15U. These results verified the feasibility of our strategy for yeast strain development.
“Candidatus Midichloriaceae” fam. nov. (Rickettsiales), an Ecologically Widespread Clade of Intracellular Alphaproteobacteria
Authors: Montagna Matteo , Sassera Davide , Epis Sara , Bazzocchi Chiara , Vannini Claudia , Lo Nathan , Sacchi Luciano , Fukatsu Takema , Petroni Giulio , Bandi Claudio 
Published: March 2013

ABSTRACT

“
Candidatus
Midichloria mitochondrii” is an intramitochondrial bacterium of the order
Rickettsiales
associated with the sheep tick
Ixodes ricinus
. Bacteria phylogenetically related to “
Ca
. Midichloria mitochondrii” (midichloria and like organisms [MALOs]) have been shown to be associated with a wide range of hosts, from amoebae to a variety of animals, including humans. Despite numerous studies focused on specific members of the MALO group, no comprehensive phylogenetic and statistical analyses have so far been performed on the group as a whole. Here, we present a multidisciplinary investigation based on 16S rRNA gene sequences using both phylogenetic and statistical methods, thereby analyzing MALOs in the overall framework of the
Rickettsiales
. This study revealed that (i) MALOs form a monophyletic group; (ii) the MALO group is structured into distinct subgroups, verifying current genera as significant evolutionary units and identifying several subclades that could represent novel genera; (iii) the MALO group ranks at the level of described
Rickettsiales
families, leading to the proposal of the novel family “
Candidatus
Midichloriaceae.” In addition, based on the phylogenetic trees generated, we present an evolutionary scenario to interpret the distribution and life history transitions of these microorganisms associated with highly divergent eukaryotic hosts: we suggest that aquatic/environmental protista have acted as evolutionary reservoirs for members of this novel family, from which one or more lineages with the capacity of infecting metazoa have evolved.
Schizosaccharomyces pombe Disaggregation Machinery Chaperones Support Saccharomyces cerevisiae Growth and Prion Propagation
Authors: Reidy Michael , Sharma Ruchika , Masison Daniel C. 
Published: March 2013

ABSTRACT

Hsp100 chaperones protect microorganisms and plants from environmental stress by cooperating with Hsp70 and its nucleotide exchange factor (NEF) and Hsp40 cochaperones to resolubilize proteins from aggregates. The
Saccharomyces cerevisiae
Hsp104 (Sc-Hsp104)-based disaggregation machinery also is essential for replication of amyloid-based prions.
Escherichia coli
ClpB can substitute for Hsp104 to propagate [
PSI
+
] prions in yeast, but only if
E. coli
DnaK and GrpE (Hsp70 and NEF) are coexpressed. Here, we tested if the reported inability of
Schizosaccharomyces pombe
Hsp104 (Sp-Hsp104) to support [
PSI
+
] propagation was due to similar species-specific chaperone requirements and find that Sp-Hsp104 alone supported propagation of three different yeast prions. Sp-Hsp70 and Sp-Fes1p (NEF) likewise functioned in place of their
Sa. cerevisiae
counterparts. Thus, chaperones of these long-diverged species possess conserved activities that function in processes essential for both cell growth and prion propagation, suggesting
Sc. pombe
can propagate its own prions. We show that curing by Hsp104 overexpression and inactivation can be distinguished and confirm the observation that, unlike Sc-Hsp104, Sp-Hsp104 cannot cure yeast of [
PSI
+
] when it is overexpressed. These results are consistent with a view that mechanisms underlying prion replication and elimination are distinct.
Complete Genome Sequence of
Escherichia
Phage ADB-2 Isolated from a Fecal Sample of Poultry
Authors: Bhensdadia D. V. , Bhimani H. D. , Rawal C. M. , Kothari V. V. , Raval V. H. , Kothari C. R. , Patel A. B. , Bhatt V. D. , Parmar N. R. , Sajnani M. R. , Koringa P. G. , Joshi C. G. , Singh S. P. , Kothari R. K. 
Published: March 2013

ABSTRACT

Escherichia
phage ADB-2 was isolated from a chicken fecal sample. It is a virulent phage and shows effective inhibition of
Escherichia coli
strains. Here we announce the completely sequenced genome of
Escherichia
phage ADB-2, and major findings from its annotation are described.
Complete Genome Sequence of Mycobacterium bovis BCG Korea, the Korean Vaccine Strain for Substantial Production
Authors: Joung Sun Myung , Jeon Sung Joo , Lim Young Ju , Lim Jong-Sung , Choi Beom-Soon , Choi Ik-Young , Yu Jeong Hee , Na Kyung-In , Cho En-Hi , Shin Sang-Sook , Park Young Kil , Kim Chang-Ki , Kim Hee-Jin , Ryoo Sung Weon 
Published: March 2013

ABSTRACT

Mycobacterium bovis
bacillus Calmette-Guérin (BCG) is the only vaccine available against tuberculosis, and the strains used worldwide represent a family of daughter strains with distinct genotypic characteristics. Here, we report the complete genome sequence of
M. bovis
BCG Korea, the strain that will be actually used in Korea for vaccine production.
Whole-Genome Sequences of an Aerobic Anoxygenic Phototroph,
Blastomonas
sp. Strain AAP53, Isolated from a Freshwater Desert Lake in Inner Mongolia, China
Authors: Zeng Yonghui , Koblížek Michal , Feng Fuying , Liu Yapeng , Wu Zaohe , Jian Jichang 
Published: March 2013

ABSTRACT

Blastomonas
is a strictly aerobic bacteriochlorophyll
a
-producing genus within the alpha-4
Proteobacteria
. Here we report the first genome sequence from this genus. The draft genome of
Blastomonas
sp. strain AAP53 contains a split photosynthesis gene cluster and two gene clusters encoding a flagellar system. Genes for the autotrophic CO
2
fixation pathway are absent.
Draft Genome of the Marine Gammaproteobacterium Halomonas titanicae
Authors: Sánchez-Porro Cristina , de la Haba Rafael R. , Cruz-Hernández Norge , González Juan M. , Reyes-Guirao Cristina , Navarro-Sampedro Laura , Carballo Modesto , Ventosa Antonio 
Published: March 2013

ABSTRACT

Halomonas titanicae
strain BH1 is a heterotrophic, aerobic marine bacterium which was isolated from rusticles of the RMS Titanic wreck. Here we report the draft genome sequence of this halophilic gammaproteobacterium.
DsbA and MgrB Regulate
steA
Expression through the Two-Component System PhoQ/PhoP in Salmonella enterica
Authors: Cardenal-Muñoz Elena , Ramos-Morales Francisco 
Published: March 2013

ABSTRACT

SteA is a protein that can be translocated into host cells through the two virulence-related type III secretion systems that are present in
Salmonella enterica
. We used the T-POP system to carry out general screens for loci that exhibited activation or repression of a
steA
::
lacZ
fusion. These screens identified the histidine kinase PhoQ and the response regulator PhoP as positive regulators of
steA
. Transcription of this gene is σ70 dependent, and the promoter of
steA
contains a PhoP-binding site that mediates direct regulation by PhoP. Our screens also detected MgrB (also known as YobG) as a negative regulator of the expression of
steA
. Disruption of the gene encoding the periplasmic disulfide oxidoreductase DsbA or addition of the reducing agent dithiothreitol increases transcription of
steA
. The effects of MgrB and DsbA on
steA
are mediated by PhoP. These results suggest that the cellular redox status is a factor contributing to regulation of
steA
and, probably, other virulence genes regulated by the PhoQ/PhoP two-component system.
Genomic Reconstruction of the Transcriptional Regulatory Network in Bacillus subtilis
Authors: Leyn Semen A. , Kazanov Marat D. , Sernova Natalia V. , Ermakova Ekaterina O. , Novichkov Pavel S. , Rodionov Dmitry A. 
Published: March 2013

ABSTRACT

The adaptation of microorganisms to their environment is controlled by complex transcriptional regulatory networks (TRNs), which are still only partially understood even for model species. Genome scale annotation of regulatory features of genes and TRN reconstruction are challenging tasks of microbial genomics. We used the knowledge-driven comparative-genomics approach implemented in the RegPredict Web server to infer TRN in the model Gram-positive bacterium
Bacillus subtilis
and 10 related
Bacillales
species. For transcription factor (TF) regulons, we combined the available information from the DBTBS database and the literature with bioinformatics tools, allowing inference of TF binding sites (TFBSs), comparative analysis of the genomic context of predicted TFBSs, functional assignment of target genes, and effector prediction. For RNA regulons, we used known RNA regulatory motifs collected in the Rfam database to scan genomes and analyze the genomic context of new RNA sites. The inferred TRN in
B. subtilis
comprises regulons for 129 TFs and 24 regulatory RNA families. First, we analyzed 66 TF regulons with previously known TFBSs in
B. subtilis
and projected them to other
Bacillales
genomes, resulting in refinement of TFBS motifs and identification of novel regulon members. Second, we inferred motifs and described regulons for 28 experimentally studied TFs with previously unknown TFBSs. Third, we discovered novel motifs and reconstructed regulons for 36 previously uncharacterized TFs. The inferred collection of regulons is available in the RegPrecise database (
http://regprecise.lbl.gov/
) and can be used in genetic experiments, metabolic modeling, and evolutionary analysis.
Archaeal DNA Polymerase D but Not DNA Polymerase B Is Required for Genome Replication in Thermococcus kodakarensis
Authors: Čuboňová Lubomira , Richardson Tomas , Burkhart Brett W. , Kelman Zvi , Connolly Bernard A. , Reeve John N. , Santangelo Thomas J. 
Published: March 2013

ABSTRACT

Three evolutionarily distinct families of replicative DNA polymerases, designated polymerase B (Pol B), Pol C, and Pol D, have been identified. Members of the Pol B family are present in all three domains of life, whereas Pol C exists only in
Bacteria
and Pol D exists only in
Archaea
. Pol B enzymes replicate eukaryotic chromosomal DNA, and as members of the Pol B family are present in all
Archaea
, it has been assumed that Pol B enzymes also replicate archaeal genomes. Here we report the construction of
Thermococcus kodakarensis
strains with mutations that delete or inactivate key functions of Pol B.
T. kodakarensis
strains lacking Pol B had no detectable loss in viability and no growth defects or changes in spontaneous mutation frequency but had increased sensitivity to UV irradiation. In contrast, we were unable to introduce mutations that inactivated either of the genes encoding the two subunits of Pol D. The results reported establish that Pol D is sufficient for viability and genome replication in
T. kodakarensis
and argue that Pol D rather than Pol B is likely the replicative DNA polymerase in this archaeon. The majority of
Archaea
contain Pol D, and, as discussed, if Pol D is the predominant replicative polymerase in
Archaea
, this profoundly impacts hypotheses for the origin(s), evolution, and distribution of the different DNA replication enzymes and systems now employed in the three domains of life.
Controlling Practitioner–patient Relationships in Acupuncture Trials: A Systematic Review and Meta-Regression
Authors: Prady Stephanie L , Burch Jane , Crouch Simon , MacPherson Hugh 
Published: March 2013

Background In trials, ‘therapist intensive’ complex interventions are typically delivered over time, during which a relationship between the practitioner and participant may develop. Such relationships are sometimes criticised as obscuring any ‘true’ treatment effect. Limiting interactions is one strategy that might be used to try to control for the effect of a therapeutic relationship. Objectives We conducted systematic review into the rationale, methods and effects of constraining relationships in controlled trials and cohort studies of acupuncture, including studies published before 2008 with an update citation search in 2010. Methods We searched six databases without keyword restrictions. Meta-analysis and meta-regression were used to explore the effect of relationship constraint on pain outcomes. Results Eighty-one of 785 (10.3%) trials reported constraining relationships. Most did not state the reason for constraint, describe the nature of the limitation, provide information on how the constrained relationship was monitored or note protocol adherence. Where a reason was reported, this was primarily to maintain participant blinding, rarely was it stated that the constraint was to control the therapeutic relationship. We found no evidence of an effect of constraint on pain outcomes (percentage heterogeneity explained, p=0.89). These results were robust to variation in trial quality and design. Conclusions Acupuncture trials appear to be constrained mostly to try to prevent participant unblinding to their allocated treatment, not to control the therapeutic relationship. The apparent lack of monitoring and negligible effects on pain outcomes of the included trials indicate the need for more high-quality randomised controlled trials investigating the effect of constraint.