bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison of image registration based measures of regional lung ventilation from dynamic spiral CT with Xe‐CT
Authors: Ding Kai , Cao Kunlin , Fuld Matthew K. , Du Kaifang , Christensen Gary E. , Hoffman Eric A. , Reinhardt Joseph M. 
Published: July 2012

Purpose:Regional lung volume change as a function of lung inflation serves as an index of parenchymal and airway status as well as an index of regional ventilation and can be used to detect pathologic changes over time. In this paper, the authors propose a new regional measure of lung mechanics—the specific air volume change by corrected Jacobian. The authors compare this new measure, along with two existing registration based measures of lung ventilation, to a regional ventilation measurement derived from xenon‐CT (Xe‐CT) imaging.Methods:4DCT and Xe‐CT datasets from four adult sheep are used in this study. Nonlinear, 3D image registration is applied to register an image acquired near end inspiration to an image acquired near end expiration. Approximately 200 annotated anatomical points are used as landmarks to evaluate registration accuracy. Three different registration based measures of regional lung mechanics are derived and compared: the specific air volume change calculated from the Jacobian (SAJ); the specific air volume change calculated by the corrected Jacobian (SACJ); and the specific air volume change by intensity change (SAI). The authors show that the commonly used SAI measure can be derived from the direct SAJ measure by using the air‐tissue mixture model and assuming there is no tissue volume change between the end inspiration and end expiration datasets. All three ventilation measures are evaluated by comparing to Xe‐CT estimates of regional ventilation.Results:After registration, the mean registration error is on the order of 1 mm. For cubical regions of interest (ROIs) in cubes with size 20 mm × 20 mm × 20 mm, the SAJ and SACJ measures show significantly higher correlation (linear regression, averager2 = 0.75 and r2 = 0.82) with the Xe‐CT based measure of specific ventilation (sV) than the SAI measure. For ROIs in slabs along the ventral‐dorsal vertical direction with size of 150 mm × 8 mm × 40 mm, the SAJ, SACJ, and SAI all show high correlation (linear regression, average r2 = 0.88, r2 = 0.92, and r2 = 0.87) with the Xe‐CT based sV without significant differences when comparing between the three methods. The authors demonstrate a linear relationship between the difference of specific air volume change and difference of tissue volume in all four animals (linear regression, average r2 = 0.86).Conclusions:Given a deformation field by an image registration algorithm, significant differences between the SAJ, SACJ, and SAI measures were found at a regional level compared to the Xe‐CT sV in four sheep that were studied. The SACJ introduced here, provides better correlations with Xe‐CT based sV than the SAJ and SAI measures, thus providing an improved surrogate for regional ventilation.
Uncoupling of Substrate-Level Phosphorylation in Escherichia coli during Glucose-Limited Growth
Authors: Sharma Poonam , Hellingwerf Klaas J. , Teixeira de Mattos Maarten J. , Bekker Martijn 
Published: July 2012

ABSTRACT

The respiratory chain of
Escherichia coli
contains three different cytochrome oxidases. Whereas the cytochrome
bo
oxidase and the cytochrome
bd
-I oxidase are well characterized and have been shown to contribute to proton translocation, physiological data suggested a nonelectrogenic functioning of the cytochrome
bd
-II oxidase. Recently, however, this view was challenged by an
in vitro
biochemical analysis that showed that the activity of cytochrome
bd
-II oxidase does contribute to proton translocation with an H
+
/e
−
stoichiometry of 1. Here, we propose that this apparent discrepancy is due to the activities of two alternative catabolic pathways: the pyruvate oxidase pathway for acetate production and a pathway with methylglyoxal as an intermediate for the production of lactate. The ATP yields of these pathways are lower than those of the pathways that have so far always been assumed to catalyze the main catabolic flux under energy-limited growth conditions (i.e., pyruvate dehydrogenase and lactate dehydrogenase). Inclusion of these alternative pathways in the flux analysis of growing
E. coli
strains for the calculation of the catabolic ATP synthesis rate indicates an electrogenic function of the cytochrome
bd
-II oxidase, compatible with an H
+
/e
−
ratio of 1. This analysis shows for the first time the extent of bypassing of substrate-level phosphorylation in
E. coli
under energy-limited growth conditions.
Microbial Community Structure and Activity Linked to Contrasting Biogeochemical Gradients in Bog and Fen Environments of the Glacial Lake Agassiz Peatland
Authors: Lin X. , Green S. , Tfaily M. M. , Prakash O. , Konstantinidis K. T. , Corbett J. E. , Chanton J. P. , Cooper W. T. , Kostka J. E. 
Published: July 2012

ABSTRACT

The abundances, compositions, and activities of microbial communities were investigated at bog and fen sites in the Glacial Lake Agassiz Peatland of northwestern Minnesota. These sites contrast in the reactivity of dissolved organic matter (DOM) and the presence or absence of groundwater inputs. Microbial community composition was characterized using pyrosequencing and clone library construction of phylogenetic marker genes. Microbial distribution patterns were linked to pH, concentrations of dissolved organic carbon and nitrogen, C/N ratios, optical properties of DOM, and activities of laccase and peroxidase enzymes. Both bacterial and archaeal richness and rRNA gene abundance were >2 times higher on average in the fen than in the bog, in agreement with a higher pH, labile DOM content, and enhanced enzyme activities in the fen. Fungi were equivalent to an average of 1.4% of total prokaryotes in gene abundance assayed by quantitative PCR. Results revealed statistically distinct spatial patterns between bacterial and fungal communities. Fungal distribution did not covary with pH and DOM optical properties and was vertically stratified, with a prevalence of
Ascomycota
and
Basidiomycota
near the surface and much higher representation of
Zygomycota
in the subsurface. In contrast, bacterial community composition largely varied between environments, with the bog dominated by
Acidobacteria
(61% of total sequences), while the
Firmicutes
(52%) dominated in the fen. Acetoclastic
Methanosarcinales
showed a much higher relative abundance in the bog, in contrast to the dominance of diverse hydrogenotrophic methanogens in the fen. This is the first quantitative and compositional analysis of three microbial domains in peatlands and demonstrates that the microbial abundance, diversity, and activity parallel with the pronounced differences in environmental variables between bog and fen sites.
Identification of a Gene Involved in the Synthesis of a Dipeptidyl Peptidase IV Inhibitor in Aspergillus oryzae
Authors: Imamura Kazuhiko , Tsuyama Yoshihito , Hirata Terukage , Shiraishi Sumihiro , Sakamoto Kazutoshi , Yamada Osamu , Akita Osamu , Shimoi Hitoshi 
Published: July 2012

ABSTRACT

WYK-1 is a dipeptidyl peptidase IV inhibitor produced by
Aspergillus oryzae
strain AO-1. Because WYK-1 is an isoquinoline derivative consisting of three
l
-amino acids, we hypothesized that a nonribosomal peptide synthetase was involved in its biosynthesis. We identified 28 nonribosomal peptide synthetase genes in the sequenced genome of
A. oryzae
RIB40. These genes were also identified in AO-1. Among them, AO090001000009 (
wykN
) was specifically expressed under WYK-1-producing conditions in AO-1. Therefore, we constructed
wykN
gene disruptants of AO-1 after nonhomologous recombination was suppressed by RNA interference to promote homologous recombination. Our results demonstrated that the disruptants did not produce WYK-1. Furthermore, the expression patterns of 10 genes downstream of
wykN
were similar to the expression pattern of
wykN
under several conditions. Additionally, homology searches revealed that some of these genes were predicted to be involved in WYK-1 biosynthesis. Therefore, we propose that
wykN
and the 10 genes identified in this study constitute the WYK-1 biosynthetic gene cluster.
Molecular and Biochemical Analyses of the GH44 Module of CbMan5B/Cel44A, a Bifunctional Enzyme from the Hyperthermophilic Bacterium Caldicellulosiruptor bescii
Authors: Ye Libin , Su Xiaoyun , Schmitz George E. , Moon Young Hwan , Zhang Jing , Mackie Roderick I. , Cann Isaac K. O. 
Published: July 2012

ABSTRACT

A large polypeptide encoded in the genome of the thermophilic bacterium
Caldicellulosiruptor bescii
was determined to consist of two glycoside hydrolase (GH) modules separated by two carbohydrate-binding modules (CBMs). Based on the detection of mannanase and endoglucanase activities in the N-terminal GH5 and the C-terminal GH44 module, respectively, the protein was designated CbMan5B/Cel44A. A GH5 module with >99% identity from the same organism was characterized previously (X. Su, R. I. Mackie, and I. K. Cann, Appl. Environ. Microbiol.
78:
2230-2240, 2012); therefore, attention was focused on CbMan5A/Cel44A-TM2 (or TM2), which harbors the GH44 module and the two CBMs. On cellulosic substrates, TM2 had an optimal temperature and pH of 85ï¿½C and 5.0, respectively. Although the amino acid sequence of the GH44 module of TM2 was similar to those of other GH44 modules that hydrolyzed cello-oligosaccharides, cellulose, lichenan, and xyloglucan, it was unique that TM2 also displayed modest activity on mannose-configured substrates and xylan. The TM2 protein also degraded Avicel with higher specific activity than activities reported for its homologs. The GH44 catalytic module is composed of a TIM-like domain and a β-sandwich domain, which consists of one β-sheet at the N terminus and nine β-sheets at the C terminus. Deletion of one or more β-sheets from the β-sandwich domain resulted in insoluble proteins, suggesting that the β-sandwich domain is essential for proper folding of the polypeptide. Combining TM2 with three other endoglucanases from
C. bescii
led to modest synergistic activities during degradation of cellulose, and based on our results, we propose a model for cellulose hydrolysis and utilization by
C. bescii
.
The Mitochondrial Dnm1-Like Fission Component Is Required for
lga2
-Induced Mitophagy but Dispensable for Starvation-Induced Mitophagy in Ustilago maydis
Authors: Nieto-Jacobo Fernanda , Pasch Denise , Basse Christoph W. 
Published: July 2012

ABSTRACT

Selective elimination of mitochondria by autophagy (mitophagy) is a crucial developmental process to dispose of disintegrated or superflous organelles. However, little is known about underlying regulatory mechanisms. We have investigated mitophagy in response to conditional overexpression of the
a2
mating-type locus gene
lga2
, which encodes a small mitochondrial protein critically involved in uniparental mitochondrial DNA inheritance during sexual development of
Ustilago maydis
. In this study, we show that conditional overexpression of
lga2
efficiently triggers mitophagy that is dependent on
atg8
and
atg11
, consistent with selective autophagy.
lga2
-triggered mitophagy is preceded by mitochondrial dysfunction, including depletion of mitochondrial RNA transcripts, and is mechanistically distinct from starvation-induced mitophagy despite a common requirement for
atg11
. In particular,
lga2
-triggered mitophagy strongly depends on the mitochondrial fission factor Dnm1, but it is only slightly affected by
N
-acetylcysteine, which is an inhibitor of starvation-induced mitophagy. To further delineate the role of mitochondrial fission, we analyzed
lga2
effects in
Δfis1
mutants. This revealed that mitochondrial fragmentation was only attenuated and mitophagy was largely unaffected. In further support of a Fis1-independent role for Dnm1, mitochondrial association of green fluorescent protein-tagged Dnm1 as well as Dnm1-opposed mitochondrial fusion during sexual development were
fis1
independent. In conclusion, our results specify the role of the mitochondrial fission factor Dnm1 in mitophagy and uncover differences between mitophagy pathways in the same cellular system.
Complete Genome Sequence of the Endophytic Bacterium Burkholderia sp. Strain KJ006
Authors: Kwak Min-Jung , Song Ju Yeon , Kim Seon-Young , Jeong Haeyoung , Kang Sung Gyun , Kim Byung Kwon , Kwon Soon-Kyeong , Lee Choong Hoon , Yu Dong Su , Park Seung-Hwan , Kim Jihyun F. 
Published: July 2012

ABSTRACT

Endophytes live inside plant tissues without causing any harm and may even benefit plants. Here, we provide the high-quality genome sequence of
Burkholderia
sp. strain KJ006, an endophytic bacterium of rice with antifungal activity. The 6.6-Mb genome, consisting of three chromosomes and a single plasmid, contains genes related to plant growth promotion or degradation of aromatic compounds.
Complete Genome Sequence of the Hyperthermophilic Archaeon Pyrococcus sp. Strain ST04, Isolated from a Deep-Sea Hydrothermal Sulfide Chimney on the Juan de Fuca Ridge
Authors: Jung Jong-Hyun , Lee Ju-Hoon , Holden James F. , Seo Dong-Ho , Shin Hakdong , Kim Hae-Yeong , Kim Wooki , Ryu Sangryeol , Park Cheon-Seok 
Published: July 2012

ABSTRACT

Pyrococcus
sp. strain ST04 is a hyperthermophilic, anaerobic, and heterotrophic archaeon isolated from a deep-sea hydrothermal sulfide chimney on the Endeavour Segment of the Juan de Fuca Ridge in the northeastern Pacific Ocean. To further understand the distinct characteristics of this archaeon at the genome level (polysaccharide utilization at high temperature and ATP generation by a Na
+
gradient), the genome of strain ST04 was completely sequenced and analyzed. Here, we present the complete genome sequence analysis results of
Pyrococcus
sp. ST04 and report the major findings from the genome annotation, with a focus on its saccharolytic and metabolite production potential.
Draft Genome Sequence of Corynebacterium bovis DSM 20582, Which Causes Clinical Mastitis in Dairy Cows
Authors: Schröder Jasmin , Glaub Alina , Schneider Jessica , Trost Eva , Tauch Andreas 
Published: July 2012

ABSTRACT

Bovine mastitis represents the most economically important disease in dairy cows and can be caused by
Corynebacterium bovis
, a commensal in the bovine udder. The draft genome sequence provides insights into the adaptation of this bacterium to the bovine habitat and its lipolytic capabilities to utilize components of cow's milk.
Draft Genome Sequence of Staphylococcus saprophyticus subsp. saprophyticus M1-1, Isolated from the Gills of a Korean Rockfish, Sebastes schlegeli Hilgendorf, after High Hydrostatic Pressure Processing
Authors: Kim Bong-Soo , Kim Chong-Tai , Park Bang Heon , Kwon Sujin , Cho Yong-Jin , Kim Namsoo , Kim Chul-Jin , Chun Jongsik , Kwak Jangyul , Maeng Jin-Soo 
Published: July 2012

ABSTRACT

A bacterium designated M1-1 was isolated from the gills of a Korean rockfish,
Sebastes schlegeli
Hilgendorf, after high hydrostatic pressure processing. Studies of 16S rRNA phylogeny and comparative genomics demonstrated that the isolate belongs to
Staphylococcus saprophyticus
subsp.
saprophyticus
. Here, we report the draft genome sequence of
S. saprophyticus
subsp.
saprophyticus
M1-1 (KACC 16562).
Draft Genome Sequence of the Marine Actinomycete Streptomyces sulphureus L180, Isolated from Marine Sediment
Authors: Zhao Xinqing , Geng Xiang , Chen Chao , Chen Liangyu , Jiao Wence , Yang Chao 
Published: July 2012

ABSTRACT

Marine-derived actinobacteria are rich sources of valuable natural products and industrial enzymes for biotechnology applications. The marine-derived
Streptomyces sulphureus
strain L180 was isolated from the marine sediment in a sea cucumber farm at a depth of about 10 m in Dalian, China, and its 16S rRNA gene sequence was determined to have the highest identity to that of
Streptomyces sulphureus
NRRL B-1627
T
(99.65%). Here, we report the draft genome sequence of this strain.
Genome Sequence of Sphingobium indicum B90A, a Hexachlorocyclohexane-Degrading Bacterium
Authors: Anand Shailly , Sangwan Naseer , Lata Pushp , Kaur Jasvinder , Dua Ankita , Singh Amit Kumar , Verma Mansi , Kaur Jaspreet , Khurana Jitendra P. , Khurana Paramjit , Mathur Saloni , Lal Rup 
Published: July 2012

ABSTRACT

Sphingobium indicum
B90A, an efficient degrader of hexachlorocyclohexane (HCH) isomers, was isolated in 1990 from sugarcane rhizosphere soil in Cuttack, India. Here we report the draft genome sequence of this bacterium, which has now become a model system for understanding the genetics, biochemistry, and physiology of HCH degradation.
Draft Genome Sequence of Serratia marcescens Strain LCT-SM213
Authors: Wang Yajuan , Yuan Yanting , Zhou Lisha , Su Qingqing , Fang Xiangqun , Li Tianzhi , Wang Junfeng , Chang De , Su Longxiang , Xu Guogang , Guo Yinghua , Yang Ruifu , Liu Changting 
Published: July 2012

ABSTRACT

Serratia marcescens
is a species of Gram-negative, rod-shaped bacterium of the family
Enterobacteriaceae
.
S. marcescens
can cause nosocomial infections, particularly catheter-associated bacteremia, urinary tract infections, and wound infections. Here, we present the draft genome sequence of
Serratia marcescens
strain LCT-SM213, which was isolated from CGMCC 1.1857.
Genome Sequence of the Plant Growth-Promoting Bacterium Enterobacter cloacae GS1
Authors: Shankar Manoharan , Ponraj Paramasivan , Ilakiam Devaraj , Rajendhran Jeyaprakash , Gunasekaran Paramasamy 
Published: July 2012

ABSTRACT

Here, we present the genome sequence of
Enterobacter cloacae
GS1. This strain proficiently colonizes rice roots and promotes plant growth by improving plant nutrition. Analyses of the
E. cloacae
GS1 genome will throw light on the genetic factors involved in root colonization, growth promotion, and ecological success of this rhizobacterium.
The Complete Genome Sequence of Bacteriophage CP21 Reveals Modular Shuffling in Campylobacter Group II Phages
Authors: Hammerl Jens A. , Jäckel Claudia , Reetz Jochen , Hertwig Stefan 
Published: July 2012

ABSTRACT

Campylobacter
group II phages described so far share a high degree of sequence similarity. We report the 182,833-bp genomic sequence of the closely related group II phage CP21 and show that it has a completely different genomic organization. As in other group II phages, the CP21 genome is composed of large modules separated by long DNA repeat regions which obviously trigger recombination and modular shuffling.
Complete Genome Sequence of a Highly Pathogenic Porcine Reproductive and Respiratory Syndrome Virus Variant
Authors: Wang Chengbao , Zhao Qin , Liang Chao , Dang Lu , Ma Yuping , Gao Jiming , Li Qiongyi , Huang Baicheng , Kong Ning , Zhang Chong , Zhou En-Min 
Published: July 2012

ABSTRACT
Following the 2006 outbreaks of the highly pathogenic porcine reproductive and respiratory syndrome, the causative agent was identified as the highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV). To investigate whether the HP-PRRSV variant continues circulating and accelerating evolution, we sequenced and analyzed the complete genome of the identified HP-PRRSV field strain SD16. The sequence data indicate that the HP-PRRSV variant continues to prevail and accelerate evolution, especially in the nonstructural protein.
Observational follow-up study following two cohorts of children with severe pneumonia after discharge from day care clinic/hospital in Dhaka, Bangladesh
Authors: Ashraf Hasan , Alam Nur H , Chisti Mohammod Jobayer , Salam Mohammed Abdus , Ahmed Tahmeed , Gyr Niklaus 
Published: July 2012

ObjectivesTo compare the features of relapse, morbidity, mortality and re-hospitalisation following successful discharge after severe pneumonia in children between a day care group and a hospital group and to explore the predictors of failures during 3 months of follow-up.DesignAn observational study following two cohorts of children with severe pneumonia for 3 months after discharge from hospital/clinic.SettingDay care was provided at the Radda Clinic and hospital care at a hospital in Dhaka, Bangladesh.ParticipantsChildren aged 2–59 months with severe pneumonia attending the clinic/hospital who survived to discharge.InterventionNo intervention was done except providing some medications for minor illnesses, if indicated.Primary outcome measuresThe primary outcome measures were the proportion of successes and failures of day care at follow-up visits as determined by estimating the OR with 95% CI in comparison to hospital care.ResultsThe authors enrolled 360 children with a mean (SD) age of 8 (7) months, 81% were infants and 61% were men. The follow-up compliance dropped from 95% at first to 85% at sixth visit. The common morbidities during the follow-up period included cough (28%), fever (17%), diarrhoea (9%) and rapid breathing (7%). During the follow-up period, significantly more day care children (n=22 (OR 12.2 (95% CI 8.2–17.8))) required re-hospitalisation after completion of initial day care compared with initial hospital care group (n=11 (OR 6.1 (95% CI 3.4–10.6))). The predictors for failure were associated with tachycardia, tachypnoea and hypoxaemia on admission and prolonged duration of stay.ConclusionsThere are considerable morbidities in children discharged following treatment of severe pneumonia like cough, fever, rapid breathing and diarrhoea during 3-month period. The findings indicate the importance of follow-up for early detection of medical problems and their management to reduce the risk of death. Establishment of an effective community follow-up would be ideal to address the problem of ‘non-compliance with follow-up’.Trial registrationThe original randomised control trial comparing day care with hospital care was registered athttp://www.clinicaltrials.gov(identifierNCT00455468).
Rosmarinus officinalisL. essential oil and the related compound 1,8-cineole do not induce direct or cross-protection inListeria monocytogenesATCC 7644 cultivated in meat broth
Authors: Gomes Neto Nelson Justino , Luz Isabelle Silva , Honório Wanessa Gonçalves , Tavares Adassa Gama , de Souza Evandro Leite 
Published: July 2012

Listeria monocytogenes has the capability of adapting to 1 or more antimicrobial compounds or procedures applied by the food industry to control the growth and survival of microorganisms in foods. In this study, the effects of Rosmarinus officinalis essential oil (EO) and the related compound 1,8-cineole on the inhibition of the growth and survival of L. monocytogenes ATCC 7644 were determined. The ability of the R. officinalis EO and 1,8-cineole to induce direct and cross-protection of bacteria against various stresses (lactic acid, pH 5.2; NaCl, 3 g/100 mL; high temperature, 45 °C) was also determined. At all concentrations tested (minimum inhibitory concentration (MIC), ½ MIC, and ¼ MIC), both compounds inhibited the cell viability of L. monocytogenes over 120 min of exposure. Overnight exposure of L. monocytogenes to sublethal amounts of either the R. officinalis EO or 1,8-cineole in meat broth revealed no induction of direct or cross-protection against lactic acid, NaCl, or high temperature. Similarly, cells subjected to 24 h cycles of adaptation with increasing amounts (½ MIC to 2× MIC) of the EO and 1,8-cineole showed no increase in direct tolerance, as they were able to survive in growth medium containing up to ½ MIC of either substance. These results show the antimicrobial efficacy of R. officinalis EO and 1,8-cineole for use in systems, particularly as anti-L. monocytogenes compounds.