bluuebunny/crossref_metadata_2025_split huggingface dataset:
Contrasting Patterns of Species Richness and Composition of Solitary Wasps and Bees (Insecta: Hymenoptera) According to Land‐use
Authors: Batista Matos Michela C. , Sousa‐Souto Leandro , Almeida Ruanno S. , Teodoro Adenir V. 
Published: May 2012

AbstractSeveral species of arthropods inhabiting forest fragments interact with managed areas. The importance of such areas to biodiversity conservation, however, is not well established. Communities of solitary wasps and bees (Insecta: Hymenoptera) play a key role in agroecosystem functioning and they have been used in studies of biodiversity assessment in different land‐use types. We aimed to assess patterns of species richness and composition of solitary wasps and bees over a 1‐yr period in a gradient of decreasing land‐use intensity formed by pastures, alley croppings, young fallows, and old fallows using trap nests. Old fallows had the highest species richness of wasps and bees, harboring all bee species and 86 percent of wasp species occurring in the region, while the remaining land‐uses had similar species richness. Vegetation structure (tree richness) and relative humidity explained most of the variance for the species richness of wasps. For bees, however, there was no influence of environmental factors on the community among land‐use types, indicating better adaptability of this group to environmental variations related to land‐use. The composition of solitary wasp communities (but not those of bees) differed among land‐use types, and the occurrence of rare species in most cases was restricted to old fallow sites. In conclusion, the community of solitary wasps and bees is contingent on land‐use, with solitary wasps more sensitive to anthropized areas. For both groups, less anthropized areas harbor a greater richness and number of rare species while more intensively managed land‐use types harbor higher abundances.
Effect of Moisture, Lipids, and Select Amino Acid Blocking Agents on the Formation and Stability of Metastable Radicals in Powdered Soy Proteins
Authors: Boatright W.L. , Lei Q. , Jahan M.S. 
Published: May 2012

Abstract:  Incremental increases in the moisture content of powdered soy protein products from 4.4% to 13.4% produced an inverse effect on the ability of soy proteins to maintain metastable free radicals. The corresponding reduction in electron paramagnetic resonance signal was not due to dielectric loss in the range of moisture contents examined. Subsequent evaluations of various treatments were conducted after drying soy proteins with molecular sieve to a water activity below 0.085 in order to minimize the influence from variations in moisture. Isolated soy protein (ISP) samples, prepared with “defatted flour” that had been further extracted with chloroform/methanol (2 : 1), had a 96% reduction in total lipids compared to the control ISP samples. The initial rate of radical accumulation in the “reduced‐lipid” ISP for the first 3 wk was not significantly different from the initial rate of radical increases in the control ISP. After 3 wk, radical accumulation in the “reduced‐lipid” ISP continued to increase, but at a rate that was less than the control. These findings indicate that the initial reactions contributing to the formation of metastable radicals in the powdered ISP are not strongly dependent on associated lipids. Blocking sulfhydryl groups during ISP preparation with N‐ethylmaleimide did not significantly slow the rate of radical accumulation compared to the control ISP. Blocking arginine residues in ISP samples with phenylglyoxal caused an increased rate of radical accumulation for the first 4 wk.Practical Application:  Levels of metastable radicals in powdered soy protein products typically range from 10 to 100 times greater than the free radicals in other food protein sources. This current research examines various compositional and treatment parameters that might be used to minimize the content of free radicals in foods containing soy proteins.
Dissociation of dysfunctional breathing and odour intolerance among adults in a general‐population study
Authors: Bonde Ellen , Andersson Eva , Brisman Jonas , Eklöf Mats , Ringsberg Karin C. , Torén Kjell 
Published: May 2012

AbstractBackground:  Many patients present with a mixture of respiratory problems such as shortness of breath, heavy breathing, coughing and odour intolerance. If these patients are diagnosed as asthma, it might sometimes be a false diagnosis. Concepts such as sensory hyperreactivity, hyperventilation, asthma‐like symptoms, odour intolerance and dysfunctional breathing are used to refer to these patients. Non‐respiratory symptoms such as headache, fatigue and bloating are sometimes also part of the clinical picture. Our aim was to use factor analysis to increase our understanding of breathing‐related symptoms in a general‐population frame.Methods:  A respiratory questionnaire was answered by 10 108 subjects in a general‐population sample. Items aiming to identify individuals with breathing‐related symptoms and asthma were included. We used factor analysis with Varimax rotation to extract discriminatory components (i.e. groups of symptoms), based on the questionnaire items. The aim was to find groups of items (factors) as distinct as possible, still allowing overlap and showing the importance of each item in the separated factor.Results:  Five distinct factors were identified in the factor analysis, representing dysfunctional breathing, odour intolerance, asthma, bronchitis and a group with mixed symptoms, respectively. These five factors explained 55% of the variance.Conclusions:  Based on our findings, we conclude that non‐asthmatic breathing‐related symptoms may be separated into at least two categories in a general population, odour intolerance and dysfunctional breathing. These two categories seem to be two distinct groups of subjects with breathing‐related symptoms and may represent different clinical entities separated from asthma and bronchitis.Please cite this paper as: Bonde E, Andersson E, Brisman J, Eklöf M, Ringsberg KC and Torén K. Dissociation of dysfunctional breathing and odour intolerance among adults in a general‐population study. Clin Respir J 2013; 7: 176–182.
Assessing the potential of wildfires as a sustainable bioenergy opportunity
Authors: Verón Santiago R. , Jobbágy Esteban G. , Di Bella Carlos M. , Paruelo José M. , Jackson Robert B. 
Published: May 2012

AbstractAs the environmental and economic consequences of fossil‐fuel use become clear, land is increasingly targeted as a source of bioenergy. We explore the potential for generating electricity from biomass vulnerable to fires as an ecologic and socioeconomic opportunity that can reduce the risk of greenhouse gas generation from wildfires and help to create incentives to preserve natural and seminatural vegetation and prevent its conversion to agriculture, including biofuel crops. On the basis of a global analysis of the energy generation and spatial distribution of fires, we show that between 2003 and 2010, global fires consumed ~8300 ± 592 PJ yr−1 of energy, equivalent to ~36–44% of the global electricity consumption in 2008 and >100% national consumption in 57 countries. Forests/woodlands, cultivated areas, shrublands, and grasslands contributed 53%, 19%, 16%, and 3.5% of the global energy released by fires. Although many agroecological, socioeconomic, and engineering challenges need to be overcome before diverting the energy lost in fires into more useable forms, done cautiously it could reconcile habitat preservation with economic yields in natural systems.
Metabolite Profiling Identifies a Key Role for Glycine in Rapid Cancer Cell Proliferation
Authors: Jain Mohit , Nilsson Roland , Sharma Sonia , Madhusudhan Nikhil , Kitami Toshimori , Souza Amanda L. , Kafri Ran , Kirschner Marc W. , Clish Clary B. , Mootha Vamsi K. 
Published: May 2012

More Glycine, PleaseTo better characterize metabolic properties of cancer cells,Jainet al.(p.1040; see the Perspective byTomita and Kami) measured systematically the concentrations of hundreds of metabolites in cell culture medium in which 60 different cancer cell lines were growing. The fastest growing cancer cells tended to consume glycine, whereas more slowly growing cells excreted some glycine. The rapidly growing cancer cells appeared to need glycine for synthesis of purine nucleotides required for continued synthesis of DNA. Interfering with glycine metabolism slowed growth of the rapidly proliferating cancer cells. Thus, an increased dependence on glycine by rapidly growing cancer cells could potentially provide a target for therapeutic intervention.
Genetically Modified Strains of Ralstonia eutropha H16 with β-Ketothiolase Gene Deletions for Production of Copolyesters with Defined 3-Hydroxyvaleric Acid Contents
Authors: Lindenkamp Nicole , Volodina Elena , Steinbüchel Alexander 
Published: May 2012

ABSTRACT

β-Ketothiolases catalyze the first step of poly(3-hydroxybutyrate) [poly(3HB)] biosynthesis in bacteria by condensation of two acetyl coenzyme A (acetyl-CoA) molecules to acetoacetyl-CoA and also take part in the degradation of fatty acids. During growth on propionate or valerate,
Ralstonia eutropha
H16 produces the copolymer poly(3-hydroxybutyrate-
co
-3-hydroxyvalerate) [poly(3HB-
co
-3HV)]. In
R. eutropha
, 15 β-ketothiolase homologues exist. The synthesis of 3-hydroxybutyryl-CoA (3HB-CoA) could be significantly reduced in an 8-fold mutant (Lindenkamp et al., Appl. Environ. Microbiol. 76:5373–5382, 2010). In this study, a 9-fold mutant deficient in nine β-ketothiolase gene homologues (
phaA
,
bktB
, H16_A1713, H16_B1771, H16_A1528, H16_B0381, H16_B1369, H16_A0170, and
pcaF
) was generated. In order to examine the polyhydroxyalkanoate production capacity when short- or long-chain and even- or odd-chain-length fatty acids were provided as carbon sources, the growth and storage behavior of several mutants from the previous study and the newly generated 9-fold mutant were analyzed. Propionate, valerate, octanoate, undecanoic acid, or oleate was chosen as the sole carbon source. On octanoate, no significant differences in growth or storage behavior were observed between wild-type
R. eutropha
and the mutants. In contrast, during the growth on oleate of a multiple mutant lacking
phaA
,
bktB
, and H16_A0170, diminished poly(3HB) accumulation occurred. Surprisingly, the amount of accumulated poly(3HB) in the multiple mutants grown on gluconate differed; it was much lower than that on oleate. The β-ketothiolase activity toward acetoacetyl-CoA in H16Δ
phaA
and all the multiple mutants remained 10-fold lower than the activity of the wild type, regardless of which carbon source, oleate or gluconate, was employed. During growth on valerate as a sole carbon source, the 9-fold mutant accumulated almost a poly(3-hydroxyvalerate) [poly(3HV)] homopolyester with 99 mol% 3HV constituents.
Engineering of a Xylose Metabolic Pathway in Rhodococcus Strains
Authors: Xiong Xiaochao , Wang Xi , Chen Shulin 
Published: May 2012

ABSTRACTThe two metabolically versatile actinobacteriaRhodococcus opacusPD630 andR. jostiiRHA1 can efficiently convert diverse organic substrates into neutral lipids mainly consisting of triacylglycerol (TAG), the precursor of energy-rich hydrocarbon. Neither, however, is able to utilize xylose, the important component present in lignocellulosic biomass, as the carbon source for growth and lipid accumulation. In order to broaden their substrate utilization range, the metabolic pathway ofd-xylose utilization was introduced into these two strains. This was accomplished by heterogenous expression of two well-selected genes,xylA, encoding xylose isomerase, andxylB, encoding xylulokinase fromStreptomyces lividansTK23, under the control of thetacpromoter with anEscherichia coli-Rhodococcusshuttle vector. The recombinantR. jostiiRHA1 bearingxylAcould grow on xylose as the sole carbon source, and additional expression ofxylBfurther improved the biomass yield. The recombinant could consume both glucose and xylose in the sugar mixture, although xylose metabolism was still affected by the presence of glucose. The xylose metabolic pathway was also introduced into the high-lipid-producing strainR. opacusPD630 by expression ofxylAandxylB. Under nitrogen-limited conditions, the fatty acid composition was determined, and lipid produced from xylose by recombinants ofR. jostiiRHA1 andR. opacusPD630 carryingxylAandxylBrepresented up to 52.5% and 68.3% of the cell dry weight (CDW), respectively. This work demonstrates that it is feasible to produce lipid from the sugars, including xylose, derived from renewable feedstock by genetic modification of rhodococcus strains.
Evaluation of Commonly Used Serological Tests for Detection of Coxiella burnetii Antibodies in Well-Defined Acute and Follow-Up Sera
Authors: Wegdam-Blans M. C. A. , Wielders C. C. H. , Meekelenkamp J. , Korbeeck J. M. , Herremans T. , Tjhie H. T. , Bijlmer H. A. , Koopmans M. P. G. , Schneeberger P. M. 
Published: May 2012

ABSTRACTIn this study, we comparedCoxiella burnetiiIgG phase I, IgG phase II, and IgM phase II detection among a commercially available enzyme-linked immunosorbent assay (ELISA) (Virion/Serion), an indirect fluorescent antibody test (IFAT) (Focus Diagnostics), and a complement fixation test (CFT) (Virion/Serion). For this, we used a unique collection of acute- and convalescent-phase sera from 126 patients with acute Q fever diagnosed by positiveCoxiella burnetiiPCR of blood. We were able to establish a reliable date of onset of disease, since DNA is detectable within 2 weeks after the start of symptoms. In acute samples, att= 0, IFAT demonstrated IgM phase II antibodies in significantly more sera than did ELISA (31.8% versus 19.7%), although the portion of solitary IgM phase II was equal for IFAT and for ELISA (18.2% and 16.7%, respectively). Twelve months after the diagnosis of acute Q fever, 83.5% and 62.2% of the sera were still positive for IgM phase II with IFAT and ELISA, respectively. At 12 months IFAT IgG phase II showed the slowest decline. Therefore, definitive serological evidence of acute Q fever cannot be based on a single serum sample in areas of epidemicity and should involve measurement of both IgM and IgG antibodies in paired serum. Based on IgG phase II antibody detection in paired samples (at 0 and 3 months) from 62 patients, IFAT confirmed more cases than ELISA and CFT, but the differences were not statically significant (100% for IFAT, 95.2% for ELISA, and 96.8% for CFT). This study demonstrated that the three serological tests are equally effective in diagnosing acute Q fever within 3 months of start of symptoms. In follow-up sera, more IgG antibodies were detected by IFAT than by ELISA or CFT, making IFAT more suitable for prevaccination screening programs.
A Lysine-Rich Region within Fungal BAG Domain-Containing Proteins Mediates a Novel Association with Ribosomes
Authors: Verghese Jacob , Morano Kevin A. 
Published: May 2012

ABSTRACT

Heat shock protein 70 (Hsp70) is a highly conserved molecular chaperone that assists in the folding of nascent chains and the repair of unfolded proteins through iterative cycles of ATP binding, hydrolysis, and nucleotide exchange tightly coupled to polypeptide binding and release. Cochaperones, including nucleotide exchange factors (NEFs), modulate the rate of ADP/ATP exchange and serve to recruit Hsp70 to distinct processes or locations. Among three nonrelated cytosolic NEFs in
Saccharomyces cerevisiae
, the Bag-1 homolog
SNL1
is unique in being tethered to the endoplasmic reticulum (ER) membrane. We demonstrate here a novel physical association between Snl1 and the intact ribosome. This interaction is both independent of and concurrent with binding to Hsp70 and is not dependent on membrane localization. The ribosome binding site is identified as a short lysine-rich motif within the amino terminus of the Snl1 BAG domain distinct from the Hsp70 interaction region. Additionally, we demonstrate a ribosome association with the
Candida albicans
Snl1 homolog and localize this putative NEF to a perinuclear/ER membrane, suggesting functional conservation in fungal BAG domain-containing proteins. We therefore propose that the Snl1 family of NEFs serves a previously unknown role in fungal protein biogenesis based on the coincident recruitment of ribosomes and Hsp70 to the ER membrane.
Novel
l
-Cysteine-Dependent Maleylpyruvate Isomerase in the Gentisate Pathway of Paenibacillus sp. Strain NyZ101
Authors: Liu Ting-Ting , Zhou Ning-Yi 
Published: May 2012

ABSTRACT

Glutathione- and mycothiol-dependent maleylpyruvate isomerases are known to be involved, respectively, in gentisate catabolism in Gram-negative and high G+C Gram-positive strains. In the present study, a low-G+C Gram-positive
Paenibacillus
sp. strain, NyZ101, was isolated and shown to degrade 3-hydroxybenzoate via gentisate. A 6.5-kb fragment containing a conserved region of gentisate 1,2-dioxygenase genes was cloned and sequenced, and four genes (
bagKLIX
) were shown to encode the enzymes involved in the catabolism to central metabolites of 3-hydroxybenzoate via gentisate. The Bag proteins share moderate identities with the reported enzymes in the 3-hydroxybenzoate catabolism, except BagL that had no obvious homology with any functionally characterized proteins. Recombinant BagL was purified to homogeneity as a His-tagged protein and likely a dimer by gel filtration. BagL was demonstrated to be a novel thiol-dependent maleylpyruvate isomerase catalyzing the isomerization of maleylpyruvate to fumarylpyruvate with
l
-cysteine, cysteinylglycine, or glutathione, as its cofactor. The

K
m

values of these three thiols for BagL were 15.5, 8.4, and 552 μM, respectively. Since cysteine and coenzyme A were reported to be abundant in low-G+C Gram-positive strains, BagL should utilize
l
-cysteine as its physiological cofactor
in vivo
. The addition of Ni
2+
increased BagL activity, and site-directed mutagenesis experiments indicated that three conserved histidines in BagL were associated with binding to Ni
2+
ion and were necessary for its enzyme activity. BagL is the first characterized
l
-cysteine-dependent catabolic enzyme in microbial metabolism and is likely a new and distinct member of DinB family, with a four-helix-bundle topology, as deduced by sequence analysis and homology modeling.
MS_RHII-RSD, a Dual-Function RNase HII-(p)ppGpp Synthetase from Mycobacterium smegmatis
Authors: Murdeshwar Maya S. , Chatterji Dipankar 
Published: May 2012

ABSTRACT

In the noninfectious soil saprophyte
Mycobacterium smegmatis
, intracellular levels of the stress alarmones guanosine tetraphosphate and guanosine pentaphosphate, together termed (p)ppGpp, are regulated by the enzyme Rel
Msm
. This enzyme consists of a single, bifunctional polypeptide chain that is capable of both synthesizing and hydrolyzing (p)ppGpp. The

rel
Msm

knockout strain of
M. smegmatis
(Δ

rel
Msm

) is expected to show a (p)ppGpp null [(p)ppGpp
0
] phenotype. Contrary to this expectation, the strain is capable of synthesizing (p)ppGpp
in vivo
. In this study, we identify and functionally characterize the open reading frame (ORF), MSMEG_5849, that encodes a second functional (p)ppGpp synthetase in
M. smegmatis
. In addition to (p)ppGpp synthesis, the 567-amino-acid-long protein encoded by this gene is capable of hydrolyzing RNA·DNA hybrids and bears similarity to the conventional RNase HII enzymes. We have classified this protein as actRel
Msm
in accordance with the recent nomenclature proposed and have named it MS_RHII-RSD, indicating the two enzymatic activities present [RHII, RNase HII domain, originally identified as
d
omain of
u
nknown
f
unction 429 (DUF429), and RSD, RelA_SpoT nucleotidyl transferase domain, the SYNTH domain responsible for (p)ppGpp synthesis activity]. MS_RHII-RSD is expressed and is constitutively active
in vivo
and behaves like a monofunctional (p)ppGpp synthetase
in vitro
. The occurrence of the RNase HII and (p)ppGpp synthetase domains together on the same polypeptide chain is suggestive of an
in vivo
role for this novel protein as a link connecting the essential life processes of DNA replication, repair, and transcription to the highly conserved stress survival pathway, the stringent response.
The
bhuQ
Gene Encodes a Heme Oxygenase That Contributes to the Ability of Brucella abortus 2308 To Use Heme as an Iron Source and Is Regulated by Irr
Authors: Ojeda Jenifer F. , Martinson David A. , Menscher Evan A. , Roop R. Martin 
Published: May 2012

ABSTRACT

The
Brucella
BhuQ protein is a homolog of the
Bradyrhizobium japonicum
heme oxygenases HmuD and HmuQ. To determine if this protein plays a role in the ability of
Brucella abortus
2308 to use heme as an iron source, an isogenic
bhuQ
mutant was constructed and its phenotype evaluated. Although the
Brucella abortus bhuQ
mutant DCO1 did not exhibit a defect in its capacity to use heme as an iron source or evidence of increased heme toxicity
in vitro
, this mutant produced increased levels of siderophore in response to iron deprivation compared to 2308. Introduction of a
bhuQ
mutation into the
B. abortus dhbC
mutant BHB2 (which cannot produce siderophores) resulted in a severe growth defect in the
dhbC bhuQ
double mutant JFO1 during cultivation under iron-restricted conditions, which could be rescued by the addition of FeCl
3
, but not heme, to the growth medium. The
bhuQ
gene is cotranscribed with the gene encoding the iron-responsive regulator RirA, and both of these genes are repressed by the other major iron-responsive regulator in the alphaproteobacteria, Irr. The results of these studies suggest that
B. abortus
2308 has at least one other heme oxygenase that works in concert with BhuQ to allow this strain to efficiently use heme as an iron source. The genetic organization of the
rirA-bhuQ
operon also provides the basis for the proposition that BhuQ may perform a previously unrecognized function by allowing the transcriptional regulator RirA to recognize heme as an iron source.
Evaluation of the New NucliSENS EasyQ KPC Test for Rapid Detection of Klebsiella pneumoniae Carbapenemase Genes (
bla
KPC
)
Authors: Spanu Teresa , Fiori Barbara , D'Inzeo Tiziana , Canu Giulia , Campoli Serena , Giani Tommaso , Palucci Ivana , Tumbarello Mario , Sanguinetti Maurizio , Rossolini Gian Maria 
Published: May 2012

ABSTRACT

KPC-type carbapenemases are emerging in
Klebsiella pneumoniae
and other Gram-negative pathogens worldwide. Rapid and sensitive detection of these resistance determinants has become relevant to clinical management and infection control. We evaluated the bioMérieux EasyQ real-time PCR assay for
bla
KPC
detection with 300 members of the
Enterobacteriaceae
, including 29 control strains producing known carbapenemases and 271 nonreplicate clinical isolates. The EasyQ assay correctly detected all of the 111 isolates harboring
bla
KPC
genes, with no false positives, and results were available within 2 h.