bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Growing Season, but Not the Farming System, Is a Food Safety Risk Determinant for Leafy Greens in the Mid-Atlantic Region of the United States
Authors: Marine Sasha C. , Pagadala Sivaranjani , Wang Fei , Pahl Donna M. , Melendez Meredith V. , Kline Wesley L. , Oni Ruth A. , Walsh Christopher S. , Everts Kathryne L. , Buchanan Robert L. , Micallef Shirley A. 
Published: January 2015

ABSTRACT

Small- and medium-size farms in the mid-Atlantic region of the United States use varied agricultural practices to produce leafy greens during spring and fall, but the impact of preharvest practices on food safety risk remains unclear. To assess farm-level risk factors, bacterial indicators,
Salmonella enterica
, and Shiga toxin-producing
Escherichia coli
(STEC) from 32 organic and conventional farms were analyzed. A total of 577 leafy greens, irrigation water, compost, field soil, and pond sediment samples were collected.
Salmonella
was recovered from 2.2% of leafy greens (
n
= 369) and 7.7% of sediment (
n
= 13) samples. There was an association between
Salmonella
recovery and growing season (fall versus spring) (
P
= 0.006) but not farming system (organic or conventional) (
P
= 0.920) or region (
P
= 0.991). No STEC was isolated. In all, 10% of samples were positive for
E. coli
: 6% of leafy greens, 18% of irrigation water, 10% of soil, 38% of sediment, and 27% of compost samples. Farming system was not a significant factor for levels of
E. coli
or aerobic mesophiles on leafy greens but was a significant factor for total coliforms (TC) (
P
< 0.001), with higher counts from organic farm samples. Growing season was a factor for aerobic mesophiles on leafy greens (
P
= 0.004), with higher levels in fall than in spring. Water source was a factor for all indicator bacteria (
P
< 0.001), and end-of-line groundwater had marginally higher TC counts than source samples (
P
= 0.059). Overall, the data suggest that seasonal events, weather conditions, and proximity of compost piles might be important factors contributing to microbial contamination on farms growing leafy greens.
Reassessment of the Transhydrogenase/Malate Shunt Pathway in Clostridium thermocellum ATCC 27405 through Kinetic Characterization of Malic Enzyme and Malate Dehydrogenase
Authors: Taillefer M. , Rydzak T. , Levin D. B. , Oresnik I. J. , Sparling R. 
Published: January 2015

ABSTRACT

Clostridium thermocellum
produces ethanol as one of its major end products from direct fermentation of cellulosic biomass. Therefore, it is viewed as an attractive model for the production of biofuels via consolidated bioprocessing. However, a better understanding of the metabolic pathways, along with their putative regulation, could lead to improved strategies for increasing the production of ethanol. In the absence of an annotated pyruvate kinase in the genome, alternate means of generating pyruvate have been sought. Previous proteomic and transcriptomic work detected high levels of a malate dehydrogenase and malic enzyme, which may be used as part of a malate shunt for the generation of pyruvate from phosphoenolpyruvate. The purification and characterization of the malate dehydrogenase and malic enzyme are described in order to elucidate their putative roles in malate shunt and their potential role in
C. thermocellum
metabolism. The malate dehydrogenase catalyzed the reduction of oxaloacetate to malate utilizing NADH or NADPH with a
k
cat
of 45.8 s
−1
or 14.9 s
−1
, respectively, resulting in a 12-fold increase in catalytic efficiency when using NADH over NADPH. The malic enzyme displayed reversible malate decarboxylation activity with a
k
cat
of 520.8 s
−1
. The malic enzyme used NADP
+
as a cofactor along with NH
4
+
and Mn
2+
as activators. Pyrophosphate was found to be a potent inhibitor of malic enzyme activity, with a

K
i

of 0.036 mM. We propose a putative regulatory mechanism of the malate shunt by pyrophosphate and NH
4
+
based on the characterization of the malate dehydrogenase and malic enzyme.
Phylogeny of Intestinal Ciliates, Including Charonina ventriculi, and Comparison of Microscopy and 18S rRNA Gene Pyrosequencing for Rumen Ciliate Community Structure Analysis
Authors: Kittelmann Sandra , Devente Savannah R. , Kirk Michelle R. , Seedorf Henning , Dehority Burk A. , Janssen Peter H. 
Published: January 2015

ABSTRACT

The development of high-throughput methods, such as the construction of 18S rRNA gene clone or pyrosequencing libraries, has allowed evaluation of ciliate community composition in hundreds of samples from the rumen and other intestinal habitats. However, several genera of mammalian intestinal ciliates have been described based only on morphological features and, to date, have not been identified using molecular methods. Here, we isolated single cells of one of the smallest but widely distributed intestinal ciliates,
Charonina ventriculi
, and sequenced its 18S rRNA gene. We verified the sequence in a full-cycle rRNA approach using fluorescence
in situ
hybridization and thereby assigned an 18S rRNA gene sequence to this species previously known only by its morphology. Based on its full-length 18S rRNA gene sequence,
Charonina ventriculi
was positioned within the phylogeny of intestinal ciliates in the subclass Trichostomatia. The taxonomic framework derived from this phylogeny was used for taxonomic assignment of trichostome ciliate 18S rRNA gene sequence data stemming from high-throughput amplicon pyrosequencing of rumen-derived DNA samples. The 18S rRNA gene-based ciliate community structure was compared to that obtained from microscopic counts using the same samples. Both methods allowed identification of dominant members of the ciliate communities and classification of the rumen ciliate community into one of the types first described by Eadie in 1962. Notably, each method is associated with advantages and disadvantages. Microscopy is a highly accurate method for evaluation of total numbers or relative abundances of different ciliate genera in a sample, while 18S rRNA gene pyrosequencing represents a valuable alternative for comparison of ciliate community structure in a large number of samples from different animals or treatment groups.
Methanobactin from Methylocystis sp. Strain SB2 Affects Gene Expression and Methane Monooxygenase Activity in Methylosinus trichosporium OB3b
Authors: Farhan Ul-Haque Muhammad , Kalidass Bhagyalakshmi , Vorobev Alexey , Baral Bipin S. , DiSpirito Alan A. , Semrau Jeremy D. 
Published: January 2015

ABSTRACT

Methanotrophs can express a cytoplasmic (soluble) methane monooxygenase (sMMO) or membrane-bound (particulate) methane monooxygenase (pMMO). Expression of these MMOs is strongly regulated by the availability of copper. Many methanotrophs have been found to synthesize a novel compound, methanobactin (Mb), that is responsible for the uptake of copper, and methanobactin produced by
Methylosinus trichosporium
OB3b plays a key role in controlling expression of MMO genes in this strain. As all known forms of methanobactin are structurally similar, it was hypothesized that methanobactin from one methanotroph may alter gene expression in another. When
Methylosinus trichosporium
OB3b was grown in the presence of 1 μM CuCl
2
, expression of
mmoX
, encoding a subunit of the hydroxylase component of sMMO, was very low.
mmoX
expression increased, however, when methanobactin from
Methylocystis
sp. strain SB2 (SB2-Mb) was added, as did whole-cell sMMO activity, but there was no significant change in the amount of copper associated with
M. trichosporium
OB3b. If
M. trichosporium
OB3b was grown in the absence of CuCl
2
, the
mmoX
expression level was high but decreased by several orders of magnitude if copper prebound to SB2-Mb (Cu-SB2-Mb) was added, and biomass-associated copper was increased. Exposure of
Methylosinus trichosporium
OB3b to SB2-Mb had no effect on expression of
mbnA
, encoding the polypeptide precursor of methanobactin in either the presence or absence of CuCl
2
.
mbnA
expression, however, was reduced when Cu-SB2-Mb was added in both the absence and presence of CuCl
2
. These data suggest that methanobactin acts as a general signaling molecule in methanotrophs and that methanobactin “piracy” may be commonplace.
Multilocus Sequence Typing of Leuconostoc gelidum subsp. gasicomitatum, a Psychrotrophic Lactic Acid Bacterium Causing Spoilage of Packaged Perishable Foods
Authors: Rahkila Riitta , Johansson Per , Säde Elina , Paulin Lars , Auvinen Petri , Björkroth Johanna 
Published: January 2015

ABSTRACT

Leuconostoc gelidum
subsp.
gasicomitatum
is a psychrotrophic lactic acid bacterium (LAB) that causes spoilage of a variety of modified-atmosphere-packaged (MAP) cold-stored food products. During the past 10 years, this spoilage organism has been increasingly reported in MAP meat and vegetable products in northern Europe. In the present study, the population structure within 252
L. gelidum
subsp.
gasicomitatum
strains was determined based on a novel multilocus sequence-typing (MLST) scheme employing seven housekeeping genes. These strains had been isolated from meat and vegetable sources over a time span of 15 years, and all 68 previously detected pulsed-field gel electrophoresis (PFGE) genotypes were represented. A total of 46 sequence types (STs) were identified, with a majority of the strains (>60%) belonging to three major STs, which were grouped into three clonal complexes (CCs) and 17 singletons by Global Optimal eBURST (goeBURST). The results by Bayesian analysis of population structure (BAPS) mostly correlated with the grouping by goeBURST. Admixture analysis by BAPS indicated a very low level of exchange of genetic material between the subpopulations. Niche specificity was observed within the subpopulations: CC1 and BAPS cluster 1 consisted mostly of strains from a variety of MAP meats, whereas vegetable strains grouped together with strains from MAP poultry within CC2 and BAPS cluster 2. The MLST scheme presented in this study provides a shareable and continuously growing sequence database enabling global comparison of strains associated with spoilage cases. This will further advance our understanding of the microbial ecology of this industrially important LAB.
Fungal Communities Respond to Long-Term CO
2
Elevation by Community Reassembly
Authors: Tu Qichao , Yuan Mengting , He Zhili , Deng Ye , Xue Kai , Wu Liyou , Hobbie Sarah E. , Reich Peter B. , Zhou Jizhong 
Published: January 2015

ABSTRACT

Fungal communities play a major role as decomposers in the Earth's ecosystems. Their community-level responses to elevated CO
2
(eCO
2
), one of the major global change factors impacting ecosystems, are not well understood. Using 28S rRNA gene amplicon sequencing and co-occurrence ecological network approaches, we analyzed the response of soil fungal communities in the BioCON (biodiversity, CO
2
, and N deposition) experimental site in Minnesota, USA, in which a grassland ecosystem has been exposed to eCO
2
for 12 years. Long-term eCO
2
did not significantly change the overall fungal community structure and species richness, but significantly increased community evenness and diversity. The relative abundances of 119 operational taxonomic units (OTU; ∼27% of the total captured sequences) were changed significantly. Significantly changed OTU under eCO
2
were associated with decreased overall relative abundance of Ascomycota, but increased relative abundance of Basidiomycota. Co-occurrence ecological network analysis indicated that eCO
2
increased fungal community network complexity, as evidenced by higher intermodular and intramodular connectivity and shorter geodesic distance. In contrast, decreased connections for dominant fungal species were observed in the eCO
2
network. Community reassembly of unrelated fungal species into highly connected dense modules was observed. Such changes in the co-occurrence network topology were significantly associated with altered soil and plant properties under eCO
2
, especially with increased plant biomass and NH
4
+
availability. This study provided novel insights into how eCO
2
shapes soil fungal communities in grassland ecosystems.
Transfer of Plasmid DNA to Clinical Coagulase-Negative Staphylococcal Pathogens by Using a Unique Bacteriophage
Authors: Winstel Volker , Kühner Petra , Krismer Bernhard , Peschel Andreas , Rohde Holger 
Published: January 2015

ABSTRACT

Genetic manipulation of emerging bacterial pathogens, such as coagulase-negative staphylococci (CoNS), is a major hurdle in clinical and basic microbiological research. Strong genetic barriers, such as restriction modification systems or clustered regularly interspaced short palindromic repeats (CRISPR), usually interfere with available techniques for DNA transformation and therefore complicate manipulation of CoNS or render it impossible. Thus, current knowledge of pathogenicity and virulence determinants of CoNS is very limited. Here, a rapid, efficient, and highly reliable technique is presented to transfer plasmid DNA essential for genetic engineering to important CoNS pathogens from a unique
Staphylococcus aureus
strain via a specific
S. aureus
bacteriophage, Φ187. Even strains refractory to electroporation can be transduced by this technique once donor and recipient strains share similar Φ187 receptor properties. As a proof of principle, this technique was used to delete the alternative transcription factor sigma B (SigB) via allelic replacement in nasal and clinical
Staphylococcus epidermidis
isolates at high efficiencies. The described approach will allow the genetic manipulation of a wide range of CoNS pathogens and might inspire research activities to manipulate other important pathogens in a similar fashion.
The ADP/ATP Carrier and Its Relationship to Oxidative Phosphorylation in Ancestral Protist Trypanosoma brucei
Authors: Gnipová Anna , Šubrtová Karolína , Panicucci Brian , Horváth Anton , Lukeš Julius , Zíková Alena 
Published: January 2015

ABSTRACT

The highly conserved ADP/ATP carrier (AAC) is a key energetic link between the mitochondrial (mt) and cytosolic compartments of all aerobic eukaryotic cells, as it exchanges the ATP generated inside the organelle for the cytosolic ADP.
Trypanosoma brucei
, a parasitic protist of medical and veterinary importance, possesses a single functional AAC protein (TbAAC) that is related to the human and yeast ADP/ATP carriers. However, unlike previous studies performed with these model organisms, this study showed that TbAAC is most likely not a stable component of either the respiratory supercomplex III+IV or the ATP synthasome but rather functions as a physically separate entity in this highly diverged eukaryote. Therefore, TbAAC RNA interference (RNAi) ablation in the insect stage of
T. brucei
does not impair the activity or arrangement of the respiratory chain complexes. Nevertheless, RNAi silencing of TbAAC caused a severe growth defect that coincides with a significant reduction of mt ATP synthesis by both substrate and oxidative phosphorylation. Furthermore, TbAAC downregulation resulted in a decreased level of cytosolic ATP, a higher mt membrane potential, an elevated amount of reactive oxygen species, and a reduced consumption of oxygen in the mitochondria. Interestingly, while TbAAC has previously been demonstrated to serve as the sole ADP/ATP carrier for ADP influx into the mitochondria, our data suggest that a second carrier for ATP influx may be present and active in the
T. brucei
mitochondrion. Overall, this study provides more insight into the delicate balance of the functional relationship between TbAAC and the oxidative phosphorylation (OXPHOS) pathway in an early diverged eukaryote.
The psychiatric inpatient physical health assessment sheet (PIPHAS): a useful tool to improve the speed, efficiency, and documentation of physical examination in new psychiatric inpatients
Authors: Pettipher Alexander , Ovens Richard 
Published: January 2015

AbstractThere is increased morbidity and mortality among patients suffering from mental illness. This is believed to be multi-factorial. Poor access to healthcare, the stigma of mental illness, reduced clinic attendance, lifestyle factors, and side effects of medications are cited as possible contributing factors. It is therefore vital to perform a physical examination to identify previously undiagnosed conditions during the admission of a psychiatric inpatient. The Royal College of Psychiatrists recommends that all patients admitted to a psychiatric hospital should receive a full physical examination on admission, or within twenty-four hours of admission.A snapshot audit was carried out at Prospect Park Hospital in Reading, which highlighted that The Royal College of Psychiatrist’s recommendation, along with Trust guidelines regarding physical examination were not being met, with only 78 out of 111 patients (70.3%) undergoing an examination during their admission. In addition to this, examinations were often poorly documented and not covering all examination domains. A psychiatric inpatient physical health assessment sheet (PIPHAS) was designed and introduced, providing a quick and standardised approach to the documentation of a physical examination. After the intervention was put into practice, its impact was assessed by performing a retrospective review of the admission clerking notes of the next 100 admissions to Prospect Park Hospital.Following the introduction of the PIPHAS form there was an increase in the number of patients undergoing physical examination on admission to hospital (75 out of 100 patients, 75%). There was also an increase in the thorough documentation of all examination domains (e.g. respiratory examination) for patients that had a completed PIPHAS form scanned within their medical records.This quality improvement project demonstrates that the PIPHAS form is a useful tool to improve the speed, efficiency, and documentation of a thorough physical examination in new psychiatric inpatients.
Predictive Utility of the Changes in Matrix Metalloproteinase‐2 in the Early Phase for Left Ventricular Reverse Remodeling After an Acute Myocardial Infarction
Authors: Morishita Tetsuji , Uzui Hiroyasu , Mitsuke Yasuhiko , Arakawa Kenichi , Amaya Naoki , Kaseno Kenichi , Ishida Kentaro , Nakaya Reiko , Lee Jong‐Dae , Tada Hiroshi 
Published: January 2015

Background

The relationship between the serum levels of matrix metalloproteinase (
MMP
) and tissue inhibitors of
MMP
(
TIMP
) and left ventricular (
LV
) reverse remodeling (
LV
‐
RR
) after an acute myocardial infarction (
AMI
) has not been sufficiently examined.

Methods and Results

In 25 patients with successful reperfusion after an
AMI
and 15 normal control subjects, the serum
MMP
‐2 and
TIMP
‐2 levels were measured on days 1, 2, 3, and 7 and at 1 and 6 months after the
AMI
onset.
LV
‐
RR
was defined as a >15% decrease in the
LV
end‐systolic volume index at 6 months after the
AMI
. The
MMP
‐2 level on day 1 and
TIMP
‐2 levels throughout the study period were comparable between the patients with and without
LV
‐
RR
. The
MMP
‐2 on day 7 (
P
<0.05) and the changes in the
MMP
‐2 from day 1 to day 7 (∆
MMP
‐2;
P
<0.01) were lower in patients with than in those without
LV
‐
RR
. The ∆
MMP
‐2 was strongly correlated with the changes in the
LV
volume and ejection fraction from 1 month to 6 months after the
AMI
. The ∆
MMP
‐2 value of <−158.5 ng/mL predicted
LV
‐
RR
with a high accuracy (91.7% sensitivity and 76.9% specificity; area under the curve=0.82).

Conclusions

Changes in
MMP
‐2 are associated with
LV
‐
RR
after an
AMI
. The Δ
MMP
‐2 might be a useful predictor of subsequent
LV
‐
RR
.
The In-between Generation. Immigrants and the Problem of a Dual Sense of Belonging
Authors: Bielenin-Lenczowska Karolina 
Published: January 2015

The In-between Generation. Immigrants and the Problem of a Dual Sense of BelongingThe aim of this paper is an anthropological analysis of three individual biographies of Macedonian-speaking Muslims migrants in Italy. An author focuses on the generation called by her in-between generation. It means young people who migrated from Macedonia with their parents at the early age. They have studied or already completed their education in Italy, they speak Italian fluently and most of their friends are Italian. However, they are still speak Macedonian at home, visit their country of origin every year and are aware of their strong belonging to the Macedonian-speaking Muslim group. Therefore, they should constantly negotiate between traditional values of their parents, and their own patterns of life. The significant issues and tensions regard religious practices, daily habits like food and dress, and – that is most sensitive – gender relations. Pokolenie pomiędzy. Imigranci a problem podwójnej przynależnościCelem artykułu jest antropologiczna analiza biografii trojga macedońskojęzycznych muzułmanów, należących do grupy imigrantów we Włoszech. Autorka skupia się na młodych ludziach, którzy na wczesnym etapie życia wyemigrowali z Macedonii z rodzicami. W literaturze nazywa się ich „pokoleniem 1,5”, podczas gdy w omawianych badaniach wybrano termin „pokolenie pomiędzy”; ponieważ rozmówcy jako imigranci znajdują się między pierwszym a drugim pokoleniem imigracyjnym, są zawieszeni pomiędzy wartościami i ideami kraju pochodzenia i kraju przyjmującego, pomiędzy dzieciństwem i dorosłością. Studiowali lub ukończyli edukację we Włoszech, mówią płynnie po włosku, a większość ich przyjaciół to Włoszki/Włosi. Jednak wciąż mówią po macedońsku w domu, co roku odwiedzają kraj pochodzenia i mają silną świadomość przynależności do grupy macedońskojęzycznych muzułmanów. Z tego względu wciąż muszą prowadzić negocjacje między tradycyjnymi wartościami rodziców a własnymi wzorami życia. Znaczący problem i źródło konfliktów stanowią praktyki religijne, elementy kultury codzienności, takie jak ubiór czy pożywienie, oraz – co najbardziej drażliwe – relacje genderowe.
The Russian Cinema of the Dissolution
Authors: Roman Katarzyna , Rawski Tomasz 
Published: January 2015

The Russian Cinema of the DissolutionThe paper takes the issue of Russian reckoning cinema after 1989. This current can be defined as comprising the films which try to lay the foundations of a new narrative about the Soviet Union (alternative to the dominant narrative). The authors reflect on the specificity of the filmmakers’ critical attitude towards the previous system. The story of the break-up of the Soviet Union turns to be a story of the great catastrophe – the tragedy of the whole society, abandoned by hypocritical intelligentsia and deceived by political elites. Rosyjskie kino rozpaduTekst podejmuje problematykę rosyjskiego kina rozliczeniowego po 1989 roku – słabo widocznego nurtu próbującego stworzyć zręby nowej narracji o Związku Radzieckim, która mogłaby stanowić alternatywę wobec narracji dominującej. Stanowi próbę namysłu nad specyfiką krytyki poprzedniego systemu przeprowadzaną przez twórców tego nurtu. Opowieść o rozpadzie Związku Radzieckiego okazuje się tu opowieścią o wielkiej katastrofie – tragedii całego społeczeństwa, opuszczonego przez obłudną inteligencję i oszukanego przez elity polityczne.