bluuebunny/crossref_metadata_2025 huggingface dataset:
Hind foot lameness: Results of magnetic resonance imaging in 38 horses (2001–2011)
Authors: Biggi M. , Dyson S.
Published: October 2012

Reasons for performing study

The distribution of lesions detected using magnetic resonance imaging (MRI) of hind feet has not been reported.

Objective

To evaluate type and distribution of lesions detected usingMRIin hind feet of lame horses and to compare the findings with those reported in front feet; to document follow‐up information.

Methods

Horses were selected if hindlimb lameness was abolished by plantar nerve blocks performed at the base of the proximal sesamoid bones. Magnetic resonance images were acquired using either a low‐field or a high‐field magnet, and all images were evaluated retrospectively by both authors. A primary diagnosis was defined as the most likely cause of lameness, based also on clinical findings and results of other imaging techniques. If ≥3 structures were equally affected, the horse was classified as having multiple injuries. Follow‐up information was collected by telephone questionnaire; outcome was classified as return to former level of athletic function, working at a lower level or retired.

Results

Thirty‐eight horses were included. Primary collateral sesamoidean ligament (CSL) injury was identified in 9 horses. Nine horses had multiple injuries, 8 had primary bone pathology, 5 had collateral desmopathy of the distal interphalangeal joint, one had primary deep digital flexor tendonitis, 2 had navicular bone pathology and 4 had lesions involving other structures within the foot. Seven horses were subjected to euthanasia shortly after diagnosis; 6 as a result of poor prognosis and one as a result of post anaesthetic complications, 4 of which had primary bone lesions, 2 multiple lesions and one distal interphalangeal joint pathology. Follow‐up information was available for 24 horses. Eleven horses returned to previous performance and 2 to a lower level of performance; 9 horses were retired because of recurrent lameness. Five of 8 horses withCSLinjury returned to previous performance and 2 to a lower level.

Conclusions and potential relevance

Collateral sesamoidean ligament injury and primary bone pathology are commonly observed onMRIexamination of hind feet, and the prognosis is reasonable.
The association of anthropometric indices in adolescence with the occurrence of the metabolic syndrome in early adulthood: Tehran Lipid and Glucose Study (TLGS)
Authors: Barzin M. , Asghari G. , Hosseinpanah F. , Mirmiran P. , Azizi F.
Published: October 2012

What is already known about this subject

Little is known about the predictive ability of anthropometric indices in adolescence for prediction of early adulthood metabolic syndrome (MetS).

There are controversies about the predictive power of body mass index (BMI) vs. waist circumference (WC) for prediction of MetS in late adolescence; some of the studies did not support the need to measure WC in mid‐adolescence, in addition to BMI; on the other hand, some other studies proposed either similar predictability or superiority of WC to identify MetS in late adolescence.

What this study adds

This is the first study to evaluate the adolescent anthropometric indices in relation to early adulthood MetS incidence one decade later in the Middle East region.

There is an important sex difference regarding the incidence of MetS in Tehranian adolescents.

It is interesting to know that all anthropometric indices in the pubertal age group (11–14 years) had better predictive ability compared to late‐pubertal (15–18 years) adolescents.

In addition, adolescent abdominal obesity surrogates, including WC and waist‐to‐height ratio, predicted adulthood MetS better than BMI in boys.

It seems that WC had an independent role beyond BMI in identification of adulthood MetS in Tehranian boys (11–18 years old).

Background

Little is known about the predictive ability of anthropometric indices in adolescence for prediction of early adulthood metabolic syndrome (MetS).

Objective

Our purpose was to explore incidence of MetS and the optimal anthropometric indicator to predict early adulthood MetS in Tehranian adolescents.

Methods

Using data from the population‐based, prospective, Tehran Lipid and Glucose Study, the utility of four anthropometric indices of adolescents in predicting early adulthood MetS (2009 Joint Scientific Statement definition) was examined among 1100 participants, aged 11–18 years, who were free of MetS at baseline, during a mean of 10.2 years of follow‐up.

Results

The cumulative incidence of MetS was 25.5% (95% confidence interval [CI]: 21.8–29.2%) for young men and 1.8% (95% CI: 0.6–3%) for young women. In boys, waist circumference (WC) had the highest odds ratio (OR) for the MetS risk, followed by waist‐to‐height ratio (WHtR). Adjusting body mass index (BMI) in addition to WC did not change the results in the 11–14‐year age group (OR for WC: 2.28 [1.64–3.16] without BMI adjustment vs. 1.98 [1.05–3.73] with BMI adjustment), suggesting that WC may predict MetS risk beyond BMI. None of the anthropometric indices were found to have significant associations with subsequent MetS risk in girls.

Conclusions

Measures of abdominal obesity including WHtR and WC predicted early adulthood MetS better than BMI in Tehranian male adolescents (11–18 years old).
An integrated model system for coastal flood prediction with a case history for Walcott, UK, on 9 November 2007
Authors: Stansby P. , Chini N. , Apsley D. , Borthwick A. , Bricheno L. , Horrillo‐Caraballo J. , McCabe M. , Reeve D. , Rogers B.D. , Saulter A. , Scott A. , Wilson C. , Wolf J. , Yan K.
Published: October 2012

An integrated model system is based on downscaling from climate models, to wave climate and continental shelf models for tides and surge, to coastal models for waves and water levels, to beach levels and overtopping of sea defences and inundation. Present operational practice in the UK is described. The model system is applied to the prediction of flooding at Walcott on 9 November 2007. Inundation levels are predicted in reasonable agreement with those at certain residential properties in Walcott as reported by the occupants. The effect of time‐varying and time‐averaged overtopping discharge is considered. Sensitivity of overtopping and inundation to uncertainties in nearshore wave height and water level is analysed, with the greatest sensitivity being to water level. Extreme joint probability analysis is undertaken, showing the event to be close to a 1 in 100‐year event. Finally, the effects of different rates of sea level rise and a climate change scenario are investigated for 2100; the simulations indicate that the return period of the equivalent 2007 event could reduce to less than 2 years with a 0.5m sea level rise.
A Raman spectroscopic study of diamond and disordered sp3‐carbon in the coesite‐bearing Straumen Eclogite Pod, Norway
Authors: SMITH D. C. , GODARD G.
Published: October 2012

Raman spectral point analysis and Raman mapping have been applied to study the nature of carbon‐bearing microinclusions C3‐1 and C5‐1 within zircon in phengite–kyanite–coesite eclogite sample 62a from the Straumen Eclogite Pod in the Western Gneiss Region (WGR), S.W. Norway. Graphitic carbon is always present with a degree of structural disorder comparable to that found in other ultra high pressure metamorphic (UHPM) terranes; it is compatible with an origin by a partial retrogression of the coexisting diamond due to depressurization by exhumation. Hematite coexists with diamond in C3‐1. In both microinclusions, the Raman wavenumber position of the diamond peak varies from point to point, from the ideal value of 1332 cm−1, frequently down to ∼1328 cm−1 and sometimes down to ∼1322 cm−1 in C3‐1. The bandwidth also increases proportionally. Some spectra reveal doublets with peaks at ∼1328 and ∼1322 cm−1 and even a triplet. These Raman data are discussed in terms of one or other kind of structural disorder of sp3‐carbon, for example metamictization, overtemperature or overpressure, nitrogen impurities and especially stacking disorder, that is, with the possible existence or coexistence of 3C, 2nH and/or 3mR polytypes in a mixture in the same monocrystal. The question of a metamorphic or a contamination origin of the diamond and the disordered sp3‐carbon in slide 62a is evaluated; numerous arguments favour the UHPM origin. These new data contribute to the ongoing debate on the various petrological and geodynamical models (including possible deviatoric stress) for the creation of diamond in UHPM rocks in general. This new locality of diamond at Straumen, the fourth in the WGR but the first in the southwestern part of the UHPM area of the WGR, provides a minimum pressure estimate for UHP metamorphism of ∼3.5 GPa. Taken together with other published P–T estimates, 3.75 ± 0.75 GPa covers all of the estimates of the minimum pressure for coesite‐, diamond‐ or orthopyroxene‐bearing eclogite types in the WGR.
Pressure‐ and stress‐induced fabric transition in olivine from peridotites in the Western Gneiss Region (Norway): implications for mantle seismic anisotropy
Authors: WANG Q. , XIA Q.‐K. , O’REILLY S. Y. , GRIFFIN W. L. , BEYER E. E. , BRUECKNER H. K.
Published: October 2012

The effects of pressure, water and differential stress on the crystallographic preferred orientation (CPO) of olivine were investigated by an integrated study on 13 peridotite samples from four areas in the Western Gneiss Region (WGR) of the Norwegian Caledonides. The highly depleted dunites are mantle residues after Archean melt extraction, while the garnet peridotites were formed by refertilization of the dunites via melt percolation in the Proterozoic. These orogenic peridotites were tectonically emplaced into Proterozoic gneisses and metasedimentary rocks of the WGR and were recrystallized under high‐pressure (HP) to ultrahigh‐pressure (UHP) conditions when the Baltic Shield was subducted beneath Laurentia during the 420–400 Ma Scandian orogeny. The CPOs of olivine, enstatite and diopside were measured using the electron backscatter diffraction technique. The weakly deformed garnet wehrlites and dunites from the HP central WGR (the Gurskøy, Almklovdalen and Tafjord areas) show the A‐type olivine fabric defined by the [100] axis subparallel to the stretching lineation and the (010) plane subparallel to the foliation, which may be a relict fabric formed at high temperature and low strain rate in the mantle wedge prior to subduction. The [001](010) fabric (B‐type) is observed in strongly sheared HP garnet peridotites and dunites from the Almklovdalen and Tafjord areas, suggesting the dominant activation of [001](010) slip system at high stress and high strain rate. Recrystallized fine olivine grains may develop a fabric different from porphyroclasts and record a gradual fabric transition. The olivine CPO in garnet lherzolites from Otrøy in the northernmost WGR is characterized by the concentration of [001] axes parallel to the stretching lineation and [100] axes normal to the foliation, indicating a prevailing [001](100) slip (C‐type fabric) at P–T conditions of >6 GPa and 850–950 °C. Despite very different deformation microstructures, Fourier transform infrared analysis reveals very low water contents (<13 ppm H2O by the Paterson calibration) in olivine for both coarse porphyroclasts and recrystallized small grains, which is consistent with the high‐degree partial melting of the peridotites during the Archean. Therefore, a combination of UHP and low temperature plays a more important role than water in promoting the C‐type olivine fabric in a dry, cold and deeply subducted continental slab. With increasing subduction depths, the C‐type olivine fabric will predominate over the A‐type fabric and make the maximum P‐wave velocity and shear wave splitting of peridotites normal to the foliation. However, the stress‐induced fabric transition in olivine from the A‐type to the B‐type may be localized in shear zones and not distinguishable in seismic anisotropy observations.
Post‐glucose load changes of plasma key metabolite and insulin concentrations during pregnancy and lactation in ewes with different susceptibility to pregnancy toxaemia
Authors: Duehlmeier R. , Fluegge I. , Schwert B. , Ganter M.
Published: October 2012

Insulin resistance during late gestation may act as a predisposing factor of ovine pregnancy toxaemia (OPT). To evaluate the insulin action on energy metabolism in ewes with different susceptibilities to OPT, intravenous glucose tolerance tests (1 mmol glucose/kg body weight) were performed in 5.6 ± 0.7 year old, slightly underfed German Blackheaded Mutton ewes [high‐risk (HR) ewes] and 2.5 year old, overnourished Finnish Landrace ewes [low‐risk (LR) ewes] during mid and late pregnancy, during early lactation and during the dry period. Plasma samples were analysed for glucose, insulin, non‐esterified fatty acids (NEFA) and β‐hydroxybutyrate (β‐HB). The glucose elimination rate and the glucose‐stimulated first‐phase insulin secretion were significantly (p < 0.05) lower in the HR, in relation to the LR group combining the data of all gestational stages. The basal rate of lipolysis was significantly increased in the HR ewes during late pregnancy, but the NEFA clearance after the glucose load was similar in both groups during all reproductive stages. Plasma β‐HB concentrations decreased only in the LR ewes after the glucose load during late pregnancy. Results indicate an insulin resistance in the HR ewes regarding the glucose utilization and the ketone body formation during late pregnancy. The insulin resistance in the HR ewes may represent one predisposing factor responsible for the susceptibility to OPT. Further scientific work is necessary to elucidate whether this insulin resistance was due to breed, age or nutritional state.
Mechanisms and functional consequences of liver failure substantially differ between endotoxaemia and faecal peritonitis in rats
Authors: Recknagel Peter , Gonnert Falk A. , Halilbasic Emina , Gajda Mieczyslaw , Jbeily Nayla , Lupp Amelie , Rubio Ignacio , Claus Ralf A. , Kortgen Andreas , Trauner Michael , Singer Mervyn , Bauer Michael
Published: October 2012

Background

Many of the concepts describing molecular mechanisms of sepsis‐induced liver failure are derived from endotoxin models. However, the biological significance of such models is questionable as the complexity of clinical sepsis and associated organ failure is only partially replicated.

Aims

Comparison of cytokine response, leucocyte recruitment, oxidative stress and markers of hepatic organ dysfunction in rat models of endotoxaemia or peritoneal contamination and infection (PCI).

Methods

Endotoxemia and polymicrobial sepsis were induced in rats by intraperitoneal injection of lipopolysaccharide (LPS) or stool suspension, respectively.

Results

Both insults produced clinical and laboratory signs of multiple organ dysfunction, including hepatic excretory dysfunction. However, TNF alpha, oxidative stress responses and the degree of cell death were significantly higher in endotoxaemia compared to PCI (e.g. serum TNF levels (pg/ml) at 1.5 h post‐insult: sham 5 ± 1.4, LPS 1 mg/kg bw 2176.92 ± 373.78, sepsis below detection limit; P P < 0.05). Cholestasis was significantly more pronounced in polymicrobial sepsis whereas serum bilirubin in endotoxaemic animals did not differ from sham‐operated controls (plasma levels of bilirubin (μmol/L) at 15 h after the insult: sham 7.1 ± 0.6, LPS 30 mg/kg 9.1 ± 0.6, sepsis 15.2 ± 1.3).

Conclusions

Polymicrobial sepsis produces profound hepatocellular dysfunction in the absence of traditional cytokine‐mediated mechanisms of cellular injury. This questions the central role of cytokines and the ensuing oxidative stress as key molecular events in mediating liver dysfunction.
Does long‐distance pollen dispersal preclude inbreeding in tropical trees? Fragmentation genetics of Dysoxylum malabaricum in an agro‐forest landscape
Authors: Ismail S. A. , Ghazoul J. , Ravikanth G. , Uma Shaanker R. , Kushalappa C. G. , Kettle C. J.
Published: October 2012

Tropical trees often display long‐distance pollen dispersal, even in highly fragmented landscapes. Understanding how patterns of spatial isolation influence pollen dispersal and interact with background patterns of fine‐scale spatial genetic structure (FSGS) is critical for evaluating the genetic consequences of habitat fragmentation. In the endangered tropical timber tree Dysoxylum malabaricum (Meliaceae), we apply eleven microsatellite markers with paternity and parentage analysis to directly estimate historic gene flow and contemporary pollen dispersal across a large area (216 km2) in a highly fragmented agro‐forest landscape. A comparison of genetic diversity and genetic structure in adult and juvenile life stages indicates an increase in differentiation and FSGS over time. Paternity analysis and parentage analysis demonstrate high genetic connectivity across the landscape by pollen dispersal. A comparison between mother trees in forest patches with low and high densities of adult trees shows that the frequency of short‐distance mating increases, as does average kinship among mates in low‐density stands. This indicates that there are potentially negative genetic consequences of low population density associated with forest fragmentation. Single isolated trees, in contrast, frequently receive heterogeneous pollen from distances exceeding 5 km. We discuss the processes leading to the observed patterns of pollen dispersal and the implications of this for conservation management of D. malabaricum and tropical trees more generally.
No inbreeding depression but increased sexual investment in highly inbred ant colonies
Authors: Kureck Ilka M. , Jongepier Evelien , Nicolai Beate , Foitzik Susanne
Published: October 2012

Inbreeding can lead to the expression of deleterious recessive alleles and to a subsequent fitness reduction. In Hymenoptera, deleterious alleles are purged in haploid males moderating inbreeding costs. However, in these haplodiploid species, inbreeding can result in the production of sterile diploid males. We investigated the effects of inbreeding on the individual and colony level in field colonies of the highly inbred ant Hypoponera opacior. In this species, outbreeding winged sexuals and nest‐mating wingless sexuals mate during two separate reproductive periods. We show that regular sib‐matings lead to high levels of homozygosity and the occasional production of diploid males, which sporadically sire triploid offspring. On the individual level, inbreeding was associated with an increased body size in workers. On the colony level, we found no evidence for inbreeding depression as productivity was unaffected by the level of homozygosity. Instead, inbred colonies altered their allocation strategies by investing more resources into sexuals than into workers. This shift towards sexual production was due to an increased investment in both males and queens, which was particularly pronounced in the dispersive generation. The absence of inbreeding depression combined with increased reproductive investment, especially in outbreeding sexuals, suggests that these ants have evolved active strategies to regulate the extent and effects of frequent inbreeding.
Biomechanical determinants of oxygen extraction during cross‐country skiing
Authors: Stöggl T. , Björklund G. , Holmberg H.‐C.
Published: October 2012

To determine the relationship of muscle activation, force production, and cycle characteristics to O2 extraction during high‐ and lower‐intensity double poling (DP), nine well‐trained male cross‐country skiers performed DP on a treadmill for 3 min at 90% VO2peak followed by 6 min at 70%. During the final minute at each workload, arterial, femoral, and subclavian venous blood were collected for determination of partial pressure of O2, partial pressure of CO2, pH, and lactate. Electromyography (EMG) was recorded from six upper and lower body muscles, leg and pole forces were measured, and cardiorespiratory variables were monitored continuously. O2 extraction was associated with time point of peak pole force (PFpeak), duration of recovery, EMG activity, and lower body use. Arm O2 extraction was lower than in the legs at both intensities (P < 0.001) and was reduced to a lesser extent upon decreasing the workload (P < 0.05). Arm root‐mean‐square EMG was higher during the poling phase and entire cycle compared with the legs (P < 0.001). Blood lactate was higher in the subclavian than in femoral vein and artery (P < 0.001) and independent of intensity. O2 extraction was correlated to low muscle activation, later PFpeak, prolonged poling time, and extensive dynamic lower body use. Cycle rate and recovery time were associated with O2 extraction during high‐intensity exercise only.
Aspect-dependent radiated noise analysis of an underway autonomous underwater vehicle
Authors: Gebbie John , Siderius Martin , Allen John S.
Published: October 2012

This paper presents an analysis of the acoustic emissions emitted by an underway REMUS-100 autonomous underwater vehicle (AUV) that were obtained near Honolulu Harbor, HI using a fixed, bottom-mounted horizontal line array (HLA). Spectral analysis, beamforming, and cross-correlation facilitate identification of independent sources of noise originating from the AUV. Fusion of navigational records from the AUV with acoustic data from the HLA allows for an aspect-dependent presentation of calculated source levels of the strongest propulsion tone.
Offspring from Oocytes Derived from in Vitro Primordial Germ Cell–like Cells in Mice
Authors: Hayashi Katsuhiko , Ogushi Sugako , Kurimoto Kazuki , Shimamoto So , Ohta Hiroshi , Saitou Mitinori
Published: October 2012

Artificially Induced Oocytes

In mice, male embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) have been shown to differentiate into primordial germ cell–like cells (PGCLCs) in vitro. Upon transplantation into testes, these PGCLCs can form fully functional sperm. Again working in mice,

Hayashi
et al.

(p.
971
, published online 4 October) found that female ESCs and iPSCs can also differentiate into PGCLCs, which, when aggregated in reconstituted ovaries, exhibited epigenetic reprogramming and meiotic potential in vitro. Upon transplantation of the reconstituted ovaries under ovarian bursa, female PGCLCs developed into fully grown oocytes that contributed to healthy offspring upon in vitro maturation and fertilization.
Evidence against Barium in the Mushroom Trogia venenata as a Cause of Sudden Unexpected Deaths in Yunnan, China
Authors: Zhang Ying , Li Yanchun , Wu Gang , Feng Bang , Yoell Shanze , Yu Zefen , Zhang Keqin , Xu Jianping
Published: October 2012

This study examined barium concentrations in the mushroom
Trogia venenata
, the leading culprit for sudden unexpected deaths in Yunnan, southwest China. We found that barium concentrations in
T. venenata
from Yunnan were low and comparable to other foods, inconsistent with barium concentrations in this mushroom as a significant contributor to these deaths.
Silage Collected from Dairy Farms Harbors an Abundance of Listeriaphages with Considerable Host Range and Genome Size Diversity
Authors: Vongkamjan Kitiya , Switt Andrea Moreno , den Bakker Henk C. , Fortes Esther D. , Wiedmann Martin
Published: October 2012

Since the food-borne pathogenListeria monocytogenesis common in dairy farm environments, it is likely that phages infecting this bacterium (“listeriaphages”) are abundant on dairy farms. To better understand the ecology and diversity of listeriaphages on dairy farms and to develop a diverse phage collection for further studies, silage samples collected on two dairy farms were screened forL. monocytogenesand listeriaphages. While only 4.5% of silage samples tested positive forL. monocytogenes, 47.8% of samples were positive for listeriaphages, containing up to >1.5 × 104PFU/g. Host range characterization of the 114 phage isolates obtained, with a reference set of 13L. monocytogenesstrains representing the nine major serotypes and four lineages, revealed considerable host range diversity; phage isolates were classified into nine lysis groups. While one serotype 3c strain was not lysed by any phage isolates, serotype 4 strains were highly susceptible to phages and were lysed by 63.2 to 88.6% of phages tested. Overall, 12.3% of phage isolates showed a narrow host range (lysing 1 to 5 strains), while 28.9% of phages represented broad host range (lysing ≥11 strains). Genome sizes of the phage isolates were estimated to range from approximately 26 to 140 kb. The extensive host range and genomic diversity of phages observed here suggest an important role of phages in the ecology ofL. monocytogeneson dairy farms. In addition, the phage collection developed here has the potential to facilitate further development of phage-based biocontrol strategies (e.g., in silage) and other phage-based tools.
Purification and Characterization of an NAD
+
-Dependent XylB-Like Aryl Alcohol Dehydrogenase Identified in Acinetobacter baylyi ADP1
Authors: Uthoff Stefan , Steinbüchel Alexander
Published: October 2012

The gene
xylB
ADP1
from
Acinetobacter baylyi
ADP1 (gene annotation number ACIAD1578), coding for a putative aryl alcohol dehydrogenase, was heterologously expressed in
Escherichia coli
BL21(DE3). The respective aryl alcohol dehydrogenase was purified by fast protein liquid chromatography to apparent electrophoretic homogeneity. The predicted molecular weight of 39,500 per subunit was confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. According to the native
M
w
as determined by gel filtration, the enzyme forms dimers and therefore seems to be XylB related. The enzyme showed the highest activity at 40°C. For both the reduction and the oxidation reactions, the pH for optimum activity was 6.5. The enzyme was NADH dependent and able to reduce medium- to long-chain
n
-alkylaldehydes, methyl-branched aldehydes, and aromatic aldehydes, with benzaldehyde yielding the highest activity. The oxidation reaction with the corresponding alcohols showed only 2.2% of the reduction activity, with coniferyl alcohol yielding the highest activity. Maximum activities for the reduction and the oxidation reaction were 104.5 and 2.3 U mg
−1
of protein, respectively. The enzyme activity was affected by low concentrations of Ag
+
and Hg
2+
and high concentrations of Cu
2+
, Zn
2+
, and Fe
2+
. The gene
xylB
ADP1
seems to be expressed constitutively and an involvement in coniferyl alcohol degradation is suggested. However, the enzyme is most probably not involved in the degradation of benzyl alcohol, anisalcohol, salicyl alcohol, vanillyl alcohol, cinnamyl alcohol, or aliphatic and isoprenoid alcohols.
Microscope-Based Imaging Platform for Large-Scale Analysis of Oral Biofilms
Authors: Karygianni L. , Follo M. , Hellwig E. , Burghardt D. , Wolkewitz M. , Anderson A. , Al-Ahmad A.
Published: October 2012

A microscopic method for noninvasively monitoring oral biofilms at the macroscale was developed to describe the spatial distribution of biofilms of different bacterial composition on bovine enamel surfaces (BES). For this purpose, oral biofilm was grown
in situ
on BES that were fixed at approximal sites of individual upper jaw acrylic devices worn by a volunteer for 3 or 5 days. Eubacteria,
Streptococcus
spp., and
Fusobacterium nucleatum
were stained using specific fluorescence
in situ
hybridization (FISH) probes. The resulting fluorescence signals were subsequently tested by confocal laser scanning microscopy (CLSM) and monitored by an automated wide-field microscope-based imaging platform (Scan∧R). Automated image processing and data analysis were conducted by microscope-associated software and followed by statistical evaluation of the results. The full segmentation of biofilm images revealed a random distribution of bacteria across the entire area of the enamel surfaces examined. Significant differences in the composition of the microflora were recorded across individual as well as between different enamel surfaces varying from sparsely colonized (47.26%) after 3 days to almost full surface coverage (84.45%) after 5 days. The enamel plates that were positioned at the back or in the middle of the oral cavity were found to be more suitable for the examination of biofilms up to 3 days old. In conclusion, automated microscopy combined with the use of FISH can enable the efficient visualization and meaningful quantification of bacterial composition over the entire sample surface. Due to the possibility of automation, Scan∧R overcomes the technical limitations of conventional CLSM.
Cellulolytic Bacteria in the Foregut of the Dromedary Camel (Camelus dromedarius)
Authors: Samsudin Anjas A. , Wright André-Denis G. , Al Jassim Rafat
Published: October 2012

Foregut digesta from five feral dromedary camels were inoculated into three different enrichment media: cotton thread, filter paper, and neutral detergent fiber. A total of 283 16S rRNA gene sequences were assigned to 33 operational taxonomic units by using 99% species-level identity. LIBSHUFF revealed significant differences in the community composition across all three libraries.
Prevalence, Environmental Loading, and Molecular Characterization of Cryptosporidium and Giardia Isolates from Domestic and Wild Animals along the Central California Coast
Authors: Oates Stori C. , Miller Melissa A. , Hardin Dane , Conrad Patricia A. , Melli Ann , Jessup David A. , Dominik Clare , Roug Annette , Tinker M. Tim , Miller Woutrina A.
Published: October 2012

The risk of disease transmission from waterborne protozoa is often dependent on the origin (e.g., domestic animals versus wildlife), overall parasite load in contaminated waterways, and parasite genotype, with infections being linked to runoff or direct deposition of domestic animal and wildlife feces. Fecal samples collected from domestic animals and wildlife along the central California coast were screened to (i) compare the prevalence and associated risk factors for fecal shedding ofCryptosporidiumandGiardiaspecies parasites, (ii) evaluate the relative importance of animal host groups that contribute to pathogen loading in coastal ecosystems, and (iii) characterize zoonotic and host-specific genotypes. Overall, 6% of fecal samples tested during 2007 to 2010 were positive forCryptosporidiumoocysts and 15% were positive forGiardiacysts. Animal host group and age class were significantly associated with detection ofCryptosporidiumandGiardiaparasites in animal feces. Fecal loading analysis revealed that infected beef cattle potentially contribute the greatest parasite load relative to other host groups, followed by wild canids. Beef cattle, however, shed host-specific, minimally zoonoticCryptosporidiumandGiardia duodenalisgenotypes, whereas wild canids shed potentially zoonotic genotypes, includingG. duodenalisassemblages A and B. Given that the parasite genotypes detected in cattle were not zoonotic, the public health risk posed by protozoan parasite shedding in cattle feces may be lower than that posed by other animals, such as wild canids, that routinely shed zoonotic genotypes.
Influence of Temperature on the Physiology and Virulence of the Insect Pathogen Serratia sp. Strain SCBI
Authors: Petersen Lauren M. , Tisa Louis S.
Published: October 2012

The physiology of a newly recognized
Serratia
species, termed South African
Caenorhabditis briggsae
Isolate (SCBI), which is both a nematode mutualist and an insect pathogen, was investigated and compared to that of
Serratia marcescens
Db11, a broad-host-range pathogen. The two
Serratia
strains had comparable levels of virulence for
Manduca sexta
and similar cytotoxic activity patterns, but motility and lipase and hemolytic activities differed significantly between them.
Calcium Causes Multimerization of the Large Adhesin LapF and Modulates Biofilm Formation by Pseudomonas putida
Authors: Martínez-Gil Marta , Romero Diego , Kolter Roberto , Espinosa-Urgel Manuel
Published: October 2012

LapF is a large secreted protein involved in microcolony formation and biofilm maturation in
Pseudomonas putida
. Its C-terminal domain shows the characteristics of proteins secreted through a type I secretion system and includes a predicted calcium binding motif. We provide experimental evidence of specific binding of Ca
2+
to the purified C-terminal domain of LapF (CLapF). Calcium promotes the formation of large aggregates, which disappear in the presence of the calcium chelator EGTA. Immunolocalization of LapF also shows the tendency of this protein to accumulate
in vivo
in certain extracellular regions. These findings, along with results showing that calcium influences biofilm formation, lead us to propose a model in which
P. putida
cells interact with each other via LapF in a calcium-dependent manner during the development of biofilms.
Transcriptional Organization and Regulatory Elements of a Pseudomonas sp. Strain ADP Operon Encoding a LysR-Type Regulator and a Putative Solute Transport System
Authors: Platero Ana Isabel , García-Jaramillo Manuel , Santero Eduardo , Govantes Fernando
Published: October 2012

The
atzS-atzT-atzU-atzV-atzW
gene cluster of the
Pseudomonas
sp. strain ADP atrazine-degradative plasmid pADP-1, which carries genes for an outer membrane protein and the components of a putative ABC-type solute transporter, is located downstream from
atzR
, which encodes the LysR-type transcriptional regulator of the cyanuric acid-degradative operon
atzDEF
. Here we describe the transcriptional organization of these genes. Our results show that all six genes are cotranscribed from the P
atzR
promoter to form the
atzRSTUVW
operon. A second, stronger promoter, P
atzT
, is found within
atzS
and directs transcription of the four distal genes. P
atzT
is σ
N
dependent, activated by NtrC in response to nitrogen limitation with the aid of IHF, and repressed by AtzR. A combination of
in vivo
mutational analysis and primer extension allowed us to locate the P
atzT
promoter and map the transcriptional start site. Similarly, we used deletion and point mutation analyses, along with
in vivo
expression studies and
in vitro
binding assays, to locate the NtrC, IHF, and AtzR binding sites and address their functionality. Our results suggest a regulatory model in which NtrC activates P
atzT
transcription via DNA looping, while AtzR acts as an antiactivator that diminishes expression by interfering with the activation process.
Genome of Enterobacteriophage Lula/phi80 and Insights into Its Ability To Spread in the Laboratory Environment
Authors: Rotman Ella , Kouzminova Elena , Plunkett Guy , Kuzminov Andrei
Published: October 2012

The novel temperate bacteriophage Lula, contaminating laboratory
Escherichia coli
strains, turned out to be the well-known lambdoid phage phi80. Our previous studies revealed that two characteristics of Lula/phi80 facilitate its spread in the laboratory environment: cryptic lysogen productivity and stealthy infectivity. To understand the genetics/genomics behind these traits, we sequenced and annotated the Lula/phi80 genome, encountering an
E. coli
-toxic gene revealed as a gap in the sequencing contig and analyzing a few genes in more detail. Lula/phi80's genome layout copies that of lambda, yet homology with other lambdoid phages is mostly limited to the capsid genes. Lula/phi80's DNA is resistant to cutting with several restriction enzymes, suggesting DNA modification, but deletion of the phage's
damL
gene, coding for DNA adenine methylase, did not make DNA cuttable. The
damL
mutation of Lula/phi80 also did not change the phage titer in lysogen cultures, whereas the host
dam
mutation did increase it almost 100-fold. Since the high phage titer in cultures of Lula/phi80 lysogens is apparently in response to endogenous DNA damage, we deleted the only Lula/phi80 SOS-controlled gene,
dinL
. We found that
dinL
mutant lysogens release fewer phage in response to endogenous DNA damage but are unchanged in their response to external DNA damage. The toxic gene of Lula/phi80,
gamL
, encodes an inhibitor of the host ATP-dependent exonucleases, RecBCD and SbcCD. Its own antidote,
agt
, apparently encoding a modifier protein, was found nearby. Interestingly, Lula/phi80 lysogens are
recD
and
sbcCD
phenocopies, so GamL and Agt are part of lysogenic conversion.
Complete Genome Sequence of the Endophytic Enterobacter cloacae subsp. cloacae Strain ENHKU01
Authors: Liu Wing-Yee , Chung Karl Ming-Kar , Wong Chi-Fat , Jiang Jing-Wei , Hui Raymond Kin-Hi , Leung Frederick Chi-Ching
Published: October 2012

Enterobacter cloacae
subsp.
cloacae
strain ENHKU01 is a Gram-negative endophyte isolated from a diseased pepper (
Capsicum annuum
) plant in Hong Kong. This is the first complete genome sequence report of a plant-endophytic strain of
E. cloacae
subsp.
cloacae
.
Staphylococcus aureus NorD, a Putative Efflux Pump Coregulated with the Opp1 Oligopeptide Permease, Contributes Selectively to Fitness
In Vivo
Authors: Ding Yanpeng , Fu Yingmei , Lee Jean C. , Hooper David C.
Published: October 2012

Staphylococcus aureus
readily infects humans, causing infections from mild superficial skin infections to lethal bacteremia and endocarditis. Transporters produced by
S. aureus
allow the pathogen to adapt to a variety of settings, including survival at sites of infection and in the presence of antibiotics. The native functions of many transporters are unknown, but their potential dual contribution to fitness and antimicrobial resistance highlights their importance in staphylococcal infections. Here, we show that
S. aureus
NorD, a newly recognized efflux pump of the major facilitator superfamily, contributes to fitness in a murine subcutaneous abscess model. In community-associated methicillin-resistant
S. aureus
(CA-MRSA) strain MW2,
norD
was selectively upregulated 36-fold at the infection site relative to growth
in vitro
, and the
norD
mutant demonstrated significant fitness impairment in abscesses, with fitness 20- to 40-fold lower than that of the parent MW2 strain. Plasmid-encoded NorD could complement the fitness defect of the MW2
norD
mutant. Chromosomal
norD
expression is polycistronic with the upstream oligopeptide permease genes (
opp1ABCDF
), which encode an ABC oligopeptide transporter. Both
norD
and
opp1
were upregulated in abscesses and iron-restricted culture medium and negatively regulated by Fur, but only NorD contributed to fitness in the murine abscess model.
Genome Sequence of Staphylococcus lentus F1142, a Strain Isolated from Korean Soybean Paste
Authors: Nam Young-Do , Chung Won-Hyong , Seo Myung-Ji , Lim Seong-Il , Yi Sung-Hun
Published: October 2012

This report describes the draft genome sequence of
Staphylococcus lentus
F1142, which was isolated from a Korean fermented soybean paste (doenjang). The draft genome sequence contained 2.79 Mbp with a G+C content of 31.8%; this is the first
S. lentus
genome to be reported.
AhpC Is Required for Optimal Production of Enterobactin by Escherichia coli
Authors: Ma Li , Payne Shelley M.
Published: October 2012

Escherichia coli
alkyl hydroperoxide reductase subunit C (AhpC) is a peroxiredoxin that detoxifies peroxides. Here we show an additional role for AhpC in cellular iron metabolism of
E. coli
. Deletion of
ahpC
resulted in reduced growth and reduced accumulation of iron by cells grown in low-iron media. Liquid chromatography-mass spectroscopy (LC-MS) analysis of culture supernatants showed that the
ahpC
mutant secreted much less enterobactin, the siderophore that chelates and transports ferric iron under iron-limiting conditions, than wild-type
E. coli
did. The
ahpC
mutant produced less 2,3-dihydroxybenzoate, the intermediate in the enterobactin biosynthesis pathway, and providing 2,3-dihydroxybenzoate restored wild-type growth of the
ahpC
mutant. These data indicated that the defect was in an early step in enterobactin biosynthesis. Providing additional copies of
entC
, which functions in the first dedicated step of enterobactin biosynthesis, but not of other enterobactin biosynthesis genes, suppressed the mutant phenotype. Additionally, providing either shikimate or a mixture of
para
-aminobenzoate, tryptophan, tyrosine, and phenylalanine, which, like enterobactin, are synthesized from the precursor chorismate, also suppressed the mutant phenotype. These data suggested that AhpC affected the activity of EntC or the availability of the chorismate substrate.
Aquaporin AqpZ Is Involved in Cell Volume Regulation and Sensitivity to Osmotic Stress in Synechocystis sp. Strain PCC 6803
Authors: Akai Masaro , Onai Kiyoshi , Morishita Megumi , Mino Hiroyuki , Shijuku Toshiaki , Maruyama Hisataka , Arai Fumihito , Itoh Shigeru , Hazama Akihiro , Checchetto Vanessa , Szabò Ildikò , Yukutake Yoshinori , Suematsu Makoto , Yasui Masato , Ishiura Masahiro , Uozumi Nobuyuki
Published: October 2012

The moderately halotolerant cyanobacterium
Synechocystis
sp. strain PCC 6803 contains a plasma membrane aquaporin, AqpZ. We previously reported that AqpZ plays a role in glucose metabolism under photomixotrophic growth conditions, suggesting involvement of AqpZ in cytosolic osmolarity homeostasis. To further elucidate the physiological role of AqpZ, we have studied its gene expression profile and its function in
Synechocystis
. The expression level of
aqpZ
was regulated by the circadian clock. AqpZ activity was insensitive to mercury in
Xenopus
oocytes and in
Synechocystis
, indicating that the AqpZ can be categorized as a mercury-insensitive aquaporin. Stopped-flow light-scattering spectrophotometry showed that addition of sorbitol and NaCl led to a slower decrease in cell volume of the
Synechocystis
Δ
aqpZ
strain than the wild type. The Δ
aqpZ
cells were more tolerant to hyperosmotic shock by sorbitol than the wild type. Consistent with this, recovery of oxygen evolution after a hyperosmotic shock by sorbitol was faster in the Δ
aqpZ
strain than in the wild type. In contrast, NaCl stress had only a small effect on oxygen evolution. The amount of AqpZ protein remained unchanged by the addition of sorbitol but decreased after addition of NaCl. This decrease is likely to be a mechanism to alleviate the effects of high salinity on the cells. Our results indicate that
Synechocystis
AqpZ functions as a water transport system that responds to daily oscillations of intracellular osmolarity.
Complete Genome of Transmissible Gastroenteritis Virus AYU Strain Isolated in Shanghai, China
Authors: Hou Yixuan , Yue Xiuwei , Cai Xuehui , Wang Shujie , Liu Yonggang , Yuan Congli , Cui Li , Hua Xiuguo , Yang Zhibiao
Published: October 2012

Transmissible gastroenteritis virus strain AYU was isolated in Shanghai. The complete genome has a length of 28,582 bp and contains seven open reading frames. Sequence analysis suggested that Shanghai strain AYU and U.S. strain Purdue P115 are derived from a common ancestor, as they have 99.6% similarity at the nucleotide level.
Nine Complete Genome Sequences of Cutaneous Human Papillomavirus Genotypes Isolated from Healthy Skin of Individuals Living in Rural He Nan Province, China
Authors: Li Jingjing , Cai Hong , Xu Zhongyao , Wang Qiyan , Hang Dong , Shen Na , Liu Mengfei , Zhang Chanyuan , Abliz Amir , Ke Yang
Published: October 2012

Nine novel human papillomavirus (HPV) types were isolated from healthy skin of individuals in rural Anyang, China. All of these isolates belong to the genus
Gammapapillomavirus
. These data will provide us with useful information for a better understanding of PV evolution and the relationship of PV with the host.
Complete Genome Sequence of Le Blanc Virus, a Third Caenorhabditis Nematode-Infecting Virus
Authors: Franz Carl J. , Zhao Guoyan , Félix Marie-Anne , Wang David
Published: October 2012

Orsay virus and Santeuil virus, the first known viruses capable of naturally infecting the nematodes
Caenorhabditis elegans
and
Caenorhabditis briggsae
, respectively, were recently identified by high-throughput sequencing of wild
Caenorhabditis
strains. By similar analysis of another wild
C. briggsae
isolate, we have now discovered and sequenced the complete genome of a third novel virus, Le Blanc virus, that is distantly related to Orsay and Santeuil viruses. All three viruses are positive-sense RNA viruses with bipartite genomes that are most closely related to nodaviruses. Identification of a third virus capable of infecting
Caenorhabditis
nematodes enables comparative analysis of this clade of viruses and strengthens this model for investigating virus-host interactions.
Genome of a Bombyx mori Nucleopolyhedrovirus Strain Isolated from India
Authors: Fan Hai-Wei , Zhang Xue-Chao , Xu Yi-Peng , Cheng Xiao-Wen , Zhang Chuan-Xi
Published: October 2012

Bombyx mori
nucleopolyhedrovirus (BmNPV), a member of the
Baculoviridae
, is a major pathogen of silkworm and has also been recently developed as an expression vector for heterologous gene expression in the silkworm larvae and pupae. To better understand the diversity of this important baculovirus, we sequenced the complete genome of the BmNPV strain isolated from India, where its host is available throughout the year due to its tropical climate. The genome of the Indian strain consists of 127,879 nucleotides, with a G+C content of 40.36%. There are 138 open reading frames (ORFs) encoding the predicted proteins of more than 50 amino acids. Genomic comparison of the Indian strain with 3 other reported BmNPV strains showed that the baculovirus repeat ORFs (
bro
) and homologous repeat regions (hr's) are highly variable. These results suggest that the BmNPV strain heterogeneity is mainly caused by single-nucleotide polymorphisms (SNPs) and changes in the hr's and
bro
genes.
Complete Genome Sequence of an H3N2 Avian Influenza Virus Isolated from a Live Poultry Market in Eastern China
Authors: Teng Qiaoyang , Hu Tao , Li Xuesong , Li Guoxin , Li Zejun
Published: October 2012

Previous studies indicate that the H3 influenza virus has the ability to establish infection upon interspecies transmission and poses a threat to mammals. Therefore, it is important to enhance the surveillance of H3 avian influenza viruses (AIVs). In this study, A/duck/Shanghai/C84/2009(H3N2) (C84) was isolated from a live poultry market in Shanghai, China. Using PCR and sequencing analyses, we obtained the whole-genome sequence of this virus. The H3N2 virus proved to be a novel multiple-gene reassortant AIV whose genes were derived from H3N2, H4N6, H6N2, and H9N2. Knowledge regarding the complete genome sequence of the C84 virus will be useful for epidemiological surveillance.
Complete Genome Sequence of a Novel Human Parechovirus
Authors: Wang Chunmei , Shan Tongling , Zheng Hao , Tong Wu , Chen Fangzhou , Hu Han , He Qigai , Tong Guangzhi
Published: October 2012

Human parechoviruses (HPeVs) belonging to the family
Picornaviridae
are widely spread pathogens among young children. We report the complete genome sequence of a novel HPeV isolated from the stool sample of a hospitalized child with diarrhea in China. The genome consists of 7,305 nucleotides, excluding the 3′ poly(A) tail, and has an open reading frame that maps between nucleotide positions 675 and 7217 and encodes a 2,180-amino-acid polyprotein. The genome sequence of the virus was sufficiently distinct from the 8 known HPeV types. Phylogenetic analysis based on the complete genome indicated that the HPeV strain represents a new genotype.
Genome of Thysanoplusia orichalcea Multiple Nucleopolyhedrovirus Lacks the Superoxide Dismutase Gene
Authors: Wang Yun-Sheng , Huang Guo-Hua , Cheng Xin-Hua , Wang Xing , Garretson Tyler A. , Dai Liang-Ying , Zhang Chuan-Xi , Cheng Xiao-Wen
Published: October 2012

Thysanoplusia orichalcea
multiple nucleopolyhedrovirus (ThorMNPV) has high virulence to
Trichoplusia ni
and
Pseudoplusia includens
larvae, with a potential for biological control of insect pests. The genome of ThorMNPV was sequenced and found to be 132,978 bp, with a G+C content of 37.9%. There are 145 predicted open reading frames (ORFs), encoding proteins of 50 or more amino acid residues with minimal overlap. Of the 145 ORFs, 141 appeared to be homologous to those of
Autographa californica
MNPV (AcMNPV). In comparison to AcMNPV, 9 ORFs of AcMNPV were absent in ThorMNPV, including the superoxide dismutase (
sod
) gene.