bluuebunny/crossref_metadata_2025_split huggingface dataset:
Steady-State Growth under Inorganic Carbon Limitation Conditions Increases Energy Consumption for Maintenance and Enhances Nitrous Oxide Production in Nitrosomonas europaea
Authors: Mellbye Brett L. , Giguere Andrew , Chaplen Frank , Bottomley Peter J. , Sayavedra-Soto Luis A. 
Published: March 2016

ABSTRACT

Nitrosomonas europaea
is a chemolithoautotrophic bacterium that oxidizes ammonia (NH
3
) to obtain energy for growth on carbon dioxide (CO
2
) and can also produce nitrous oxide (N
2
O), a greenhouse gas. We interrogated the growth, physiological, and transcriptome responses of
N. europaea
to conditions of replete (>5.2 mM) and limited inorganic carbon (IC) provided by either 1.0 mM or 0.2 mM sodium carbonate (Na
2
CO
3
) supplemented with atmospheric CO
2
. IC-limited cultures oxidized 25 to 58% of available NH
3
to nitrite, depending on the dilution rate and Na
2
CO
3
concentration. IC limitation resulted in a 2.3-fold increase in cellular maintenance energy requirements compared to those for NH
3
-limited cultures. Rates of N
2
O production increased 2.5- and 6.3-fold under the two IC-limited conditions, increasing the percentage of oxidized NH
3
-N that was transformed to N
2
O-N from 0.5% (replete) up to 4.4% (0.2 mM Na
2
CO
3
). Transcriptome analysis showed differential expression (
P
≤ 0.05) of 488 genes (20% of inventory) between replete and IC-limited conditions, but few differences were detected between the two IC-limiting treatments. IC-limited conditions resulted in a decreased expression of ammonium/ammonia transporter and ammonia monooxygenase subunits and increased the expression of genes involved in C
1
metabolism, including the genes for RuBisCO (
cbb
gene cluster), carbonic anhydrase, folate-linked metabolism of C
1
moieties, and putative C salvage due to oxygenase activity of RuBisCO. Increased expression of nitrite reductase (gene cluster NE0924 to NE0927) correlated with increased production of N
2
O. Together, these data suggest that
N. europaea
adapts physiologically during IC-limited steady-state growth, which leads to the uncoupling of NH
3
oxidation from growth and increased N
2
O production.

IMPORTANCE
Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, is an important process in the global nitrogen cycle. This process is generally dependent on ammonia-oxidizing microorganisms and nitrite-oxidizing bacteria. Most nitrifiers are chemolithoautotrophs that fix inorganic carbon (CO
2
) for growth. Here, we investigate how inorganic carbon limitation modifies the physiology and transcriptome of
Nitrosomonas europaea
, a model ammonia-oxidizing bacterium, and report on increased production of N
2
O, a potent greenhouse gas. This study, along with previous work, suggests that inorganic carbon limitation may be an important factor in controlling N
2
O emissions from nitrification in soils and wastewater treatment.
Culturing and Characterization of Gut Symbiont Burkholderia spp. from the Southern Chinch Bug, Blissus insularis (Hemiptera: Blissidae)
Authors: Xu Yao , Buss Eileen A. , Boucias Drion G. 
Published: March 2016

ABSTRACT

The phloem-feeding Southern chinch bug,
Blissus insularis
, harbors a high density of the exocellular bacterial symbiont
Burkholderia
in the lumen of specialized midgut crypts. Here we developed an organ culture method that initially involved incubating the
B. insularis
crypts in osmotically balanced insect cell culture medium. This approach enabled the crypt-inhabiting
Burkholderia
spp. to make a transition to an
in vitro
environment and to be subsequently cultured in standard bacteriological media. Examinations using ribotyping and BOX-PCR fingerprinting techniques demonstrated that most
in vitro
-produced bacterial cultures were identical to their crypt-inhabiting
Burkholderia
counterparts. Genomic and physiological analyses of gut-symbiotic
Burkholderia
spp. that were isolated individually from two separate
B. insularis
laboratory colonies revealed that the majority of individual insects harbored a single
Burkholderia
ribotype in their midgut crypts, resulting in a diverse
Burkholderia
community within each colony. The diversity was also exhibited by the phenotypic and genotypic characteristics of these
Burkholderia
cultures. Access to cultures of crypt-inhabiting bacteria provides an opportunity to investigate the interaction between symbiotic
Burkholderia
spp. and the
B. insularis
host. Furthermore, the culturing method provides an alternative strategy for establishing
in vitro
cultures of other fastidious insect-associated bacterial symbionts.

IMPORTANCE
An organ culture method was developed to establish
in vitro
cultures of a fastidious
Burkholderia
symbiont associated with the midgut crypts of the Southern chinch bug,
Blissus insularis
. The identities of the resulting cultures were confirmed using the genomic and physiological features of
Burkholderia
cultures isolated from
B. insularis
crypts, showing that host insects maintained the diversity of
Burkholderia
spp. over multiple generations. The availability of characterized gut-symbiotic
Burkholderia
cultures provides a resource for genetic manipulation of these bacteria and for examination of the mechanisms underlying insect-bacterium symbiosis.
Genetic Diversity of Flavobacterium psychrophilum Isolates from Three Oncorhynchus spp. in the United States, as Revealed by Multilocus Sequence Typing
Authors: Van Vliet Danielle , Wiens Gregory D. , Loch Thomas P. , Nicolas Pierre , Faisal Mohamed 
Published: March 2016

ABSTRACT

The use of a multilocus sequence typing (MLST) technique has identified the intraspecific genetic diversity of U.S.
Flavobacterium psychrophilum
, an important pathogen of salmonids worldwide. Prior to this analysis, little U.S.
F. psychrophilum
genetic information was known; this is of importance when considering targeted control strategies, including vaccine development. Herein, MLST was used to investigate the genetic diversity of 96
F. psychrophilum
isolates recovered from rainbow trout (
Oncorhynchus mykiss
), coho salmon (
Oncorhynchus kisutch
), and Chinook salmon (
Oncorhynchus tshawytscha
) that originated from nine U.S. states. The isolates fell into 34 distinct sequence types (STs) that clustered in 5 clonal complexes (CCs) (
n
= 63) or were singletons (
n
= 33). The distribution of STs varied spatially, by host species, and in association with mortality events. Several STs (i.e., ST9, ST10, ST30, and ST78) were found in multiple states, whereas the remaining STs were localized to single states. With the exception of ST256, which was recovered from rainbow trout and Chinook salmon, all STs were found to infect a single host species. Isolates that were collected during bacterial cold water disease outbreaks most frequently belonged to CC-ST10 (e.g., ST10 and ST78). Collectively, the results of this study clearly demonstrate the genetic diversity of
F. psychrophilum
within the United States and identify STs of clinical significance. Although the majority of STs described herein were novel, some (e.g., ST9, ST10, ST13, ST30, and ST31) were previously recovered on other continents, which demonstrates the transcontinental distribution of
F. psychrophilum
genotypes.

IMPORTANCE
Flavobacterium psychrophilum
is the causative agent of bacterial cold water disease (BCWD) and rainbow trout fry syndrome (RTFS) and is an important bacterial pathogen of wild and farmed salmonids worldwide. These infections are responsible for large economic losses globally, yet the genetic diversity of this pathogen remains to be fully investigated. Previous studies have identified the genetic diversity of this pathogen in other main aquaculture regions; however, little effort has been focused on the United States. In this context, this study aims to examine the genetic diversity of
F. psychrophilum
from the United States, as this region remains important in salmonid aquaculture.
Type III-Dependent Translocation of HrpB2 by a Nonpathogenic
hpaABC
Mutant of the Plant-Pathogenic Bacterium Xanthomonas campestris pv. vesicatoria
Authors: Scheibner Felix , Schulz Steve , Hausner Jens , Marillonnet Sylvestre , Büttner Daniela 
Published: March 2016

ABSTRACT

The plant-pathogenic bacterium
Xanthomonas campestris
pv. vesicatoria employs a type III secretion (T3S) system to translocate effector proteins into plant cells. The T3S apparatus spans both bacterial membranes and is associated with an extracellular pilus and a channel-like translocon in the host plasma membrane. T3S is controlled by the switch protein HpaC, which suppresses secretion and translocation of the predicted inner rod protein HrpB2 and promotes secretion of translocon and effector proteins. We previously reported that HrpB2 interacts with HpaC and the cytoplasmic domain of the inner membrane protein HrcU (C. Lorenz, S. Schulz, T. Wolsch, O. Rossier, U. Bonas, and D. Büttner, PLoS Pathog
4:
e1000094, 2008,
http://dx.doi.org/10.1371/journal.ppat.1000094
). However, the molecular mechanisms underlying the control of HrpB2 secretion are not yet understood. Here, we located a T3S and translocation signal in the N-terminal 40 amino acids of HrpB2. The results of complementation experiments with HrpB2 deletion derivatives revealed that the T3S signal of HrpB2 is essential for protein function. Furthermore, interaction studies showed that the N-terminal region of HrpB2 interacts with the cytoplasmic domain of HrcU, suggesting that the T3S signal of HrpB2 contributes to substrate docking. Translocation of HrpB2 is suppressed not only by HpaC but also by the T3S chaperone HpaB and its secreted regulator, HpaA. Deletion of
hpaA
,
hpaB
, and
hpaC
leads to a loss of pathogenicity but allows the translocation of fusion proteins between the HrpB2 T3S signal and effector proteins into leaves of host and non-host plants.

IMPORTANCE
The T3S system of the plant-pathogenic bacterium
Xanthomonas campestris
pv. vesicatoria is essential for pathogenicity and delivers effector proteins into plant cells. T3S depends on HrpB2, which is a component of the predicted periplasmic inner rod structure of the secretion apparatus. HrpB2 is secreted during the early stages of the secretion process and interacts with the cytoplasmic domain of the inner membrane protein HrcU. Here, we localized the secretion and translocation signal of HrpB2 in the N-terminal 40 amino acids and show that this region is sufficient for the interaction with the cytoplasmic domain of HrcU. Our results suggest that the T3S signal of HrpB2 is required for the docking of HrpB2 to the secretion apparatus. Furthermore, we provide experimental evidence that the N-terminal region of HrpB2 is sufficient to target effector proteins for translocation in a nonpathogenic
X. campestris
pv. vesicatoria strain.
Epoxyalkane:Coenzyme M Transferase Gene Diversity and Distribution in Groundwater Samples from Chlorinated-Ethene-Contaminated Sites
Authors: Liu Xikun , Mattes Timothy E. 
Published: March 2016

ABSTRACT

Epoxyalkane:coenzyme M transferase (EaCoMT) plays a critical role in the aerobic biodegradation and assimilation of alkenes, including ethene, propene, and the toxic chloroethene vinyl chloride (VC). To improve our understanding of the diversity and distribution of EaCoMT genes in the environment, novel EaCoMT-specific terminal-restriction fragment length polymorphism (T-RFLP) and nested-PCR methods were developed and applied to groundwater samples from six different contaminated sites. T-RFLP analysis revealed 192 different EaCoMT T-RFs. Using clone libraries, we retrieved 139 EaCoMT gene sequences from these samples. Phylogenetic analysis revealed that a majority of the sequences (78.4%) grouped with EaCoMT genes found in VC- and ethene-assimilating
Mycobacterium
strains and
Nocardioides
sp. strain JS614. The four most-abundant T-RFs were also matched with EaCoMT clone sequences related to
Mycobacterium
and
Nocardioides
strains. The remaining EaCoMT sequences clustered within two emergent EaCoMT gene subgroups represented by sequences found in propene-assimilating
Gordonia rubripertincta
strain B-276 and
Xanthobacter autotrophicus
strain Py2. EaCoMT gene abundance was positively correlated with VC and ethene concentrations at the sites studied.

IMPORTANCE
The EaCoMT gene plays a critical role in assimilation of short-chain alkenes, such as ethene, VC, and propene. An improved understanding of EaCoMT gene diversity and distribution is significant to the field of bioremediation in several ways. The expansion of the EaCoMT gene database and identification of incorrectly annotated EaCoMT genes currently in the database will facilitate improved design of environmental molecular diagnostic tools and high-throughput sequencing approaches for future bioremediation studies. Our results further suggest that potentially significant aerobic VC degraders in the environment are not well represented in pure culture. Future research should aim to isolate and characterize aerobic VC-degrading bacteria from these underrepresented groups.
Soil Characteristics Driving Arbuscular Mycorrhizal Fungal Communities in Semiarid Mediterranean Soils
Authors: Alguacil Maria del Mar , Torres Maria Pilar , Montesinos-Navarro Alicia , Roldán Antonio 
Published: March 2016

ABSTRACTWe investigated communities of arbuscular mycorrhizal fungi (AMF) in the roots and the rhizosphere soil ofBrachypodium retusumin six different natural soils under field conditions. We explored phylogenetic patterns of AMF composition using indicator species analyses to find AMF associated with a given habitat (root versus rhizosphere) or soil type. We tested whether the AMF characteristics of different habitats or contrasting soils were more closely related than expected by chance. Then we used principal-component analysis and multivariate analysis of variance to test for the relative contribution of each factor in explaining the variation in fungal community composition. Finally, we used redundancy analysis to identify the soil properties that significantly explained the differences in AMF communities across soil types. The results pointed out a tendency of AMF communities in roots to be closely related and different from those in the rhizosphere soil. The indicator species analyses revealed AMF associated with rhizosphere soil and the root habitat. Soil type also determined the distribution of AMF communities in soils, and this effect could not be attributed to a single soil characteristic, as at least three soil properties related to microbial activity, i.e., pH and levels of two micronutrients (Mn and Zn), played significant roles in triggering AMF populations.IMPORTANCECommunities of arbuscular mycorrhizal fungi (AMF) are main components of soil biota that can determine the productivity of ecosystems. These fungal assemblages vary across host plants and ecosystems, but the main ecological processes that shape the structures of these communities are still largely unknown. A field study in six different soil types from semiarid areas revealed that AMF communities are significantly influenced by habitat (soil versus roots) and soil type. In addition, three soil properties related to microbiological activity (i.e., pH and manganese and zinc levels) were the main factors triggering the distribution of AMF. These results contribute to a better understanding of the ecological factors that can shape AMF communities, an important soil microbial group that affects multiple ecosystem functions.
Permanent congenital hypothyroidism with blood spot thyroid stimulating hormone <10 mU/L
Authors: Jones Jeremy H , Smith Sarah , Dorrian Catherine , Mason Avril , Shaikh M Guftar 
Published: March 2016

BackgroundThe UK recommended lower threshold for neonatal blood spot thyroid stimulating hormone (TSH) screening for congenital hypothyroidism (CHT) is 10.0 mU/L. Some laboratories use lower thresholds. This will lead to referral of mildly or unaffected infants but some will require thyroxine therapy.MethodsLaboratory referrals with a first or repeat capillary TSH between 8.0 and <10.0 mU/L were identified (January 2004 to March 2014). The outcome of these cases was examined.Results26 infants had one or more blood spot TSH values between 8.0 and 9.99 mU/L; 65% had transient elevated neonatal TSH while one is awaiting diagnostic challenge. The remaining eight (31%) have permanent CHT; three with dyshormonogenesis, two with thyroid ectopia and the others met the criteria for definite CHT. Two out of three with dyshormonogenesis presented with decompensated hypothyroidism.ConclusionsInfants with permanent and occasionally severe CHT may have a screening TSH below the UK recommended lower cut-off.
Patterns of orodental injury and mouthguard use in Dutch field hockey
Authors: Vucic Strahinja , Drost Rosalin W , van Wijk Arjen J , Wesselink Paul R , Wolvius Eppo B 
Published: March 2016

BackgroundOrodental injuries in field hockey are a growing cause of concern that requires attention.ObjectiveThe objective of this cross-sectional study was to investigate the patterns of orodental injury, and the use of mouthguards in Dutch national field hockey.Materials and methodsIn the period from 1 May to 31 July 2014, a 33-item questionnaire about orodental injury and mouthguard use was sent to 7 field hockey clubs in the Netherlands. Data were analysed using 2 multivariable logistic (non-)linear regression per outcome measurement: (1) orodental injury and (2) type of mouthguard.ResultsOut of 6585 players, 1299 (20%) responded sufficiently and were eligible for the study. In total, 214 hockey players (16%) experienced at least 1 orodental injury in their career. The injuries were less severe in athletes who wore a mouthguard during an accident than in those who did not, OR=2.1 to 3.3, p≤0.05. Players without mouthguard sustained broken and knocked out teeth more frequently, while players with a mouthguard had more lip cuts (p≤0.05). Players complained less about custom-made than about mouth-moulded mouthguards (p≤0.05). Also, males were more at risk for an orodental injury, OR=1.4 (95% CI 1.0 to 1.9), and were less likely to have a custom-made mouthguard, OR=0.7 (95% CI 0.6 to 0.9), than females.ConclusionsA substantial number of field hockey players suffers from orodental injury. Mouthguards should be included in prevention strategies as they are associated with less severe injuries and patterns of injury are to be taken into account when targeting specific groups.
Physiotherapy for pain: a meta-epidemiological study of randomised trials
Authors: Ginnerup-Nielsen Elisabeth , Christensen Robin , Thorborg Kristian , Tarp Simon , Henriksen Marius 
Published: March 2016

ObjectivesTo empirically assess the clinical effects of physiotherapy on pain in adults.DesignUsing meta-epidemiology, we report on the effects of a ‘physiotherapy’ intervention on self-reported pain in adults. For each trial, the group difference in the outcome ‘pain intensity’ was assessed as standardised mean differences (SMD) with 95% CIs. Stratified analyses were conducted according to patient population (International Classification of Diseases-10 classes), type of physiotherapy intervention, their interaction, as well as type of comparator group and risks of bias. The quality of the body of evidence was assessed based on GRADE methodology.Data sourcesSystematic searches were carried out in MEDLINE and PEDro from 1 January 2004–31 December 2013. 174 trials (224 comparisons) met the inclusion criteria for the meta-analysis.Eligibility criteria for selecting studiesRandomised trials using ‘no intervention’ or of a sham-controlled design were selected. Only articles written in English were eligible.ResultsAn overall moderate effect of physiotherapy on pain corresponding to 0.65 SD-units (95% CI 0.57 to 0.73) was found based on a moderate inconsistency (I2=51%). Stratified exploration showed that therapeutic exercise for musculoskeletal diseases tended to be more beneficial than multimodal interventions (difference 0.30 95% CI 0.03 to 0.57; p=0.03). Trials with a ‘no intervention’ comparator tended to have a higher overall effect size than trials with a sham comparator (difference 0.25; 95% CI 0.09 to 0.41; p=0.004). In general, our confidence in the estimates was low, mainly due to high risk of performance biases and between-study heterogeneity.ConclusionsPhysiotherapy reduces pain in adults, but standardisation of interventions and focus on trial research with low risks of bias and reproducible treatment modalities are needed.Trial registration numberCRD42014008754.
Fracture epidemiology in male elite football players from 2001 to 2013: ‘How long will this fracture keep me out?’
Authors: Larsson David , Ekstrand Jan , Karlsson Magnus K 
Published: March 2016

BackgroundDetermining fracture risk and rehabilitation periods after specific fractures in professional football is essential for team planning.AimTo identify fracture epidemiology and absences after different types of fractures in male professional football players.Methods2439 players from 41 professional male teams in 10 countries were followed prospectively from 2001 to 2013. Team medical staff registered fractures, absences after fractures and player exposure.Results364 fractures were recorded, with an incidence of 0.27/1000 h of exposure (95% CI 0.25 to 0.30). The incidence of traumatic fractures was 0.25 (0.22 to 0.27) and that of stress fractures was 0.03 (0.02 to 0.04). 45% of traumatic fractures and 86% of stress fractures affected the lower extremities. Absence after a fracture was 32 days (1–278) (median (range)), compared to that after a traumatic fracture of 30 days (1–278) and a stress fracture of 65 days (6–168) (p<0.001). Annual fracture incidence was stable during the study period (R2=0.051, b=−0.011 (95% CI −0.043 to 0.021)). Young players had a relative risk of 10.9 (3.3 to 35.6) of sustaining stress fractures compared to old players (p<0.01). The fracture incidence did not differ between individuals in different playing positions (p=0.10).SummaryA male professional football team can expect 1 to 2 fractures per season. There are more traumatic fractures than stress fractures; while most fractures affect the lower extremities, stress fractures yield longer absences than traumatic fractures and young players have more stress fractures than old players. There is no difference in risk among players at different playing positions.