bluuebunny/crossref_metadata_2025_split huggingface dataset:
Degradation of Granular Starch by the Bacterium Microbacterium aurum Strain B8.A Involves a Modular α-Amylase Enzyme System with FNIII and CBM25 Domains
Authors: Valk Vincent , Eeuwema Wieger , Sarian Fean D. , van der Kaaij Rachel M. , Dijkhuizen Lubbert 
Published: July 2015

ABSTRACT

The bacterium
Microbacterium aurum
strain B8.A, originally isolated from a potato plant wastewater facility, is able to degrade different types of starch granules. Here we report the characterization of an unusually large, multidomain
M. aurum
B8.A α-amylase enzyme (MaAmyA). MaAmyA is a 1,417-amino-acid (aa) protein with a predicted molecular mass of 148 kDa. Sequence analysis of MaAmyA showed that its catalytic core is a family GH13_32 α-amylase with the typical ABC domain structure, followed by a fibronectin (FNIII) domain, two carbohydrate binding modules (CBM25), and another three FNIII domains. Recombinant expression and purification yielded an enzyme with the ability to degrade wheat and potato starch granules by introducing pores. Characterization of various truncated mutants of MaAmyA revealed a direct relationship between the presence of CBM25 domains and the ability of MaAmyA to form pores in starch granules, while the FNIII domains most likely function as stable linkers. At the C terminus, MaAmyA carries a 300-aa domain which is uniquely associated with large multidomain amylases; its function remains to be elucidated. We concluded that
M. aurum
B8.A employs a multidomain enzyme system to initiate degradation of starch granules via pore formation.
The Role of the Microbiome of Truffles in Aroma Formation: a Meta-Analysis Approach
Authors: Vahdatzadeh Maryam , Deveau Aurélie , Splivallo Richard 
Published: July 2015

ABSTRACT

Truffles (
Tuber
spp.) are ascomycete subterraneous fungi that form ectomycorrhizas in a symbiotic relationship with plant roots. Their fruiting bodies are appreciated for their distinctive aroma, which might be partially derived from microbes. Indeed, truffle fruiting bodies are colonized by a diverse microbial community made up of bacteria, yeasts, guest filamentous fungi, and viruses. The aim of this minireview is two-fold. First, the current knowledge on the microbial community composition of truffles has been synthesized to highlight similarities and differences among four truffle (
Tuber
) species (
T. magnatum
,
T. melanosporum
,
T. aestivum
, and
T. borchii
) at various stages of their life cycle. Second, the potential role of the microbiome in truffle aroma formation has been addressed for the same four species. Our results suggest that on one hand, odorants, which are common to many truffle species, might be of mixed truffle and microbial origin, while on the other hand, less common odorants might be derived from microbes only. They also highlight that bacteria, the dominant group in the microbiome of the truffle, might also be the most important contributors to truffle aroma not only in
T. borchii
, as already demonstrated, but also in
T. magnatum
,
T. aestivum
, and
T. melanosporum
.
Three of a Kind: Genetically Similar Tsukamurella Phages TIN2, TIN3, and TIN4
Authors: Dyson Zoe A. , Tucci Joseph , Seviour Robert J. , Petrovski Steve 
Published: July 2015

ABSTRACT

Three
Tsukamurella
phages, TIN2, TIN3, and TIN4, were isolated from activated sludge treatment plants located in Victoria, Australia, using conventional enrichment techniques. Illumina and 454 whole-genome sequencing of these
Siphoviridae
viruses revealed that they had similar genome sequences, ranging in size between 76,268 bp and 76,964 bp. All three phages shared 74% nucleotide sequence identity to the previously described
Gordonia
phage GTE7. Genome sequencing suggested that phage TIN3 had suffered a mutation in one of its lysis genes compared to the sequence of phage TIN4, to which it is genetically very similar. Mass spectroscopy data showed the unusual presence of a virion structural gene in the DNA replication module of phage TIN4, disrupting the characteristic modular genome architecture of
Siphoviridae
phages. All three phages appeared highly virulent on strains of
Tsukamurella inchonensis
and
Tsukamurella paurometabola
.
Involvement of Coat Proteins in Bacillus subtilis Spore Germination in High-Salinity Environments
Authors: Nagler Katja , Setlow Peter , Reineke Kai , Driks Adam , Moeller Ralf 
Published: July 2015

ABSTRACT

The germination of spore-forming bacteria in high-salinity environments is of applied interest for food microbiology and soil ecology. It has previously been shown that high salt concentrations detrimentally affect
Bacillus subtilis
spore germination, rendering this process slower and less efficient. The mechanistic details of these salt effects, however, remained obscure. Since initiation of nutrient germination first requires germinant passage through the spores' protective integuments, the aim of this study was to elucidate the role of the proteinaceous spore coat in germination in high-salinity environments. Spores lacking major layers of the coat due to chemical decoating or mutation germinated much worse in the presence of NaCl than untreated wild-type spores at comparable salinities. However, the absence of the crust, the absence of some individual nonmorphogenetic proteins, and the absence of either CwlJ or SleB had no or little effect on germination in high-salinity environments. Although the germination of spores lacking GerP (which is assumed to facilitate germinant flow through the coat) was generally less efficient than the germination of wild-type spores, the presence of up to 2.4 M NaCl enhanced the germination of these mutant spores. Interestingly, nutrient-independent germination by high pressure was also inhibited by NaCl. Taken together, these results suggest that (i) the coat has a protective function during germination in high-salinity environments; (ii) germination inhibition by NaCl is probably not exerted at the level of cortex hydrolysis, germinant accessibility, or germinant-receptor binding; and (iii) the most likely germination processes to be inhibited by NaCl are ion, Ca
2+
-dipicolinic acid, and water fluxes.
Lactic Acid Bacteria in Durum Wheat Flour Are Endophytic Components of the Plant during Its Entire Life Cycle
Authors: Minervini Fabio , Celano Giuseppe , Lattanzi Anna , Tedone Luigi , De Mastro Giuseppe , Gobbetti Marco , De Angelis Maria 
Published: July 2015

ABSTRACTThis study aimed at assessing the dynamics of lactic acid bacteria and otherFirmicutesassociated with durum wheat organs and processed products. 16S rRNA gene-based high-throughput sequencing showed thatLactobacillus,Streptococcus,Enterococcus, andLactococcuswere the main epiphytic and endophytic genera among lactic acid bacteria.Bacillus,Exiguobacterium,Paenibacillus, andStaphylococcuscompleted the picture of the core genus microbiome. The relative abundance of each lactic acid bacterium genus was affected by cultivars, phenological stages, otherFirmicutesgenera, environmental temperature, and water activity (aw) of plant organs. Lactobacilli, showing the highest sensitivity to aw, markedly decreased during milk development (Odisseo) and physiological maturity (Saragolla). At these stages,Lactobacilluswas mainly replaced byStreptococcus,Lactococcus, andEnterococcus. However, a key sourdough species,Lactobacillus plantarum, was associated with plant organs during the life cycle of Odisseo and Saragolla wheat. The composition of the sourdough microbiota and the overall quality of leavened baked goods are also determined throughout the phenological stages of wheat cultivation, with variations depending on environmental and agronomic factors.
High-Pressure Inactivation of Rotaviruses: Role of Treatment Temperature and Strain Diversity in Virus Inactivation
Authors: Araud Elbashir , DiCaprio Erin , Yang Zhihong , Li Xinhui , Lou Fangfei , Hughes John H. , Chen Haiqiang , Li Jianrong 
Published: July 2015

ABSTRACT

Rotavirus (RV) is the major etiological agent of acute gastroenteritis in infants worldwide. Although high-pressure processing (HPP) is a popular method to inactivate enteric pathogens in food, the sensitivity of different virus strains within same species and serotype to HPP is variable. This study aimed to compare the barosensitivities of seven RV strains derived from four serotypes (serotype G1, strains Wa, Ku, and K8; serotype G2, strain S2; serotype G3, strains SA-11 and YO; and serotype G4, strain ST3) following high-pressure treatment. RV strains showed various responses to HPP based on the initial temperature and had different inactivation profiles. Ku, K8, S2, SA-11, YO, and ST3 showed enhanced inactivation at 4°C compared to 20°C. In contrast, strain Wa was not significantly impacted by the initial treatment temperature. Within serotype G1, strain Wa was significantly (
P
< 0.05) more resistant to HPP than strains Ku and K8. Overall, the resistance of the human RV strains to HPP at 4°C can be ranked as Wa > Ku = K8 > S2 > YO > ST3, and in terms of serotype the ranking is G1 > G2 > G3 > G4. In addition, pressure treatment of 400 MPa for 2 min was sufficient to eliminate the Wa strain, the most pressure-resistant RV, from oyster tissues. HPP disrupted virion structure but did not degrade viral protein or RNA, providing insight into the mechanism of viral inactivation by HPP. In conclusion, HPP is capable of inactivating RV at commercially acceptable pressures, and the efficacy of inactivation is strain dependent.
Use of 16S rRNA Gene-Targeted Group-Specific Primers for Real-Time PCR Analysis of Predominant Bacteria in Mouse Feces
Authors: Yang Yun-Wen , Chen Mang-Kun , Yang Bing-Ya , Huang Xian-Jie , Zhang Xue-Rui , He Liang-Qiang , Zhang Jing , Hua Zi-Chun 
Published: July 2015

ABSTRACT

Mouse models are widely used for studying gastrointestinal (GI) tract-related diseases. It is necessary and important to develop a new set of primers to monitor the mouse gut microbiota. In this study, 16S rRNA gene-targeted group-specific primers for
Firmicutes
,
Actinobacteria
,
Bacteroidetes
,
Deferribacteres
, “
Candidatus
Saccharibacteria,”
Verrucomicrobia
,
Tenericutes
, and
Proteobacteria
were designed and validated for quantification of the predominant bacterial species in mouse feces by real-time PCR. After confirmation of their accuracy and specificity by high-throughput sequencing technologies, these primers were applied to quantify the changes in the fecal samples from a trinitrobenzene sulfonic acid-induced colitis mouse model. Our results showed that this approach efficiently predicted the occurrence of colitis, such as spontaneous chronic inflammatory bowel disease in transgenic mice. The set of primers developed in this study provides a simple and affordable method to monitor changes in the intestinal microbiota at the phylum level.
Identification of Bradyrhizobium elkanii Genes Involved in Incompatibility with Soybean Plants Carrying the
Rj4
Allele
Authors: Faruque Omar M. , Miwa Hiroki , Yasuda Michiko , Fujii Yoshiharu , Kaneko Takakazu , Sato Shusei , Okazaki Shin 
Published: July 2015

ABSTRACT

Symbioses between leguminous plants and soil bacteria known as rhizobia are of great importance to agricultural production and nitrogen cycling. While these mutualistic symbioses can involve a wide range of rhizobia, some legumes exhibit incompatibility with specific strains, resulting in ineffective nodulation. The formation of nodules in soybean plants (
Glycine max
) is controlled by several host genes, which are referred to as
Rj
genes. The soybean cultivar BARC2 carries the
Rj4
gene, which restricts nodulation by specific strains, including
Bradyrhizobium elkanii
USDA61. Here we employed transposon mutagenesis to identify the genetic locus in USDA61 that determines incompatibility with soybean varieties carrying the
Rj4
allele. Introduction of the Tn
5
transposon into USDA61 resulted in the formation of nitrogen fixation nodules on the roots of soybean cultivar BARC2 (
Rj4 Rj4
). Sequencing analysis of the sequence flanking the Tn
5
insertion revealed that six genes encoding a putative histidine kinase, transcriptional regulator, DNA-binding transcriptional activator, helix-turn-helix-type transcriptional regulator, phage shock protein, and cysteine protease were disrupted. The cysteine protease mutant had a high degree of similarity with the type 3 effector protein XopD of
Xanthomonas campestris
. Our findings shed light on the diverse and complicated mechanisms that underlie these highly host-specific interactions and indicate the involvement of a type 3 effector in
Rj4
nodulation restriction, suggesting that
Rj4
incompatibility is partly mediated by effector-triggered immunity.
Temperature-Sensitive Salmonella enterica Serovar Enteritidis PT13a Expressing Essential Proteins of Psychrophilic Bacteria
Authors: Duplantis Barry N. , Puckett Stephanie M. , Rosey Everett L. , Ameiss Keith A. , Hartman Angela D. , Pearce Stephanie C. , Nano Francis E. 
Published: July 2015

ABSTRACT

Synthetic genes based on deduced amino acid sequences of the NAD-dependent DNA ligase (
ligA
) and CTP synthetase (
pyrG
) of psychrophilic bacteria were substituted for their native homologues in the genome of
Salmonella enterica
serovar Enteritidis phage type 13a (PT13a). The resulting strains were rendered temperature sensitive (TS) and did not revert to temperature resistance at a detectable level. At permissive temperatures, TS strains grew like the parental strain in broth medium and in macrophage-like cells, but their growth was slowed or stopped when they were shifted to a restrictive temperature. When injected into BALB/c mice at the base of the tail, representing a cool site of the body, the strains with restrictive temperatures of 37, 38.5, and 39°C persisted for less than 1 day, 4 to 7 days, and 20 to 28 days, respectively. The wild-type strain persisted at the site of inoculation for at least 28 days. The wild-type strain, but not the TS strains, was also found in spleen-plus-liver homogenates within 1 day of inoculation of the tail and was detectable in these organs for at least 28 days. Intramuscular vaccination of White Leghorn chickens with the PT13a strain carrying the psychrophilic
pyrG
gene provided some protection against colonization of the reproductive tract and induced an anti-
S. enterica
antibody response.
AllR Controls the Expression of Streptomyces coelicolor Allantoin Pathway Genes
Authors: Navone Laura , Macagno Juan Pablo , Licona-Cassani Cuauhtémoc , Marcellin Esteban , Nielsen Lars K. , Gramajo Hugo , Rodriguez Eduardo 
Published: July 2015

ABSTRACT

Streptomyces
species are native inhabitants of soil, a natural environment where nutrients can be scarce and competition fierce. They have evolved ways to metabolize unusual nutrients, such as purines and its derivatives, which are highly abundant in soil. Catabolism of these uncommon carbon and nitrogen sources needs to be tightly regulated in response to nutrient availability and environmental stimulus. Recently, the allantoin degradation pathway was characterized in
Streptomyces coelicolor
. However, there are questions that remained unanswered, particularly regarding pathway regulation. Here, using a combination of proteomics and genetic approaches, we identified the negative regulator of the allantoin pathway, AllR.
In vitro
studies confirmed that AllR binds to the promoter regions of allantoin catabolic genes and determined the AllR DNA binding motif. In addition, effector studies showed that allantoic acid, and glyoxylate, to a lesser extent, inhibit the binding of AllR to the DNA. Inactivation of AllR repressor leads to the constitutive expression of the AllR regulated genes and intriguingly impairs actinorhodin and undecylprodigiosin production. Genetics and proteomics analysis revealed that among all genes from the allantoin pathway that are upregulated in the
allR
mutant, the
hyi
gene encoding a hydroxypyruvate isomerase (Hyi) is responsible of the impairment of antibiotic production.
The geological CO2 degassing history of a long-lived caldera
Authors: Chiodini Giovanni , Pappalardo L. , Aiuppa A. , Caliro S. 
Published: July 2015

Abstract
The majority of the ∼100 Holocene calderas on Earth host vigorously active hydrothermal systems, the heat and volatile budgets of which are sustained by degassing of deeply stored magma. Calderas may thus contribute a nontrivial, although poorly quantified, fraction of the global budget of magmatic volatiles such as CO2. Here we use original isotopic and petrological results from Campi Flegrei volcano, Italy, to propose that hydrothermal calcites are natural mineral archives for the magmatic CO2 that reacted with reservoir rocks during the geological history of a caldera. We show that Campi Flegrei calcites, identified in core samples extracted from 3-km-deep geothermal wells, formed at isotopic equilibrium with magmatic fluids having δ18OH2O of +8.7‰ to +12.7‰, and δ13CCO2 of ∼−1.5‰. This inferred fossil fluid composition is virtually identical to that of present-day fumaroles, demonstrating a stable carbon source during the caldera’s (&lt;40 k.y.) history. We use the mass of calcites stored in the hydrothermal system to estimate that 12 Gt of magmatic CO2 reacted with the Campi Flegrei rocks during the caldera history; this corresponds to a time-averaged CO2 flux of ∼800 t d–1. This long-term CO2 flux, the first of its kind in the geological literature, is similar to the present-day soil CO2 degassing flux (1100 ± 200 t d–1). We conclude that the actual magmatic CO2 degassing flux from calderas may be severely underestimated if subsurface calcite precipitation is not taken into account.
Boxing injury epidemiology in the Great Britain team: a 5-year surveillance study of medically diagnosed injury incidence and outcome
Authors: Loosemore Michael , Lightfoot Joseph , Palmer-Green Deborah , Gatt Ian , Bilzon James , Beardsley Chris 
Published: July 2015

ObjectivesThere has been no comprehensive injury report of elite-level amateur boxers in competition and training. We reviewed injuries in training and competition in the Great Britain (GB) amateur boxing squad between 2005 and 2009.MethodsLongitudinal, prospective injury surveillance over 5 years of the GB boxing squad from 2005 to 2009. 66 boxers passed through the squad. The location, region affected, description, and the duration of each injury were recorded by the team doctor and team physiotherapist. We recorded whether the injury occurred during competition or training, and also whether it was a new or a recurrent injury. The injury rate during competition was calculated as the number of injuries per 1000 h.ResultsMore injuries affected the hand than any other body location. This was the case overall, in training and competition individually, and for both new and recurrent injuries. More injuries occurred during training than during competition, and most injuries were new rather than recurrent. Total injury rate during competition was 828 per 1000 h and hand injury rate in competition was 302 injuries per 1000 h. Hand injury rate in competition was significantly higher than at the other locations. The incidence of concussion is comparatively low.ConclusionsInjury prevention should aim to protect the hands and wrists of elite amateur boxers.
Risk factors associated with lower extremity stress fractures in runners: a systematic review with meta-analysis
Authors: Wright Alexis A , Taylor Jeffrey B , Ford Kevin R , Siska Lindsey , Smoliga James M 
Published: July 2015

BackgroundStress fractures are common overuse injuries with up to 95% occurring in the lower extremities. Among runners, stress fractures account for 15–20% of all musculoskeletal injuries.PurposeWe systematically reviewed and critiqued the evidence regarding risk factors associated with increased risk of lower extremity stress fractures in runners.Study designSystematic review.MethodsA systematic, computerised literature search of Medline, Embase, PubMed, SPORTDiscus, and CINAHL databases (from database inception through 9 January 2014) using keywords related to risk factors and stress fractures. This systematic review with meta-analysis utilised the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines for the search and reporting phases of the study. Inverse variance meta-analyses, using a random effects model were used to summarise ORs.Results8 articles met the inclusion criteria; 7 were considered low risk. 4 articles qualified for meta-analysis. Results of the meta-analysis identified previous history of stress fracture and female sex as the primary risk factors for future stress fracture with a pooled OR of 4.99 (95% CI 2.91 to 8.56; p<0.001; I2=0%) and 2.31 (95% CI 1.24 to 4.29; p<0.01; I2=0%), respectively.ConclusionsCurrently, only previous history of stress fracture and female sex are risk factors for lower extremity stress fractures strongly supported by the data.
Injury and illness surveillance during the 24th Men's Handball World Championship 2015 in Qatar
Authors: Bere Tone , Alonso Juan-Manuel , Wangensteen Arnlaug , Bakken Arnhild , Eirale Cristiano , Dijkstra H Paul , Ahmed Hosny , Bahr Roald , Popovic Nebojsa 
Published: July 2015

BackgroundThe IOC encourages international federations to establish systematic athlete injury and illness surveillance programmes.ObjectiveTo describe pattern of injuries and illnesses during the 24th Men's Handball World Championship 2015 by implementing the IOC injury and illness surveillance protocol.MethodsThe medical staff of participating teams (n=24) were requested to report all new injuries and illnesses during matches and/or training on a daily basis throughout the event (15 January to 1 February, 2015). Exposure (number of player-hours) during all matches was calculated for all players (n=384) and for each of the 4 player positions (wing, back, line and goalkeeper).ResultsMedical staff of all teams submitted 96.7% (n=325) of the daily report forms. In total, 27.1% of the players were injured, and of the 132 injuries reported, 40% were time-loss injuries. The total incidence of injuries was 104.5 per 1000 player-hours. The highest risk of injury was found among line players, and more injuries occurred during the first half of the matches. The most frequent injury location was the ankle, followed by the thigh, knee and head/face. The majority of injuries were contusion, sprain or strain. In total, 10.9% of the players were affected by an illness during the event. Of the 42 cases recorded, 31 (73.8%) were reported as respiratory tract infection.ConclusionsThe risk of injury in handball is high among Olympic sports. Preventive measures should focus on contusions, ankle sprains, and thigh muscle strains, as well as measures aimed to reduce upper respiratory tract infections.