bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protonation–state‐Coupled Conformational Dynamics in Reaction Mechanisms of Channel and Pump Rhodopsins
Authors: Bondar Ana‐Nicoleta , Smith Jeremy C. 
Published: May 2017

AbstractChannel and pump rhodopsins use energy from light absorbed by a covalently bound retinal chromophore to transport ions across membranes of microbial cells. Ion transfer steps, including proton transfer, can couple to changes in protein conformational dynamics and water positions. Although general principles of how microbial rhodopsins function are largely understood, key issues pertaining to reaction mechanisms remain unclear. In this review, we compare the protonation‐coupled dynamics of pump and channelrhodopsins, highlighting the roles that water dynamics, protein electrostatics and protein flexibility can have in ion transport mechanisms. We discuss observations supporting important functional roles of inter‐ and intra‐helical carboxylate/hydroxyl hydrogen‐bonding motifs. As specific examples, we use the proton pump bacteriorhodopsin, the sodium pump KR2, channelrhodopsins and Anabaena sensory rhodopsin. We outline the usefulness of theoretic biophysics approaches to the study of retinal proteins, challenges in studying the hydrogen‐bond dynamics of rhodopsin active sites, and implications for conformational coupling in membrane transporters.
Study on the Basic Performance of Three‐phase Fluidized Bed Equipment for Solar Photocatalysis–Membrane Separation
Authors: Sha Li , Xie Liping , Li Miaomiao , Fei Xuening , Du Jinshan , Zou Chenxi 
Published: May 2017

AbstractIn this study, three‐phase fluidized bed equipment for the solar photocatalysis–membrane separation (E‐SPME), comprising solar photocatalytic degradation and membrane separation zones, was first introduced, and the photocatalytic degradation of acid red B wastewater (ARBW) with a TiO2 photocatalyst was investigated using the E‐SPME. The experimental results indicated the circulating flow of wastewater between the two zones and the increase in the ARBW photocatalytic degradation efficiency with decreasing membrane flux. The same experimental phenomenon was observed with the change in the aeration rate in the lower water tank from 0.10 to 0.40 m3 h−1, but the degradation efficiency started to decrease with further increase in the aeration rate to 0.50 m3 h−1. The degradation efficiency on a clear day was greater than that on a cloudy day; however, it was significantly improved with the opened UV lamps on a cloudy day. The steady operation of the E‐SPME was still possible by the opening of the UV lamps on completely cloudy and clear days with a solar light intensity of <13.0 W m−2.
Ultrastructural study on the interaction between Physcomitrella patens and Botrytis cinerea
Authors: Yan H. Q. , Zhang T. T. , Lan S. C. , Jiang S. 
Published: May 2017

Little is known about the interactions of bryophytes with their pathogens compared with those of flowering plants. This study used the moss Physcomitrella patens and fungal pathogen Botrytis cinerea to investigate their interaction at the ultrastructural level. Infection behaviour of B. cinerea in moss tissues was observed for 1–7 days after inoculation. Some appressoria directly penetrated P. patens cytoplasm through leaf cell walls, and others entered the intercellular spaces of leaves and infected cytoplasm. Infection hyphae were observed in sclerenchyma cells of P. patens stems for the first time. The results demonstrated that the ratio of hyphae‐inoculated leaf cells to leaf numbers could be used to quantify the disease development process at 24 h after inoculation. The ultrastructural studies revealed two responses of P. patens to B. cinerea inoculation: reinforcement of cell walls, including papillae formation; and cell death. This was the first observation of papillae for P. patens–B. cinerea interaction at the ultrastructural level. Papillae in P. patens had a similar ultrastructure to those of higher plants, and may be involved in the defence response to B. cinerea infection. Thus papillae formation is probably an evolutionarily conserved defence mechanism from the early land colonization by plants. Cell death during the P. patens–B. cinerea interaction had some features of programmed cell death, with hydrogen peroxide produced in cytoplasm membranes, suggesting something like a hypersensitive response. These ultrastructural studies suggest that P. patens could be a useful system for studying phytopathogens and could provide theoretical bases for defence mechanisms in evolutionary development.
Anaerobic soil disinfestation is an alternative to soil fumigation for control of some soilborne pathogens in strawberry production
Authors: Shennan C. , Muramoto J. , Koike S. , Baird G. , Fennimore S. , Samtani J. , Bolda M. , Dara S. , Daugovish O. , Lazarovits G. , Butler D. , Rosskopf E. , Kokalis‐Burelle N. , Klonsky K. , Mazzola M. 
Published: May 2017

Alternatives to soil fumigation are needed for soilborne disease control. The aim of this study was to test anaerobic soil disinfestation (ASD) as an alternative to soil fumigation for control of critical soilborne pathogens in Californian strawberry production. Controlled environment experiments were conducted at 25 and 15 °C to test different materials as carbon sources for ASD using soil inoculated with Verticillium dahliae. Field trials were conducted in three locations comparing ASD with 20 Mg ha−1 rice bran (RB) against fumigated and untreated controls, steam, mustard seed meal and fish emulsion. In ASD‐treated soils, temperature and extent of anaerobic conditions were critical for control of V. dahliae, but multiple carbon inputs reduced inoculum by 80–100%. In field trials, ASD with RB provided control of a number of pathogens, and in three of four trials produced marketable fruit yields equivalent to fumigation. Little weed control benefit from ASD was found. ASD with RB also induced changes in the soil microbiome that persisted through the growing season. When equivalent yields were obtained, net returns above harvest and treatment costs with ASD RB were 92–96% of those with bed fumigation based on average prices over the previous 5 years. ASD can be a viable alternative for control of some soilborne pathogens. Growers are adopting ASD in California strawberry production, but research to determine optimal soil temperatures, anaerobicity thresholds and carbon sources for effective control of specific pathogens is needed.
Outcome and complications in dogs with appendicular primary bone tumors treated with stereotactic radiotherapy and concurrent surgical stabilization
Authors: Boston Sarah E. , Vinayak Arathi , Lu Xiaomin , Larue Susan , Bacon Nicholas J. , Bleedorn Jason A. , Souza Carlos H. M. , Ehrhart Nicole P. 
Published: May 2017

AbstractObjectiveTo document the outcome of dogs with appendicular primary bone tumors treated with stereotactic radiotherapy (SRT) and concurrent stabilization.Study designMulti‐institutional retrospective case series.AnimalsEighteen dogs with presumptive or definitive diagnosis of appendicular osteosarcoma.MethodsMedical records of dogs with appendicular primary bone tumors treated with SRT and stabilization were reviewed for signalment, preoperative staging and diagnostics, radiation dose, stabilization method, and outcome.ResultsThe distal radius was affected in 13/18 cases. Osteosarcoma or sarcoma was confirmed cytologically or histologically in 15/18 cases. Seven dogs were diagnosed with a pathological fracture at the time of treatment, and 11 were considered at high risk for pathological fracture. Dogs received a single dose (n = 5) or 3 doses (n = 13) of SRT. Surgical stabilization was performed under the same anesthetic event as the final dose of SRT in 10 dogs. Stabilization was achieved with a bone plate (n = 15) or interlocking nail (n = 3). Seventeen dogs received adjuvant chemotherapy. Complications occurred in 16/17 dogs, 15/17 of those being considered major complications. Four dogs experienced more than one complication. Infection was the most common complication, diagnosed in 15/17 cases, and considered as a major complication in 13/15 cases. Postoperative fracture was recorded as a major complication in 3 cases. Nine dogs were amputated at a median of 152 days. The median survival time was 344 days.ConclusionTreatment of bone tumors with SRT and concurrent stabilization was associated with a prohibitively high complication rate in dogs. Alternative methods for limb salvage should be considered for dogs at risk for pathologic fracture.
Oral l‐tyrosine supplementation augments the vasoconstriction response to whole‐body cooling in older adults
Authors: Lang James A. , Smaller Kevin A. 
Published: May 2017

New Findings
What is the central question of this study?
Ageing is associated with altered sympathetic responses to stress, which are explained in part by reduced noradrenergic function. The impact of supplementation with oral l‐tyrosine, the amino acid precursor for catecholamine synthesis, on the effector responses to cold and exercise stress has yet to be examined.

What is the main finding and its importance?
Oral l‐tyrosine ingestion augmented the sympathetically mediated vasoconstriction response to cold exposure in aged skin. This suggests that l‐tyrosine supplementation might improve thermoregulatory function in older adults.

l‐Tyrosine is the primary substrate for noradrenaline biosynthesis within sympathetic axon terminals. In stressful conditions requiring increased catecholamine production, the axonal l‐tyrosine concentration may limit the full expression of the sympathetic effector response and this may be particularly evident in older adults. We hypothesize that oral l‐tyrosine supplementation will increase the sympathetic response to whole‐body cooling and muscle metaboreflex activation. In a randomized, double‐blind design, 11 young (Y = 24 ± 1 years) and 11 older participants (O = 68 ± 4 years) ingested either 150 mg kg−1 of l‐tyrosine or placebo before commencing 30 min of whole‐body cooling to induce a gradual decline in skin temperature from 34 to 30.5°C. Laser Doppler flux (LDF) was measured at the ventral forearm, and cutaneous vascular conductance (CVC) was calculated as CVC = LDF/mean arterial pressure and expressed as a percentage change from baseline (%ΔCVC). Two minutes of static hand‐grip exercise (35% maximal voluntary contraction) followed by 3 min of postexercise ischaemia were implemented before and toward the end of the cooling bout. l‐Tyrosine supplementation did not affect blood pressure or heart rate responses to exercise or postexercise ischaemia. However, the blunted vasoconstriction response to whole‐body cooling in older adults (placebo: Y = 39 ± 5%ΔCVC and O = 16 ± 2 %ΔCVC; P < 0.05) was augmented after l‐tyrosine supplementation (l‐tyrosine: Y = 40 ± 4%ΔCVC and O = 32 ± 5 %ΔCVC; P < 0.05). These results suggest that l‐tyrosine bioavailability might limit thermoregulatory function in an older population.
Genome Stability in Engineered Strains of the Extremely Thermophilic Lignocellulose-Degrading Bacterium Caldicellulosiruptor bescii
Authors: Williams-Rhaesa Amanda M. , Poole Farris L. , Dinsmore Jessica T. , Lipscomb Gina L. , Rubinstein Gabriel M. , Scott Israel M. , Conway Jonathan M. , Lee Laura L. , Khatibi Piyum A. , Kelly Robert M. , Adams Michael W. W. 
Published: May 2017

ABSTRACT

Caldicellulosiruptor bescii
is the most thermophilic cellulose degrader known and is of great interest because of its ability to degrade nonpretreated plant biomass. For biotechnological applications, an efficient genetic system is required to engineer it to convert plant biomass into desired products. To date, two different genetically tractable lineages of
C. bescii
strains have been generated. The first (JWCB005) is based on a random deletion within the pyrimidine biosynthesis genes
pyrFA
, and the second (MACB1018) is based on the targeted deletion of
pyrE
, making use of a kanamycin resistance marker. Importantly, an active insertion element, IS
Cbe4
, was discovered in
C. bescii
when it disrupted the gene for lactate dehydrogenase (
ldh
) in strain JWCB018, constructed in the JWCB005 background. Additional instances of IS
Cbe4
movement in other strains of this lineage are presented herein. These observations raise concerns about the genetic stability of such strains and their use as metabolic engineering platforms. In order to investigate genome stability in engineered strains of
C. bescii
from the two lineages, genome sequencing and Southern blot analyses were performed. The evidence presented shows a dramatic increase in the number of single nucleotide polymorphisms, insertions/deletions, and IS
Cbe4
elements within the genome of JWCB005, leading to massive genome rearrangements in its daughter strain, JWCB018. Such dramatic effects were not evident in the newer MACB1018 lineage, indicating that JWCB005 and its daughter strains are not suitable for metabolic engineering purposes in
C. bescii
. Furthermore, a facile approach for assessing genomic stability in
C. bescii
has been established.

IMPORTANCE
Caldicellulosiruptor bescii
is a cellulolytic extremely thermophilic bacterium of great interest for metabolic engineering efforts geared toward lignocellulosic biofuel and bio-based chemical production. Genetic technology in
C. bescii
has led to the development of two uracil auxotrophic genetic background strains for metabolic engineering. We show that strains derived from the genetic background containing a random deletion in uracil biosynthesis genes (
pyrFA
) have a dramatic increase in the number of single nucleotide polymorphisms, insertions/deletions, and IS
Cbe4
insertion elements in their genomes compared to the wild type. At least one daughter strain of this lineage also contains large-scale genome rearrangements that are flanked by these IS
Cbe4
elements. In contrast, strains developed from the second background strain developed using a targeted deletion strategy of the uracil biosynthetic gene
pyrE
have a stable genome structure, making them preferable for future metabolic engineering studies.
Effects of High Pressure on Bacillus licheniformis Spore Germination and Inactivation
Authors: Borch-Pedersen Kristina , Mellegård Hilde , Reineke Kai , Boysen Preben , Sevenich Robert , Lindbäck Toril , Aspholm Marina 
Published: May 2017

ABSTRACT

Bacillus
and
Clostridium
species form spores, which pose a challenge to the food industry due to their ubiquitous nature and extreme resistance. Pressurization at <300 MPa triggers spore germination by activating germination receptors (GRs), while pressurization at >300 MPa likely triggers germination by opening dipicolinic acid (DPA) channels present in the inner membrane of the spores. In this work, we expose spores of
Bacillus licheniformis
, a species associated with food spoilage and occasionally with food poisoning, to high pressure (HP) for holding times of up to 2 h. By using mutant spores lacking one or several GRs, we dissect the roles of the GerA, Ynd, and GerK GRs in moderately HP (mHP; 150 MPa)-induced spore germination. We show that Ynd alone is sufficient for efficient mHP-induced spore germination. GerK also triggers germination with mHP, although at a reduced germination rate compared to that of Ynd. GerA stimulates mHP-induced germination but only in the presence of either the intact GerK or Ynd GR. These results suggests that the effectiveness of the individual GRs in mHP-induced germination differs from their effectiveness in nutrient-induced germination, where GerA plays an essential role. In contrast to
Bacillus subtilis
spores, treatment with very HP (vHP) of 550 MPa at 37°C did not promote effective germination of
B. licheniformis
spores. However, treatment with vHP in combination with elevated temperatures (60°C) gave a synergistic effect on spore germination and inactivation. Together, these results provide novel insights into how HP affects
B. licheniformis
spore germination and inactivation and the role of individual GRs in this process.

IMPORTANCE
Bacterial spores are inherently resistant to food-processing regimes, such as high-temperature short-time pasteurization, and may therefore compromise food durability and safety. The induction of spore germination facilitates subsequent inactivation by gentler processing conditions that maintain the sensory and nutritional qualities of the food. High-pressure (HP) processing is a nonthermal food-processing technology used to eliminate microbes from food. The application of this technology for spore eradication in the food industry requires a better understanding of how HP affects the spores of different bacterial species. The present study provides novel insights into how HP affects
Bacillus licheniformis
spores, a species associated with food spoilage and occasionally food poisoning. We describe the roles of different germination receptors in HP-induced germination and the effects of two different pressure levels on the germination and inactivation of spores. This study will potentially contribute to the effort to implement HP technology for spore inactivation in the food industry.
Defining Genetic Fitness Determinants and Creating Genomic Resources for an Oral Pathogen
Authors: Narayanan Ajay M. , Ramsey Matthew M. , Stacy Apollo , Whiteley Marvin 
Published: May 2017

ABSTRACT

Periodontitis is a microbial infection that destroys the structures that support the teeth. Although it is typically a chronic condition, rapidly progressing, aggressive forms are associated with the oral pathogen
Aggregatibacter actinomycetemcomitans
. One of this bacterium's key virulence traits is its ability to attach to surfaces and form robust biofilms that resist killing by the host and antibiotics. Though much has been learned about
A. actinomycetemcomitans
since its initial discovery, we lack insight into a fundamental aspect of its basic biology, as we do not know the full set of genes that it requires for viability (the essential genome). Furthermore, research on
A. actinomycetemcomitans
is hampered by the field's lack of a mutant collection. To address these gaps, we used rapid transposon mutant sequencing (Tn-seq) to define the essential genomes of two strains of
A. actinomycetemcomitans
, revealing a core set of 319 genes. We then generated an arrayed mutant library comprising >1,500 unique insertions and used a sequencing-based approach to define each mutant's position (well and plate) in the library. To demonstrate its utility, we screened the library for mutants with weakened resistance to subinhibitory erythromycin, revealing the multidrug efflux pump AcrAB as a critical resistance factor. During the screen, we discovered that erythromycin induces
A. actinomycetemcomitans
to form biofilms. We therefore devised a novel Tn-seq-based screen to identify specific factors that mediate this phenotype and in follow-up experiments confirmed 4 mutants. Together, these studies present new insights and resources for investigating the basic biology and disease mechanisms of a human pathogen.

IMPORTANCE
Millions suffer from gum disease, which often is caused by
Aggregatibacter actinomycetemcomitans
, a bacterium that forms antibiotic-resistant biofilms. To fully understand any organism, we should be able to answer: what genes does it require for life? Here, we address this question for
A. actinomycetemcomitans
by determining the genes in its genome that cannot be mutated. As for the genes that can be mutated, we archived these mutants into a library, which we used to find genes that contribute to antibiotic resistance, leading us to discover that antibiotics cause
A. actinomycetemcomitans
to form biofilms. We then devised an approach to find genes that mediate this process and confirmed 4 genes. These results illuminate new fundamental traits of a human pathogen.
Soil Bacterial and Fungal Communities Show Distinct Recovery Patterns during Forest Ecosystem Restoration
Authors: Sun Shan , Li Song , Avera Bethany N. , Strahm Brian D. , Badgley Brian D. 
Published: May 2017

ABSTRACT
Bacteria and fungi are important mediators of biogeochemical processes and play essential roles in the establishment of plant communities, which makes knowledge about their recovery after extreme disturbances valuable for understanding ecosystem development. However, broad ecological differences between bacterial and fungal organisms, such as growth rates, stress tolerance, and substrate utilization, suggest they could follow distinct trajectories and show contrasting dynamics during recovery. In this study, we analyzed both the intra-annual variability and decade-scale recovery of bacterial and fungal communities in a chronosequence of reclaimed mined soils using next-generation sequencing to quantify their abundance, richness, β-diversity, taxonomic composition, and cooccurrence network properties. Bacterial communities shifted gradually, with overlapping β-diversity patterns across chronosequence ages, while shifts in fungal communities were more distinct among different ages. In addition, the magnitude of intra-annual variability in bacterial β-diversity was comparable to the changes across decades of chronosequence age, while fungal communities changed minimally across months. Finally, the complexity of bacterial cooccurrence networks increased with chronosequence age, while fungal networks did not show clear age-related trends. We hypothesize that these contrasting dynamics of bacteria and fungi in the chronosequence result from (i) higher growth rates for bacteria, leading to higher intra-annual variability; (ii) higher tolerance to environmental changes for fungi; and (iii) stronger influence of vegetation on fungal communities.

IMPORTANCE
Both bacteria and fungi play essential roles in ecosystem functions, and information about their recovery after extreme disturbances is important for understanding whole-ecosystem development. Given their many differences in phenotype, phylogeny, and life history, a comparison of different bacterial and fungal recovery patterns improves the understanding of how different components of the soil microbiota respond to ecosystem recovery. In this study, we highlight key differences between soil bacteria and fungi during the restoration of reclaimed mine soils in the form of long-term diversity patterns, intra-annual variability, and potential interaction networks. Cooccurrence networks revealed increasingly complex bacterial community interactions during recovery, in contrast to much simpler and more isolated fungal network patterns. This study compares bacterial and fungal cooccurrence networks and reveals cooccurrences persisting through successional ages.