bluuebunny/crossref_metadata_2025_split huggingface dataset:
Limited differences among habitats in deep‐sea macro‐infaunal communities off New Zealand: implications for their vulnerability to anthropogenic disturbance
Authors: Leduc Daniel , Rowden Ashley A. , Clark Malcolm R. , Bowden David A. , Thurber Andrew R. 
Published: April 2016

AbstractThe spread of human activities into the deep sea may pose a high risk to benthic communities and affect ecosystem integrity. The deep sea is characterized by physical and biological heterogeneity and different habitat types are likely to differ in their vulnerability to anthropogenic impacts. However, across‐habitat comparisons are rare, and no comprehensive ecological risk assessment has yet been developed. To address this gap in our knowledge, we compared macro‐infaunal community structure in four habitats (slope, canyons, seamounts and methane seeps) at depths between 700 and 1500 m in the Hikurangi Margin and Bay of Plenty regions off New Zealand. The most striking contrast in community structure was between the two study regions, due to an order of magnitude difference in macro‐infaunal abundance that we believe was caused by differences in surface productivity and food availability at the sea bed. We found differences in structural and functional attributes of macro‐infaunal communities among some habitats in the Hikurangi Margin (slope, canyon and seep), but not in the Bay of Plenty. We posit that differences between canyon and slope communities on the Hikurangi Margin are due to enhanced food availability inside canyons compared with adjacent slope habitats. Seep communities were characterized by elevated abundance of both symbiont‐bearing and heterotrophic taxa, and were the most distinct, and variable, among the habitats that we considered on the Hikurangi Margin. Communities of seamounts were not distinct from slope or canyon communities on the Hikurangi Margin, probably reflecting similar environmental conditions in these habitats. The communities of deep‐sea canyon and seep habitats on the Hikurangi Margin were sufficiently dissimilar from each other and from slope habitats to warrant separate management consideration. By contrast, the low dissimilarity between communities of canyon and slope habitats in the Bay of Plenty suggests that habitat‐based management is not required in this region, for macro‐infauna at least. Although the two study regions share similar species pools, populations of the Hikurangi Margin region may be less vulnerable than the sparser populations of the Bay of Plenty due to the higher availability of potential colonizers and faster population growth. Thus regions, and habitats in some regions, should be subject to separate ecological risk assessment to help identify the key risks and consequences of human activities, and to inform options for reducing or mitigating impacts.
Does physiological acclimation to climate warming stabilize the ratio of canopy respiration to photosynthesis?
Authors: Drake John E. , Tjoelker Mark G. , Aspinwall Michael J. , Reich Peter B. , Barton Craig V. M. , Medlyn Belinda E. , Duursma Remko A. 
Published: April 2016

Summary

Given the contrasting short‐term temperature dependences of gross primary production (GPP) and autotrophic respiration, the fraction of GPP respired by trees is predicted to increase with warming, providing a positive feedback to climate change. However, physiological acclimation may dampen or eliminate this response.

We measured the fluxes of aboveground respiration (Ra), GPP and their ratio (Ra/GPP) in large, field‐grown Eucalyptus tereticornis trees exposed to ambient or warmed air temperatures (+3°C). We report continuous measurements of whole‐canopy CO2 exchange, direct temperature response curves of leaf and canopy respiration, leaf and branch wood respiration, and diurnal photosynthetic measurements.

Warming reduced photosynthesis, whereas physiological acclimation prevented a coincident increase in Ra. Ambient and warmed trees had a common nonlinear relationship between the fraction of GPP that was respired above ground (Ra/GPP) and the mean daily temperature. Thus, warming significantly increased Ra/GPP by moving plants to higher positions on the shared Ra/GPP vs daily temperature relationship, but this effect was modest and only notable during hot conditions.

Despite the physiological acclimation of autotrophic respiration to warming, increases in temperature and the frequency of heat waves may modestly increase tree Ra/GPP, contributing to a positive feedback between climate warming and atmospheric CO2 accumulation.
Impact of end‐stage renal disease on psychological status and quality of life
Authors: Kilicoglu Ali Guven , Bahali Kayhan , Canpolat Nur , Bilgic Ayhan , Mutlu Caner , Yalçın Özhan , Pehlivan Gulseren , Sever Lale 
Published: April 2016

AbstractBackgroundThe aim of this study was to assess depression, anxiety, and quality of life (QOL) in a cohort of children and adolescents with end‐stage renal disease (ESRD), to compare these findings with healthy controls, and to evaluate the association between these psychological symptoms, QOL, and clinical variables related to ESRD.MethodsThirty‐two children and adolescents 8–18 years of age were enrolled in the study. The sociodemographic data were evaluated. Questionnaires were used to evaluate the psychological status and QOL of the patients and healthy controls.ResultsThere was a significant difference in mean depression score, which was significantly higher for the ESRD patients. Mean state anxiety score was significantly lower for ESRD patients than for controls. Regarding QOL score, there were significant differences between the ESRD patients and control groups for both child‐rated and parent‐rated QOL scores, which were significantly lower for ESRD patients. Trait anxiety was a negative predictor of all subscales of the Pediatric Quality of Life Inventory 4.ConclusionsEnd‐stage renal disease was related to significant morbidity and poorer QOL. The assessment and enhancement of QOL and comorbid psychiatric disorders in ESRD should be a part of disease management.
Rauvolfia serpentina N‐methyltransferases involved in ajmaline and Nβ‐methylajmaline biosynthesis belong to a gene family derived from γ‐tocopherol C‐methyltransferase
Authors: Cázares‐Flores Paulo , Levac Dylan , De Luca Vincenzo 
Published: April 2016

SummaryAjmaline biosynthesis in Rauvolfia serpentina has been one of the most studied monoterpenoid indole alkaloid (MIA) pathways within the plant family Apocynaceae. Detailed molecular and biochemical information on most of the steps involved in the pathway has been generated over the last 30 years. Here we report the identification, molecular cloning and functional expression in Escherichia coli of two R. serpentinacDNAs that are part of a recently discovered γ‐tocopherol‐like N‐methyltransferase (γ‐TLMT) family and are involved in indole and side‐chain N‐methylation of ajmaline. Recombinant proteins showed remarkable substrate specificity for molecules with an ajmalan‐type backbone and strict regiospecific N‐methylation. Furthermore, N‐methyltransferase gene transcripts and enzyme activity were enriched in R. serpentina roots which correlated with accumulation of ajmaline alkaloid. This study elucidates the final step in the ajmaline biosynthetic pathway and describes the enzyme responsible for the formation of Nβ‐methylajmaline, an unusual charged MIA found in R. serpentina.
Different flowering response to various fruit loads in apple cultivars correlates with degree of transcript reaccumulation of a TFL1‐encoding gene
Authors: Haberman Amnon , Ackerman Michal , Crane Omer , Kelner Jean‐Jacques , Costes Evelyne , Samach Alon 
Published: April 2016

SummaryIn many perennial fruit trees, flowering in the year following a year with heavy fruit load can be quite limited. This biennial cycle of fruiting, termed alternate bearing, was described 170 years ago in apple (Malus domestica). Apple inflorescences are mainly found on short branches (spurs). Bourse shoots (BS) develop from the leaf axils of the spur. BS apices may terminate ~100 days after flowering, with formation of next year's inflorescences. We sought to determine how developing fruit on the spur prevents the adjacent BS apex from forming an inflorescence. The presence of adjacent fruit correlated with reaccumulation of transcript encoding a potential flowering inhibitor, MdTFL1‐2, in BS apices prior to inflorescence initiation. BS apices without adjacent fruit that did not flower due to late fruitlet removal, neighbouring fruit on the tree, or leaf removal, also reaccumulated the MdTFL1‐2 transcript. Fruit load and gibberellin (GA) application had similar effects on the expression of MdTFL1‐2 and genes involved in GA biosynthesis and metabolism. Some apple cultivars are less prone to alternate bearing. We show that the response of a BS apex to different numbers of adjacent fruit differs among cultivars in both MdTFL1‐2 accumulation and return flowering. These results provide a working model for the further study of alternate bearing, and help clarify the need for cultivar‐specific approaches to reach stable fruit production.
Antibacterial effect of N‐acetylcysteine on common canine otitis externa isolates
Authors: May Elizabeth R. , Conklin Katherine A. , Bemis David A. 
Published: April 2016

BackgroundN‐Acetylcysteine (NAC) has the potential to be a useful therapeutic agent for the treatment of otitis externa due to its antimicrobial and mucolytic properties, as well as its ability to disrupt bacterial biofilm.Hypothesis/ObjectivesTo determine the antibacterial activity of NAC against common bacterial isolates associated with canine otitis externa.AnimalsTwenty two isolates from canine clinical cases of otitis externa were identified and tested, including five Staphylococcus pseudintermedius, six Pseudomonas aeruginosa, five Corynebacterium spp. and six β‐haemolytic Streptococcus spp. isolates.MethodsEach isolate was grown on blood agar for 24 h and transferred to Mueller Hinton Broth (MHB) to achieve a final concentration of 5 × 105 CFU/mL. NAC was diluted in MHB to a starting concentration of 160 mg/mL and serial two‐fold microdilution assays were performed in triplicate with negative controls for all isolates tested. Concentrations of NAC tested ranged from 0.125 to 80 mg/mL. A 50 μL volume of bacterial suspension was used to inoculate each well.ResultsThe minimum inhibitory concentration (MIC) of NAC for all isolates tested ranged from 5 to 20 mg/mL.Conclusions and Clinical RelevanceN‐Acetylcysteine inhibits clinically relevant and drug resistant bacteria in vitro, and has potential for use as a novel agent for treatment of otitis externa.
Serotonin in the solitary tract nucleus shortens the laryngeal chemoreflex in anaesthetized neonatal rats
Authors: Donnelly William T. , Bartlett Donald , Leiter J. C. 
Published: April 2016

New FindingsWhat is the central question of this study?Failure to terminate apnoea and arouse is likely to contribute to sudden infant death syndrome (SIDS). Serotonin is deficient in the brainstems of babies who died of SIDS. Therefore, we tested the hypothesis that serotonin in the nucleus of the solitary tract (NTS) would shorten reflex apnoea.What is the main finding and its importance?Serotonin microinjected into the NTS shortened the apnoea and respiratory inhibition associated with the laryngeal chemoreflex. Moreover, this effect was achieved through a 5‐HT3receptor. This is a new insight that is likely to be relevant to the pathogenesis of SIDS.The laryngeal chemoreflex (LCR), an airway‐protective reflex that causes apnoea and bradycardia, has long been suspected as an initiating event in the sudden infant death syndrome. Serotonin (5‐HT) and 5‐HT receptors may be deficient in the brainstems of babies who die of sudden infant death syndrome, and 5‐HT seems to be important in terminating apnoeas directly or in causing arousals or as part of the process of autoresuscitation. We hypothesized that 5‐HT in the brainstem would limit the duration of the LCR. We studied anaesthetized rat pups between 7 and 21 days of age and made microinjections into the cisterna magna or into the nucleus of the solitary tract (NTS). Focal, bilateral microinjections of 5‐HT into the caudal NTS significantly shortened the LCR. The 5‐HT1areceptor antagonist, WAY 100635, did not affect the LCR consistently, nor did a 5‐HT2receptor antagonist, ketanserin, alter the duration of the LCR. The 5‐HT3specific agonist, 1‐(3‐chlorophenyl)‐biguanide, microinjected bilaterally into the caudal NTS significantly shortened the LCR. Thus, endogenous 5‐HT released within the NTS may curtail the respiratory depression that is part of the LCR, and serotonergic shortening of the LCR may be attributed to activation of 5‐HT3receptors within the NTS. 5‐HT3receptors are expressed presynaptically on C fibre afferents of the superior laryngeal nerve, and serotonergic shortening of the LCR may be mediated presynaptically by enhanced activation of inhibitory interneurons within the NTS.
Parenteral Vaccination Can Be an Effective Means of Inducing Protective Mucosal Responses
Authors: Clements John D. , Freytag Lucy C. 
Published: April 2016

ABSTRACTThe current paradigm in vaccine development is that nonreplicating vaccines delivered parenterally fail to induce immune responses in mucosal tissues. However, both clinical and experimental data have challenged this concept, and numerous studies have shown that induction of mucosal immune responses after parenteral vaccination is not a rare occurrence and might, in fact, significantly contribute to the protection against mucosal infections afforded by parenteral vaccines. While the mechanisms underlying this phenomenon are not well understood, the realization that parenteral vaccination can be an effective means of inducing protective mucosal responses is paradigm-shifting and has potential to transform the way vaccines are designed and delivered.
Comparison of Culture-Based Methods for Identification of Colonization with Methicillin-Resistant and Methicillin-Susceptible Staphylococcus aureus in the Context of Cocolonization
Authors: Davis Meghan F. , Hu Baofeng , Carroll Karen C. , Bilker Warren B. , Tolomeo Pam , Cluzet Valerie C. , Baron Patrick , Ferguson Jacqueline M. , Morris Daniel O. , Rankin Shelley C. , Lautenbach Ebbing , Nachamkin Irving 
Published: April 2016

ABSTRACT

Two screening methods to detect staphylococcal colonization in humans were compared. Direct plating to CHROMagar (BD Diagnostics) was compared to a broth preenrichment followed by plating to Baird-Parker agar. The broth-enrichment method was comparable to CHROMagar for methicillin-resistant
Staphylococcus aureas
(MRSA) detection, but the enrichment method was optimum for recovery of coagulase-positive
Staphylococcus
spp.
Use of Shotgun Metagenome Sequencing To Detect Fecal Colonization with Multidrug-Resistant Bacteria in Children
Authors: Andersen Heidi , Connolly Natalia , Bangar Hansraj , Staat Mary , Mortensen Joel , Deburger Barbara , Haslam David B. 
Published: April 2016

ABSTRACT

Prevention of multidrug-resistant (MDR) bacterial infections relies on accurate detection of these organisms. We investigated shotgun metagenome sequencing for the detection of methicillin-resistant
Staphylococcus aureus
(MRSA), vancomycin-resistant
Enterococcus
(VRE), and MDR
Enterobacteriaceae
. Fecal metagenomes were analyzed from high-risk inpatients and compared to those of low-risk outpatients and controls with minimal risk for a MDR bacterial infection. Principal-component analysis clustered patient samples into distinct cohorts, confirming that the microbiome composition was significantly different between cohorts (
P
= 0.006). Microbial diversity and relative anaerobe abundance were preserved in outpatients compared to those in controls. Relative anaerobe abundance was significantly reduced in inpatients compared to that in outpatients (
P
= 0.006). Although the potential for MDR bacteria was increased in inpatients and outpatients compared to that in controls (
P
< 0.001), there was no difference between inpatients and outpatients. However, 9 (53%) inpatients had colonization with a MDR bacterium that was not identified by culture. Unlike culture, shotgun sequencing quantitatively characterizes the burdens of multiple MDR bacteria relative to all of the microbiota within the intestinal community. We propose consideration of key microbiome features, such as diversity and relative anaerobe abundance, in addition to the detection of MDR bacteria by shotgun metagenome sequencing as a novel method that might better identify patients who are at increased risk of a MDR infection.
Furin Cleavage of L2 during Papillomavirus Infection: Minimal Dependence on Cyclophilins
Authors: Bronnimann Matthew P. , Calton Christine M. , Chiquette Samantha F. , Li Shuaizhi , Lu Mingfeng , Chapman Janice A. , Bratton Kristin N. , Schlegel Angela M. , Campos Samuel K. 
Published: April 2016

ABSTRACT

Despite an abundance of evidence supporting an important role for the cleavage of minor capsid protein L2 by cellular furin, direct cleavage of capsid-associated L2 during human papillomavirus 16 (HPV16) infection remains poorly characterized. The conserved cleavage site, close to the L2 N terminus, confounds observation and quantification of the small cleavage product by SDS-PAGE. To overcome this difficulty, we increased the size shift by fusing a compact protein domain, the
Propionibacterium shermanii
transcarboxylase domain (PSTCD), to the N terminus of L2. The infectious PSTCD-L2 virus displayed an appreciable L2 size shift during infection of HaCaT keratinocytes. Cleavage under standard cell culture conditions rarely exceeded 35% of total L2. Cleavage levels were enhanced by the addition of exogenous furin, and the absolute levels of infection correlated to the level of L2 cleavage. Cleavage occurred on both the HaCaT cell surface and extracellular matrix (ECM). Contrary to current models, experiments on the involvement of cyclophilins revealed little, if any, role for these cellular enzymes in the modulation of furin cleavage. HPV16 L2 contains two consensus cleavage sites, Arg5 (
2
RHKR
5
) and Arg12 (
9
RTKR
12
). Mutant PSTCD-L2 viruses demonstrated that although furin can cleave either site, cleavage must occur at Arg12, as cleavage at Arg5 alone is insufficient for successful infection. Mutation of the conserved cysteine residues revealed that the Cys22-Cys28 disulfide bridge is not required for cleavage. The PSTCD-L2 virus or similar N-terminal fusions will be valuable tools to study additional cellular and viral determinants of furin cleavage.

IMPORTANCE
Furin cleavage of minor capsid protein L2 during papillomavirus infection has been difficult to directly visualize and quantify, confounding efforts to study this important step of HPV infection. Fusion of a small protein domain to the N terminus greatly facilitates direct visualization of the cleavage product, revealing important characteristics of this critical process. Contrary to the current model, we found that cleavage is largely independent of cyclophilins, suggesting that cyclophilins act either in parallel to or downstream of furin to trigger exposure of a conserved N-terminal L2 epitope (RG-1) during infection. Based on this finding, we strongly caution against using L2 RG-1 epitope exposure as a convenient but indirect proxy of furin cleavage.
Characterization of Human and Murine T-Cell Immunoglobulin Mucin Domain 4 (TIM-4) IgV Domain Residues Critical for Ebola Virus Entry
Authors: Rhein Bethany A. , Brouillette Rachel B. , Schaack Grace A. , Chiorini John A. , Maury Wendy 
Published: April 2016

ABSTRACT

Phosphatidylserine (PtdSer) receptors that are responsible for the clearance of dying cells have recently been found to mediate enveloped virus entry. Ebola virus (EBOV), a member of the
Filoviridae
family of viruses, utilizes PtdSer receptors for entry into target cells. The PtdSer receptors human and murine T-cell immunoglobulin mucin (TIM) domain proteins TIM-1 and TIM-4 mediate filovirus entry by binding to PtdSer on the virion surface via a conserved PtdSer binding pocket within the amino-terminal IgV domain. While the residues within the TIM-1 IgV domain that are important for EBOV entry are characterized, the molecular details of virion–TIM-4 interactions have yet to be investigated. As sequences and structural alignments of the TIM proteins suggest distinct differences in the TIM-1 and TIM-4 IgV domain structures, we sought to characterize TIM-4 IgV domain residues required for EBOV entry. Using vesicular stomatitis virus pseudovirions bearing EBOV glycoprotein (EBOV GP/VSVΔG), we evaluated virus binding and entry into cells expressing TIM-4 molecules mutated within the IgV domain, allowing us to identify residues important for entry. Similar to TIM-1, residues in the PtdSer binding pocket of murine and human TIM-4 (mTIM-4 and hTIM-4) were found to be important for EBOV entry. However, additional TIM-4-specific residues were also found to impact EBOV entry, with a total of 8 mTIM-4 and 14 hTIM-4 IgV domain residues being critical for virion binding and internalization. Together, these findings provide a greater understanding of the interaction of TIM-4 with EBOV virions.

IMPORTANCE
With more than 28,000 cases and over 11,000 deaths during the largest and most recent Ebola virus (EBOV) outbreak, there has been increased emphasis on the development of therapeutics against filoviruses. Many therapies under investigation target EBOV cell entry. T-cell immunoglobulin mucin (TIM) domain proteins are cell surface factors important for the entry of many enveloped viruses, including EBOV. TIM family member TIM-4 is expressed on macrophages and dendritic cells, which are early cellular targets during EBOV infection. Here, we performed a mutagenesis screening of the IgV domain of murine and human TIM-4 to identify residues that are critical for EBOV entry. Surprisingly, we identified more human than murine TIM-4 IgV domain residues that are required for EBOV entry. Defining the TIM IgV residues needed for EBOV entry clarifies the virus-receptor interactions and paves the way for the development of novel therapeutics targeting virus binding to this cell surface receptor.