bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dead fungal mycelium in forest soil represents a decomposition hotspot and a habitat for a specific microbial community
Authors: Brabcová Vendula , Nováková Monika , Davidová Anna , Baldrian Petr 
Published: February 2016

Summary

Turnover of fungal biomass in forest litter and soil represents an important process in the environment. To date, knowledge of mycelial decomposition has been derived primarily from short‐term studies, and the guild of mycelium decomposers has been poorly defined.

Here, we followed the fate of the fruiting bodies of an ectomycorrhizal fungus in litter and soil of a temperate forest over 21 wk. The community of associated microbes and enzymatic processes in this specific substrate were described.

The decomposition of fungal fruiting bodies exhibited biphasic kinetics. The rapid initial phase, which included the disappearance of DNA, was followed by a slower turnover of the recalcitrant fraction. Compared with the surrounding litter and soil, the mycelium represented a hotspot of activity of several biopolymer‐degrading enzymes and high bacterial biomass. Specific communities of bacteria and fungi were associated with decomposing mycelium. These communities differed between the initial and late phases of decomposition. The bacterial community associated with decomposing mycelia typically contained the genera Pedobacter, Pseudomonas, Variovorax, Chitinophaga, Ewingella and Stenotrophomonas, whereas the fungi were mostly nonbasidiomycetous r‐strategists of the genera Aspergillus, Penicillium, Mortierella, Cladosporium and several others.

Decomposing ectomycorrhizal fungal mycelium exhibits high rates of decomposition and represents a specific habitat supporting a specific microbial community.
Evidence for the long‐term maintenance of a rare self‐incompatibility system in Oleaceae
Authors: Vernet Philippe , Lepercq Pierre , Billiard Sylvain , Bourceaux Angélique , Lepart Jacques , Dommée Bertrand , Saumitou‐Laprade Pierre 
Published: February 2016

Summary

A rare homomorphic diallelic self‐incompatibility (DSI) system discovered in Phillyrea angustifolia (family Oleaceae, subtribe Oleinae) can promote the transition from hermaphroditism to androdioecy. If widespread and stable in Oleaceae, DSI may explain the exceptionally high rate of androdioecious species reported in this plant family. Here, we set out to determine whether DSI occurs in another Oleaceae lineage.

We tested for DSI in subtribe Fraxininae, a lineage that diverged from subtribe Oleinae c. 40 million yr ago. We explored the compatibility relationships in Fraxinus ornus using 81 hermaphrodites and 25 males from one natural stand and two naturalized populations using intra‐ and interspecific stigma tests performed on F. ornus and P. angustifolia testers.

We uncovered a DSI system with hermaphrodites belonging to one of two self‐incompatibility (SI) groups and males compatible with both groups, making for a truly androdioecious reproductive system. The two human‐founded populations contained only one of the two SI groups.

Our results provide evidence for the evolutionary persistence of DSI. We discuss how its stability over time may have affected transitions to other sexual systems, such as dioecy.
Growth temperature impact on leaf form and function in Arabidopsis thaliana ecotypes from northern and southern Europe
Authors: Stewart Jared J. , Demmig‐Adams Barbara , Cohu Christopher M. , Wenzl Coleman A. , Muller Onno , Adams William W. 
Published: February 2016

AbstractThe plasticity of leaf form and function in European lines of Arabidopsis thaliana was evaluated in ecotypes from Sweden and Italy grown under contrasting (cool versus hot) temperature regimes. Although both ecotypes exhibited acclimatory adjustments, the Swedish ecotype exhibited more pronounced responses to the two contrasting temperature regimes in several characterized features. These responses included thicker leaves with higher capacities for photosynthesis, likely facilitated by a greater number of phloem cells per minor vein for the active loading and export of sugars, when grown under cool temperature as opposed to leaves with a higher vein density and a greater number of tracheary elements per minor vein, likely facilitating higher rates of transpirational water loss (and thus evaporative cooling), when grown under hot temperature with high water availability. In addition, only the Swedish ecotype exhibited reduced rosette growth and greater levels of foliar tocopherols under the hot growth temperature. These responses, and the greater responsiveness of the Swedish ecotype compared with the Italian ecotype, are discussed in the context of redox signalling networks and transcription factors, and the greater range of environmental conditions experienced by the Swedish versus the Italian ecotype during the growing season in their native habitats.
Hip joint pathology: relationship between patient history, physical tests, and arthroscopy findings in clinical practice
Authors: Tijssen M. , van Cingel R. E. H. , de Visser E. , Hölmich P. , Nijhuis‐van der Sanden M. W. G. 
Published: February 2016

The purpose of this retrospective cohort study was to (a) describe the clinical presentation of femoroacetabular impingement (FAI) and hip labral pathology; (b) describe the accuracy of patient history and physical tests for FAI and labral pathology as confirmed by hip arthroscopy. Patients (18–65 years) were included if they were referred to a physical therapist to gather pre‐operative data and were then diagnosed during arthroscopy. Results of pre‐operative patient history and physical tests were collected and compared to arthroscopy. Data of 77 active patients (mean age: 37 years) were included. Groin as main location of pain, the Anterior Impingement test (AIT), Flexion‐Abduction‐External Rotation (FABER) test, and Fitzgerald test had a high sensitivity (range 0.72–0.91). Sensitivity increased when combining these tests (0.97) as either groin as main location of pain and a positive FABER test or a positive AIT and a positive FABER test were the shortest most sensitive combinations. The results of this study point out that in clinical practice absence of groin as main location of pain combined with a negative FABER test or the combination of a negative AIT and a negative FABER test are suggested to rule out the diagnosis of symptomatic FAI and/or labral pathology.
Somaclonal variation does not preclude the use of rice transformants for genetic screening
Authors: Wei Fu‐Jin , Kuang Lin‐Yun , Oung Hui‐Min , Cheng Sin‐Yuan , Wu Hshin‐Ping , Huang Lin‐Tzu , Tseng Yi‐Tzu , Chiou Wan‐Yi , Hsieh‐Feng Vicki , Chung Cheng‐Han , Yu Su‐May , Lee Lan‐Ying , Gelvin Stanton B. , Hsing Yue‐Ie C. 
Published: February 2016

SummaryRice (Oryza sativa) is one of the world's most important crops. Rice researchers make extensive use of insertional mutants for the study of gene function. Approximately half a million flanking sequence tags from rice insertional mutant libraries are publicly available. However, the relationship between genotype and phenotype is very weak. Transgenic plant assays have been used frequently for complementation, overexpression or antisense analysis, but sequence changes caused by callus growth, Agrobacterium incubation medium, virulence genes, transformation and selection conditions are unknown. We used high‐throughput sequencing of DNA from rice lines derived from Tainung 67 to analyze non‐transformed and transgenic rice plants for mutations caused by these parameters. For comparison, we also analyzed sequence changes for two additional rice varieties and four T‐DNA tagged transformants from the Taiwan Rice Insertional Mutant resource. We identified single‐nucleotide polymorphisms, small indels, large deletions, chromosome doubling and chromosome translocations in these lines. Using standard rice regeneration/transformation procedures, the mutation rates of regenerants and transformants were relatively low, with no significant differences among eight tested treatments in the Tainung 67 background and in the cultivars Taikeng 9 and IR64. Thus, we could not conclusively detect sequence changes resulting from Agrobacterium‐mediated transformation in addition to those caused by tissue culture‐induced somaclonal variation. However, the mutation frequencies within the two publically available tagged mutant populations, including TRIM transformants or Tos17 lines, were about 10‐fold higher than the frequency of standard transformants, probably because mass production of embryogenic calli and longer callus growth periods were required to generate these large libraries.
Eradication of feral goats enhances expansion of the invasive shrub Leucaena leucocephala on Nakoudo‐jima, an oceanic island
Authors: Osawa T , Hata K , Kachi N 
Published: February 2016

SummaryMany introduced species can co‐exist within the same ecosystem and sometimes interact with each other. Under such situations, eradication of one species may cause unexpected negative effects. Nakoudo‐jima in the Ogasawara (Bonin) Islands is an oceanic island that had feral goats that were introduced in the 1880s, but eradicated in 1999. Following their eradication, the alien invasive shrub Leucaena leucocephala (Fabaceae) was predicted to increase drastically. In this study, we tested the hypothesis that the eradication of feral goats enhanced the expansion of L. leucocephala using four time‐series aerial photographs and validation work based on current field surveys of Nakoudo‐jima. Our results showed that following feral goat elimination, bare ground areas decreased and forest cover increased. This was particularly true of areas dominated by L. leucocephala. Thus, feral goats appear to have limited the expansion of L. leucocephala on Nakoudo‐jima. Grassland cover also increased following feral goat elimination, but this may have occurred prior to L. leucocephala expansion. These results suggest that L. leucocephala‐dominated forest might invade grassland areas and that grasslands may have mediated the expansion of L. leucocephala after feral goat elimination. Future management of L. leucocephala should target the species in the high‐risk expansion zones adjacent to grasslands.
Untargeted Metabolomics To Ascertain Antibiotic Modes of Action
Authors: Vincent Isabel M. , Ehmann David E. , Mills Scott D. , Perros Manos , Barrett Michael P. 
Published: February 2016

ABSTRACT

Deciphering the mode of action (MOA) of new antibiotics discovered through phenotypic screening is of increasing importance. Metabolomics offers a potentially rapid and cost-effective means of identifying modes of action of drugs whose effects are mediated through changes in metabolism. Metabolomics techniques also collect data on off-target effects and drug modifications. Here, we present data from an untargeted liquid chromatography-mass spectrometry approach to identify the modes of action of eight compounds: 1-[3-fluoro-4-(5-methyl-2,4-dioxo-pyrimidin-1-yl)phenyl]-3-[2-(trifluoromethyl)phenyl]urea (AZ1), 2-(cyclobutylmethoxy)-5′-deoxyadenosine, triclosan, fosmidomycin, CHIR-090, carbonyl cyanide
m
-chlorophenylhydrazone (CCCP), 5-chloro-2-(methylsulfonyl)-
N
-(1,3-thiazol-2-yl)-4-pyrimidinecarboxamide (AZ7), and ceftazidime. Data analysts were blind to the compound identities but managed to identify the target as thymidylate kinase for AZ1, isoprenoid biosynthesis for fosmidomycin, acyl-transferase for CHIR-090, and DNA metabolism for 2-(cyclobutylmethoxy)-5′-deoxyadenosine. Changes to cell wall metabolites were seen in ceftazidime treatments, although other changes, presumably relating to off-target effects, dominated spectral outputs in the untargeted approach. Drugs which do not work through metabolic pathways, such as the proton carrier CCCP, have no discernible impact on the metabolome. The untargeted metabolomics approach also revealed modifications to two compounds, namely, fosmidomycin and AZ7. An untreated control was also analyzed, and changes to the metabolome were seen over 4 h, highlighting the necessity for careful controls in these types of studies. Metabolomics is a useful tool in the analysis of drug modes of action and can complement other technologies already in use.
Population Structure Analysis of Carbapenem-Resistant Acinetobacter baumannii Clinical Isolates from Brazil Reveals Predominance of Clonal Complexes 1, 15, and 79
Authors: Camargo Carlos Henrique , Tiba Monique Ribeiro , Saes Marta Regina , Vasconcellos Francielli Mahnic de , Santos Luis Fernando dos , Romero Eliete Caló , Garcia Doroti de Oliveira 
Published: February 2016

ABSTRACT

The population structure of 71 carbapenem-resistant
Acinetobacter baumannii
clinical isolates from several hospitals in Brazil was investigated by ApaI pulsed-field gel electrophoresis,
bla
OXA-51
-like subtyping, and multilocus sequence typing (Institute Pasteur scheme). In addition to the predominance of strains carrying
bla
OXA-23
, we detected the presence of
bla
OXA-72
and
bla
OXA-231
. We observed a predominance of clonal complex 1 (CC1), CC15, and CC79 and representative strains of the worldwide-disseminated international clone I.
Global Urine Metabolomics in Patients Treated with First-Line Tuberculosis Drugs and Identification of a Novel Metabolite of Ethambutol
Authors: Das Mrinal Kumar , Arya Rakesh , Debnath Sanjita , Debnath Rahul , Lodh Anindita , Bishwal Subasa Chandra , Das Anjan , Nanda Ranjan Kumar 
Published: February 2016

ABSTRACT

Population level variation of drug metabolism phenotype (DMP) has great implications in treatment outcome, drug-related side effects, and resistance development. In this study, we used a gas chromatography-time of flight-mass spectrometry (GC-TOF-MS)-based untargeted urine metabolomics approach to understand the DMP of a tuberculosis (TB) patient cohort (
n
= 20) from Tripura, a state in the northeastern part of India. Urine samples collected at different postdose time points (2 h, 6 h, 12 h, 24 h, 36 h, and 48 h) from these newly diagnosed TB patients receiving first-line anti-TB drugs were analyzed, and we have successfully detected three of the four first-line drugs,
viz
., isoniazid (INH), ethambutol (ETB), and pyrazinamide (PZA). The majority of their known metabolites, acetyl-isoniazid (AcINH), isonicotinic acid (INA), isonicotinuric acid (INTA), 2,2′-(ethylenediimino)-dibutyric acid (EDBA), 5-hydroxypyrazinamide (5OH-PZA), pyrazinoic acid (POA), and 5-hydroxypyrazinoic acid (5OH-POA), were also detected. Analyzing the variation in abundances of drugs and their known metabolites and calculating the metabolic ratios in these samples, we offer comprehensive DMP information on this small patient cohort that represents Tripura, India. The majority (75%) of these patients are found to be slow acetylators of INH. The average metabolic ratios of POA/PZA and 5OH-POA/POA are 3.16 ± 3.03 and 6.09 ± 6.15, respectively. Employing correlation analysis of the metabolomics metadata and a manual prediction of drug catabolism, we have proposed 2-aminobutyric acid (AABA) as a novel metabolite of ETB. These observations indicate the usefulness of GC-MS-based metabolomics to characterize the DMP at a population level and also to identify novel drug metabolites.
Role of the Stringent Stress Response in the Antibiotic Resistance Phenotype of Methicillin-Resistant Staphylococcus aureus
Authors: Aedo Sandra , Tomasz Alexander 
Published: February 2016

ABSTRACT

Resistance to beta-lactam antibiotics in methicillin-resistant
Staphylococcus aureus
(MRSA) requires the presence of an acquired genetic determinant,
mecA
or
mecC
, which encode penicillin-binding protein PBP2A or PBP2A′, respectively. Although all MRSA strains share a mechanism of resistance, the phenotypic expression of beta-lactam resistance shows considerable strain-to-strain variation. The stringent stress response, a stress response that results from nutrient limitation, was shown to play a key role in determining the resistance level of an MRSA strain. In the present study, we validated the impact of the stringent stress response on transcription and translation of
mecA
in the MRSA clinical isolate strain N315, which also carries known regulatory genes (
mecI/mecR1
/
mecR2
and
blaI/blaR1
) for
mecA
transcription. We showed that the impact of the stringent stress response on the resistance level may be restricted to beta-lactam resistance based on a “foreign” determinant such as
mecA
, as opposed to resistance based on mutations in the native
S. aureus
determinant
pbpB
(encoding PBP2). Our observations demonstrate that high-level resistance mediated by the stringent stress response follows the current model of beta-lactam resistance in which the native PBP2 protein is also essential for expression of the resistance phenotype. We also show that the
Staphylococcus sciuri pbpD
gene (also called
mecAI
), the putative evolutionary precursor of
mecA
, confers oxacillin resistance in an
S. aureus
strain, generating a heterogeneous phenotype that can be converted to high and homogenous resistance by induction of the stringent stress response in the bacteria.
The Recombinant Bacteriophage Endolysin HY-133 Exhibits
In Vitro
Activity against Different African Clonal Lineages of the Staphylococcus aureus Complex, Including Staphylococcus schweitzeri
Authors: Idelevich Evgeny A. , Schaumburg Frieder , Knaack Dennis , Scherzinger Anna S. , Mutter Wolfgang , Peters Georg , Peschel Andreas , Becker Karsten 
Published: February 2016

ABSTRACT

HY-133 is a recombinant bacteriophage endolysin with bactericidal activity against
Staphylococcus aureus
. Here, HY-133 showed
in vitro
activity against major African methicillin-susceptible and methicillin-resistant
S. aureus
lineages and ceftaroline/ceftobiprole- and borderline oxacillin-resistant isolates. HY-133 was also active against
Staphylococcus schweitzeri
, a recently described species of the
S. aureus
complex. The activity of HY-133 on the tested isolates (MIC
50
, 0.25 μg/ml; MIC
90
, 0.5 μg/ml; range, 0.125 to 0.5 μg/ml) was independent of the species and strain background or antibiotic resistance.
Complement Activation by Giardia duodenalis Parasites through the Lectin Pathway Contributes to Mast Cell Responses and Parasite Control
Authors: Li Erqiu , Tako Ernest A. , Singer Steven M. 
Published: February 2016

ABSTRACTInfection withGiardia duodenalisis one of the most common causes of diarrheal disease in the world. While numerous studies have identified important contributions of adaptive immune responses to parasite control, much less work has examined innate immunity and its connections to the adaptive response during this infection. We explored the role of complement in immunity toGiardiausing mice deficient in mannose-binding lectin (Mbl2) or complement factor 3a receptor (C3aR). Both strains exhibited delayed clearance of parasites and a reduced ability to recruit mast cells in the intestinal submucosa. C3aR-deficient mice had normal production of antiparasite IgA, butex vivoT cell recall responses were impaired. These data suggest that complement is a key factor in the innate recognition ofGiardiaand that recruitment of mast cells and activation of T cell immunity through C3a are important for parasite control.
Short-Stalked Prosthecomicrobium hirschii Cells Have a Caulobacter-Like Cell Cycle
Authors: Williams Michelle , Hoffman Michelle D. , Daniel Jeremy J. , Madren Seth M. , Dhroso Andi , Korkin Dmitry , Givan Scott A. , Jacobson Stephen C. , Brown Pamela J. B. 
Published: February 2016

ABSTRACTThe dimorphic alphaproteobacteriumProsthecomicrobium hirschiihas both short-stalked and long-stalked morphotypes. Notably, these morphologies do not arise from transitions in a cell cycle. Instead, the maternal cell morphology is typically reproduced in daughter cells, which results in microcolonies of a single cell type. In this work, we further characterized the short-stalked cells and found that these cells have aCaulobacter-like life cycle in which cell division leads to the generation of two morphologically distinct daughter cells. Using a microfluidic device and total internal reflection fluorescence (TIRF) microscopy, we observed that motile short-stalked cells attach to a surface by means of a polar adhesin. Cells attached at their poles elongate and ultimately release motile daughter cells. Robust biofilm growth occurs in the microfluidic device, enabling the collection of synchronous motile cells and downstream analysis of cell growth and attachment. Analysis of a draftP. hirschiigenome sequence indicates the presence of CtrA-dependent cell cycle regulation. This characterization ofP. hirschiiwill enable future studies on the mechanisms underlying complex morphologies and polymorphic cell cycles.IMPORTANCEBacterial cell shape plays a critical role in regulating important behaviors, such as attachment to surfaces, motility, predation, and cellular differentiation; however, most studies on these behaviors focus on bacteria with relatively simple morphologies, such as rods and spheres. Notably, complex morphologies abound throughout the bacteria, with striking examples, such asP. hirschii, found within the stalkedAlphaproteobacteria.P. hirschiiis an outstanding candidate for studies of complex morphology generation and polymorphic cell cycles. Here, the cell cycle and genome ofP. hirschiiare characterized. This work sets the stage for future studies of the impact of complex cell shapes on bacterial behaviors.
Lanthanide-Dependent Regulation of Methanol Oxidation Systems in Methylobacterium extorquens AM1 and Their Contribution to Methanol Growth
Authors: Vu Huong N. , Subuyuj Gabriel A. , Vijayakumar Srividhya , Good Nathan M. , Martinez-Gomez N. Cecilia , Skovran Elizabeth 
Published: February 2016

ABSTRACT

Methylobacterium extorquens
AM1 has two distinct types of methanol dehydrogenase (MeDH) enzymes that catalyze the oxidation of methanol to formaldehyde. MxaFI-MeDH requires pyrroloquinoline quinone (PQQ) and Ca in its active site, while XoxF-MeDH requires PQQ and lanthanides, such as Ce and La. Using MeDH mutant strains to conduct growth analysis and MeDH activity assays, we demonstrate that
M. extorquens
AM1 has at least one additional lanthanide-dependent methanol oxidation system contributing to methanol growth. Additionally, the abilities of different lanthanides to support growth were tested and strongly suggest that both XoxF and the unknown methanol oxidation system are able to use La, Ce, Pr, Nd, and, to some extent, Sm. Further, growth analysis using increasing La concentrations showed that maximum growth rate and yield were achieved at and above 1 μM La, while concentrations as low as 2.5 nM allowed growth at a reduced rate. Contrary to published data, we show that addition of exogenous lanthanides results in differential expression from the
xox1
and
mxa
promoters, upregulating genes in the
xox1
operon and repressing genes in the
mxa
operon. Using transcriptional reporter fusions, intermediate expression from both the
mxa
and
xox1
promoters was detected when 50 to 100 nM La was added to the growth medium, suggesting that a condition may exist under which
M. extorquens
AM1 is able to utilize both enzymes simultaneously. Together, these results suggest that
M. extorquens
AM1 actively senses and responds to lanthanide availability, preferentially utilizing the lanthanide-dependent MeDHs when possible.

IMPORTANCE
The biological role of lanthanides is a nascent field of study with tremendous potential to impact many areas in biology. Our studies demonstrate that there is at least one additional lanthanide-dependent methanol oxidation system, distinct from the MxaFI and XoxF MeDHs, that may aid in classifying additional environmental organisms as methylotrophs. Further, our data suggest that
M. extorquens
AM1 has a mechanism to regulate which MeDH is transcribed, depending on the presence or absence of lanthanides. While the mechanism controlling differential regulation is not yet understood, further research into how methylotrophs obtain and use lanthanides will facilitate their cultivation in the laboratory and their use as a biomining and biorecycling strategy for recovery of these commercially valuable rare-earth elements.