bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community
Authors: Embree Mallory , Nagarajan Harish , Movahedi Narjes , Chitsaz Hamidreza , Zengler Karsten 
Published: October 2013

Abstract
Microbial interactions have a key role in global geochemical cycles. Although we possess significant knowledge about the general biochemical processes occurring in microbial communities, we are often unable to decipher key functions of individual microorganisms within the environment in part owing to the inability to cultivate or study them in isolation. Here, we circumvent this shortcoming through the use of single-cell genome sequencing and a novel low-input metatranscriptomics protocol to reveal the intricate metabolic capabilities and microbial interactions of an alkane-degrading methanogenic community. This methanogenic consortium oxidizes saturated hydrocarbons under anoxic conditions through a thus-far-uncharacterized biochemical process. The genome sequence of a dominant bacterial member of this community, belonging to the genus Smithella, was sequenced and served as the basis for subsequent analysis through metabolic reconstruction. Metatranscriptomic data generated from less than 500 pg of mRNA highlighted metabolically active genes during anaerobic alkane oxidation in comparison with growth on fatty acids. These data sets suggest that Smithella is not activating hexadecane by fumarate addition. Differential expression assisted in the identification of hypothetical proteins with no known homology that may be involved in hexadecane activation. Additionally, the combination of 16S rDNA sequence and metatranscriptomic data enabled the study of other prevalent organisms within the consortium and their interactions with Smithella, thus yielding a comprehensive characterization of individual constituents at the genome scale during methanogenic alkane oxidation.
Quantitative and qualitative impact of hospital effluent on dissemination of the integron pool
Authors: Stalder Thibault , Barraud Olivier , Jové Thomas , Casellas Magali , Gaschet Margaux , Dagot Christophe , Ploy Marie- Cécile 
Published: October 2013

Abstract
There is increasing evidence that human activity, and especially the resulting effluent, has a major role in the dissemination of bacterial antibiotic-resistance determinants in the environment. Hospitals are the major antibiotic consumers and thus facilitate the spread of antibiotic resistance. Questions are increasingly being raised about the management of hospital effluents, but their involvement in antibiotic-resistance dissemination has never been assessed. Integrons are a paradigm of genetic transfer between the environmental resistome and both commensal and pathogenic bacteria. In order to assess the impact of hospital activities on antibiotic-resistance dissemination in the environment, we monitored integrons and their gene cassettes in hospital effluents, and their release in the environment. We found that bacterial communities present in a hospital effluent contained a high proportion of integrons. In terms of both their gene cassette diversity and gene cassette arrays, the urban effluent and municipal wastewater treatment plant (WWTP) influent were most similar, whereas the hospital effluent and recirculation sludge exhibited very specific patterns. We found that anthropogenic activities led to the release of abundant integrons and antibiotic-resistance gene cassettes, but we observed no specific impact of hospital activities on the receiving environment. Furthermore, although the WWTP did not reduce the normalized integron copy number, it reduced the diversity of gene cassette arrays contained in the raw wastewater, underlining the effect of the biological treatment on the anthropogenic integron pool arriving at the WWTP.
Modular community structure suggests metabolic plasticity during the transition to polar night in ice-covered Antarctic lakes
Authors: Vick-Majors Trista J , Priscu John C , Amaral-Zettler Linda A 
Published: October 2013

Abstract
High-latitude environments, such as the Antarctic McMurdo Dry Valley lakes, are subject to seasonally segregated light–dark cycles, which have important consequences for microbial diversity and function on an annual basis. Owing largely to the logistical difficulties of sampling polar environments during the darkness of winter, little is known about planktonic microbial community responses to the cessation of photosynthetic primary production during the austral sunset, which lingers from approximately February to April. Here, we hypothesized that changes in bacterial, archaeal and eukaryotic community structure, particularly shifts in favor of chemolithotrophs and mixotrophs, would manifest during the transition to polar night. Our work represents the first concurrent molecular characterization, using 454 pyrosequencing of hypervariable regions of the small-subunit ribosomal RNA gene, of bacterial, archaeal and eukaryotic communities in permanently ice-covered lakes Fryxell and Bonney, before and during the polar night transition. We found vertically stratified populations that varied at the community and/or operational taxonomic unit-level between lakes and seasons. Network analysis based on operational taxonomic unit level interactions revealed nonrandomly structured microbial communities organized into modules (groups of taxa) containing key metabolic potential capacities, including photoheterotrophy, mixotrophy and chemolithotrophy, which are likely to be differentially favored during the transition to polar night.
Integrated transcriptomic and proteomic analysis of the global response of Wolbachia to doxycycline-induced stress
Authors: Darby Alistair C , Gill A Christina , Armstrong Stuart D , Hartley Catherine S , Xia Dong , Wastling Jonathan M , Makepeace Benjamin L 
Published: October 2013

Abstract
The bacterium Wolbachia (order Rickettsiales), representing perhaps the most abundant vertically transmitted microbe worldwide, infects arthropods and filarial nematodes. In arthropods, Wolbachia can induce reproductive alterations and interfere with the transmission of several arthropod-borne pathogens. In addition, Wolbachia is an obligate mutualist of the filarial parasites that cause lymphatic filariasis and onchocerciasis in the tropics. Targeting Wolbachia with tetracycline antibiotics leads to sterilisation and ultimately death of adult filariae. However, several weeks of treatment are required, restricting the implementation of this control strategy. To date, the response of Wolbachia to stress has not been investigated, and almost nothing is known about global regulation of gene expression in this organism. We exposed an arthropod Wolbachia strain to doxycycline in vitro, and analysed differential expression by directional RNA-seq and label-free, quantitative proteomics. We found that Wolbachia responded not only by modulating expression of the translation machinery, but also by upregulating nucleotide synthesis and energy metabolism, while downregulating outer membrane proteins. Moreover, Wolbachia increased the expression of a key component of the twin-arginine translocase (tatA) and a phosphate ABC transporter ATPase (PstB); the latter is associated with decreased susceptibility to antimicrobials in free-living bacteria. Finally, the downregulation of 6S RNA during translational inhibition suggests that this small RNA is involved in growth rate control. Despite its highly reduced genome, Wolbachia shows a surprising ability to regulate gene expression during exposure to a potent stressor. Our findings have general relevance for the chemotherapy of obligate intracellular bacteria and the mechanistic basis of persistence in the Rickettsiales.
Base excision repair AP endonucleases and mismatch repair act together to induce checkpoint-mediated autophagy
Authors: SenGupta Tanima , Torgersen Maria Lyngaas , Kassahun Henok , Vellai Tibor , Simonsen Anne , Nilsen Hilde 
Published: October 2013

AbstractCellular responses to DNA damage involve distinct DNA repair pathways, such as mismatch repair (MMR) and base excision repair (BER). UsingCaenorhabditis elegansas a model system, we present genetic and molecular evidence of a mechanistic link between processing of DNA damage and activation of autophagy. Here we show that the BER AP endonucleases APN-1 and EXO-3 function in the same pathway as MMR, to elicit DNA-directed toxicity in response to 5-fluorouracil, a mainstay of systemic adjuvant treatment of solid cancers. Immunohistochemical analyses suggest that EXO-3 generates the DNA nicks required for MMR activation. Processing of DNA damage via this pathway, in which both BER and MMR enzymes are required, leads to induction of autophagy inC. elegansand human cells. Hence, our data show that MMR- and AP endonuclease-dependent processing of 5-fluorouracil-induced DNA damage leads to checkpoint activation and induction of autophagy, whose hyperactivation contributes to cell death.
CD72 regulates the growth of KIT-mutated leukemia cell line Kasumi-1
Authors: Kataoka Tatsuki R. , Kumanogoh Atsushi , Hirata Masahiro , Moriyoshi Koki , Ueshima Chiyuki , Kawahara Masahiro , Tsuruyama Tatsuaki , Haga Hironori 
Published: October 2013

AbstractGain-of-function mutations in KIT, a member of the receptor type tyrosine kinases, are observed in certain neoplasms, including mast cell tumors (MCTs) and acute myelogenous leukemias (AMLs). A MCT line HMC1.2 harboring the KIT mutation was reported to express CD72, which could suppress the cell proliferation. Here, we examined the ability of CD72 to modify the growth of AMLs harboring gain-of-function KIT mutations. CD72 was expressed on the surface of the AML cell line, Kasumi-1. CD72 ligation by an agonistic antibody BU40 or by a natural ligand CD100, suppressed the proliferation of the Kasumi-1 cells and enhanced cell death, as monitored by caspase-3 cleavage. These responses were associated with the phosphorylation of CD72, the formation of the CD72 - SHP-1 complex and dephosphorylation of src family kinases and JNK. Thus, these results seemed to suggest that CD72 was the therapeutic potential for AML, as is the case of MCTs.
Cellular network entropy as the energy potential in Waddington's differentiation landscape
Authors: Banerji Christopher R. S. , Miranda-Saavedra Diego , Severini Simone , Widschwendter Martin , Enver Tariq , Zhou Joseph X. , Teschendorff Andrew E. 
Published: October 2013

AbstractDifferentiation is a key cellular process in normal tissue development that is significantly altered in cancer. Although molecular signatures characterising pluripotency and multipotency exist, there is, as yet, no single quantitative mark of a cellular sample's position in the global differentiation hierarchy. Here we adopt a systems view and consider the sample's network entropy, a measure of signaling pathway promiscuity, computable from a sample's genome-wide expression profile. We demonstrate that network entropy provides a quantitative, in-silico, readout of the average undifferentiated state of the profiled cells, recapitulating the known hierarchy of pluripotent, multipotent and differentiated cell types. Network entropy further exhibits dynamic changes in time course differentiation data, and in line with a sample's differentiation stage. In disease, network entropy predicts a higher level of cellular plasticity in cancer stem cell populations compared to ordinary cancer cells. Importantly, network entropy also allows identification of key differentiation pathways. Our results are consistent with the view that pluripotency is a statistical property defined at the cellular population level, correlating with intra-sample heterogeneity, and driven by the degree of signaling promiscuity in cells. In summary, network entropy provides a quantitative measure of a cell's undifferentiated state, defining its elevation in Waddington's landscape.
From Hopeless to Curious? Thoughts on Hausman's “Dubious to Hopeless” Critique of Contingent Valuation
Authors: Haab Timothy C. , Interis Matthew G. , Petrolia Daniel R. , Whitehead John C. 
Published: October 2013

AbstractHausman “selectively” reviewed the contingent valuation method (CVM) literature in 2012 and failed to find progress in the method during the 18 years since Diamond and Hausman argued that unquantified benefits and costs are preferred to those quantified by CVM. In this manuscript, we provide counter‐arguments to Hausman's claims, not with the intent to convince the reader that the debate over CVM is settled in favor of the method, but rather to argue that the intellectual debate over CVM is ongoing, that dismissing CVM is unwarranted, and that plenty of work remains to be done for the truly curious researcher.
Principles of International Investment Law
Authors: Dolzer Rudolf , Schreuer Christoph 
Published: October 2013

Abstract
This book outlines the principles behind the international law of foreign investment, focusing on the law governed by bilateral and multilateral investment treaties. The book traces the purpose, context, and evolution of the clauses and provisions characteristic of contemporary investment treaties, and analyses the case law interpreting the issues raised by standard clauses. Particular consideration is given to broad treaty-rules whose understanding in practice has mainly been shaped by their interpretation and application by international tribunals. In addition, the book introduces the dispute settlement mechanisms for enforcing investment law, outlining the operation of State vs. State and Investor vs. State arbitration. Combining a systematic analytical study of the texts and principles underlying investment law with a jurisprudential analysis of the case law arising in international tribunals, this book introduces the principles of international investment law and arbitration.
Herschel observations and a model for IRAS 08572+3915: a candidate for the most luminous infrared galaxy in the local (
z &lt; 0.2) Universe
Authors: Efstathiou A. , Pearson C. , Farrah D. , Rigopoulou D. , Graciá-Carpio J. , Verma A. , Spoon H. W. W. , Afonso J. , Bernard-Salas J. , Clements D. L. , Cooray A. , Cormier D. , Etxaluze M. , Fischer J. , González-Alfonso E. , Hurley P. , Lebouteiller V. , Oliver S. J. , Rowan-Robinson M. , Sturm E. 
Published: October 2013

Abstract
We present Herschel photometry and spectroscopy, carried out as part of the Herschel ultraluminous infrared galaxy (ULIRG) survey, and a model for the infrared to submillimetre emission of the ULIRG IRAS 08572+3915. This source shows one of the deepest known silicate absorption features and no polycyclic aromatic hydrocarbon emission. The model suggests that this object is powered by an active galactic nucleus (AGN) with a fairly smooth torus viewed almost edge-on and a very young starburst. According to our model, the AGN contributes about 90 per cent of the total luminosity of 1.1 × 1013 L⊙, which is about a factor of 5 higher than previous estimates. The large correction of the luminosity is due to the anisotropy of the emission of the best-fitting torus. Similar corrections may be necessary for other local and high-z analogues. This correction implies that IRAS 08572+3915 at a redshift of 0.058 35 may be the nearest hyperluminous infrared galaxy and probably the most luminous infrared galaxy in the local (z &lt; 0.2) Universe. IRAS 08572+3915 shows a low ratio of [C ii] to IR luminosity (log L[Cii]/LIR &lt; −3.8) and a [O i]63 μm to [C ii]158 μm line ratio of about 1 that supports the model presented in this Letter.
Proposed Methodology for Quality Preselection of Rice Populations
Authors: Moreira Adriane M. , Bassinello Priscila Z. , Caliari Márcio , Borba Tereza C. O. 
Published: October 2013

ABSTRACTThe evaluation of culinary and sensory characteristics of a particular cultivar is an important trait for rice grain quality because it guides decisions for breeding programs and allows the prediction of rice market acceptance. The aim of this study was to apply direct and indirect tests for the characterization of the grain quality in a segregating rice population under different treatments (2 × 2). A methodology was proposed from the data based on mathematical equations to aid rice breeding programs in the preselection of promising genotypes. Grain samples were evaluated for apparent amylose content, gelatinization temperature, and viscoamylographic profile. In addition, the samples were subjected to a cooking test. The evaluated parameters were weighted and grouped into two linear equations, yielding scores that were subjected to the selection criteria. Using this methodology, families of the studied population were preselected, which reduced the number of samples for final selection by at least 76%. The physical‐chemical analysis did not indicate a direct positive correlation to accurately infer the culinary and sensorial quality of the rice for human consumption, but this analysis was shown to be useful in the preselection of lineages through the proposed strategy.
First Report of Acidovorax avenae subsp. avenae Causing Sugarcane Red Stripe in Gabon
Authors: Girard J.-C. , Noëll J. , Larbre F. , Roumagnac P. , Rott P. 
Published: October 2013

During a disease inspection at the sugarcane estate SUCAF near Franceville, Gabon, in March 2011, 1- to 3-mm wide and several dm long dark red stripes were observed on sugarcane (Saccharum spp.) leaves of many plants of cultivar R570. These plants were 5.5 months old in the first ratoon crop. Additionally, spindle leaves of several stalks were rotted and could be easily pulled out of the top of the stalk. Longitudinal sections of diseased stalks showed reddish-brown discoloration of the upper stem and the rotted spindle had an unpleasant odor. Circular, convex, smooth, yellow-cream pigmented bacterial colonies with 2 to 3 mm diameter were isolated after 3 days at 28°C from young leaf lesions on YPGA (yeast extract 7 g/L, peptone 7 g/L, glucose 7 g/L, agar 15 g/L, pH 6.8 to 7.0). The 16S-23S internal transcribed spacer (ITS) of two representative colonies was PCR amplified, and the nucleotide sequences were shown to be 99% identical to the 16S-23S ITS sequence from the genome of Acidovorax avenae subsp. avenae strain ATCC 19860 (GenBank: CP002521.1). One of these A. avenae subsp. avenae isolates from Gabon was inoculated into greenhouse grown plants of sugarcane cultivar R570. Plants were inoculated by injection into the sheath of spindle leaves above the meristem with the bacterial strain (12 plants) or with a water control (six plants). In this method, the bacteria (108 CFU/ml) were injected using a syringe through the leaf sheath until filling the leaf whorl. Three weeks post-inoculation, one to several cm long red-brown stripes were observed on leaves of 11 of 12 inoculated plants. Seven weeks post-inoculation, all plants exhibited symptoms, from red, brown, or black stripes to leaf necrosis, rotting, and death of the spindle leaves (six plants). All six control plants were symptomless. In a second experiment, 6 of 12 plants showed symptoms 3 weeks post inoculation, and the pathogen was successfully re-isolated from all six symptomatic plants with YPGA medium. The 16S-23S ITS of three single colonies obtained each from different symptomatic plants were PCR amplified and the nucleotide sequences were again found 99% identical to the 16S-23S ITS sequence from the genome of A. avenae subsp. avenae ATCC 19860. To our knowledge, this is the first report of A. avenae subsp. avenae, the causal agent of sugarcane red stripe (also reported as top rot), in Gabon. It is also the first description of the occurrence of the top rot form of the disease in R570, a cultivar that is grown in several locations of Africa, the Mascarene Islands, and the French West Indies. A large-scale survey needs to be undertaken to determine the distribution of red stripe in Gabon, a disease for which several outbreaks have been reported recently worldwide (1,2). References: (1) M. P. Grisham and R. M. Johnson. Phytopathology 101:564, 2011. (2) S. Zia-ul-Hussnain et al. Afr. J. Biotechnol. 10:7191, 2011.
Isoflurane-induced Apoptosis of Neurons and Oligodendrocytes in the Fetal Rhesus Macaque Brain
Authors: Creeley Catherine E. , Dikranian Krikor T. , Dissen Gregory A. , Back Stephen A. , Olney John W. , Brambrink Ansgar M. 
Published: October 2013

Abstract

Background:
The authors have previously shown that exposure of the neonatal nonhuman primate (NHP) brain to isoflurane for 5 h causes widespread acute apoptotic degeneration of neurons and oligodendrocyte. The current study explored the potential apoptogenic action of isoflurane in the fetal NHP brain.

Methods:
Fetal rhesus macaques at gestational age of 120 days (G120) were exposed in utero for 5 h to isoflurane anesthesia (n = 5) or to no anesthesia (control condition; n = 4), and all regions of the brain were systematically evaluated 3 h later for evidence of apoptotic degeneration of neurons or glia.

Results:
Exposure of the G120 fetal NHP brain to isoflurane caused a significant increase in apoptosis of neurons and of oligodendrocytes at a stage when oligodendrocytes were just beginning to myelinate axons. The neuroapoptosis response was most prominent in the cerebellum, caudate, putamen, amygdala, and several cerebrocortical regions. Oligodendrocyte apoptosis was diffusely distributed over many white matter regions. The total number of apoptotic profiles (neurons + oligodendrocytes) in the isoflurane-exposed brains was increased 4.1-fold, compared with the brains from drug-naive controls. The total number of oligodendrocytes deleted by isoflurane was higher than the number of neurons deleted.

Conclusions:
Isoflurane anesthesia for 5 h causes death of neurons and oligodendrocytes in the G120 fetal NHP brain. In the fetal brain, as the authors previously found in the neonatal NHP brain, oligodendrocytes become vulnerable when they are just achieving myelination competence. The neurotoxic potential of isoflurane increases between the third trimester (G120) and the neonatal period in the NHP brain.
Postoperative Changes in Sleep-disordered Breathing and Sleep Architecture in Patients with Obstructive Sleep Apnea
Authors: Chung Frances , Liao Pu , Yegneswaran Balaji , Shapiro Colin M. , Kang Weimin 
Published: October 2013

Abstract

Background:
Anesthetics, analgesics, and surgery may profoundly affect sleep architecture and aggravate sleep-related breathing disturbances. The authors hypothesized that patients with preoperative polysomnographic evidence of obstructive sleep apnea (OSA) would experience greater changes in these parameters than patients without OSA.

Methods:
After obtaining approvals from the Institutional Review Boards, consented patients underwent portable polysomnography preoperatively and on postoperative nights (N) 1, 3, 5, and 7 at home or in hospital. The primary and secondary outcome measurements were polysomnographic parameters of sleep-disordered breathing and sleep architecture.

Results:
Of the 58 patients completed the study, 38 patients had OSA (apnea hypopnea index [AHI] >5) with median preoperative AHI of 18 events per hour and 20 non-OSA patients had median preoperative AHI of 2. AHI was increased after surgery in both OSA and non-OSA patients (P < 0.05), with peak increase on postoperative N3 (OSA vs. non-OSA, 29 [14, 57] vs. 8 [2, 18], median [25th, 75th percentile], P < 0.05). Hypopnea index accounted for 72% of the postoperative increase in AHI. The central apnea index was low (median = 0) but was significantly increased on postoperative N1 in only non-OSA patients. Sleep efficiency, rapid eye movement sleep, and slow-wave sleep were decreased on N1 in both groups, with gradual recovery.

Conclusions:
Postoperatively, sleep architecture was disturbed and AHI was increased in both OSA and non-OSA patients. Although the disturbances in sleep architecture were greatest on postoperative N1, breathing disturbances during sleep were greatest on postoperative N3.