bluuebunny/crossref_metadata_2025_split huggingface dataset:
The DnaA inhibitor SirA acts in the same pathway as Soj (ParA) to facilitate oriC segregation during Bacillus subtilis sporulation
Authors: Duan Yi , Huey Jack D. , Herman Jennifer K. 
Published: August 2016

SummaryDNA replication and chromosome segregation must be carefully regulated to ensure reproductive success. During Bacillus subtilis sporulation, chromosome copy number is reduced to two, and cells divide asymmetrically to produce the future spore (forespore) compartment. For successful sporulation, oriC must be captured in the forespore. New rounds of DNA replication are prevented in part by SirA, a protein that utilizes residues in its N‐terminus to directly target Domain I of the bacterial initiator, DnaA. Using a quantitative forespore chromosome organization assay, we show that SirA also acts in the same pathway as another DnaA regulator, Soj, to promote oriC capture in the forespore. By analyzing loss‐of‐function variants of both SirA and DnaA, we observe that SirA's ability to inhibit DNA replication can be genetically separated from its role in oriC capture. In addition, we identify substitutions near the C‐terminus of SirA and in DnaA Domain III that enhance interaction between the two proteins. One such variant, SirAP141T, remained functional in regard to inhibiting replication, but was unable to support oriC capture. Collectively, our results support a model in which SirA targets DnaA Domain I to inhibit DNA replication, and DnaA Domain III to facilitate Soj‐dependent oriC capture in the forespore.
Time of day determines Arabidopsis transcriptome and growth dynamics under mild drought
Authors: Dubois Marieke , Claeys Hannes , Van den Broeck Lisa , Inzé Dirk 
Published: August 2016

AbstractDrought stress is a major problem for agriculture worldwide, causing significant yield losses. Plants have developed highly flexible mechanisms to deal with drought, including organ‐ and developmental stage‐specific responses. In young leaves, growth is repressed as an active mechanism to save water and energy, increasing the chances of survival but decreasing yield. Despite its importance, the molecular basis for this growth inhibition is largely unknown. Here, we present a novel approach to explore early molecular mechanisms controlling Arabidopsis leaf growth inhibition following mild drought. We found that growth and transcriptome responses to drought are highly dynamic. Growth was only repressed by drought during the day, and our evidence suggests that this may be due to gating by the circadian clock. Similarly, time of day strongly affected the extent, specificity, and in certain cases even direction of drought‐induced changes in gene expression. These findings underscore the importance of taking into account diurnal patterns to understand stress responses, as only a small core of drought‐responsive genes are affected by drought at all times of the day. Finally, we leveraged our high‐resolution data to demonstrate that phenotypic and transcriptome responses can be matched to identify putative novel regulators of growth under mild drought.
Stochastic analysis of production dynamics of male and female redclaw crayfish (Cherax quadricarinatus) reared under commercial intensive cultivation
Authors: Nuñez‐Amao Lavinia , Villarreal Humberto , Naranjo‐Paramo José , Hernandez‐Llamas Alfredo 
Published: August 2016

AbstractWe used a stochastic model to simulate, over time, total biomass production of male and female Australian redclaw crayfish (Cherax quadricarinatus), so as production of commercial‐sized crayfish (40–60 and 61–90 g). The model was calibrated with a database from an intensive commercial farm. Results showed that uncertainty in obtaining production of the 61–90 g grade diminished with time. In the case of 40–60 g grade and total biomass, uncertainty was minimal at 69 days (males 40–60 g grade), 84 days (females 40–60 g grade), 92 days (male total biomass) and 94 days (female total biomass). The model predicted that, at harvesting time, there is 95% confidence intervals that males produce 2.96–3.29 t ha−1 (mean = 3.13 t ha−1) and females produce 2.49–2.72 t ha−1 (mean = 2.60 t ha−1), of biomass, closely approximating biomass production registered in the database. When increasing sample size from one pond to 16 ponds, variability in production was reduced in 75.5% (males) and 65.2% (females). Sensitivity analysis showed that individual weight, and percentages corresponding to the total commercial population and the 40–60 g size were the variables mostly influencing the variance of yields. The results showed that the dynamics of production of commercial biomass strongly differ among ponds. We conclude that the model is a useful tool for analysis of the stochastic processes governing production dynamics of redclaw crayfish biomass.
Novel and designed ecosystems
Authors: Higgs Eric 
Published: August 2016

AbstractGrowing attention to novel and designed ecosystems, and the confusion that follows from the overlap of these distinct ecosystem approaches, risks a loss of focus on ecological values at the core of restoration ecology. Novel ecosystems originate in ecosystems that are transformed beyond which the practical efforts of conventional restoration are feasible. They are also self‐sustaining in the sense that they take time to form, and do not typically receive regular management. In this respect, they arise differently than designed ecosystems, which are assembled with specific goals in mind and are often heavily managed. Designed (or engineered) ecosystems comprise a variety of ecological approaches including reclamation (return a degraded ecosystem to productive capacity), green infrastructure, and agroecological systems. There are three elements that distinguish novel and designed ecosystems. Designed ecosystems typically require intensive intervention to create them, and ongoing management to sustain them; novel ecosystems do not. Second, the human intentions behind designed and novel ecosystems are usually different. Designed ecosystems exist in the service of human interests, including specific services (e.g. filtration, cooling, nature appreciation), aesthetics, and shifting value commitments toward green infrastructure; novel ecosystems arise typically through inadvertent human activity. Third, designed and novel ecosystems have different developmental pathways. Historical ecosystems are the starting point for restored, hybrid, and novel ecosystems; designed ecosystems are intentionally created. Designed ecosystems stand apart as providing a new origin for ecosystems of the future, including those that become novel ecosystems.
The effect of blood transfusion on central venous oxygen saturation in critically ill patients admitted to a neurointensive care unit
Authors: Surve R. M. , Muthuchellappan R. , Rao G.S.U. , Philip M. 
Published: August 2016

SUMMARYBackgroundLiterature suggests poorer outcomes during anaemia as well as following red blood cell transfusion (BT) in brain injured patients. Recently, central venous oxygen saturation (ScvO2) has been proposed as a physiological trigger to guide red BT. In this study, we looked at ScvO2 changes following BT in patients admitted to a neurointensive care unit (NICU).Study designIn this prospective, observational study, adult, acutely ill neurological patients of >18 years were recruited. The following parameters were measured before and immediately after transfusion and then at 6, 12, 18 and 24 h after transfusion: haemoglobin (Hb), ScvO2 and central venous oxygen partial pressure (PcvO2) (blood sampled from central venous catheter). Simultaneously, hemodynamic parameters [central venous pressure (CVP), heart rate (HR), mean arterial pressure (MAP) and systolic blood pressure (SBP)] were also noted.ResultsData from 70 adult patients were analysed. Following BT, significant improvement was noted in Hb, ScvO2 and all hemodynamic parameters. The ScvO2 changes correlated significantly with the number of units of BT (P = 0·039), pre‐transfusion Hb (P = 0·010), ScvO2 (P = 0·001) and PcvO2 (P = 0·001). When receiver operating characteristic (ROC) curves were drawn, optimum cut‐off values of baseline ScvO2 and Hb to predict the need for transfusion in terms of oxygen delivery were 70% and 8·6 gm dL−1 respectively.DiscussionBaseline ScvO2<70% appears to be a useful physiological trigger for deciding the need for BT in brain injured patients. Whether improvement in ScvO2 leads to improvement in regional brain oxygenation needs to be studied.
Incorporating catchment to reach scale processes into hydromorphological assessment in the UK
Authors: England Judy , Gurnell Angela M. 
Published: August 2016

AbstractHydromorphological pressures and the measures undertaken to address them are an important element of the delivery of the WFD within the United Kingdom. While assessment procedures currently employed gather useful morphological information for river reaches and their immediate margins and some process information, crucial information on key processes is missing and information gathered on the riparian zone and floodplain is limited. This article presents a newly developed framework that enables existing data to be placed within a multiscale, process‐based context. The framework has great promise for diagnosing hydromorphological pressures, identifying where and how natural recovery is likely to take place, and where more interventionist restoration techniques may be needed. The ability to consider trajectories of river channel adjustments could help us understand how watercourses are still responding to historic changes, improve our confidence in applying restoration measures and the likely hydromorphological consequences of future climate changes.
Characterization of CTX-M-140, a Variant of CTX-M-14 Extended-Spectrum β-Lactamase with Decreased Cephalosporin Hydrolytic Activity, from Cephalosporin-Resistant Proteus mirabilis
Authors: Tian Guo-Bao , Jiang Yi-Qi , Huang Ying-Min , Qin Yun , Feng Lian-Qiang , Zhang Xue-Fei , Li Hong-Yu , Zhong Lan-Lan , Zeng Kun-Jiao , Patil Sandip , Xing Yong , Huang Xi 
Published: August 2016

ABSTRACT

CTX-M-140, a novel CTX-M-type extended-spectrum β-lactamase (ESBL), was identified in cephalosporin-resistant clinical isolates of
Proteus mirabilis
. CTX-M-140 contained an alanine-to-threonine substitution at position 109 compared to its putative progenitor, CTX-M-14. When it was expressed in an
Escherichia coli
isogenic background, CTX-M-140 conferred 4- to 32-fold lower MICs of cephalosporins than those with CTX-M-14, indicating that the phenotype was attributable to this single substitution. For four mutants of CTX-M-14 that were constructed by site-directed mutagenesis (A109E, A109D, A109K, and A109R mutants), MICs of cephalosporins were similar to those for the
E. coli
host strain, which suggested that the alanine at position 109 was essential for cephalosporin hydrolysis. The kinetic properties of native CTX-M-14 and CTX-M-140 were consistent with the MICs for the
E. coli
clones. Compared with that of CTX-M-14, a lower hydrolytic activity against cephalosporins was observed for CTX-M-140.
bla
CTX-M-140
is located on the chromosome as determined by I-CeuI pulsed-field gel electrophoresis (I-CeuI-PFGE) and Southern hybridization. The genetic environment surrounding
bla
CTX-M-140
is identical to the sequence found in different plasmids with
bla
CTX-M-9-group
genes among the
Enterobacteriaceae
. Genome sequencing and analysis showed that
P. mirabilis
strains with
bla
CTX-M-140
have a genome size of ∼4 Mbp, with a GC content of 38.7% and 23 putative antibiotic resistance genes. Our results indicate that alanine at position 109 is critical for the hydrolytic activity of CTX-M-14 against oxyimino-cephalosporins.
Comparative Characterization of CTX-M-64 and CTX-M-14 Provides Insights into the Structure and Catalytic Activity of the CTX-M Class of Enzymes
Authors: He Dandan , Chiou Jiachi , Zeng Zhenling , Chan Edward Wai-Chi , Liu Jian-Hua , Chen Sheng 
Published: August 2016

ABSTRACT

Clinical isolates producing hybrid CTX-M β-lactamases, presumably due to recombination between the
bla
CTX-M-15
and
bla
CTX-M-14
elements, have emerged in recent years. Among the hybrid enzymes, CTX-M-64 and CTX-M-14 display the most significant difference in catalytic activity. This study aims to investigate the mechanisms underlying such differential enzymatic activities in order to provide insight into the structure/function relationship of this class of enzymes. Sequence alignment analysis showed that the major differences between the amino acid composition of CTX-M-64 and CTX-M-14 lie at both the N and C termini of the enzymes. Single or multiple amino acid substitutions introduced into CTX-M-64 and CTX-M-14 were found to produce only minor effects on hydrolytic functions; such a finding is consistent with the notion that the discrepancy between the functional activities of the two enzymes is not the result of only a few amino acid changes but is attributable to interactions between a unique set of amino acid residues in each enzyme. This theory is supported by the results of the thermal stability assay, which confirmed that CTX-M-64 is significantly more stable than CTX-M-14. Our data confirmed that, in addition to the important residues located in the active site, residues distal to the active site also contribute to the catalytic activity of the enzyme through stabilizing its structural integrity.
Validation of the HIV Tropism Test TROCAI Using the Virological Response to a Short-Term Maraviroc Monotherapy Exposure
Authors: Gonzalez-Serna A. , Genebat M. , De Luna-Romero M. , Tarancon-Diez L. , Dominguez-Molina B. , Pacheco Y. M. , Muñoz-Fernández M. A. , Leal M. , Ruiz-Mateos E. 
Published: August 2016

ABSTRACT
TROCAI is a phenotypic tropism test developed using the virological response to a short-term exposure to maraviroc monotherapy (Maraviroc Clinical Test [MCT]). It was found that with TROCAI, a cutoff of <0.5% of dual/mixed viruses was needed to predict R5 HIV tropism. Here, we have validated TROCAI, using this cutoff, in a new cohort of 42 patients, finding a very high concordance between TROCAI and MCT (98%), and a good concordance (71 to 87%) with other genotypic/phenotypic methods.
Pyrimidine Pathway-Dependent and -Independent Functions of the Toxoplasma gondii Mitochondrial Dihydroorotate Dehydrogenase
Authors: Hortua Triana Miryam Andrea , Cajiao Herrera Daniela , Zimmermann Barbara H. , Fox Barbara A. , Bzik David J. 
Published: August 2016

ABSTRACT

Dihydroorotate dehydrogenase (DHODH) mediates the fourth step of
de novo
pyrimidine biosynthesis and is a proven drug target for inducing immunosuppression in therapy of human disease as well as a rapidly emerging drug target for treatment of malaria. In
Toxoplasma gondii
, disruption of the first, fifth, or sixth step of
de novo
pyrimidine biosynthesis induced uracil auxotrophy. However, previous attempts to generate uracil auxotrophy by genetically deleting the mitochondrion-associated DHODH of
T. gondii
(
Tg
DHODH) failed. To further address the essentiality of
Tg
DHODH, mutant gene alleles deficient in
Tg
DHODH activity were designed to ablate the enzyme activity. Replacement of the endogenous
DHODH
gene with catalytically deficient
DHODH
gene alleles induced uracil auxotrophy. Catalytically deficient
Tg
DHODH localized to the mitochondria, and parasites retained mitochondrial membrane potential. These results show that
Tg
DHODH is essential for the synthesis of pyrimidines and suggest that
Tg
DHODH is required for a second essential function independent of its role in pyrimidine biosynthesis.
Neisseria gonorrhoeae Evades Calprotectin-Mediated Nutritional Immunity and Survives Neutrophil Extracellular Traps by Production of TdfH
Authors: Jean Sophonie , Juneau Richard A. , Criss Alison K. , Cornelissen Cynthia N. 
Published: August 2016

ABSTRACTNeisseria gonorrhoeaesuccessfully overcomes host strategies to limit essential nutrients, termed nutritional immunity, by production of TonB-dependent transporters (TdTs)—outer membrane proteins that facilitate nutrient transport in an energy-dependent manner. Four gonococcal TdTs facilitate utilization of iron or iron chelates from host-derived proteins, including transferrin (TbpA), lactoferrin (LbpA), and hemoglobin (HpuB), in addition to xenosiderophores from other bacteria (FetA). The roles of the remaining four uncharacterized TdTs (TdfF, TdfG, TdfH, and TdfJ) remain elusive. Regulatory data demonstrating that production of gonococcal TdfH and TdfJ are unresponsive to or upregulated under iron-replete conditions led us to evaluate the role of these TdTs in the acquisition of nutrients other than iron. In this study, we found that production of gonococcal TdfH is both Zn and Zur repressed. We also found that TdfH confers resistance to calprotectin, an immune effector protein highly produced in neutrophils that has antimicrobial activity due to its ability to sequester Zn and Mn. We found that TdfH directly binds calprotectin, which enables gonococcal Zn accumulation in a TdfH-dependent manner and enhances bacterial survival after exposure to neutrophil extracellular traps (NETs). These studies highlight Zn sequestration by calprotectin as a key functional arm of NET-mediated killing of gonococci. We demonstrate for the first time thatN. gonorrhoeaeexploits this host strategy in a novel defense mechanism, in which TdfH production hijacks and directly utilizes the host protein calprotectin as a zinc source and thereby evades nutritional immunity.
The Glycolytic Enzyme Triosephosphate Isomerase of Trichomonas vaginalis Is a Surface-Associated Protein Induced by Glucose That Functions as a Laminin- and Fibronectin-Binding Protein
Authors: Miranda-Ozuna Jesús F. T. , Hernández-García Mar S. , Brieba Luis G. , Benítez-Cardoza Claudia G. , Ortega-López Jaime , González-Robles Arturo , Arroyo Rossana 
Published: August 2016

ABSTRACTTriosephosphate isomerase ofTrichomonas vaginalis(TvTIM) is a 27-kDa cytoplasmic protein encoded by two genes,tvtim1andtvtim2, that participates in glucose metabolism.TvTIM is also localized to the parasite surface. Thus, the goal of this study was to identify the novel functions of the surface-associatedTvTIM inT. vaginalisand to assess the effect of glucose as an environmental factor that regulates its expression and localization. Reverse transcription-PCR (RT-PCR) showed that thetvtimgenes were differentially expressed in response to glucose concentration.tvtim1was overexpressed under glucose-restricted (GR) conditions, whereastvtim2was overexpressed under glucose-rich, or high-glucose (HG), conditions. Western blot and indirect immunofluorescence assays also showed that glucose positively affected the amount and surface localization ofTvTIM inT. vaginalis. Affinity ligand assays demonstrated that the recombinantTvTIM1 andTvTIM2 proteins bound to laminin (Lm) and fibronectin (Fn) but not to plasminogen. Moreover, higher levels of adherence to Lm and Fn were detected in parasites grown under HG conditions than in those grown under GR conditions. Furthermore, pretreatment of trichomonads with an anti-TvTIMr polyclonal antibody or pretreatment of Lm- or Fn-coated wells with both recombinant proteins (TvTIM1r andTvTIM2r) specifically reduced the binding of live parasites to Lm and Fn in a concentration-dependent manner. Moreover,T. vaginaliswas exposed to different glucose concentrations during vaginal infection of women with trichomoniasis. Our data indicate thatTvTIM is a surface-associated protein under HG conditions that mediates specific binding to Lm and Fn as a novel virulence factor ofT. vaginalis.
Osmium isotope evidence for two pulses of increased continental weathering linked to Early Jurassic volcanism and climate change
Authors: Percival L.M.E. , Cohen A.S. , Davies M.K. , Dickson A.J. , Hesselbo S.P. , Jenkyns H.C. , Leng M.J. , Mather T.A. , Storm M.S. , Xu W. 
Published: August 2016

Abstract
Large igneous provinces (LIPs) are proposed to have caused a number of episodes of abrupt environmental change by increasing atmospheric CO2 levels, which were subsequently alleviated by drawdown of CO2 via enhanced continental weathering and burial of organic matter. Here the sedimentary records of two such episodes of environmental change, the Toarcian oceanic anoxic event (T-OAE) and preceding Pliensbachian–Toarcian (Pl-To) event (both possibly linked to the Karoo-Ferrar LIP), are investigated using a new suite of geochemical proxies that have not been previously compared. Stratigraphic variations in osmium isotope (187Os/188Os) records are compared with those of mercury (Hg) and carbon isotopes (δ13C) in samples from the Mochras core, Llanbedr Farm, Cardigan Bay Basin, Wales. These sedimentary rocks are confirmed as recording an open-marine setting by analysis of molybdenum/uranium enrichment trends, indicating that the Os isotope record in these samples reflects the isotopic composition of the global ocean. The Os isotope data include the first results across the Pl-To boundary, when seawater 187Os/188Os increased from ∼0.40 to ∼0.53, in addition to new data that show elevated 187Os/188Os (from ∼0.42 to ∼0.68) during the T-OAE. Both increases in 187Os/188Os correlate with negative carbon isotope excursions and increased mercury concentrations, supporting an interplay between terrestrial volcanism, weathering, and climate that was instrumental in driving these distinct episodes of global environmental change. These observations also indicate that the environmental impact of the Karoo-Ferrar LIP was not limited solely to the T-OAE.
Shock-metamorphosed rutile grains containing the high-pressure polymorph TiO2-II in four Neoarchean spherule layers
Authors: Smith Frank C. , Glass Billy P. , Simonson Bruce M. , Smith Joseph P. , Krull-Davatzes Alexandra E. , Booksh Karl S. 
Published: August 2016

Abstract
At least 17 spherule layers are presently known within stratigraphic units deposited between ca. 3.47 and 2.49 Ga. The spherule layers contain varying amounts of formerly molten, millimeter-sized and smaller spherules. The aggregate thickness of spherules in these layers commonly ranges from ∼1 cm to as much as a few decimeters. Several lines of evidence support the interpretation that the spherule layers represent distal impact ejecta layers. Previously, only one shock-metamorphosed grain (quartz) had been documented from the spherule layers. Therefore, a key diagnostic criterion for the impact origin of these layers has remained elusive for 30 years. We report the discovery, using micro-Raman spectroscopy, of shock-induced TiO2-II, a high-pressure polymorph of TiO2, in 34 grains from four Neoarchean spherule layers deposited between ca. 2.65 and 2.54 Ga. As all the TiO2-II-bearing grains contain rutile, we interpret them as shock-metamorphosed rutile grains. Shock-metamorphosed rutile grains, which may be more abundant in the upper parts of three of the layers, provide unambiguous physical evidence to further support an impact origin for these four layers. Our results demonstrate that TiO2-II can survive for &gt;2.5 b.y. in supracrustal successions that have undergone low-grade metamorphism. Because TiO2-II transforms to rutile at a temperature ≥440 °C, TiO2-II in impact ejecta layers is a potential geothermometer. To our knowledge, this is the first report of a shock-induced, high-pressure polymorph formed by an Archean impact.