The multifaceted histone chaperone RbAp46/48 in Plasmodium falciparum: structural insights, production, and characterization

RbAp46/RBBP7 and RbAp48/RBBP4 are WD40-repeat histone chaperones and chromatin adaptors that reside in multiple complexes involved in maintenance of chromatin structure. RbAp48 is the essential subunit of the chromatin assembly factor-1 (CAF-1) complex, therefore also named as CAF-1C. A detailed in silico sequence and structure analysis of homologs of RbAp46/48 in Plasmodium falciparum (PF3D7_0110700 and PF3D7_1433300) exhibited conservation of characteristic features in both the protein-seven-bladed WD40 β-propeller conformation and different binding interfaces. A comparative structural analysis highlighted species-specific features of the parasite, yeast, drosophila, and human RbAp46/48. In the present study, we report cloning, expression, and characterization of P. falciparum PF3D7_0110700, a putative RbAp46/48 (PfRbAp46/48). PfRbAp46/48 was cloned into pTEM11 vector in fusion with 6xHistidine tag and over-expressed in Escherichia coli B834 cells. The protein was purified by Ni-NTA followed by gel permeation chromatography. The protein expressed in all the three asexual blood stages and exhibited nuclear localization. We showed direct interaction of the purified rPfRbAp46/48 with the histone H4. These findings further our understanding of RbAp46/48 proteins and role of these proteins in the parasite biology.

Unraveling CAF-1 family in Plasmodium falciparum: comparative genome-wide identification and phylogenetic analysis among eukaryotes, expression profiling and protein-protein interaction studies

The present research reports a detailed in silico analysis of chromatin assembly factor-1 (CAF-1) family in human malaria parasite Plasmodium falciparum. Our analysis revealed five chromatin assembly factor-1 genes in P. falciparum (PfCAF-1) and the PfCAF-1 family was divided into two classes where, Class A belongs to the CAF-1 complex and others are kept in Class B. For comparative studies, orthologs of PfCAF-1 family were identified across 53 eukaryotic species and evolutionary relationships were drawn for different CAF-1 subfamilies. The phylogenetic analysis revealed grouping of evolutionary-related species together, although, divergence was observed in branching pattern. A detailed analysis of domain composition highlighted species-specific features viz. species-specific KDDS repeats of 84 amino acids were identified in PfCAF-1A whereas, members of CAF-1C/RbAp48 and RbAp46 subfamily exhibited least variation in size and domain composition. The qRT-PCR analysis revealed upregulation of PfCAF-1 members in trophozoite or schizont stage. Furthermore, a comparative expression analysis of the available transcriptome and proteome data along with qRT-PCR analysis revealed mixed expression patterns (coordination as well as non-coordination between different studies). Protein-protein interaction network analyses of PfCAF-1 family were carried out highlighting important complexes based on interologs. The PfRbAp48 was found to be highly connected with a total of 108 PPIs followed by PfRbAp46. The results unravel insights into the PfCAF-1 family and identify unique features, thus opening new perspectives for further targeted developments to understand and combat malaria menace.

Randomized evaluation of fibrinogen vs placebo in complex cardiovascular surgery (REPLACE): a double-blind phase III study of haemostatic therapy

BACKGROUND

Single-dose human fibrinogen concentrate (FCH) might have haemostatic benefits in complex cardiovascular surgery.

METHODS

Patients undergoing elective aortic surgery requiring cardiopulmonary bypass were randomly assigned to receive FCH or placebo. Study medication was administered to patients with a 5 min bleeding mass of 60-250 g after separation from bypass and surgical haemostasis. A standardized algorithm for allogeneic blood product transfusion was followed if bleeding continued after study medication.

RESULTS

519 patients from 34 centres were randomized, of whom 152 (29%) met inclusion criteria for study medication. Median (IQR) pretreatment 5 min bleeding mass was 107 (76-138) and 91 (71-112) g in the FCH and placebo groups, respectively (P=0.13). More allogeneic blood product units were administered during the first 24 h after FCH, 5.0 (2.0-11.0), when compared with placebo, 3.0 (0.0-7.0), P=0.026. Fewer patients avoided transfusion in the FCH group (15.4%) compared with placebo (28.4%), P=0.047. The FCH immediately increased plasma fibrinogen concentration and fibrin-based clot strength. Adverse event rates were comparable in each group.

CONCLUSIONS

Human fibrinogen concentrate was associated with increased allogeneic blood product transfusion, an unexpected finding contrary to previous studies. Human fibrinogen concentrate may not be effective in this setting when administered according to 5-minute bleeding mass. Low bleeding rates and normal-range plasma fibrinogen concentrations before study medication, and variability in adherence to the complex transfusion algorithm, may have contributed to these results.

CLINICAL TRIAL REGISTRATION

ClinicalTrials.gov identifier no. NCT01475669; EudraCT trial no. 2011-002685-20.

Impact of exercise on productivity, behavior, and immune functioning of weaned Bos indicus-cross calves housed in drylots

The effects of 2 exercise regimes on cattle productivity, immune function, and behavior were evaluated against a control ( = 4 pens/treatment) using weaned -cross calves ( = 203) housed in drylots (16-18 calves/single sex pens). Three treatments were applied 3 times per week for 4 wk: 1) programmatic exercise (PRO), in which cattle and a stockperson walked in the alleyway behind their home pen for 20 min; 2) free exercise (FREE), in which cattle were moved into the drovers alley for 60 min, not exercised by a stockperson, and were allowed free access to their home pen and alleyway; and 3) control (CON), in which calves were removed from their home pen only for routine husbandry. Behavior observations were conducted on d -2 and -1 relative to treatment implementation (d 0) and on d 5, 6, 12, 13, 19, 20, 26, and 27. Instantaneous scan sampling was used to create behavioral profiles for cattle (posture: stand, lie, and walk; and behavior: feed, drink, and ruminate). Focal observations recorded the incidence of social behaviors (allogrooming, social play, and agonistic interactions) and animal-environment interactions (AEI; fencepost licking, rock eating, tongue rolling, and cross-suckling). Body weights, exit velocities, and antibody titers to a bovine viral diarrhea virus type 1b vaccine were measured on d -10, 10, and 28. A linear mixed model (PROC MIXED) was used to evaluate the impact of exercise treatment, sex, time, and their interactions on cattle behavior, health, and productivity. Statistical differences were not observed ( = 0.11) for overall ADG among cattle receiving FREE (1.00 kg ± 0.04) PRO (0.85 kg ± 0.04), or CON (0.86 kg ± 0.05) exercise treatments. Allogrooming ( = 0.05), lying ( < 0. 01), AEI ( < 0.01), rumination ( < 0.01), and agonistic interactions ( < 0.01) increased over time. Comfort-related behaviors (e.g., lying, rumination) increased over the evaluation period, suggesting that calves became acclimated to the environment. Exercise did not alter behaviors or vaccine response and did not reduce the performance of production-critical (e.g., feeding, resting, ruminating) behaviors.

Pain and compression neuropathy in primary inguinal hernia

PURPOSE

Enlargement of the ilioinguinal nerve at the external inguinal ring is observed in 34% of patients undergoing primary open inguinal herniorrhaphy; in 88% of patients it occurs at the fascial edge where the hernia mushrooms with abdominal pressure. Compression neuropathy occurs near many anatomical nerve constriction sites and is associated with enlargement of the peripheral nerve accompanied by sensory changes.

METHODS

In this prospective study, Carolina Comfort Scale (CCS) questionnaire data was collected for 35 primary hernia repairs. Each patient underwent primary inguinal herniorrhaphy that included ilioinguinal neurectomy. All nerves were sampled proximal to the external inguinal ring. Any nerves with grossly increased overall diameter to any degree distal to the external ring were additionally sampled in the thickened portions. A neuropathologist performed histologic evaluation of the H&E-stained cross sections.

RESULTS

Paired comparison of proximal and distal nerves revealed a greater overall diameter and greater measured nerve-specific diameter in distal nerve segments. Nerves with increased overall diameter were also found to have a statistically significant positive correlation with four of eight pain measures. Additionally, increased nerve-specific diameter correlates with increased pain on four of eight pain values, but age effect on nerve diameter blunts this finding.

CONCLUSIONS

Increased preoperative CCS pain values in primary open inguinal hernia are significantly correlated with gross enlargement of the overall diameter and nerve-specific diameter of the ilioinguinal nerve beyond the external inguinal ring. This is consistent with a compression neuropathy.

Identification of mega-environments and rice genotypes for general and specific adaptation to saline and alkaline stresses in India

In the present study, a total of 53 promising salt-tolerant genotypes were tested across 18 salt-affected diverse locations for three years. An attempt was made to identify ideal test locations and mega-environments using GGE biplot analysis. The CSSRI sodic environment was the most discriminating location in individual years as well as over the years and could be used to screen out unstable and salt-sensitive genotypes. Genotypes CSR36, CSR-2K-219, and CSR-2K-262 were found ideal across years. Overall, Genotypes CSR-2K-219, CSR-2K-262, and CSR-2K-242 were found superior and stable among all genotypes with higher mean yields. Different sets of genotypes emerged as winners in saline soils but not in sodic soils; however, Genotype CSR-2K-262 was the only genotype that was best under both saline and alkaline environments over the years. The lack of repeatable associations among locations and repeatable mega-environment groupings indicated the complexity of soil salinity. Hence, a multi-location and multi-year evaluation is indispensable for evaluating the test sites as well as identifying genotypes with consistently specific and wider adaptation to particular agro-climatic zones. The genotypes identified in the present study could be used for commercial cultivation across edaphically challenged areas for sustainable production.

Low level exposure to inorganic mercury interferes with B cell receptor signaling in transitional type 1 B cells

Mercury (Hg) has been implicated as a factor contributing to autoimmune disease in animal models and humans. However the mechanism by which this occurs has remained elusive. Since the discovery of B cells it has been appreciated by immunologists that during the normal course of B cell development, some immature B cells must be generated that produce immunoglobulin reactive to self-antigens (auto-antibodies). However in the course of normal development, the vast majority of immature auto-reactive B cells are prevented from maturing by processes collectively known as tolerance. Autoimmune disease arises when these mechanisms of tolerance are disrupted. In the B cell compartment, it is firmly established that tolerance depends in part upon negative selection of self-reactive immature (transitional type 1) B cells. In these cells negative selection depends upon signals generated by the B Cell Receptor (BCR), in the sense that those T1 B cells who's BCRs most strongly bind to, and so generate the strongest signals to self-antigens are neutralized. In this report we have utilized multicolor phosphoflow cytometry to show that in immature T1 B cells Hg attenuates signal generation by the BCR through mechanisms that may involve Lyn, a key tyrosine kinase in the BCR signal transduction pathway. We suggest that exposure to low, environmentally relevant levels of Hg, disrupts tolerance by interfering with BCR signaling in immature B cells, potentially leading to the appearance of mature auto-reactive B cells which have the ability to contribute to auto-immune disease.

Evolution of the Reactor Antineutrino Flux and Spectrum at Daya Bay

The Daya Bay experiment has observed correlations between reactor core fuel evolution and changes in the reactor antineutrino flux and energy spectrum. Four antineutrino detectors in two experimental halls were used to identify 2.2 million inverse beta decays (IBDs) over 1230 days spanning multiple fuel cycles for each of six 2.9 GW_{th} reactor cores at the Daya Bay and Ling Ao nuclear power plants. Using detector data spanning effective ^{239}Pu fission fractions F_{239} from 0.25 to 0.35, Daya Bay measures an average IBD yield σ[over ¯]_{f} of (5.90±0.13)×10^{-43}  cm^{2}/fission and a fuel-dependent variation in the IBD yield, dσ_{f}/dF_{239}, of (-1.86±0.18)×10^{-43}  cm^{2}/fission. This observation rejects the hypothesis of a constant antineutrino flux as a function of the ^{239}Pu fission fraction at 10 standard deviations. The variation in IBD yield is found to be energy dependent, rejecting the hypothesis of a constant antineutrino energy spectrum at 5.1 standard deviations. While measurements of the evolution in the IBD spectrum show general agreement with predictions from recent reactor models, the measured evolution in total IBD yield disagrees with recent predictions at 3.1σ. This discrepancy indicates that an overall deficit in the measured flux with respect to predictions does not result from equal fractional deficits from the primary fission isotopes ^{235}U, ^{239}Pu, ^{238}U, and ^{241}Pu. Based on measured IBD yield variations, yields of (6.17±0.17) and (4.27±0.26)×10^{-43}  cm^{2}/fission have been determined for the two dominant fission parent isotopes ^{235}U and ^{239}Pu. A 7.8% discrepancy between the observed and predicted ^{235}U yields suggests that this isotope may be the primary contributor to the reactor antineutrino anomaly.

Transfusion in critical care - a UK regional audit of current practice

A consistent message within critical care publications has been that a restrictive transfusion strategy is non-inferior, and possibly superior, to a liberal strategy for stable, non-bleeding critically ill patients. Translation into clinical practice has, however, been slow. Here, we describe the degree of adherence to UK best practice guidelines in a regional network of nine intensive care units within Wessex. All transfusions given during a 2-month period were included (n = 444). Those given for active bleeding or within 24 h of major surgery, trauma or gastrointestinal bleeding were excluded (n = 148). The median (IQR [range]) haemoglobin concentration before transfusion was 73 (68-77 [53-106]) g.l^-1 , with only 34% of transfusion episodes using a transfusion threshold of < 70 g.l^-1 . In a subgroup analysis that did not study patients with a history of cardiac disease (n = 42), haemoglobin concentration before transfusion was 72 (68-77 [50-98]) g.l^-1 , with only 36% of transfusion episodes using a threshold of < 70 g.l^-1 (see Fig. 3). Most blood transfusions given to critically ill patients who were not bleeding in this audit used a haemoglobin threshold > 70 g.l^-1 . The reason why recommendations on transfusion triggers have not translated into clinical practice is unclear. With a clear national drive to decrease usage of blood products and clear evidence that a threshold of 70 g.l^-1 is non-inferior, it is surprising that a scarce and potentially dangerous resource is still being overused within critical care. Simple solutions such as electronic patient records that force pause for thought before blood transfusion, or prescriptions that only allow administration of a single unit in non-emergency circumstances may help to reduce the incidence of unnecessary blood transfusions.

Structural studies of substrate and product complexes of 5-aminolaevulinic acid dehydratase from humans,Escherichia coliand the hyperthermophilePyrobaculum calidifontis

A number of X-ray analyses of an enzyme involved in a key early stage of tetrapyrrole biosynthesis are reported. Two structures of human 5-aminolaevulinate dehydratase (ALAD), native and recombinant, have been determined at 2.8 Å resolution, showing that the enzyme adopts an octameric quaternary structure in accord with previously published analyses of the enzyme from a range of other species. However, this is in contrast to the finding that a disease-related F12L mutant of the human enzyme uniquely forms hexamers [Breiniget al.(2003),Nature Struct. Biol.10, 757–763]. Monomers of all ALADs adopt the TIM-barrel fold; the subunit conformation that assembles into the octamer includes the N-terminal tail of one monomer curled around the (α/β)8barrel of a neighbouring monomer. Both crystal forms of the human enzyme possess two monomers per asymmetric unit, termedAandB. In the native enzyme there are a number of distinct structural differences between theAandBmonomers, with the latter exhibiting greater disorder in a number of loop regions and in the active site. In contrast, the second monomer of the recombinant enzyme appears to be better defined and the active site of both monomers clearly possesses a zinc ion which is bound by three conserved cysteine residues. In native human ALAD, theAmonomer also has a ligand resembling the substrate ALA which is covalently bound by a Schiff base to one of the active-site lysines (Lys252) and is held in place by an ordered active-site loop. In contrast, these features of the active-site structure are disordered or absent in theBsubunit of the native human enzyme. The octameric structure of the zinc-dependent ALAD from the hyperthermophilePyrobaculum calidifontisis also reported at a somewhat lower resolution of 3.5 Å. Finally, the details are presented of a high-resolution structure of theEscherichia coliALAD enzyme co-crystallized with a noncovalently bound moiety of the product, porphobilinogen (PBG). This structure reveals that the pyrrole side-chain amino group is datively bound to the active-site zinc ion and that the PBG carboxylates interact with the enzymeviahydrogen bonds and salt bridges with invariant residues. A number of hydrogen-bond interactions that were previously observed in the structure of yeast ALAD with a cyclic intermediate resembling the product PBG appear to be weaker in the new structure, suggesting that these interactions are only optimal in the transition state.

Quantitative CT Measures of Bronchiectasis in Smokers

BACKGROUND

Bronchiectasis is frequent in smokers with COPD; however, there are only limited data on objective assessments of this process. The objective was to assess bronchovascular morphology, calculate the ratio of the diameters of bronchial lumen and adjacent artery (BA ratio), and identify those measurements able to discriminate bronchiectasis.

METHODS

We collected quantitative CT (QCT) measures of BA ratios, peak wall attenuation, wall thickness (WT), wall area, and wall area percent (WA%) at matched fourth through sixth airway generations in 21 ever smokers with bronchiectasis (cases) and 21 never-smoking control patients (control airways). In cases, measurements were collected at both bronchiectatic and nonbronchiectatic airways. Logistic analysis and the area under receiver operating characteristic curve (AUC) were used to assess the predictive ability of QCT measurements for bronchiectasis.

RESULTS

The whole-lung and fourth through sixth airway generation BA ratio, WT, and WA% were significantly greater in bronchiectasis cases than control patients. The AUCs for the BA ratio to predict bronchiectasis ranged from 0.90 (whole lung) to 0.79 (fourth-generation). AUCs for WT and WA% ranged from 0.72 to 0.75 and from 0.71 to 0.75. The artery diameters but not bronchial diameters were smaller in bronchiectatic than both nonbronchiectatic and control airways (P < .01 for both).

CONCLUSIONS

Smoking-related increases in the BA ratio appear to be driven by reductions in vascular caliber. QCT measures of BA ratio, WT, and WA% may be useful to objectively identify and quantify bronchiectasis in smokers.

TRIAL REGISTRY

ClinicalTrials.gov; No.: NCT00608764; URL: www.clinicaltrials.gov.

Limits on Active to Sterile Neutrino Oscillations from Disappearance Searches in the MINOS, Daya Bay, and Bugey-3 Experiments

Searches for a light sterile neutrino have been performed independently by the MINOS and the Daya Bay experiments using the muon (anti)neutrino and electron antineutrino disappearance channels, respectively. In this Letter, results from both experiments are combined with those from the Bugey-3 reactor neutrino experiment to constrain oscillations into light sterile neutrinos. The three experiments are sensitive to complementary regions of parameter space, enabling the combined analysis to probe regions allowed by the Liquid Scintillator Neutrino Detector (LSND) and MiniBooNE experiments in a minimally extended four-neutrino flavor framework. Stringent limits on sin^{2}2θ_{μe} are set over 6 orders of magnitude in the sterile mass-squared splitting Δm_{41}^{2}. The sterile-neutrino mixing phase space allowed by the LSND and MiniBooNE experiments is excluded for Δm_{41}^{2}<0.8  eV^{2} at 95%  CL_{s}.

Improved Search for a Light Sterile Neutrino with the Full Configuration of the Daya Bay Experiment

This Letter reports an improved search for light sterile neutrino mixing in the electron antineutrino disappearance channel with the full configuration of the Daya Bay Reactor Neutrino Experiment. With an additional 404 days of data collected in eight antineutrino detectors, this search benefits from 3.6 times the statistics available to the previous publication, as well as from improvements in energy calibration and background reduction. A relative comparison of the rate and energy spectrum of reactor antineutrinos in the three experimental halls yields no evidence of sterile neutrino mixing in the 2×10^{-4}≲|Δm_{41}^{2}|≲0.3  eV^{2} mass range. The resulting limits on sin^{2}2θ_{14} are improved by approx imately a factor of 2 over previous results and constitute the most stringent constraints to date in the |Δm_{41}^{2}|≲0.2  eV^{2} region.