A protein interaction map of Drosophila melanogaster

Drosophila melanogaster is a proven model system for many aspects of human biology. Here we present a two-hybrid-based protein-interaction map of the fly proteome. A total of 10,623 predicted transcripts were isolated and screened against standard and normalized complementary DNA libraries to produce a draft map of 7048 proteins and 20,405 interactions. A computational method of rating two-hybrid interaction confidence was developed to refine this draft map to a higher confidence map of 4679 proteins and 4780 interactions. Statistical modeling of the network showed two levels of organization: a short-range organization, presumably corresponding to multiprotein complexes, and a more global organization, presumably corresponding to intercomplex connections. The network recapitulated known pathways, extended pathways, and uncovered previously unknown pathway components. This map serves as a starting point for a systems biology modeling of multicellular organisms, including humans.

Intravascular susceptibility contrast mechanisms in tissues

The factors affecting the rate of loss of transverse magnetization in gradient echo and spin-echo pulse sequences have been quantified using computer modeling for media containing arrays of susceptibility variations. The results are particularly relevant for describing the signal losses that occur in tissues containing capillaries of altered intrinsic susceptibility from the administration of exogenous contrast agents or arising from changes in blood oxygenation. The precise magnitudes and relationship of gradient echo and spin-echo decay rates depend on geometrical factors such as the sizes and spacings of the inhomogeneities, the rate of water diffusion, field strength, and echo times. The conventional separation of contributions to transverse decay rates arising from so-called static field effects and diffusion is shown to be inappropriate for many situations of practical interest because diffusion introduces a motional averaging of the static field even in gradient echo sequences. The result of diffusion in some regimes is to reduce the decay rate from field inhomogeneities in gradient echo sequences, so that T2* is longer in media such as tissue where water diffuses reasonably rapidly, than would be the case for stationary nuclei. The effects of different types of contrast agent and the implications for functional imaging based on the effects of deoxyhemoglobin in brain tissue are considered.

Human CAP18: a novel antimicrobial lipopolysaccharide-binding protein

CAP18 (18-kDa cationic antimicrobial protein) is a protein originally identified and purified from rabbit leukocytes on the basis of its capacity to bind and inhibit various activities of lipopolysaccharide (LPS). Here we report the cloning of human CAP18 and characterize the anti-LPS activity of the C-terminal fragment. Oligonucleotide probes designed from the rabbit CAP18 cDNA were used to identify human CAP18 from a bone marrow cDNA library. The cDNA encodes a protein composed of a 30-amino-acid signal peptide, a 103-amino-acid N-terminal domain of unknown function, and a C-terminal domain of 37 amino acids homologous to the LPS-binding antimicrobial domain of rabbit CAP18, designated CAP18(104-140). A human CAP18-specific antiserum was generated by using CAP18 expressed as a fusion protein with the maltose-binding protein. Western blots (immunoblots) with this antiserum showed specific expression of human CAP18 in granulocytes. Synthetic human CAP18(104-140) and a more active truncated fragment, CAP18(104-135), were shown to (i) bind to erythrocytes coated with diverse strains of LPS, (ii) inhibit LPS-induced release of nitric oxide from macrophages, (iii) inhibit LPS-induced generation of tissue factor, and (iv) protect mice from LPS lethality. CAP18(104-140) may have therapeutic utility for conditions associated with elevated concentrations of LPS.

Theoretical model for water diffusion in tissues

Water diffusion in a tissue model is studied both analytically and numerically. Tissue is regarded as a periodic array of boxes surrounded by partially permeable membranes (cells), embedded in an extracellular medium. intracellular and extracellular diffusion coefficients may differ. Expressions for the apparent diffusion coefficients (ADC) in isotropic and nonisotropic tissues are derived and compared with Monte Carlo simulations. Calculated ADCs disagree with values obtained from the widely used "fast exchange" formula. Effects of differences between intracellular and extracellular T2 relaxation times on measured values of ADC and T2 are discussed. The general analysis is specifically applied to the changes occurring in ADC following ischemic insults to brain tissue. It is found that although membranes affect ADC significantly, the observed changes in diffusion cannot be due to reduced membrane permeabilities. They may result from the combined effect of changes in cellular volume fraction, extracellular and intracellular diffusion.

Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana

The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.

Expression of mRNAs encoding subunits of the NMDA receptor in developing rat brain

Developmental changes in the levels of N-methyl-D-aspartate (NMDA) receptor subunit mRNAs were identified in rat brain using solution hybridization/RNase protection assays. Pronounced increases in the levels of mRNAs encoding NR1 and NR2A were seen in the cerebral cortex, hippocampus, and cerebellum between postnatal days 7 and 20. In cortex and hippocampus, the expression of NR2B mRNA was high in neonatal rats and remained relatively constant over time. In contrast, in cerebellum, the level of NR2B mRNA was highest at postnatal day 1 and declined to undetectable levels by postnatal day 28. NR2C mRNA was not detectable in cerebellum before postnatal day 11, after which it increased to reach adult levels by postnatal day 28. In cortex, the expression of NR2A and NR2B mRNAs corresponds to the previously described developmental profile of NMDA receptor subtypes having low and high affinities for ifenprodil, i.e., a delayed expression of NR2A correlating with the late expression of low-affinity ifenprodil sites. In cortex and hippocampus, the predominant splice variants of NR1 were those without the 5' insert and with or without both 3' inserts. In cerebellum, however, the major NR1 variants were those containing the 5' insert and lacking both 3' inserts. The results show that the expression of NR1 splice variants and NR2 subunits is differentially regulated in various brain regions during development. Changes in subunit expression are likely to underlie some of the changes in the functional and pharmacological properties of NMDA receptors that occur during development.

Factors influencing contrast in fast spin-echo MR imaging

Multi-echo pulse sequences for producing T2-weighted images in much reduced imaging times have recently been developed for routine clinical use. A number of recent articles have described the contrast obtained with fast spin-echo (FSE) sequences and have generally indicated that they depict tissues very similarly to conventional spin-echo (SE) imaging. There are, however, some important differences in contrast between some tissues in FSE images. This work presents a detailed study of the contrast obtained with FSE imaging sequences and examines the image sequence and tissue parameters which influence contrast. The use of multiple refocusing pulses produces several subtle effects not seen in conventional SE imaging sequences, and in this study the precise nature and extent of such effects are described. The relative contributions to image contrast of magnetization transfer, the decoupling of J-modulation effects, the production of stimulated echoes and direct saturation effects, of diffusion and of the effects of the differential attenuation of different spatial frequencies, are each quantified. The mechanisms responsible for the brighter fat signal seen in FSE images, as well as the loss of signal from some other tissues, are explained. Computer simulations, phantom experiments, and clinical images are all used to support the conclusions.

Changes in water diffusion and relaxation properties of rat cerebrum during status epilepticus

Diffusion-weighted (DW) imaging has been used to record changes associated with status epilepticus (SE) in rat brain. It was found that the apparent diffusion coefficient (ADC) of water in brain decreased 14-18% during SE, and it fell a further 20-22% when the animals were sacrificed. The transverse decay time constant T2* showed corresponding reductions, but no significant changes were seen in relaxation times T1 or T2 values. Changes in ADC in status epilepticus are similar to those seen in stroke and ischemia but occur under very different conditions of blood flow and metabolism.

Regulation of cardiac and smooth muscle Ca(2+) channels (Ca(V)1.2a,b) by protein kinases

High voltage-activated Ca(2+) channels of the Ca(V)1.2 class (L-type) are crucial for excitation-contraction coupling in both cardiac and smooth muscle. These channels are regulated by a variety of second messenger pathways that ultimately serve to modulate the level of contractile force in the tissue. The specific focus of this review is on the most recent advances in our understanding of how cardiac Ca(V)1.2a and smooth muscle Ca(V)1.2b channels are regulated by different kinases, including cGMP-dependent protein kinase, cAMP-dependent protein kinase, and protein kinase C. This review also discusses recent evidence regarding the regulation of these channels by protein tyrosine kinase, calmodulin-dependent kinase, purified G protein subunits, and identification of possible amino acid residues of the channel responsible for kinase regulation.

Blood pressure-lowering effects of GLP-1 receptor agonists exenatide and liraglutide: a meta-analysis of clinical trials

AIMS

Aside from lowering blood glucose, glucagon-like peptide-1 receptor agonists (GLP-1 RAs) attract much attention because of their cardioprotective effects. The aim of this study was to assess the blood pressure-lowering effects of the GLP-1 RAs exenatide and liraglutide compared with other common drugs used to treat type 2 diabetes (T2DM) based on randomized controlled trials (RCTs) including data describing complete blood pressure (BP) changes from baseline.

METHODS

We searched the major databases for published or unpublished RCTs that had been performed in patients with T2DM and compared the effects of exenatide and liraglutide to those of other common drugs used to treat T2DM. The RCTs that included data describing BP changes between the baseline and the end of the study were selected for further analysis.

RESULTS

A total of 16 RCTs that enrolled 3443 patients in the GLP-1 RA treatment group and 2417 subjects in the control group were included in this meta-analysis. The GLP-1 RA exenatide reduced systolic blood pressure (SBP) when compared with both placebo and insulin glargine, with mean differences of -5.24 and -3.46 mmHg, respectively, and with 95% confidence intervals (CI) of -6.88 to -3.59, p < 0.00001 and -3.63 to -3.29, p < 0.00001, respectively. Meanwhile, in the exenatide-treated group, diastolic blood pressure (DBP) was reduced by -5.91 mmHg, with a 95% CI of -7.53 to -4.28, p < 0.00001 compared with the placebo group, and -0.99 mmHg with a 95% CI of -1.12 to -0.87, p < 0.00001 compared with the sitagliptin group. SBP changes in this meta-analysis were assessed in the groups treated with 1.2 or 1.8 mg liraglutide per day. In the 1.2 mg-treated group, liraglutide treatment reduced SBP compared with placebo and glimepiride treatment, with mean differences of -5.60 and -2.38 mmHg, and 95% CIs of -5.84 to -5.36, p < 0.00001 and -4.75 to -0.01, p = 0.05, respectively. In the 1.8-mg-treated group, liraglutide also reduced SBP compared with placebo and glimepiride treatment with mean differences of -4.49 and -2.62 mmHg, and a 95% CI of -4.73 to -4.26, p < 0.00001, and -2.91 to -2.33, p < 0.00001, respectively.

CONCLUSION

Treatment with the GLP-1 RAs exenatide and liraglutide reduced SBP and DBP by 1 to 5 mmHg compared with some other anti-diabetic drugs including insulin, glimepiride and placebo for patients with T2DM. GLP-1 RAs may offer an alternative therapy for these patients and will help provide extra cardiovascular benefits.

Inhibition of apoptosis as a mechanism of tumor promotion

Recent evidence supports the concept that tumor growth in vivo depends on evasion of normal homeostatic control mechanisms that operate through induction of cell death by apoptosis. This study tested the hypothesis that a common property shared by known or suspected tumor promoters is the ability to block the process of apoptosis. A total of 10 tumor promoters were tested and all were found to inhibit DNA fragmentation and cell death of 7 different cell lines triggered into apoptosis by diverse agents. Resistance to apoptosis could be induced rapidly (within 1 h) by treating with relatively high concentrations of promoters. However, low physiological concentrations of promoters could also induce complete resistance to apoptosis after prolonged exposure (5-15 days of culture). Like tumor promotion in vivo, promoter-induced resistance to apoptosis was reversible after culturing in the absence of promoter. These findings provide new insight into the mechanism of tumor promotion and suggest a novel in vitro screening assay to detect new tumor-promoting agents in the environment.

Group II introns as controllable gene targeting vectors for genetic manipulation of bacteria

Mobile group II introns can be retargeted to insert into virtually any desired DNA target. Here we show that retargeted group II introns can be used for highly specific chromosomal gene disruption in Escherichia coli and other bacteria at frequencies of 0.1-22%. Furthermore, the introns can be used to introduce targeted chromosomal breaks, which can be repaired by transformation with a homologous DNA fragment, enabling the introduction of point mutations. Because of their wide host range, mobile group II introns should be useful for genetic engineering and functional genomics in a wide variety of bacteria.

A double-stranded RNA binding protein required for activation of repressed messages in mammalian germ cells

Chromatin packaging in mammalian spermatozoa requires an ordered replacement of the somatic histones by two classes of spermatid-specific basic proteins, the transition proteins and the protamines. Temporal expression of transition proteins and protamines during spermatid differentiation is under translational control, and premature translation of protamine 1 leads to precocious nuclear condensation and sterility. We have previously suggested that the double-stranded (ds) RNA binding protein Prbp (encoded by the gene Tarbp2) functions as a translational regulator during mouse spermatogenesis. Here we show that Prbp is required for proper translational activation of the mRNAs encoding the protamines. We generated mice that carry a targeted disruption of Tarbp2 and determined that they were sterile and severely oligospermic. Using immunohistological analysis, we determined that the endogenous Prm2 mRNA and a reporter mRNA carrying protamine 1 translational-control elements were translated in a mosaic pattern. We showed that failure to synthesize the protamines resulted in delayed replacement of the transition proteins and subsequent failure of spermiation. The timing of Prbp expression suggests that it may function as a chaperone in the assembly of specific translationally regulated ribonucleoprotein particles.

Performance of the ATLAS trigger system in 2015

During 2015 the ATLAS experiment recorded [Formula: see text] of proton-proton collision data at a centre-of-mass energy of [Formula: see text]. The ATLAS trigger system is a crucial component of the experiment, responsible for selecting events of interest at a recording rate of approximately 1 kHz from up to 40 MHz of collisions. This paper presents a short overview of the changes to the trigger and data acquisition systems during the first long shutdown of the LHC and shows the performance of the trigger system and its components based on the 2015 proton-proton collision data.

Processing and properties of sol-gel bioactive glasses

Melt derived 45S5 Bioglass(R) has been studied for more than 25 years. Bioglass(R) has excellent biocompatibility, and its surface reactivity has contributed to its clinical success over the past 10 years. Recently, porous bioactive glasses have been derived through sol-gel processing in an attempt to increase the specific surface area, and, thus, the surface reactivity and degradability of the material. This allows the material to be replaced ultimately by natural tissue while it stimulates bone regeneration. In this work, the processing and properties of these sol-gel bioactive glasses are discussed, and a new drying method and treatment is described to make homogeneous particulate and monoliths on a production scale.

Green tea polyphenol extract attenuates inflammation in interleukin-2-deficient mice, a model of autoimmunity

Green tea polyphenols (GrTP) have been previously shown to decrease endotoxin-induced tumor necrosis factor-alpha production and lethality in mice. Our present studies demonstrate that GrTP inhibit inflammatory responses and may be useful in treating chronic inflammatory states, such as inflammatory bowel disease. In this preliminary study, we examined whether GrTP decrease disease activity in interleukin-2-deficient (IL-2(-/-) mice. Eight-week old IL-2(-/-) C57BL/6J mice who were fed nonpurified diet were randomly assigned to receive water with GrTP (5 g/L) or water alone (control) for up to 6 wk. After 1 wk, explant colon and lamina propria lymphocyte (LPL) cultures were established from a subgroup of mice and supernatants collected. Culture supernatants from GrTP-treated mice showed decreased spontaneous interferon-gamma and tumor necrosis factor-alpha secretion compared with that of controls. At 6 wk, the GrTP group had less severe colitis as demonstrated by lower histologic scores and wet colon weights. This was associated with lower plasma levels of serum amyloid A, increased weight gain and improved hematocrits. These results show that GrTP attenuated inflammation in IL-2(-/-) mice and suggest a role for GrTP in treating chronic inflammatory diseases such as inflammatory bowel disease.

Diffusion-weighted imaging in tissues: theoretical models

Typical diffusion measurements use Stejskal-Tanner pulsed gradient spin echo sequences to provide information about the average diffusion and displacement profiles of particles in a sample. To derive structural information, a measured displacement profile has to be related by means of a model to the physical and geometrical properties of the tissue, such as diffusion coefficients and shapes of semi-permeable membranes of compartments in the system. The behavior of the NMR signal and the measured ADC are greatly affected by the cellular architecture of a tissue, mainly because cellular membranes are relatively impermeable to water. For long diffusion times, and small signal attenuations, ADC is relatively insensitive to how it is measured. In general, however, ADC values are not readily interpreted unless the measuring conditions are specified in detail. For given measuring conditions, ADC depends on intra- and extracellular diffusion coefficients, membrane permeabilities, cell sizes and the cellular volume fraction. If intra- and extracellular T2 relaxation rates are different enough, ADC may also depend on the relaxation properties of the system and the echo time. An improved understanding of the precise influence of these factors has been obtained by detailed consideration of theoretical and computer models that can be related to experimental data in simple systems. Further refinements of such models should advance our understanding of water diffusion in tissues.

Percentage signal recovery derived from MR dynamic susceptibility contrast imaging is useful to differentiate common enhancing malignant lesions of the brain

BACKGROUND AND PURPOSE

Differentiation of enhancing malignant lesions on conventional MR imaging can be difficult and various newer imaging techniques have been suggested. Our aim was to evaluate the role of PSR obtained from DSC perfusion measurements in differentiating lymphoma, GBM, and metastases. The effectiveness of PSR was compared with that of rCBV. We hypothesized that the newly defined parameter of PSR is more sensitive and specific in differentiating these lesions.

MATERIALS AND METHODS

This retrospective study included 66 patients (39 men and 27 women; age range: 27-82 years) with a pathologically proved diagnosis of primary CNS lymphoma, GBM, or metastases (22 patients in each group). Mean PSR, min PSR, max PSR, and rCBV were calculated. The classification accuracy of these parameters was investigated by using ROC.

RESULTS

Mean PSR was high (113.15 ± 41.59) in lymphoma, intermediate in GBM (78.22 ± 14.27), and low in metastases (53.46 ± 12.87) with a P value < .000. F values obtained from 1-way ANOVA analysis for mean, min, and max PSR ratios were 29.9, 39.4, and 23.4, respectively, which were better than those of rCBV (11.1) in differentiating the 3 groups. Max PSR yielded the best ROC characteristics with an A(z) of 0.934 (95% CI, 0.877-0.99) in differentiating lymphoma from metastases and GBM. The A(z) for mean and min PSR of 0.938 (95% CI, 0.0.884-0.990) and 0.938 (95% CI, 0.884-0.991), respectively, was better than rCBV (A(z), 0.534; 95% CI, 0.391-0.676) in the differentiation of metastases from GBM and lymphoma (P ≤ .0001).

CONCLUSIONS

PSR appears to be a parameter that helps in differentiating intracerebral malignant lesions such as GBM, metastases, and lymphoma.

The regulation of phosphorylation of tau in SY5Y neuroblastoma cells: the role of protein phosphatases

In Alzheimer disease brain the microtubule associated protein (MAP) tau is abnormally hyperphosphorylated. The role of protein phosphatases (PP) in the regulation of phosphorylation of tau was studied in undifferentiated SY5Y cells. In cells treated with 10 nM okadaic acid (OA), a PP-2A/PP-1 inhibitor, the PP-1 and -2A activities decreased by 60% and 100% respectively and the activities of MAPKs, cdc2 kinase and cdk5, but not of GSK-3, increased. OA increased the phosphorylation of tau at Thr-231/Ser-235 and Ser-3961404, but not at Ser-262/356 or Ser-199/202. An increase in tyrosinated/detyrosinated tubulin ratio, a decrease in the microtubule binding activities of tau, MAP1b and MAP2, and cell death were observed. Treatment with 1 microm taxol partially inhibited the cell death. These data suggest (1) that OA induced hyperphosphorylation of tau is probably the result of activated MAPK and cdks in addition to decreased PP-2A and PP-1 activities and (2) that in SY5Y cells the OA induced cell death is associated with a decrease in stable microtubules.

Cospeciation in the triplex symbiosis of termite gut protists (Pseudotrichonympha spp.), their hosts, and their bacterial endosymbionts

A number of cophylogenetic relationships between two organisms namely a host and a symbiont or parasite have been studied to date; however, organismal interactions in nature usually involve multiple members. Here, we investigated the cospeciation of a triplex symbiotic system comprising a hierarchy of three organisms -- termites of the family Rhinotermitidae, cellulolytic protists of the genus Pseudotrichonympha in the guts of these termites, and intracellular bacterial symbionts of the protists. The molecular phylogeny was inferred based on two mitochondrial genes for the termites and nuclear small-subunit rRNA genes for the protists and their endosymbionts, and these were compared. Although intestinal microorganisms are generally considered to have looser associations with the host than intracellular symbionts, the Pseudotrichonympha protists showed almost complete codivergence with the host termites, probably due to strict transmissions by proctodeal trophallaxis or coprophagy based on the social behaviour of the termites. Except for one case, the endosymbiotic bacteria of the protists formed a monophyletic lineage in the order Bacteroidales, and the branching pattern was almost identical to those of the protists and the termites. However, some non-codivergent evolutionary events were evident. The members of this triplex symbiotic system appear to have cospeciated during their evolution with minor exceptions; the evolutionary relationships were probably established by termite sociality and the complex microbial community in the gut.