CD18-dependent activation of the neutrophil NADPH oxidase during phagocytosis of Escherichia coli or Staphylococcus aureus is regulated by class III but not class I or II PI3Ks

Phagocytosis and activation of the NADPH oxidase are important mechanisms by which neutrophils and macrophages engulf and kill microbial pathogens. We investigated the role of PI3K signaling pathways in the regulation of the oxidase during phagocytosis of Staphylococcus aureus and Escherichia coli by mouse and human neutrophils, a mouse macrophage-like cell line and a human myeloid-like cell line. Phagocytosis of these bacteria was promoted by serum, independent of serum-derived antibodies, and effectively abolished in mouse neutrophils lacking the beta(2)-integrin common chain, CD18. A combination of PI3K isoform-selective inhibitors, mouse knock-outs, and RNA-interference indicated CD18-dependent activation of the oxidase was independent of class I and II PI3Ks, but substantially dependent on the single class III isoform (Vps34). Class III PI3K was responsible for the synthesis of PtdIns( 3) P on phagosomes containing either bacteria. The use of mouse neutrophils carrying an appropriate knock-in mutation indicated that PtdIns(3) P binding to the PX domain of their p40(phox) oxidase subunit is important for oxidase activation in response to both S aureus and E coli. This interaction does not, however, account for all the PI3K sensitivity of these responses, particularly the oxidase response to E coli, suggesting that additional mechanisms for PtdIns( 3) P-regulation of the oxidase must exist. ( Blood. 2008; 112: 5202-5211)

Genome-wide Association Study Implicates HLA-C*01:02 as a Risk Factor at the Major Histocompatibility Complex Locus in Schizophrenia

BACKGROUND: We performed a genome-wide association study (GWAS) to identify common risk variants for schizophrenia. METHODS: The discovery scan included 1606 patients and 1794 controls from Ireland, using 6,212,339 directly genotyped or imputed single nucleotide polymorphisms (SNPs). A subset of this sample (270 cases and 860 controls) was subsequently included in the Psychiatric GWAS Consortium-schizophrenia GWAS meta-analysis. RESULTS: One hundred eight SNPs were taken forward for replication in an independent sample of 13,195 cases and 31,021 control subjects. The most significant associations in discovery, corrected for genomic inflation, were (rs204999, p combined = 1.34 × 10(-9) and in combined samples (rs2523722 p combined = 2.88 × 10(-16)) mapped to the major histocompatibility complex (MHC) region. We imputed classical human leukocyte antigen (HLA) alleles at the locus; the most significant finding was with HLA-C*01:02. This association was distinct from the top SNP signal. The HLA alleles DRB1*03:01 and B*08:01 were protective, replicating a previous study. CONCLUSIONS: This study provides further support for involvement of MHC class I molecules in schizophrenia. We found evidence of association with previously reported risk alleles at the TCF4, VRK2, and ZNF804A loci.

Targeted genome-wide investigation identifies novel SNP's associated with diabetic nephropathy

Loci contributing to complex disease have been identified by focusing on genome-wide scans utilising non-synonymous single nucleotide polymorphisms (nsSNPs). We employed Illumina’s HNS12 BeadChip (13,917 high-value SNPs) which was specifically designed to capture nsSNPs and ideally complements more dense genome-wide association studies that fail to consider many of these putatively functional variants. The HNS12 panel also includes 870 tag SNPs covering the major histocompatibility region. All individuals genotyped in this study were Caucasians with (cases) and without (controls) diabetic nephropathy. About 449 individuals with type 2 diabetes (203 cases, 246 controls) were genotyped in the initial study. 1,467 individuals with type 1 diabetes (718 cases, 749 controls) were genotyped in the follow up study. 11,152 SNPs were successfully analysed and ranked for association with diabetic nephropathy based on significance (P) values. The top ranked 32 SNPs were subsequently genotyped using MassARRAY iPLEX™ and TaqMan technologies to investigate association of these polymorphisms with nephropathy in individuals with type 1 diabetes. The top ranked nsSNP, rs1543547 (P = 10-5), is located in RAET1L, a major histocompatibility class I-related gene at 6q25.1. Of particular interest, multiple nsSNPs within the top ranked (0.2%) SNPs are within several plausible candidate genes for nephropathy on 3q21.3 and 6p21.3.

Infrequent Expression of the Cancer-Testis Antigen, PASD1, in Ovarian Cancer

Ovarian cancer is very treatable in the early stages of disease; however, it is usually detected in the later stages, at which time, treatment is no longer as effective. If discovered early (Stage I), there is a 90% chance of five-year survival. Therefore, it is imperative that early-stage biomarkers are identified to enhance the early detection of ovarian cancer. Cancer-testis antigens (CTAs), such as Per ARNT SIM (PAS) domain containing 1 (PASD1), are unique in that their expression is restricted to immunologically restricted sites, such as the testis and placenta, which do not express MHC class I, and cancer, making them ideally positioned to act as targets for immunotherapy as well as potential biomarkers for cancer detection where expressed. We examined the expression of PASD1a and b in a number of cell lines, as well as eight healthy ovary samples, eight normal adjacent ovarian tissues, and 191 ovarian cancer tissues, which were predominantly stage I (n = 164) and stage II (n = 14) disease. We found that despite the positive staining of skin cancer, only one stage Ic ovarian cancer patient tissue expressed PASD1a and b at detectable levels. This may reflect the predominantly stage I ovarian cancer samples examined. To examine the restriction of PASD1 expression, we examined endometrial tissue arrays and found no expression in 30 malignant tumor tissues, 23 cases of hyperplasia, or 16 normal endometrial tissues. Our study suggests that the search for a single cancer-testes antigen/biomarker that can detect early ovarian cancer must continue.

Australia Telescope Compact Array 1.2cm Observations of the Massive Star Forming Region G305.2+0.2

We report on Australia Telescope Compact Array observations of the massive star-forming region G305.2+0.2 at 1.2 cm. We detected emission in five molecules towards G305A, confirming its hot core nature. We determined a rotational temperature of 26 K for methanol. A non-local thermodynamic equilibrium excitation calculation suggests a kinematic temperature of the order of 200 K. A time-dependent chemical model is also used to model the gas-phase chemistry of the hot core associated with G305A. A comparison with the observations suggest an age of between 2 × 104 and 1.5 × 105 yr. We also report on a feature to the south-east of G305A which may show weak Class I methanol maser emission in the line at 24.933 GHz. The more evolved source G305B does not show emission in any of the line tracers, but strong Class I methanol maser emission at 24.933 GHz is found 3 arcsec to the east. Radio continuum emission at 18.496 GHz is detected towards two H ii regions. The implications of the non-detection of radio continuum emission towards G305A and G305B are also discussed.

Analysis of malts by capillary electrophoresis

A range of malts, as well as their high- and low-molecular-mass fractions, has been examined by capillary electrophoresis in phosphate buffer, pH 2.5, and in carbonate buffer, pH 9.5, and the results have been compared with those for roasted barley and for caramels. The malts fall into two categories: (i) the lightly roasted malts, where the high-molecular-mass coloured fraction is negatively charged at pH 9.5 and positively charged at pH 2.5; and (ii) the highly roasted malts (and the roasted barley), where the high-molecular-mass fraction migrates close to the electro-osmotic flow at both pH 9.5 and 2.5, implying that it carries little or no charge. The former category shows migration patterns similar to Class III caramels, whereas the latter migrates differently from Class I, III and IV caramels as well as from the former. Capillary electrophoresis therefore has considerable potential for differentiating between malts and between malts and caramels and roasted barley. (C) 2002 Society of Chemical Industry.

Hypoglycaemia, liver necrosis and perinatal death in mice lacking all isoforms of phosphoinositide 3-kinase p85 alpha

Phosphoinositide 3-kinases produce 3'-phosphorylated phosphoinositides that act as second messengers to recruit other signalling proteins to the membrane(1). Pi3ks are activated by many extracellular stimuli and have been implicated in a variety of cellular responses(1). The Pi3k gene family is complex and the physiological roles of different classes and isoforms are not clear. The gene Pik3r1 encodes three proteins (p85 alpha, p55 alpha and p50 alpha) that serve as regulatory subunits of class I-A Pi3ks (ref. 2). Mice lacking only the p85a isoform are viable but display hypoglycaemia and increased insulin sensitivity correlating with upregulation of the p55 alpha and p50 alpha variants(3). Here we report that loss of all protein products of Pik3r1 results in perinatal lethality. We observed, among other abnormalities, extensive hepatocyte necrosis and chylous ascites, We also noted enlarged skeletal muscle fibres, brown fat necrosis and calcification of cardiac tissue. In liver and muscle, loss of the major regulatory isoform caused a great decrease in expression and activity of class I-A Pi3k catalytic subunits: nevertheless, homozygous mice still displayed hypoglycaemia, lower insulin levels and increased glucose tolerance. Our findings reveal that p55 alpha and/or p50 alpha are required for survival, but not for development of hypoglycaemia, in mice lacking p85 alpha.

What is Irish Standard English?

Standard English need not be a matter of prescriptivism or any attempt to ‘create’ a particular standard, but, rather, can be a matter of observation of actual linguistic behaviour. For Hudson (2000), standard English is the kind of English which is written in published work, which is spoken in situations where published writing is most influential – especially in university level education and so in post-university professions – and which is spoken ‘natively’ at home by the ‘professional class’, i.e. people who are most influenced by published writing. In the papers in Bex and Watts (eds, 1999), it is recurrently claimed that, when speaking English, what the ‘social group with highest degree of power, wealth or prestige’ or more neutrally ‘educated people’ or ‘socially admired people’ speak is the variety known as ‘standard English’. However, ‘standard English’ may also mean that shared aspect of English which makes global communication possible. This latter perspective allows for two meanings of ‘standard’: it may refer both to an idealised set of shared features, and also to different sets of national features, reflecting different demographic and political histories and language influences. The methodology adopted in the International Corpus of English (henceforth ICE – cf. Greenbaum, 1996) enables us to observe and investigate each set of features, showing what everybody shares and also what makes each national variety of English different.

Computational identification of self-inhibitory peptides from envelope proteins

Fusion process is known to be the initial step of viral infection and hence targeting the entry process is a promising strategy to design antiviral therapy. The self-inhibitory peptides derived from the enveloped (E) proteins function to inhibit the proteinprotein interactions in the membrane fusion step mediated by the viral E protein. Thus, they have the potential to be developed into effective antiviral therapy. Herein, we have developed a Monte Carlo-based computational method with the aim to identify and optimize potential peptide hits from the E proteins. The stability of the peptides, which indicates their potential to bind in situ to the E proteins, was evaluated by two different scoring functions, dipolar distance-scaled, finite, ideal-gas reference state and residue-specific all-atom probability discriminatory function. The method was applied to a-helical Class I HIV-1 gp41, beta-sheet Class II Dengue virus (DENV) type 2 E proteins, as well as Class III Herpes Simplex virus-1 (HSV-1) glycoprotein, a E protein with a mixture of a-helix and beta-sheet structural fold. The peptide hits identified are in line with the druggable regions where the self-inhibitory peptide inhibitors for the three classes of viral fusion proteins were derived. Several novel peptides were identified from either the hydrophobic regions or the functionally important regions on Class II DENV-2 E protein and Class III HSV-1 gB. They have potential to disrupt the proteinprotein interaction in the fusion process and may serve as starting points for the development of novel inhibitors for viral E proteins. 

Cathepsin F cysteine protease of the human liver fluke, Opisthorchis viverrini

The liver fluke Opisthorchis viverrini is classified as a class I carcinogen due to the association between cholangiocarcinoma and chronic O. viverrini infection. During its feeding activity within the bile duct, the parasite secretes several cathepsin F cysteine proteases that may induce or contribute to the pathologies associated with hepatobiliary abnormalities.

The impact of body mass index on maternal and neonatal outcomes: a retrospective study in a UK obstetric population, 2004-2011

Objective: To assess the prevalence of overweight and obesity, and the impact of body mass index (BMI) on maternal and neonatal outcomes, in a UK obstetric population.
Design: Retrospective study.
Setting: A tertiary referral unit in Northern Ireland.
Population: A total of 30 298 singleton pregnancies over an 8-year period, 2004–2011.
Methods: Women were categorised according to World Health Organization classification: underweight (BMI < 18.50 kg/m2); normal weight (BMI 18.50–24.99 kg/m2; reference group); overweight (BMI 25.00–29.99 kg/m2); obese class I (BMI 30.00–34.99 kg/m2); obese class II (BMI 35–39.99 kg/m2); and obese class III (BMI = 40 kg/m2). Maternal and neonatal outcomes were examined using logistic regression, adjusted for confounding variables.
Main outcome measures: Maternal and neonatal outcomes.
Results: Compared with women of normal weight, women who were overweight or obese class I were at significantly increased risk of hypertensive disorders of pregnancy (OR 1.9, 99% CI 1.7–2.3; OR 3.5, 99% CI 2.9–4.2); gestational diabetes mellitus (OR 1.7, 99% CI 1.3–2.3; OR 3.7, 99% CI 2.8–5.0); induction of labour (OR 1.2, 99% CI 1.1–1.3; OR 1.3, 99% CI 1.2–1.5); caesarean section (OR 1.4, 99% CI 1.3–1.5; OR 1.8, 99% CI 1.6–2.0); postpartum haemorrhage (OR 1.4, 99% CI 1.3–1.5; OR 1.8, 1.6–2.0); and macrosomia (OR 1.5, 99% CI 1.3–1.6; OR 1.9, 99% CI 1.6–2.2), with the risks increasing for obese classes II and III. Women in obese class III were at increased risk of preterm delivery (OR 1.6, 99% CI 1.1–2.5), stillbirth (OR 3.0, 99% CI 1.0–9.3), postnatal stay > 5 days (OR 2.1, 99% CI 1.5–3.1), and infant requiring admission to a neonatal unit (OR 1.6, 99% CI 1.0–2.6).
Conclusions: By categorising women into overweight and obesity subclassifications (classes I –III), this study clearly demonstrates an increasing risk of adverse outcomes across BMI categories, with women who are overweight also at significant risk.
Keywords Body mass index, maternal and neonatal outcomes,obesity, pregnancy

Corneal Allograft Rejection:Risk Factors, Diagnosis, Prevention, and Treatment

Recent advances in corneal graft technology, including donor tissue retrieval, storage and surgical techniques, have greatly improved the clinical outcome of corneal grafts. Despite these advances, immune mediated corneal graft rejection remains the single most important cause of corneal graft failure. Several host factors have been identified as conferring a "high risk" status to the host. These include: more than two quadrant vascularisation, with associated lymphatics, which augment the afferent and efferent arc of the immune response; herpes simplex keratitis; uveitis; silicone oil keratopathy; previous failed (rejected) grafts; "hot eyes"; young recipient age; and multiple surgical procedures at the time of grafting. Large grafts, by virtue of being closer to the host limbus, with its complement of vessels and antigen-presenting Langerhans cells, also are more susceptible to rejection. The diagnosis of graft rejection is entirely clinical and in its early stages the clinical signs could be subtle. Graft rejection is largely mediated by the major histocompatibility antigens, minor antigens and perhaps blood group ABO antigens and some cornea-specific antigens. Just as rejection is mediated by active immune mediated events, the lack of rejection (tolerance) is also sustained by active immune regulatory mechanisms. The anterior chamber associated immune deviation (ACAID) and probably, conjunctiva associated lymphoid tissue (CALT) induced mucosal tolerance, besides others, play an important role. Although graft rejection can lead to graft failure, most rejections can be readily controlled if appropriate management is commenced at the proper time. Topical steroids are the mainstay of graft rejection management. In the high-risk situations however, systemic steroids, and other immunosuppressive drugs such as cyclosporin and tacrolimus (FK506) are of proven benefit, both for treatment and prevention of rejection.

Impact of oncogenic driver mutations on feedback between the PI3K and MEK pathways in cancer cells

Inhibition of the PI3K (phosphoinositide 3-kinase)/Akt/mTORC1 (mammalian target of rapamycin complex 1) and Ras/MEK [MAPK (mitogen-activated protein kinase)/ERK (extracellular-signal-regulated kinase) kinase]/ERK pathways for cancer therapy has been pursued for over a decade with limited success. Emerging data have indicated that only discrete subsets of cancer patients have favourable responses to these inhibitors. This is due to genetic mutations that confer drug insensitivity and compensatory mechanisms. Therefore understanding of the feedback mechanisms that occur with respect to specific genetic mutations may aid identification of novel biomarkers that predict patient response. In the present paper, we show that feedback between the PI3K/Akt/mTORC1 and Ras/MEK/ERK pathways is cell-line-specific and highly dependent on the activating mutation of K-Ras or overexpression c-Met. We found that cell lines exhibited differential signalling and apoptotic responses to PD184352, a specific MEK inhibitor, and PI103, a second-generation class I PI3K inhibitor. We reveal that feedback from the PI3K/Akt/mTORC1 to the Ras/MEK/ERK pathway is present in cancer cells harbouring either K-Ras activating mutations or amplification of c-Met but not the wild-type counterparts. Moreover, we demonstrate that inhibition of protein phosphatase activity by OA (okadaic acid) restored PI103-mediated feedback in wild-type cells. Together, our results demonstrate a novel mechanism for feedback between the PI3K/Akt/mTORC1 and the Ras/MEK/ERK pathways that only occurs in K-Ras mutant and c-Met amplified cells but not the isogenic wild-type cells through a mechanism that may involve inhibition of a specific endogenous phosphatase(s) activity. We conclude that monitoring K-Ras and c-Met status are important biomarkers for determining the efficacy of PI103 and other PI3K/Akt inhibitors in cancer therapy.

Young Stellar Object VARiability (YSOVAR): Long Timescale Variations in the Mid-infrared

The YSOVAR (Young Stellar Object VARiability) Spitzer Space Telescope observing program obtained the first extensive mid-infrared (3.6 and 4.5 μm) time series photometry of the Orion Nebula Cluster plus smaller footprints in 11 other star-forming cores (AFGL 490, NGC 1333, Mon R2, GGD 12-15, NGC 2264, L1688, Serpens Main, Serpens South, IRAS 20050+2720, IC 1396A, and Ceph C). There are ~29,000 unique objects with light curves in either or both IRAC channels in the YSOVAR data set. We present the data collection and reduction for the Spitzer and ancillary data, and define the "standard sample" on which we calculate statistics, consisting of fast cadence data, with epochs roughly twice per day for ~40 days. We also define a "standard sample of members" consisting of all the IR-selected members and X-ray-selected members. We characterize the standard sample in terms of other properties, such as spectral energy distribution shape. We use three mechanisms to identify variables in the fast cadence data—the Stetson index, a χ2 fit to a flat light curve, and significant periodicity. We also identified variables on the longest timescales possible of six to seven years by comparing measurements taken early in the Spitzer mission with the mean from our YSOVAR campaign. The fraction of members in each cluster that are variable on these longest timescales is a function of the ratio of Class I/total members in each cluster, such that clusters with a higher fraction of Class I objects also have a higher fraction of long-term variables. For objects with a YSOVAR-determined period and a [3.6]-[8] color, we find that a star with a longer period is more likely than those with shorter periods to have an IR excess. We do not find any evidence for variability that causes [3.6]-[4.5] excesses to appear or vanish within our data set; out of members and field objects combined, at most 0.02% may have transient IR excesses.