Faculty Bibliography

Neither breakpoints (BPs) nor epidemiological cutoff values (ECVs) have been established for Candida spp. with anidulafungin, caspofungin, and micafungin when using the Sensititre YeastOne (SYO) broth dilution colorimetric method. In addition, reference caspofungin MICs have so far proven to be unreliable. Candida species wild-type (WT) MIC distributions (for microorganisms in a species/drug combination with no detectable phenotypic resistance) were established for 6,007 Candida albicans, 186 C. dubliniensis, 3,188 C. glabrata complex, 119 C. guilliermondii, 493 C. krusei, 205 C. lusitaniae, 3,136 C. parapsilosis complex, and 1,016 C. tropicalis isolates. SYO MIC data gathered from 38 laboratories in Australia, Canada, Europe, Mexico, New Zealand, South Africa, and the United States were pooled to statistically define SYO ECVs. ECVs for anidulafungin, caspofungin, and micafungin encompassing >/=97.5% of the statistically modeled population were, respectively, 0.12, 0.25, and 0.06 mug/ml for C. albicans, 0.12, 0.25, and 0.03 mug/ml for C. glabrata complex, 4, 2, and 4 mug/ml for C. parapsilosis complex, 0.5, 0.25, and 0.06 mug/ml for C. tropicalis, 0.25, 1, and 0.25 mug/ml for C. krusei, 0.25, 1, and 0.12 mug/ml for C. lusitaniae, 4, 2, and 2 mug/ml for C. guilliermondii, and 0.25, 0.25, and 0.12 mug/ml for C. dubliniensis. Species-specific SYO ECVs for anidulafungin, caspofungin, and micafungin correctly classified 72 (88.9%), 74 (91.4%), 76 (93.8%), respectively, of 81 Candida isolates with identified fks mutations. SYO ECVs may aid in detecting non-WT isolates with reduced susceptibility to anidulafungin, micafungin, and especially caspofungin, since testing the susceptibilities of Candida spp. to caspofungin by reference methodologies is not recommended.

Intratumoral heterogeneity in glioblastoma (GBM) is exemplified by the diversity of tumor microenvironments, which include normoxic hypervascular areas and necrotic regions, which are considered hypoxic. GBM stem cells (GSCs) play a central role in tumor growth and therapy resistance. How GSCs adapt to diverse GBM microenvironments remains an important and unanswered question. We recently discovered that CD133-expressing GSCs are metabolically adept at expanding in hypoxic conditions and do not require Notch signaling for their self-renewal. Transcriptional analysis indicated that CD133+ GSCs have 17.8+/-8.8-fold enriched expression of GPR133 (n = 3 biospecimens), a member of the adhesion family of Gproteincoupled receptors. Immunostaining with GPR133 antibody revealed that GPR133 expression is restricted to hypoxic regions within GBM tumors (12/12 GBM biospecimens) and not present in normal brain. We observed that GPR133 mRNA expression correlates with hypoxia-induced transcripts, such as CA9 and VEFGA (n = 3 primary cultures). To test the hypothesis that GPR133 expression is regulated by oxygen tension, we subjected GBM cultures to 1% O2 in vitro and found that GPR133 transcript was consistently upregulated (n = 5 cultures). To examine whether GPR133 is important for GSC self-renewal, we tested the effect of shRNA-mediated knockdown on in vitro tumorsphere formation ability. GPR133 knockdown depleted CD133+ GSCs and inhibited tumorsphere formation under both normoxic and hypoxic conditions (p< 0.05). GPR133 knockdown also reduced in vivo tumorigenicity and increased survival of implanted mice (n = 3). Using colorimetric assays, we found that CD133+ GSCs have 26.2+/-12.53% higher cAMP levels compared to CD133- GBM cells (n = 3) and that GPR133 knockdown downregulated cAMP levels to 47.25+/-27.27% of scramble control (n = 3), suggesting that GPR133 signals through activation of adenylate cyclase and cAMP elevation

OBJECTIVE: Highly publicized incidents in which people with apparent mental illnesses use guns to victimize strangers have important implications for public views of people with mental illnesses and the formation of mental health and gun policy. The study aimed to provide more data about this topic. METHODS: MacArthur Violence Risk Assessment Study data were analyzed to determine the prevalence of violence by 951 patients after discharge from a psychiatric hospital, including gun violence, violence toward strangers, and gun violence toward strangers. RESULTS: Two percent of patients committed a violent act involving a gun, 6% committed a violent act involving a stranger, and 1% committed a violent act involving both a gun and a stranger. CONCLUSIONS: When public perceptions and policies regarding mental illness are shaped by highly publicized but infrequent instances of gun violence toward strangers, they are unlikely to help people with mental illnesses or to improve public safety.

Identifying a bona fide population of cardiac stem cells (CSCs) is a critical step for developing cell-based therapies for heart failure patients. Previously, cardiac c-kit(+) cells were reported to be CSCs with a potential to become myocardial, endothelial and smooth muscle cells in vitro and after cardiac injury. Here we provide further insights into the nature of cardiac c-kit(+) cells. By targeting the c-kit locus with multiple reporter genes in mice, we find that c-kit expression rarely co-localizes with the expression of the cardiac progenitor and myogenic marker Nkx2.5, or that of the myocardial marker, cardiac troponin T (cTnT). Instead, c-kit predominantly labels a cardiac endothelial cell population in developing and adult hearts. After acute cardiac injury, c-kit(+) cells retain their endothelial identity and do not become myogenic progenitors or cardiomyocytes. Thus, our work strongly suggests that c-kit(+) cells in the murine heart are endothelial cells and not CSCs.

The endoplasmic reticulum (ER)-localized peroxiredoxin 4 (PRDX4) supports disulfide bond formation in eukaryotic cells lacking endoplasmic reticulum oxidase 1 (ERO1). The source of peroxide that fuels PRDX4-mediated disulfide bond formation has remained a mystery, because ERO1 is believed to be a major producer of hydrogen peroxide (H2O2) in the ER lumen. We report on a simple kinetic technique to track H2O2 equilibration between cellular compartments, suggesting that the ER is relatively isolated from cytosolic or mitochondrial H2O2 pools. Furthermore, expression of an ER-adapted catalase to degrade lumenal H2O2 attenuated PRDX4-mediated disulfide bond formation in cells lacking ERO1, whereas depletion of H2O2 in the cytosol or mitochondria had no similar effect. ER catalase did not effect the slow residual disulfide bond formation in cells lacking both ERO1 and PRDX4. These observations point to exploitation of a hitherto unrecognized lumenal source of H2O2 by PRDX4 and a parallel slow H2O2-independent pathway for disulfide formation.

Cellular metabolism is increasingly recognized as a controller of immune cell fate and function. MicroRNA-33 (miR-33) regulates cellular lipid metabolism and represses genes involved in cholesterol efflux, HDL biogenesis, and fatty acid oxidation. Here, we determined that miR-33-mediated disruption of the balance of aerobic glycolysis and mitochondrial oxidative phosphorylation instructs macrophage inflammatory polarization and shapes innate and adaptive immune responses. Macrophage-specific Mir33 deletion increased oxidative respiration, enhanced spare respiratory capacity, and induced an M2 macrophage polarization-associated gene profile. Furthermore, miR-33-mediated M2 polarization required miR-33 targeting of the energy sensor AMP-activated protein kinase (AMPK), but not cholesterol efflux. Notably, miR-33 inhibition increased macrophage expression of the retinoic acid-producing enzyme aldehyde dehydrogenase family 1, subfamily A2 (ALDH1A2) and retinal dehydrogenase activity both in vitro and in a mouse model. Consistent with the ability of retinoic acid to foster inducible Tregs, miR-33-depleted macrophages had an enhanced capacity to induce forkhead box P3 (FOXP3) expression in naive CD4+ T cells. Finally, treatment of hypercholesterolemic mice with miR-33 inhibitors for 8 weeks resulted in accumulation of inflammation-suppressing M2 macrophages and FOXP3+ Tregs in plaques and reduced atherosclerosis progression. Collectively, these results reveal that miR-33 regulates macrophage inflammation and demonstrate that miR-33 antagonism is atheroprotective, in part, by reducing plaque inflammation by promoting M2 macrophage polarization and Treg induction.

DnaK/Hsp70 chaperones form oligomers of poorly understood structure and functional significance. Site-specific proteolysis and crosslinking were used to probe the architecture of oligomers formed by the endoplasmic reticulum (ER) Hsp70, BiP. These were found to consist of adjacent protomers engaging the interdomain linker of one molecule in the substrate binding site of another, attenuating the chaperone function of oligomeric BiP. Native gel electrophoresis revealed a rapidly-modulated reciprocal relationship between the burden of unfolded proteins and BiP oligomers and slower equilibration between oligomers and inactive, covalently-modified BiP. Lumenal ER calcium depletion caused rapid oligomerization of mammalian BiP and a coincidental diminution in substrate binding, pointing to the relative inertness of the oligomers. Thus, equilibration between inactive oligomers and active monomeric BiP is poised to buffer fluctuations in ER unfolded protein load on a rapid timescale attainable neither by inter-conversion of active and covalently-modified BiP nor by the conventional unfolded protein response.

UNLABELLED:DamID is a powerful technique for identifying regions of the genome bound by a DNA-binding (or DNA-associated) protein. Currently, no method exists for automatically processing next-generation sequencing DamID (DamID-seq) data, and the use of DamID-seq datasets with normalization based on read-counts alone can lead to high background and the loss of bound signal. DamID-seq thus presents novel challenges in terms of normalization and background minimization. We describe here damidseq_pipeline, a software pipeline that performs automatic normalization and background reduction on multiple DamID-seq FASTQ datasets. AVAILABILITY AND IMPLEMENTATION/METHODS:Open-source and freely available from http://owenjm.github.io/damidseq_pipeline. The damidseq_pipeline is implemented in Perl and is compatible with any Unix-based operating system (e.g. Linux, Mac OSX). CONTACT/BACKGROUND:o.marshall@gurdon.cam.ac.uk SUPPLEMENTARY INFORMATION/BACKGROUND:Supplementary data are available at Bioinformatics online.

Despite the central importance of germ cells for transmission of genetic material, our understanding of the molecular programs that control primordial germ cell (PGC) specification and differentiation are limited. Here, we present findings that X nondisjunction factor-1 (xnd-1), known for its role in regulating meiotic crossover formation, is an early determinant of germ cell fates in Caenorhabditis elegans. xnd-1 mutant embryos display a novel "one PGC" phenotype due to G2 cell cycle arrest of the P4 blastomere. Larvae and adults display smaller germ lines and reduced brood sized consistent with a role for XND-1 in germ cell proliferation. Maternal XND-1 proteins are found in P4 and exclusively localized to the nucleus in the PGCs, Z2 and Z3. Zygotic XND-1 turns on shortly thereafter, at the approximately 300-cell stage, making XND-1 the earliest zygotically-expressed gene in the worm PGCs. Strikingly, a subset of xnd-1 mutants lack germ cells, a phenotype shared with nos-2, a member of the conserved Nanos family of germline determinants. We generated a nos-2 null allele and show that nos-2; xnd-1 double mutants display synthetic sterility. Further removal of nos-1 leads to almost complete sterility, with the vast majority of animals without germ cells. The sterility in xnd-1 mutants is correlated with an increase in the transcriptional activation-associated histone modification and aberrant expression of somatic transgenes. Together, these data strongly suggest that xnd-1 defines a new branch for PGC development that functions redundantly with nos-2 and nos-1 to promote germline fates by maintaining transcriptional quiescence and regulating germ cell proliferation.