Cellular Fatty Acid Toxicity: Extrapolating Yeast Screens into Mammalian Models

Fatty acid deposition in non-adipose tissue leads to a cellular dysfunction known as lipotoxicity. Neutral lipid synthesis is known to protect against lipotoxicity but many additional pathways are likely to be integral in this process. In order to identify pathways protective against lipid induced cell death, we performed a genome-wide unsaturated fatty acid (UFA) sensitivity screen in yeast. Of the ~5,500 gene mutants tested, we identified 156 which resulted in sensitivity to growth on media containing palmitoleate. These genes identified many cellular processes, including vesicular trafficking, lipid metabolism and vacuolar protein sorting. Deletion of three members of the GET complex, a complex essential for tail anchored protein insertion into the ER, caused vulnerability to fatty acids. We went on to assess the role of GET3 in cellular lipid metabolism and found that ablation of GET3 results in a defect in vacuolar hydrolysis and a reduction in lipid droplet number; pathways which we hypothesize to be integrally related. Furthermore, a major goal of this study was to find mammalian genes playing an integral role in pathways of lipoprotection. Of the 156 gene deletions found to confer fatty acid sensitivity in yeast, 68 have been conserved in mammals. We demonstrate that two of these mammalian orthologs, ARV1and ASNA1, are vulnerable to fatty acid treatment upon knockdown in the MIN6 pancreatic beta-cell line. These mammalian genes, which were identified through the fatty acid sensitivity screen in yeast, are involved in lipid induced cellular dysfunction in pancreatic beta-cells and, in the case of ARV1, hepatocytes. Therefore, these genes likely play a role in the progression of the lipotoxic diseases; type 2 diabetes and nonalcoholic fatty liver disease

Statistical coherence of primary schooling in population census microdata: IPUMS-International integrated samples compared for fifteen African countries

The IPUMS-International project, now in its fifteenth year, integrates and disseminates population microdata for twenty-two African countries (82 countries world-wide) and the number continues to increase as more National Statistical Offices cooperate with the initiative. Statistical quality is a serious concern both for the producers of the microdata as well as the researchers who use them. This paper applies the intra-cohort comparison method to pairs of integrated (harmonized) samples for fifteen African countries to assess statistical coherence using as a benchmark the proportion completing primary school by single years of birth. Samples for six countries show near perfect coherence (R2 > .9, and regression coefficients ~1.0 +/- <0.08). For a second group of five countries, coefficients are only slightly larger (R2 > 0.6 <0.9). Large deviations from 1.0 characterize samples for only four countries. On the whole, the results suggest that samples for the fifteen countries have considerable utility for socio-demographic analysis

The Risks of LASIK Corrective Eye Surgery: A Mass Transfer Approach to a Universal Concern

The laser vision correction procedure, LASIK, requires a thin flap of the cornea to be created by a microkeratome knife. The focus of this project was to study and quantify the moisture loss from the tiny corneal flap using the concepts of mass transfer. Significant (10 fold) moisture concentration differences between the bottom and top surface of the corneal flap were observed, in conjunction with a strong dependence on the diffusivity of the flap as well as the length of the procedure time. Outer edges of the flap suffered the most water loss. Amount of moisture loss (85% in two minutes) in addition to the location(s) of ?dry spots? were hypothesized to influence one of the few recurrent complications of LASIK, flap misalignment

Syndemic factors associated with non-fatal overdose among young opioid users in New York City

IntroductionRates of illicit opioid use are particularly high among young adults, yet research on overdose experience and factors associated with overdose in this population remains limited. This study examines the experiences and correlates of non-fatal overdose among young adults using illicit opioids in New York City (NYC).Methods539 participants were recruited via Respondent-Driven Sampling in 2014-2016. Eligibility criteria included: aged 18–29 years old; current residence in NYC; and nonmedical prescription opioid (PO) use and/or heroin use in the past 30 days. Participants completed structured interviews to assess their socio-demographics, drug use trajectories, current substance use and lifetime and most recent overdose experiences, and were tested on-site for hepatitis C virus (HCV) antibodies.Results43.9% of participants reported lifetime overdose experience; of these, 58.8% had experienced two or more overdose events. The majority of participants’ most recent overdoses (63.5%) were due to polysubstance use. In bivariable analyses, after RDS adjustment, having ever overdosed was correlated with: household income of >$100,00 growing up (vs.$51,000-100,000); lifetime homelessness; HCV antibody-positive status; lifetime engagement in regular nonmedical benzodiazepine use, regular heroin injection and regular PO injection; and using a non-sterile syringe in the past 12 months. Multivariable logistic regression identified childhood household income >$100,00 (AOR=1.88), HCV-positive status (AOR=2.64), benzodiazepine use (AOR=2.15), PO injection (AOR=1.96) and non-sterile syringe use (AOR=1.70) as significant independent correlates of lifetime overdose. A multivariable model with multiple overdoses (vs. one) found only lifetime regular heroin use and PO injection to be strong correlates.DiscussionResults indicate a high prevalence of lifetime and repeated overdose among opioid-using young adults in NYC, highlighting a need for intensified overdose prevention efforts for this population. The strong associations of HCV and indices of polydrug use with overdose suggest that prevention efforts should address the complex risk environment in which overdose occurs, attending to the overlapping nature of disease-related risk behavior and overdose risk behavior among young people who inject opioids. Overdose prevention efforts tailored for this group may find it useful to adopt a syndemic conception of overdose that understands such events as resulting from multiple, and often interrelated, risk factors

Profiling the Essential Nature of Lipid Metabolism in Asexual Blood and Gametocyte Stages of Plasmodium falciparum

SummaryDuring its life cycle, Plasmodium falciparum undergoes rapid proliferation fueled by de novo synthesis and acquisition of host cell lipids. Consistent with this essential role, Plasmodium lipid synthesis enzymes are emerging as potential drug targets. To explore their broader potential for therapeutic interventions, we assayed the global lipid landscape during P. falciparum sexual and asexual blood stage (ABS) development. Using liquid chromatography-mass spectrometry, we analyzed 304 lipids constituting 24 classes in ABS parasites, infected red blood cell (RBC)-derived microvesicles, gametocytes, and uninfected RBCs. Ten lipid classes were previously uncharacterized in P. falciparum, and 70%–75% of the lipid classes exhibited changes in abundance during ABS and gametocyte development. Utilizing compounds that target lipid metabolism, we affirmed the essentiality of major classes, including triacylglycerols. These studies highlight the interplay between host and parasite lipid metabolism and provide a comprehensive analysis of P. falciparum lipids with candidate pathways for drug discovery efforts

Spirit, mind and body: the archaeology of monastic healing

Archaeology and material culture are used in this chapter to consider how monastic experience responded to illness, ageing and disability. The approach taken is influenced by the material study of religion, which interrogates how bodies and things engage to construct the sensory experience of religion, and by practice-based approaches in archaeology, which examine the active role of space and material culture in shaping religious agency and embodiment. The archaeology of monastic healing focuses on the full spectrum of healing technologies, from managing the body in order to prevent illness, through to the treatment of the sick and preparation of the corpse for burial

Proteogenomics connects somatic mutations to signalling in breast cancer

Somatic mutations have been extensively characterized in breast cancer, but the effects of these genetic alterations on the proteomic landscape remain poorly understood. We describe quantitative mass spectrometry-based proteomic and phosphoproteomic analyses of 105 genomically annotated breast cancers of which 77 provided high-quality data. Integrated analyses allowed insights into the somatic cancer genome including the consequences of chromosomal loss, such as the 5q deletion characteristic of basal-like breast cancer. The 5q trans effects were interrogated against the Library of Integrated Network-based Cellular Signatures, thereby connecting CETN3 and SKP1 loss to elevated expression of EGFR, and SKP1 loss also to increased SRC. Global proteomic data confirmed a stromal-enriched group in addition to basal and luminal clusters and pathway analysis of the phosphoproteome identified a G Protein-coupled receptor cluster that was not readily identified at the mRNA level. Besides ERBB2, other amplicon-associated, highly phosphorylated kinases were identified, including CDK12, PAK1, PTK2, RIPK2 and TLK2. We demonstrate that proteogenomic analysis of breast cancer elucidates functional consequences of somatic mutations, narrows candidate nominations for driver genes within large deletions and amplified regions, and identifies therapeutic targets

An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer

Improvements in mass spectrometry (MS)-based peptide sequencing provide a new opportunity to determine whether polymorphisms, mutations, and splice variants identified in cancer cells are translated. Herein, we apply a proteogenomic data integration tool (QUILTS) to illustrate protein variant discovery using whole genome, whole transcriptome, and global proteome datasets generated from a pair of luminal and basal-like breast-cancer-patient-derived xenografts (PDX). The sensitivity of proteogenomic analysis for singe nucleotide variant (SNV) expression and novel splice junction (NSJ) detection was probed using multiple MS/MS sample process replicates defined here as an independent tandem MS experiment using identical sample material. Despite analysis of over 30 sample process replicates, only about 10% of SNVs (somatic and germline) detected by both DNA and RNA sequencing were observed as peptides. An even smaller proportion of peptides corresponding to NSJ observed by RNA sequencing were detected (<0.1%). Peptides mapping to DNA-detected SNVs without a detectable mRNA transcript were also observed, suggesting that transcriptome coverage was incomplete (∼80%). In contrast to germline variants, somatic variants were less likely to be detected at the peptide level in the basal-like tumor than in the luminal tumor, raising the possibility of differential translation or protein degradation effects. In conclusion, this large-scale proteogenomic integration allowed us to determine the degree to which mutations are translated and identify gaps in sequence coverage, thereby benchmarking current technology and progress toward whole cancer proteome and transcriptome analysis

Economic-demographic interactions in long-run growth

Cliometrics confirms that Malthus’ model of the pre-industrial economy, in which increases in productivity raise population but higher population drives down wages, is a good description for much of demographic/economic history. A contributor to the Malthusian equilibrium was the Western European Marriage Pattern, the late age of female first marriage, which promised to retard the fall of living standards by restricting fertility. The demographic transition and the transition from Malthusian economies to modern economic growth attracted many Cliometric models surveyed here. A popular model component is that lower levels of mortality over many centuries increased the returns to, or preference for, human capital investment so that technical progress eventually accelerated. This initially boosted birth rates and population growth accelerated. Fertility decline was earliest and most striking in late eighteenth century France. By the 1830s the fall in French marital fertility is consistent with a response to the rising opportunity cost of children. The rest of Europe did not begin to follow until end of the nineteenth century. Interactions between the economy and migration have been modelled with Cliometric structures closely related to those of natural increase and the economy. Wages were driven up by emigration from Europe and reduced in the economies receiving immigrants