Proteome profiling by label‐free mass spectrometry reveals differentiated response of Campylobacter jejuni 81–176 to sublethal concentrations of bile acids.

Purpose Bile acids are crucial components of the intestinal antimicrobial defense and represent a significant stress factor for enteric pathogens. Adaptation processes of Campylobacter jejuni to this hostile environment are analyzed in this study by a proteomic approach. Experimental design Proteome profiling by label-free mass spectrometry (SWATH-MS) has been used to characterize the adaptation of C. jejuni to sublethal concentrations of seven bile acids. Results The bile acids with the lowest inhibitory concentration (IC50), deoxycholic and chenodeoxycholic acid, induce the most significant proteome changes. Overall a downregulation of all basic biosynthetic pathways and a general decrease in the transcription machinery are found. Concurrently, an induction of factors involved in detoxification of reactive oxygen species, protein folding, and bile acid exporting efflux pumps is detected. Exposure to deoxycholic and chenodeoxycholic acid results in an increased expression of components of the more energy-efficient aerobic respiration pathway, while the anaerobic branches of the electron transport chain are down-expressed. Conclusions and clinical relevance The results show that C. jejuni has a differentiated system of adaptation to bile acid stresses. The findings enhance the understanding of the pathogenesis of campylobacteriosis, especially for survival of C. jejuni in the human intestine, and may provide clues to future medical treatment

SITOTOKSISITAS BEBERAPA JENIS TERIPANG YANG DIKOLEKSI DARI PULAU SEIRA DAN PULAU LUANG

Sitotoksik beberapa jenis teripang asal dari pulau Seira dan pulau Luang, terhadap larva udang, Artemia salina telah diteliti dilakukan. Penyarian senyawa kimianya dari teripang dilakukan dengan 2 metode ekstraksi yaitu cara maserasi dengan etanol 96% (6 kali), dan cara dekok dengan akuades (3 kali).  Hasil penelitian menunjukkan bahwa ada perbedaan yang signifikan daya sitotoksik di antara ekstrak etanol dan ekstrak air. Daya toksisitas ekstrak etanol 96 % memberikan LC50 degan level sedang 39,87 ppm dan 66,06 ppm untuk teripang Stichopus hermanii, dan Stichopus vostus.  Sedangkan untuk ekstrak air menunjukkan sitotoksik yang sangat lemah yaitu berkisar 707,94 ~ 67.608 ppm. Hasil ini menunjukkan bahwa ekstrak air banyak mengandung senyawa garam.   

The Infrared Einstein Ring in the Gravitational Lens MG1131+0456 and the Death of the Dusty Lens Hypothesis

We have obtained and modeled new NICMOS images of the lens system MG1131+0456, which show that its lens galaxy is an H=18.6 mag, transparent, early-type galaxy at a redshift of about z_l = 0.85; it has a major axis effective radius R_e=0.68+/-0.05 arcsec, projected axis ratio b/a=0.77+/-0.02, and major axis PA=60+/-2 degrees. The lens is the brightest member of a group of seven galaxies with similar R-I and I-H colors, and the two closest group members produce sufficient tidal perturbations to explain the ring morphology. The host galaxy of the MG1131+0456 source is a z_s > 2 ERO (``extremely red object'') which is lensed into optical and infrared rings of dramatically different morphologies. These differences imply a strongly wavelength-dependent source morphology that could be explained by embedding the host in a larger, dusty disk. At 1.6 micron (H), the ring is spectacularly luminous, with a total observed flux of H=17.4 mag and a de-magnified flux of 19.3 mag, corresponding to a 1-2L_* galaxy at the probable source redshift of z_s > 2. Thus, it is primarily the stellar emission of the radio source host galaxy that produces the overall colors of two of the reddest radio lenses, MG1131+0456 and B~1938+666, aided by the suppression of optical AGN emission by dust in the source galaxy. The dusty lens hypothesis -- that many massive early-type galaxies with 0.2 < z_l < 1.0 have large, uniform dust opacities -- is ruled out.Comment: 27 pages, 8 COLOR figures, submitted to ApJ. Black and white version available at http://cfa-www.harvard.edu/castle

Iceberg or cut off - how adult stutterer articulate fluent-sounding utterances

Whether fluent-sounding utterances of adults who stutter (AWS) are normally articulated is unclear. We asked 15 AWS and 17 matched adults who do not stutter (ANS) to utter the pseudoword "natscheitideut" 15 times in a 3 T MRI scanner while recording real-time MRI videos at 55 frames per per second in a mid-sagittal plane. All stuttered or otherwise dysfluent runs were discarded. We used sophisticated analyses to model the movement of the tip of the tongue, lips and velum. We observed reproducible movement patterns of the inner and outer articulators which were similar in both groups. Speech duration was similar in both groups and decreased over repetitions, more so in ANS than in AWS. The variability of the movement patterns of tongue, lips and velum decreased over repetitions. The extent of variability decrease was similar in both groups. Across all participants, this repetition effect on movement variability for the lips and the tip of the tongue was less pronounced in severely as compared to mildly stuttering individuals. We conclude that there is no major difference in the movement patterns of a fluent-sounding utterance in both groups. This encourages studies looking at state rather than trait markers of speech dysfluency

Direct proteomic and high-resolution microscopy biopsy analysis identifies distinct ventricular fates in severe aortic stenosis

The incidence of aortic valve stenosis (AS), the most common reason for aortic valve replacement (AVR), increases with population ageing. While untreated AS is associated with high mortality, different hemodynamic subtypes range from normal left-ventricular function to severe heart failure. However, the molecular nature underlying four different AS subclasses, suggesting vastly different myocardial fates, is unknown. Here, we used direct proteomic analysis of small left-ventricular biopsies to identify unique protein expression profiles and subtype-specific AS mechanisms. Left-ventricular endomyocardial biopsies were harvested from patients during transcatheter AVR, and inclusion criteria were based on echocardiographic diagnosis of severe AS and guideline-defined AS-subtype classification: 1) normal ejection fraction (EF)/high-gradient; 2) low EF/high-gradient; 3) low EF/low-gradient; and 4) paradoxical low-flow/low-gradient AS. Samples from non-failing donor hearts served as control. We analyzed 25 individual left-ventricular biopsies by data-independent acquisition mass spectrometry (DIA-MS), and 26 biopsies by histomorphology and cardiomyocytes by STimulated Emission Depletion (STED) superresolution microscopy. Notably, DIA-MS reliably detected 2273 proteins throughout each individual left-ventricular biopsy, of which 160 proteins showed significant abundance changes between AS-subtype and non-failing samples including the cardiac ryanodine receptor (RyR2). Hierarchical clustering segregated unique proteotypes that identified three hemodynamic AS-subtypes. Additionally, distinct proteotypes were linked with AS-subtype specific differences in cardiomyocyte hypertrophy. Furthermore, superresolution microscopy of immunolabeled biopsy sections showed subcellular RyR2-cluster fragmentation and disruption of the functionally important association with transverse tubules, which occurred specifically in patients with systolic dysfunction and may hence contribute to depressed left-ventricular function in AS

Population-scale proteome variation in human induced pluripotent stem cells

Human disease phenotypes are driven primarily by alterations in protein expression and/or function. To date, relatively little is known about the variability of the human proteome in populations and how this relates to variability in mRNA expression and to disease loci. Here, we present the first comprehensive proteomic analysis of human induced pluripotent stem cells (iPSC), a key cell type for disease modelling, analysing 202 iPSC lines derived from 151 donors, with integrated transcriptome and genomic sequence data from the same lines. We characterised the major genetic and non-genetic determinants of proteome variation across iPSC lines and assessed key regulatory mechanisms affecting variation in protein abundance. We identified 654 protein quantitative trait loci (pQTLs) in iPSCs, including disease-linked variants in protein-coding sequences and variants with trans regulatory effects. These include pQTL linked to GWAS variants that cannot be detected at the mRNA level, highlighting the utility of dissecting pQTL at peptide level resolution

Identifying Extrinsic versus Intrinsic Drivers of Variation in Cell Behavior in Human iPSC Lines from Healthy Donors

Large cohorts of human induced pluripotent stem cells (iPSCs) from healthy donors are a potentially powerful tool for investigating the relationship between genetic variants and cellular behavior. Here, we integrate high content imaging of cell shape, proliferation, and other phenotypes with gene expression and DNA sequence datasets from over 100 human iPSC lines. By applying a dimensionality reduction approach, Probabilistic Estimation of Expression Residuals (PEER), we extracted factors that captured the effects of intrinsic (genetic concordance between different cell lines from the same donor) and extrinsic (cell responses to different fibronectin concentrations) conditions. We identify genes that correlate in expression with intrinsic and extrinsic PEER factors and associate outlier cell behavior with genes containing rare deleterious non-synonymous SNVs. Our study, thus, establishes a strategy for examining the genetic basis of inter-individual variability in cell behavior

Structural brain anomalies in patients with FOXG1 syndrome and in Foxg1+/- mice

Objective FOXG1 syndrome is a rare neurodevelopmental disorder associated with heterozygous FOXG1 variants or chromosomal microaberrations in 14q12. The study aimed at assessing the scope of structural cerebral anomalies revealed by neuroimaging to delineate the genotype and neuroimaging phenotype associations. Methods We compiled 34 patients with a heterozygous (likely) pathogenic FOXG1 variant. Qualitative assessment of cerebral anomalies was performed by standardized re-analysis of all 34 MRI data sets. Statistical analysis of genetic, clinical and neuroimaging data were performed. We quantified clinical and neuroimaging phenotypes using severity scores. Telencephalic phenotypes of adult Foxg1+/- mice were examined using immunohistological stainings followed by quantitative evaluation of structural anomalies. Results Characteristic neuroimaging features included corpus callosum anomalies (82%), thickening of the fornix (74%), simplified gyral pattern (56%), enlargement of inner CSF spaces (44%), hypoplasia of basal ganglia (38%), and hypoplasia of frontal lobes (29%). We observed a marked, filiform thinning of the rostrum as recurrent highly typical pattern of corpus callosum anomaly in combination with distinct thickening of the fornix as a characteristic feature. Thickening of the fornices was not reported previously in FOXG1 syndrome. Simplified gyral pattern occurred significantly more frequently in patients with early truncating variants. Higher clinical severity scores were significantly associated with higher neuroimaging severity scores. Modeling of Foxg1 heterozygosity in mouse brain recapitulated the associated abnormal cerebral morphology phenotypes, including the striking enlargement of the fornix. Interpretation Combination of specific corpus callosum anomalies with simplified gyral pattern and hyperplasia of the fornices is highly characteristic for FOXG1 syndrome.Peer reviewe

Common genetic variation drives molecular heterogeneity in human iPSCs.

Technology utilizing human induced pluripotent stem cells (iPS cells) has enormous potential to provide improved cellular models of human disease. However, variable genetic and phenotypic characterization of many existing iPS cell lines limits their potential use for research and therapy. Here we describe the systematic generation, genotyping and phenotyping of 711 iPS cell lines derived from 301 healthy individuals by the Human Induced Pluripotent Stem Cells Initiative. Our study outlines the major sources of genetic and phenotypic variation in iPS cells and establishes their suitability as models of complex human traits and cancer. Through genome-wide profiling we find that 5-46% of the variation in different iPS cell phenotypes, including differentiation capacity and cellular morphology, arises from differences between individuals. Additionally, we assess the phenotypic consequences of genomic copy-number alterations that are repeatedly observed in iPS cells. In addition, we present a comprehensive map of common regulatory variants affecting the transcriptome of human pluripotent cells

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

Abstract: Recent developments in stem cell biology have enabled the study of cell fate decisions in early human development that are impossible to study in vivo. However, understanding how development varies across individuals and, in particular, the influence of common genetic variants during this process has not been characterised. Here, we exploit human iPS cell lines from 125 donors, a pooled experimental design, and single-cell RNA-sequencing to study population variation of endoderm differentiation. We identify molecular markers that are predictive of differentiation efficiency of individual lines, and utilise heterogeneity in the genetic background across individuals to map hundreds of expression quantitative trait loci that influence expression dynamically during differentiation and across cellular contexts