Ranking noncanonical 5' splice site usage by genome-wide RNA-seq analysis and splicing reporter assays.

Most human pathogenic mutations in 5' splice sites affect the canonical GT in positions +1 and +2, leading to noncanonical dinucleotides. On the other hand, noncanonical dinucleotides are observed under physiological conditions in ∼1% of all human 5'ss. It is therefore a challenging task to understand the pathogenic mutation mechanisms underlying the conditions under which noncanonical 5'ss are used. In this work, we systematically examined noncanonical 5' splice site selection, both experimentally using splicing competition reporters and by analyzing a large RNA-seq data set of 54 fibroblast samples from 27 subjects containing a total of 2.4 billion gapped reads covering 269,375 exon junctions. From both approaches, we consistently derived a noncanonical 5'ss usage ranking GC > TT > AT > GA > GG > CT. In our competition splicing reporter assay, noncanonical splicing was strictly dependent on the presence of upstream or downstream splicing regulatory elements (SREs), and changes in SREs could be compensated by variation of U1 snRNA complementarity in the competing 5'ss. In particular, we could confirm splicing at different positions (i.e., -1, +1, +5) of a splice site for all noncanonical dinucleotides "weaker" than GC. In our comprehensive RNA-seq data set analysis, noncanonical 5'ss were preferentially detected in weakly used exon junctions of highly expressed genes. Among high-confidence splice sites, they were 10-fold overrepresented in clusters with a neighboring, more frequently used 5'ss. Conversely, these more frequently used neighbors contained only the dinucleotides GT, GC, and TT, in accordance with the above ranking.

Succession of splicing regulatory elements determines cryptic 5΄ss functionality.

A critical step in exon definition is the recognition of a proper splice donor (5΄ss) by the 5' end of U1 snRNA. In the selection of appropriate 5΄ss, cis-acting splicing regulatory elements (SREs) are indispensable. As a model for 5΄ss recognition, we investigated cryptic 5΄ss selection within the human fibrinogen Bß-chain gene (FGB) exon 7, where we identified several exonic SREs that simultaneously acted on up- and downstream cryptic 5΄ss. In the FGB exon 7 model system, 5΄ss selection iteratively proceeded along an alternating sequence of U1 snRNA binding sites and interleaved SREs which in principle supported different 3' exon ends. Like in a relay race, SREs either suppressed a potential 5΄ss and passed the splicing baton on or splicing actually occurred. From RNA-Seq data, we systematically selected 19 genes containing exons with silent U1 snRNA binding sites competing with nearby highly used 5΄ss. Extensive SRE analysis by different algorithms found authentic 5΄ss significantly more supported by SREs than silent U1 snRNA binding sites, indicating that our concept may permit generalization to a model for 5΄ss selection and 3' exon end definition.

The release of cardioprotective humoral factors after remote ischemic preconditioning in humans is age- and sex-dependent.

BACKGROUND: Preclinical and proof-of-concept studies suggest a cardioprotective effect of remote ischemic preconditioning (RIPC). However, two major clinical trials (ERICCA and RIPHeart) failed to show cardioprotection by RIPC. Aging and gender might be confounding factors of RIPC affecting the inter-organ signalling. Theoretically, confounding factors might prevent the protective potency of RIPC by interfering with cardiac signalling pathways, i.e. at the heart, and/or by affecting the release of humoral factor(s) from the remote organ, e.g. from the upper limb. This study investigated the effect of age and sex on the release of cardioprotective humoral factor(s) after RIPC in humans. METHODS: Blood samples were taken from young and aged, male and female volunteers before (control) and after RIPC (RIPC). To investigate the protective potency of the different plasma groups obtained from the human volunteers, isolated perfused hearts of young rats were used as bioassay. For this, hearts were perfused with the volunteer plasma (0.5% of coronary flow) before hearts underwent global ischemia and reperfusion. In addition, to characterize the protective potency of humoral factor(s) after RIPC to initiate protection not only in young but also aged hearts, plasma from young male volunteers were transferred to isolated hearts of aged rats. At the end of the experimental protocol, infarct sizes were determined by TTC-staining (expressed as % of left ventricle). RESULTS: RIPC plasma of young male volunteers reduced infarct size in young rat hearts from 47 ± 5 to 31 ± 10% (p = 0.02). In contrast, RIPC plasma of aged male volunteers had no protective effect. Infarct size after application of control plasma of young female volunteers was 33 ± 10%, and female RIPC plasma did not lead to an infarct size reduction. RIPC plasma of old female initiated no cardioprotection. RIPC plasma of young male volunteers reduced infarct size in isolated hearts from aged rats (41 ± 5% vs. 51 ± 5%; p < 0.001). CONCLUSIONS: The release of humoral factor(s) into the blood after RIPC in humans is affected by both age and sex. In addition, these blood borne factor(s) are capable to initiate cardioprotection within the aged heart.

Hierarchical Clustering of DNA k-mer Counts in RNAseq Fastq Files Identifies Sample Heterogeneities.

We apply hierarchical clustering (HC) of DNA k-mer counts on multiple Fastq files. The tree structures produced by HC may reflect experimental groups and thereby indicate experimental effects, but clustering of preparation groups indicates the presence of batch effects. Hence, HC of DNA k-mer counts may serve as a diagnostic device. In order to provide a simple applicable tool we implemented sequential analysis of Fastq reads with low memory usage in an R package (seqTools) available on Bioconductor. The approach is validated by analysis of Fastq file batches containing RNAseq data. Analysis of three Fastq batches downloaded from ArrayExpress indicated experimental effects. Analysis of RNAseq data from two cell types (dermal fibroblasts and Jurkat cells) sequenced in our facility indicate presence of batch effects. The observed batch effects were also present in reads mapped to the human genome and also in reads filtered for high quality (Phred > 30). We propose, that hierarchical clustering of DNA k-mer counts provides an unspecific diagnostic tool for RNAseq experiments. Further exploration is required once samples are identified as outliers in HC derived trees.

Immunohistochemical detection of lymph node-DTCs in patients with node-negative HNSCC.

This study was performed to systematically assess the prevalence, topography and prognostic impact of disseminated tumor cells (DTCs) in lymph nodes (LN) of patients with primary, regional and distant metastasis-free head and neck squamous cell carcinoma (HNSCC) who underwent resection with elective neck dissection. From the routinely processed resection specimen, we could prospectively analyze a total of 1.137 exactly mapped LNs of 50 pN0-HNSCC patients, classified as tumor free by routine histopathology. Three immunohistochemistry (IHC) assays using antibodies directed against CK5/14, a broad spectrum of CKs (1-8, 10, 14-16 and 19), and CD44v6, respectively, were applied on 4.190 LN sections to detect DTCs. The IHC results were correlated with clinicopathologic parameters and clinical follow-up data. We detected seven micrometastases (MM) in five patients and 31 DTCs in 12 patients. Overall, 15 (30%) patients were positive for DTCs or MMs. Strikingly, the anatomical distribution of LN affected with DTCs was not random, but was dependent on the lateralization of the primary tumor and clustered significantly most proximal to the primary tumor. None of the investigated patients developed loco-regional lymphatic or distant metastasis during the mean follow-up period of 71 months. Our results reveal clinically occult tumor cell dissemination as an early and frequent event in HNSCC. Considering that higher rates of recurrences in therapeutic LN dissection concepts have been reported than in elective neck dissection strategies, our DTC-data support to perform elective neck dissections, since they appear to be effective in preventing loco-regional lymphatic recurrence from LN DTCs or MMs.

Sample Size Estimation for Detection of Splicing Events in Transcriptome Sequencing Data.

Merging data from multiple samples is required to detect low expressed transcripts or splicing events that might be present only in a subset of samples. However, the exact number of required replicates enabling the detection of such rare events often remains a mystery but can be approached through probability theory. Here, we describe a probabilistic model, relating the number of observed events in a batch of samples with observation probabilities. Therein, samples appear as a heterogeneous collection of events, which are observed with some probability. The model is evaluated in a batch of 54 transcriptomes of human dermal fibroblast samples. The majority of putative splice-sites (alignment gap-sites) are detected in (almost) all samples or only sporadically, resulting in an U-shaped pattern for observation probabilities. The probabilistic model systematically underestimates event numbers due to a bias resulting from finite sampling. However, using an additional assumption, the probabilistic model can predict observed event numbers within a <10% deviation from the median. Single samples contain a considerable amount of uniquely observed putative splicing events (mean 7122 in alignments from TopHat alignments and 86,215 in alignments from STAR). We conclude that the probabilistic model provides an adequate description for observation of gap-sites in transcriptome data. Thus, the calculation of required sample sizes can be done by application of a simple binomial model to sporadically observed random events. Due to the large number of uniquely observed putative splice-sites and the known stochastic noise in the splicing machinery, it appears advisable to include observation of rare splicing events into analysis objectives. Therefore, it is beneficial to take scores for the validation of gap-sites into account.

Validation of Splicing Events in Transcriptome Sequencing Data.

Genomic alignments of sequenced cellular messenger RNA contain gapped alignments which are interpreted as consequence of intron removal. The resulting gap-sites, genomic locations of alignment gaps, are landmarks representing potential splice-sites. As alignment algorithms report gap-sites with a considerable false discovery rate, validations are required. We describe two quality scores, gap quality score (gqs) and weighted gap information score (wgis), developed for validation of putative splicing events: While gqs solely relies on alignment data wgis additionally considers information from the genomic sequence. FASTQ files obtained from 54 human dermal fibroblast samples were aligned against the human genome (GRCh38) using TopHat and STAR aligner. Statistical properties of gap-sites validated by gqs and wgis were evaluated by their sequence similarity to known exon-intron borders. Within the 54 samples, TopHat identifies 1,000,380 and STAR reports 6,487,577 gap-sites. Due to the lack of strand information, however, the percentage of identified GT-AG gap-sites is rather low. While gap-sites from TopHat contain ≈89% GT-AG, gap-sites from STAR only contain ≈42% GT-AG dinucleotide pairs in merged data from 54 fibroblast samples. Validation with gqs yields 156,251 gap-sites from TopHat alignments and 166,294 from STAR alignments. Validation with wgis yields 770,327 gap-sites from TopHat alignments and 1,065,596 from STAR alignments. Both alignment algorithms, TopHat and STAR, report gap-sites with considerable false discovery rate, which can drastically be reduced by validation with gqs and wgis.

rbamtools: an R interface to samtools enabling fast accumulative tabulation of splicing events over multiple RNA-seq samples.

The open source environment R isf the most widely used software to statistically explore biological data sets including sequence alignments. BAM is the de facto standard file format for sequence alignment. With rbamtools, we provide now a full spectrum of accessibility to BAM for R users such as reading, writing, extraction of subsets and plotting of alignment depth where the script syntax closely follows the SAM/BAM format. Additionally, rbamtools enables fast accumulative tabulation of splicing events over multiple BAM files.

Identification of amino acid determinants in CYP4B1 for optimal catalytic processing of 4-ipomeanol.

Mammalian CYP4B1 enzymes are cytochrome P450 mono-oxygenases that are responsible for the bioactivation of several exogenous pro-toxins including 4-ipomeanol (4-IPO). In contrast with the orthologous rabbit enzyme, we show here that native human CYP4B1 with a serine residue at position 427 is unable to bioactivate 4-IPO and does not cause cytotoxicity in HepG2 cells and primary human T-cells that overexpress these enzymes. We also demonstrate that a proline residue in the meander region at position 427 in human CYP4B1 and 422 in rabbit CYP4B1 is important for protein stability and rescues the 4-IPO bioactivation of the human enzyme, but is not essential for the catalytic activity of the rabbit CYP4B1 protein. Systematic substitution of native and p.S427P human CYP4B1 with peptide regions from the highly active rabbit enzyme reveals that 18 amino acids in the wild-type rabbit CYP4B1 protein are key for conferring high 4-IPO metabolizing activity. Introduction of 12 of the 18 amino acids that are also present at corresponding positions in other human CYP4 family members into the p.S427P human CYP4B1 protein results in a mutant human enzyme (P+12) that is as stable and as active as the rabbit wild-type CYP4B1 protein. These 12 mutations cluster in the predicted B-C loop through F-helix regions and reveal new amino acid regions important to P450 enzyme stability. Finally, by minimally re-engineering the human CYP4B1 enzyme for efficient activation of 4-IPO, we have developed a novel human suicide gene system that is a candidate for adoptive cellular therapies in humans.

Analysis of Documentation Speed Using Web-Based Medical Speech Recognition Technology: Randomized Controlled Trial.

BACKGROUND: Clinical documentation has undergone a change due to the usage of electronic health records. The core element is to capture clinical findings and document therapy electronically. Health care personnel spend a significant portion of their time on the computer. Alternatives to self-typing, such as speech recognition, are currently believed to increase documentation efficiency and quality, as well as satisfaction of health professionals while accomplishing clinical documentation, but few studies in this area have been published to date. OBJECTIVE: This study describes the effects of using a Web-based medical speech recognition system for clinical documentation in a university hospital on (1) documentation speed, (2) document length, and (3) physician satisfaction. METHODS: Reports of 28 physicians were randomized to be created with (intervention) or without (control) the assistance of a Web-based system of medical automatic speech recognition (ASR) in the German language. The documentation was entered into a browser's text area and the time to complete the documentation including all necessary corrections, correction effort, number of characters, and mood of participant were stored in a database. The underlying time comprised text entering, text correction, and finalization of the documentation event. Participants self-assessed their moods on a scale of 1-3 (1=good, 2=moderate, 3=bad). Statistical analysis was done using permutation tests. RESULTS: The number of clinical reports eligible for further analysis stood at 1455. Out of 1455 reports, 718 (49.35%) were assisted by ASR and 737 (50.65%) were not assisted by ASR. Average documentation speed without ASR was 173 (SD 101) characters per minute, while it was 217 (SD 120) characters per minute using ASR. The overall increase in documentation speed through Web-based ASR assistance was 26% (P=.04). Participants documented an average of 356 (SD 388) characters per report when not assisted by ASR and 649 (SD 561) characters per report when assisted by ASR. Participants' average mood rating was 1.3 (SD 0.6) using ASR assistance compared to 1.6 (SD 0.7) without ASR assistance (P<.001). CONCLUSIONS: We conclude that medical documentation with the assistance of Web-based speech recognition leads to an increase in documentation speed, document length, and participant mood when compared to self-typing. Speech recognition is a meaningful and effective tool for the clinical documentation process.

AKT1 and AKT2 induce distinct phosphorylation patterns in HL-1 cardiac myocytes.

The protein kinase AKT is a central kinase in the heart and has a major impact on growth/hypertrophy, survival/apoptosis, and metabolism. To gain more insight into AKT isoform-specific signaling at the molecular level, we investigated the phosphoproteome of HL-1 cardiomyocytes carrying AKT1 or AKT2 isoform-specific knock down, respectively. We combined stable isotope labeling with high resolution mass spectrometry and identified 377 regulated phosphopeptides. Although AKT1 is expressed at 4-fold higher levels, insulin stimulation mainly activated AKT2, which might in part rely on a preferred interaction of AKT2 with the mammalian target of rapamycin complex 2. In line with this result, the highest number of regulated phosphopeptides was identified in the AKT2 knock down cells. Isoform-specific regulation of AKT targets not previously described could be observed, and specific regulation of indirect target sites allows a deeper insight into affected biological processes. In the myocardial context, we identified many phosphosites supporting a connection of AKT to excitation-contraction coupling. Phosphoproteins identified included L-type calcium channel, ryanodine receptor, junctophilin, histidine-rich calcium binding protein, phospholamban, heat shock protein beta-6, and Ca²âº/calmodulin-dependent kinase II. In conclusion, AKT isoform-specific knock down combined with quantitative phosphoproteomics provided a powerful strategy to unravel AKT isoform-specific signaling.

An intronic G run within HIV-1 intron 2 is critical for splicing regulation of vif mRNA.

Within target T lymphocytes, human immunodeficiency virus type I (HIV-1) encounters the retroviral restriction factor APOBEC3G (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G; A3G), which is counteracted by the HIV-1 accessory protein Vif. Vif is encoded by intron-containing viral RNAs that are generated by splicing at 3' splice site (3'ss) A1 but lack splicing at 5'ss D2, which results in the retention of a large downstream intron. Hence, the extents of activation of 3'ss A1 and repression of D2, respectively, determine the levels of vif mRNA and thus the ability to evade A3G-mediated antiviral effects. The use of 3'ss A1 can be enhanced or repressed by splicing regulatory elements that control the recognition of downstream 5'ss D2. Here we show that an intronic G run (G(I2)-1) represses the use of a second 5'ss, termed D2b, that is embedded within intron 2 and, as determined by RNA deep-sequencing analysis, is normally inefficiently used. Mutations of G(I2)-1 and activation of D2b led to the generation of transcripts coding for Gp41 and Rev protein isoforms but primarily led to considerable upregulation of vif mRNA expression. We further demonstrate, however, that higher levels of Vif protein are actually detrimental to viral replication in A3G-expressing T cell lines but not in A3G-deficient cells. These observations suggest that an appropriate ratio of Vif-to-A3G protein levels is required for optimal virus replication and that part of Vif level regulation is effected by the novel G run identified here.

Comparative analysis of diagnostic ultrasound and histopathology for detecting cervical lymph node metastases in head and neck cancer.

PURPOSE: We evaluated the current performance of diagnostic ultrasound (US) for detecting cervical lymph node (LN) metastases based on objective measures and subjective findings in comparison to the gold standard, histopathological evaluation. PATIENTS AND METHODS: From 2007 to 2016, we prospectively included patients with head and neck cancer who were scheduled for surgical therapy including neck dissection. LNs were examined by multimodal US by a level III head and neck sonologist and individually assigned to a map containing six AAO-HNS neck LN levels preoperatively. During the operation, LNs were dissected and then assessed by routine histopathology, with 86% of them examined individually and the remaining LNs (14%) per AAO-HNS neck LN level. The optimal cutoff points (OCPs) of four defined LN diameters and 2D and 3D roundness indices per AAO-HNS neck LN level were determined. RESULTS: In total, 235 patients were included, and 4539 LNs were analyzed by US, 7237 by histopathology and 2684 by both methods. Of these, 259 (9.65%) were classified as suspicious for metastasis by US, whereas 299 (11.14%) were found to be positive by histopathology. Subjective US sensitivity and specificity were 0.79 and 0.99, respectively. The OCPs of the individual LN diameters and the 2D and 3D roundness index were determined individually for all AAO-HNS neck LN levels. Across all levels, the OCP for the 2D index was 1.79 and the 3D index was 14.97. The predictive performance of all distances, indices, and subjective findings improved with increasing metastasis size. Anticipation of pN stage was best achieved with subjective US findings and the smallest diameter (Cohen's κ = 0.713 and 0.438, respectively). CONCLUSION: Our LN mapping and meticulous 1:1 node-by-node comparison reveals the usefulness of US for detecting metastatic involvement of neck LNs in head and neck carcinomas as compared to histopathology. The predictive ability for small tumor deposits less than 8 mm in size remains weak and urgently needs improvement.

Is the prediction of one or two ipsilateral positive lymph nodes by computerized tomography and ultrasound reliable enough to restrict therapeutic neck dissection in oral squamous cell carcinoma (OSCC) patients?

INTRODUCTION: Proper management of the clinically involved neck in OSCC patients continues to be a matter of debate. Our aim was to analyze the accuracy of computerized tomography (CT) and ultrasound (US) in anticipating the exact location of lymph node (LN) metastases of OSCC patients across the AAO-HNS (American Academy of Otolaryngology-Head and Neck Surgery) levels ipsi- and contralaterally. Furthermore, we wanted to assess the suitability of therapeutic selective neck dissection (SND) in patients with one or two ipsilateral positive nodes upon clinical staging (cN1/cN2a and cN2b(2/x) patients). METHODS: We prospectively analyzed the LN status of patients with primary OSCC using CT and US from 2007 to 2013. LNs were individually assigned to a map containing the AAO-HNS levels; patients bearing a single or just two ipsilateral positive nodes (designated cN1/cN2a or cN2b(2/x) patients either by CT (CT group) or US alone (US group) or in a group combining findings of CT and US (CTUS group)) received an ipsi-ND (I-V) and a contra-ND (I-IV). 78% of the LNs were sent individually for routine histopathological examination; the remaining were dissected and analyzed per neck level. RESULTS: Upon the analysis of 1.670 LNs of 57 patients, the exact location of pathology proven LN metastases in cN1 patients was more precisely predicted by US compared to CT with confirmed findings only in levels IA, IB und IIA. Clearly decreasing the number of missed lesions, the findings in the CTUS group nearly kept the spatial reliability of the US group. The same analysis for patients with exactly two supposed ipsilateral lesions (cN2b(2/x)) yielded confirmed metastases from levels I to V for both methods individually and in combination and, therefore, render SND insufficient for these cases. CONCLUSION: Our findings stress the importance of conducting both, CT and US, in patients with primary OSCC. Only the combination of their findings warrants the application of therapeutic SND in patients with a single ipsilateral LN metastasis (cN1/cN2a patients) but not in patients with more than one lesion upon clinical staging (≥ cN2b).

Biomechanical assessment of healthy and keratoconic corneas (with/without crosslinking) using dynamic ultrahigh-speed Scheimpflug technology and the relevance of the parameter (A1L-A2L).

AIMS: To examine corneal biomechanics in healthy and keratoconic eyes, with or without crosslinking obtained by ultrahigh-speed Scheimpflug measurements (Corvis ST). METHODS: One hundred and seventeen eyes were studied in three groups: group 1 (n=39) contained keratoconic eyes without crosslinking. Group 2 (CXL; n=28) comprised keratoconic eyes after crosslinking. These were compared with a control group (n=50 matched healthy eyes). In addition, 10 keratoconus patients, before and after CXL treatment, respectively, were examined. RESULTS: The novel parameter A1L-A2L demonstrated highly significant differences between crosslinked corneas and untreated keratoconic or healthy corneas. Velocity during second applanation (A2V) and deformation amplitude (DA) were significantly increased in crosslinked keratoconic eyes both compared with untreated keratoconic eyes and with healthy controls. Radius at highest curvature also was significant among all groups. Inward applanation length (A1L) was significantly increased in controls, whereas outward applanation length (A2L) was significantly reduced in crosslinked keratoconic eyes compared with both other groups. The follow-up analysis revealed statistically significant changes in pachymetry and intraocular pressure and showed tendencies towards significance in applanation times 1 and 2 and in DA. CONCLUSIONS: Both A2V and A2L are viable parameters to discriminate healthy from keratoconic but also crosslinked from non-crosslinked keratoconic corneas. The difference of A1L-A2L could reliably discriminate crosslinked from non-crosslinked and healthy corneas. Follow-up examination in a small cohort allows distinction between crosslinked and untreated keratoconus in follow-up examinations. The difference of A1L-A2L could reliably discriminate crosslinked from non-crosslinked and healthy corneas. Measurements of corneal deformation using dynamic ultrahigh-speed Scheimpflug technology are reproducible and provide useful information about keratoconus assessment and biomechanics. Therefore, the Corvis ST seems to provide useful technology to monitor therapeutic success of crosslinking treatment.

High Concentration of Low-Density Lipoprotein Results in Disturbances in Mitochondrial Transcription and Functionality in Endothelial Cells.

Concentrations of low-density lipoprotein (LDL) above 0.8 mg/ml have been associated with increased risk for cardiovascular diseases and impaired endothelial functionality. Here, we demonstrate that high concentrations of LDL (1 mg/ml) decreased NOS3 protein and RNA levels in primary human endothelial cells. In addition, RNA sequencing data, in particular splice site usage analysis, showed a shift in NOS3 exon-exon junction reads towards those specifically assigned to nonfunctional transcript isoforms further diminishing the functional NOS3 levels. The reduction in NOS3 was accompanied by decreased migratory capacity, which depends on intact mitochondria and ATP formation. In line with these findings, we also observed a reduced ATP content. While mitochondrial mass was unaffected by high LDL, we found an increase in mitochondrial DNA copy number and mitochondrial RNA transcripts but decreased expression of nuclear genes coding for respiratory chain proteins. Therefore, high LDL treatment most likely results in an imbalance between respiratory chain complex proteins encoded in the mitochondria and in the nucleus resulting in impaired respiratory chain function explaining the reduction in ATP content. In conclusion, high LDL treatment leads to a decrease in active NOS3 and dysregulation of mitochondrial transcription, which is entailed by reduced ATP content and migratory capacity and thus, impairment of endothelial cell functionality.

Echocardiographic Analysis of Cardiac Function after Infarction in Mice: Validation of Single-Plane Long-Axis View Measurements and the Bi-Plane Simpson Method.

Although echocardiography is commonly used to analyze cardiac function in small animal models of cardiac remodeling after myocardial infarction, the different echocardiographic methods are validated poorly. End-diastolic volume, end-systolic volume and ejection fraction were analyzed using either standard single-plane analysis from parasternal long-axis B-mode views (PSLAX) or the bi-plane Simpson method (using PSLAX and three short-axis views) and validated using magnetic resonance imaging as standard. Ejection fraction measured by PSLAX was moderately correlated with a coefficient of R2 = 0.49. The standard deviation of residuals was 9.91. Simpson analysis revealed an improved correlation coefficient of R2 = 0.77 and a reduction in standard deviation of residuals by 45% (5.45 vs. 9.92, p = 0.014). Subgroup analysis revealed that the high variation in PSLAX is due to changes in ventricular geometry after myocardial infarction. Our results indicate that the bi-plane Simpson method is advantageous for the assessment of cardiac function after myocardial infarction.

Age, gender and UV-exposition related effects on gene expression in in vivo aged short term cultivated human dermal fibroblasts.

Ageing, the progressive functional decline of virtually all tissues, affects numerous living organisms. Main phenotypic alterations of human skin during the ageing process include reduced skin thickness and elasticity which are related to extracellular matrix proteins. Dermal fibroblasts, the main source of extracellular fibrillar proteins, exhibit complex alterations during in vivo ageing and any of these are likely to be accompanied or caused by changes in gene expression. We investigated gene expression of short term cultivated in vivo aged human dermal fibroblasts using RNA-seq. Therefore, fibroblast samples derived from unaffected skin were obtained from 30 human donors. The donors were grouped by gender and age (Young: 19 to 25 years, Middle: 36 to 45 years, Old: 60 to 66 years). Two samples were taken from each donor, one from a sun-exposed and one from a sun-unexposed site. In our data, no consistently changed gene expression associated with donor age can be asserted. Instead, highly correlated expression of a small number of genes associated with transforming growth factor beta signalling was observed. Also, known gene expression alterations of in vivo aged dermal fibroblasts seem to be non-detectable in cultured fibroblasts.

FTO is a relevant factor for the development of the metabolic syndrome in mice.

The metabolic syndrome is a worldwide problem mainly caused by obesity. FTO was found to be a obesity-risk gene in humans and FTO deficiency in mice led to reduction in adipose tissue. Thus, FTO is an important factor for the development of obesity. Leptin-deficient mice are a well characterized model for analysing the metabolic syndrome. To determine the relevance of FTO for the development of the metabolic syndrome we analysed different parameters in combined homozygous deficient mice (Lep(ob/ob);Fto(-/-)). Lep(ob/ob);Fto(-/-) mice showed an improvement in analysed hallmarks of the metabolic syndrome in comparison to leptin-deficient mice wild type or heterozygous for Fto. Lep(ob/ob);Fto(-/-) mice did not develop hyperglycaemia and showed an improved glucose tolerance. Furthermore, extension of beta-cell mass was prevented in Lep(ob/ob);Fto(-/-)mice and accumulation of ectopic fat in the liver was reduced. In conclusion this study demonstrates that FTO deficiency has a protective effect not only on the development of obesity but also on the metabolic syndrome. Thus, FTO plays an important role in the development of metabolic disorders and is an interesting target for therapeutic agents.