Evidence for widespread translation of 5' untranslated regions.

Ribosome profiling experiments support the translation of a range of novel human open reading frames. By contrast, most peptides from large-scale proteomics experiments derive from just one source, 5' untranslated regions. Across the human genome we find evidence for 192 translated upstream regions, most of which would produce protein isoforms with extended N-terminal ends. Almost all of these N-terminal extensions are from highly abundant genes, which suggests that the novel regions we detect are just the tip of the iceberg. These upstream regions have characteristics that are not typical of coding exons. Their GC-content is remarkably high, even higher than 5' regions in other genes, and a large majority have non-canonical start codons. Although some novel upstream regions have cross-species conservation - five have orthologues in invertebrates for example - the reading frames of two thirds are not conserved beyond simians. These non-conserved regions also have no evidence of purifying selection, which suggests that much of this translation is not functional. In addition, non-conserved upstream regions have significantly more peptides in cancer cell lines than would be expected, a strong indication that an aberrant or noisy translation initiation process may play an important role in translation from upstream regions.

Preovulatory follicular fluid secretome added to in vitro maturation medium influences the metabolism of equine cumulus-oocyte complexes.

BACKGROUND: In vitro embryo production is a highly demanded reproductive technology in horses, which requires the recovery (in vivo or post-mortem) and in vitro maturation (IVM) of oocytes. Oocytes subjected to IVM exhibit poor developmental competence compared to their in vivo counterparts, being this related to a suboptimal composition of commercial maturation media. The objective of this work was to study the effect of different concentrations of secretome obtained from equine preovulatory follicular fluid (FF) on cumulus-oocyte complexes (COCs) during IVM. COCs retrieved in vivo by ovum pick up (OPU) or post-mortem from a slaughterhouse (SLA) were subjected to IVM in the presence or absence of secretome (Control: 0 µg/ml, S20: 20 µg/ml or S40: 40 µg/ml). After IVM, the metabolome of the medium used for oocyte maturation prior (Pre-IVM) and after IVM (Post-IVM), COCs mRNA expression, and oocyte meiotic competence were analysed. RESULTS: IVM leads to lactic acid production and an acetic acid consumption in COCs obtained from OPU and SLA. However, glucose consumption after IVM was higher in COCs from OPU when S40 was added (Control Pre-IVM vs. S40 Post-IVM: 117.24 ± 7.72 vs. 82.69 ± 4.24; Mean µM ± SEM; p < 0.05), while this was not observed in COCs from SLA. Likewise, secretome enhanced uptake of threonine (Control Pre-IVM vs. S20 Post-IVM vs. S40 Post-IVM: 4.93 ± 0.33 vs. 3.04 ± 0.25 vs. 2.84 ± 0.27; Mean µM ± SEM; p < 0.05) in COCs recovered by OPU. Regarding the relative mRNA expression of candidate genes related to metabolism, Lactate dehydrogenase A (LDHA) expression was significantly downregulated when secretome was added during IVM at 20-40 µg/ml in OPU-derived COCs (Control vs. S20 vs. S40: 1.77 ± 0.14 vs. 1 ± 0.25 vs. 1.23 ± 0.14; fold change ± SEM; p < 0.05), but not in SLA COCs. CONCLUSIONS: The addition of secretome during in vitro maturation (IVM) affects the gene expression of LDHA, glucose metabolism, and amino acid turnover in equine cumulus-oocyte complexes (COCs), with diverging outcomes observed between COCs retrieved using ovum pick up (OPU) and slaughterhouse-derived COCs (SLA).

APPRIS: selecting functionally important isoforms.

APPRIS (https://appris.bioinfo.cnio.es) is a well-established database housing annotations for protein isoforms for a range of species. APPRIS selects principal isoforms based on protein structure and function features and on cross-species conservation. Most coding genes produce a single main protein isoform and the principal isoforms chosen by the APPRIS database best represent this main cellular isoform. Human genetic data, experimental protein evidence and the distribution of clinical variants all support the relevance of APPRIS principal isoforms. APPRIS annotations and principal isoforms have now been expanded to 10 model organisms. In this paper we highlight the most recent updates to the database. APPRIS annotations have been generated for two new species, cow and chicken, the protein structural information has been augmented with reliable models from the EMBL-EBI AlphaFold database, and we have substantially expanded the confirmatory proteomics evidence available for the human genome. The most significant change in APPRIS has been the implementation of TRIFID functional isoform scores. TRIFID functional scores are assigned to all splice isoforms, and APPRIS uses the TRIFID functional scores and proteomics evidence to determine principal isoforms when core methods cannot.

Analysis of the Association between Copy Number Variation and Ventricular Fibrillation in ST-Elevation Acute Myocardial Infarction.

Sudden cardiac death due to ventricular fibrillation (VF) during ST-elevation acute myocardial infarction (STEAMI) significantly contributes to cardiovascular-related deaths. Although VF has been linked to genetic factors, variations in copy number variation (CNV), a significant source of genetic variation, have remained largely unexplored in this context. To address this knowledge gap, this study performed whole exome sequencing analysis on a cohort of 39 patients with STEAMI who experienced VF, aiming to elucidate the role of CNVs in this pathology. The analysis revealed CNVs in the form of duplications in the PARP2 and TTC5 genes as well as CNVs in the form of deletions in the MUC15 and PPP6R1 genes, which could potentially serve as risk indicators for VF during STEAMI. The analysis also underscores notable CNVs with an average gene copy number equal to or greater than four in DEFB134, FCGR2C, GREM1, PARM1, SCG5, and UNC79 genes. These findings provide further insight into the role of CNVs in VF in the context of STEAMI.

Influence of base designs on the manufacturing accuracy of vat-polymerized diagnostic casts using two different technologies.

STATEMENT OF PROBLEM: Diagnostic casts can incorporate different base designs and be manufactured using different vat-polymerization technologies. However, the influence of the interrelation between the base design and the 3D printing technology on the casts' final accuracy remains unclear. PURPOSE: The purpose of this in vitro study was to assess the influence of different base designs of 3D printed casts on the accuracy of 2 vat-polymerization technologies. MATERIAL AND METHODS: A digital maxillary cast was obtained and used to generate 3 different base designs: solid (S group), honeycombed (HC group), and hollow (H group). The HC and H groups were subdivided based on the wall thickness of the cast design, resulting in 2 subgroups with thicknesses of 1 mm (HC1 and H1) and 2 mm (HC2 and H2) (N=100, n=10). Eleven reference cubes were added to each specimen for subsequent measurements. Specimens were manufactured by using 2 vat-polymerization 3D printers: Nextdent 5100 (ND group) and Sonic Mini 4K (SM4K group) and a resin material suitable for both 3D printers (Nextdent Model 2.0). A coordinate measuring machine quantified the linear and 3-dimensional discrepancies between the digital cast and each reference specimen. Trueness was defined as the average absolute dimensional discrepancy between the virtual cast and the specimens produced through additive manufacturing (AM), while precision was delineated as the standard deviation in dimensional discrepancies between the digital cast and the AM specimens. The data were analyzed using the Kruskal-Wallis and Mann-Whitney U pairwise comparison tests (α=.05). RESULTS: For the NextDent group the trueness ranged from 21.83 µm to 28.35 µm, and the precision ranged from 17.82 µm to 37.70 µm. For the Phrozen group, the trueness ranged from 45.15 µm to 64.51 µm, and the precision ranged from 33.51 µm to 48.92 µm. The Kruskal-Wallis test showed significant differences on the x-, y-, and z-axes and in the 3D discrepancy (all P<.001). On the x-axis, the Mann-Whitney U test showed significant differences for the Phrozen group between the H-2 and H-1 groups (P=.001), H-2 and S groups (P<.001), and HC-2 and S groups (P=.012). On the y-axis, significant differences were found in the Phrozen group between the H-2 and H-1 groups (P=.001), the H-2 and S, H-1 and HC-1, and HC-1 and S groups (P<.001), the H-1 and HC-2 groups (P=.007), and the HC-2 and S groups (P=.009). The NextDent group exhibited significant differences, particularly among the HC-1 and H-2 groups (P=.004), H-1 (P=.020), and HC-2 (P=.001) groups; and on the z-axis significant differences were found in the Phrozen group between the H-2 and H-1 and S groups and the HC-2 group and H-1 and S groups (both P<.001). In the NextDent group, significant differences were found between the H-2 and HC-2 (P=.047) and HC-1 (P=.028) groups. For the 3D discrepancy analysis, significant differences were found in the Phrozen group between the H-2 and H-1 and S groups (P<.001), the H-1 and HC-2 groups (P=.001), the S and HC-1 and HC-2 groups (P<.001), and the H-1 and HC-1 groups (P=.002). In the NextDent group, significant differences were observed between the H-2 and HC-1 groups (P=.012). CONCLUSIONS: The accuracy of digital casts depends on the manufacturing trinomial and base design of the casts. The honeycomb and hollow based designs provided the highest accuracy in the NextDent and Phrozen groups respectively for the material polymer tested. All specimens fell in the clinically acceptable range.

Satisfaction and use of the didactic simulator for learning the nursing process: an observational study.

INTRODUCTION: The implementation of Information and Communication Technology (ICT) in daily healthcare practice has become standardized. In relation to education within the nursing degree, ICTs make it possible to carry out practical immersion training from the" classroom or from any other place with an Internet connection, as evidenced by circumstances that have occurred in recent years, such as the pandemic caused by COVID-19. OBJECTIVE: Design and assess a didactic simulation program for the training of the nursing process that promotes learning in the nursing care METHODOLOGY: The methodological approach is quantitative and it is a descriptive cross-sectional study. The sampling method used was non-probabilistic by convenience. RESULTS: When observing the comparison of the averages of student satisfaction with respect to the didactic simulator, it is worth mentioning that all the items are above 2.80 on a score in which "0" is the minimum value and "5" the maximum value. The results of the use of the computer tool by the students, we highlight as significant data that all the items present an average equal to or lower than 3.04 out of 7, where "1" corresponds to a lot of use and "7" to little use. CONCLUSION: The implication of ICT in the teaching-learning process among Nursing Degree students, it is considered optimal. when analyzing the answers obtained in the items that refer to a higher ease in the execution of development of Care plans, a fundamental work in Nursing performance.

Is erenumab an efficient alternative for the prevention of episodic and chronic migraine in Spain? Results of a cost-effectiveness analysis.

BACKGROUND: The reimbursement of erenumab in Spain and other European countries is currently restricted because of the cost of this novel therapy to patients with migraine who have experienced previous failures to traditional preventive treatments. However, this reimbursement policy should be preferably based on cost-effectiveness studies, among other criteria. This study performed a cost-effectiveness analysis of erenumab versus topiramate for the prophylactic treatment of episodic migraine (EM) and versus placebo for chronic migraine (CM). METHODS: A Markov model with a 10-year time horizon, from the perspective of the Spanish National Healthcare System, was constructed based on data from responder and non-responder patients. A responder was defined as having a minimum 50% reduction in the number of monthly migraine days (MMD). A hypothetical cohort of patients with EM with one or more prior preventive treatment failures and patients with CM with more than two treatment failures was considered. The effectiveness score was measured as an incremental cost per quality-adjusted life year (QALY) gained and cost per migraine day (MD) avoided. Data from clinical outcomes and patient characteristics were obtained from erenumab clinical trials (NCT02066415, STRIVE, ARISE, LIBERTY and HER-MES). Deterministic and probabilistic sensitivity analyses were performed to validate the robustness of the model. RESULTS: After a 10-year follow-up, the estimated QALYs were 5.88 and 6.11 for patients with EM treated with topiramate and erenumab, respectively. Erenumab showed an incremental cost per patient of €4,420 vs topiramate. For CM patients, erenumab resulted in 0.756 QALYs gained vs placebo; and an incremental cost of €1,814. Patients treated with erenumab achieved reductions in MD for both EM and CM (172 and 568 MDs, respectively). The incremental cost per QALY gained with erenumab was below the Spanish threshold of €30,000/QALY for both health and societal perspectives (EM €19,122/QALY and CM €2,398/QALY). CONCLUSIONS: Erenumab is cost-effective versus topiramate as a preventive treatment for EM and versus placebo for patients with CM from the perspective of the Spanish National Health System.

APPRIS principal isoforms and MANE Select transcripts define reference splice variants.

MOTIVATION: Selecting the splice variant that best represents a coding gene is a crucial first step in many experimental analyses, and vital for mapping clinically relevant variants. This study compares the longest isoforms, MANE Select transcripts, APPRIS principal isoforms, and expression data, and aims to determine which method is best for selecting biological important reference splice variants for large-scale analyses. RESULTS: Proteomics analyses and human genetic variation data suggest that most coding genes have a single main protein isoform. We show that APPRIS principal isoforms and MANE Select transcripts best describe these main cellular isoforms, and find that using the longest splice variant as the representative is a poor strategy. Exons unique to the longest splice isoforms are not under selective pressure, and so are unlikely to be functionally relevant. Expression data are also a poor means of selecting the main splice variant. APPRIS principal and MANE Select exons are under purifying selection, while exons specific to alternative transcripts are not. There are MANE and APPRIS representatives for almost 95% of genes, and where they agree they are particularly effective, coinciding with the main proteomics isoform for over 98.2% of genes. AVAILABILITY AND IMPLEMENTATION: APPRIS principal isoforms for human, mouse and other model species can be downloaded from the APPRIS database (https://appris.bioinfo.cnio.es), GENCODE genes (https://www.gencodegenes.org/) and the Ensembl website (https://www.ensembl.org). MANE Select transcripts for the human reference set are available from the Ensembl, GENCODE and RefSeq databases (https://www.ncbi.nlm.nih.gov/refseq/). Lists of splice variants where MANE and APPRIS coincide are available from the APPRIS database. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Prognostic impact of coronary lesions and its revascularization in a 5-year follow-up after the TAVI procedure.

BACKGROUND: Coronary artery disease (CAD) is a common finding in patients undergoing transcatheter aortic valve implantation (TAVI). However, its prognostic significance and its management remains controversial. AIMS: This study sought to determine whether the presence of CAD, its complexity, and angiography-guided percutaneous coronary intervention (PCI) are associated with outcomes after TAVI. METHODS: All patients undergoing TAVI at a tertiary referral center between 2008 and 2018 were included in a prospective observational study. Baseline SYNTAX (Synergy between PCI with Taxus and Cardiac Surgery) score (SS) and a residual SS after PCI were calculated. The endpoints on the 5 year follow-up were all-cause mortality and a composite of mayor cardiovascular adverse events (MACE). RESULTS: In 379 patients, the presence of CAD and its complexity were not significantly associated with worse 5-year survival after TAVI, with a mortality for SS0 of 45%; for SS 1-22 of 36.5% (HR 0.77; 95% CI 0.53-1.11, p = 0.15) and for SS > 22 of 42.1% (HR 1.24; 95% CI 0.59-2.63, p = 0.57). Regarding the combined event of MACE, there were also no statistically significant differences between patients with CAD and without CAD (56.8% in patients without CAD and 54.9% in patients with CAD; HR 1.06; 95% CI 0.79-1.43, p = 0.7). Angiography-guided PCI or completeness of revascularization was not associated with different outcomes. CONCLUSIONS: In the present analysis, neither the presence nor the extent of CAD, nor the degree of revascularization, was associated with a prognostic impact in patients undergoing TAVI at 5-year follow-up.

Use of rivaroxaban attenuates renal function impairment in patients with atrial fibrillation: insights of the EMIR study.

BACKGROUND: In atrial fibrillation (AF) patients on vitamin K antagonists, a progressive deterioration of renal function is common but there is limited evidence with long-term use of rivaroxaban. Herein, we investigated the change in renal function in AF patients after 2 years of rivaroxaban treatment. METHODS: The EMIR registry is an observational and multicentre study including AF patients treated with rivaroxaban for at least 6 months prior to inclusion. Changes in analytical parameters were recorded during 2 years of follow-up. Renal function was estimated using the Cockroft-Gault equation. RESULTS: 1433 patients (638, 44.5% women, mean age of 74.2 ± 9.7 years) were included. Creatinine clearance (CrCl) was available at baseline and at 2 years in 1085 patients. At inclusion, 33.2% of patients had impaired renal function (CrCl <60 ml/min). At 2 years, we were not able to find changes in the proportion of patients with impaired renal function, which increased to 34.6% (p = 0.290). However, the baseline mean CrCl was 76.0 ± 30.5 ml/min and slightly improved at 2 years (77.0 ± 31.8 ml/min; p = 0.014). Overall, the proportion of patients with CrCl <60 ml/min at baseline that had CrCl ≥60 ml/min at 2 years was significantly higher compared to that of patients with CrCl ≥60 ml/min at baseline and CrCl <60 ml/min after (22.2% vs. 13.1%; p < 0.001) CONCLUSIONS: In AF patients on long-term rivaroxaban therapy, a decrease in renal function was not observed. We even observed a slight improvement in the patients with renal impairment. These results reinforce the idea that rivaroxaban may be a safe option even in patients with renal impairment.

Laparoscopic surgery in 3D improves results and surgeon convenience in sleeve gastrectomy for morbid obesity.

PURPOSE: Advanced laparoscopic procedures are still challenging. One critical issue is the lack of stereoscopic vision. The aim of this surgical study is to evaluate whether 3D vision offers any advantages for surgical performance over 2D vision during sleeve gastrectomy for morbid obesity using a laparoscopic system that allows changing between 2D and 3D optics. METHODS: A total of 78 patients were analyzed, with 37 in the 2D group and 41 in the 3D group. Performance time, hospital stay, complications, and early outcomes were collected. To assess the quality of the 2D and 3D techniques, visual analog scales from 0 to 10 were designed, and image quality, depth of field, precision in performing tasks, and general ergonomics were measured. RESULTS: According to the vision system used, the mean duration of surgery was 85 ± 16.8 min for patients operated on with the 2D system and 69 ± 16.9 min for those operated on with the 3D system. There were no significant differences between the overall percentages of complications according to the type of vision used. However, postoperative complications were more severe in the 2D laparoscopy group. The average length of stay was shorter for patients in the 3D group. Regarding the differences perceived by the surgeon, the depth of field and the precision of tasks were better in the 3D vision group. CONCLUSION: The 3D system provided greater depth perception and precision in more complex tasks, enabling safer surgery. This led to a reduction in the operative time and hospital stay. Moreover, the severity of complications was less.

Endometrial area of the blood flow as a marker of endometritis in equine.

In this study, uterine blood flow area (BFA) has been evaluated for the first time using power Doppler ultrasound (PD) as a marker of endometritis in mares and jennies. The uterine BFA in healthy mares was greater in oestrus than in diestrus (p < .001). However, differences in endometrial blood flow between oestrus and diestrus were not observed in mares with endometritis. The uterine blood flow in healthy jennies is not affected by the oestrus cycle. Both species showed an increase in endometrial BFA in pathological uterine conditions compared to controls. BFA was a good marker of endometritis with an area under curve (AUC) (estrus:0.94 (p < .001) diestrus:0.98 (p < .001) in mares and AUC (0.91 (p < .0001) in jennies. The results of this preliminary study suggest that PD ultrasound in combination with computerized image analysis has the potential to be a very useful tool in the diagnosis of endometritis.

Rare Variants in Genes of the Cholesterol Pathway Are Present in 60% of Patients with Acute Myocardial Infarction.

Acute myocardial infarction (AMI) is a pandemic in which conventional risk factors are inadequate to detect who is at risk early in the asymptomatic stage. Although gene variants in genes related to cholesterol, which may increase the risk of AMI, have been identified, no studies have systematically screened the genes involved in this pathway. In this study, we included 105 patients diagnosed with AMI with an elevation of the ST segment (STEMI) and treated with primary percutaneous coronary intervention (PPCI). Using next-generation sequencing, we examined the presence of rare variants in 40 genes proposed to be involved in lipid metabolism and we found that 60% of AMI patients had a rare variant in the genes involved in the cholesterol pathway. Our data show the importance of considering the wide scope of the cholesterol pathway in order to assess the genetic risk related to AMI.

Exercise testing in COVID-19 era: Clinical profile, results and feasibility wearing a facemask.

BACKGROUND: No data are available about whether Coronavirus disease 2019 (COVID-19) pandemic have led to changes in clinical profiles or results of exercise testing once the usual activity was reassumed, as well as if wearing a facemask has any impact on the tests. The aim of this study is to evaluate differences in the patients referred to exercise stress testing in the context of COVID-19 pandemic and analyse the feasibility and results of these tests wearing a facemask. METHODS: We included all patients referred for an exercise test from 1 June to 30 September 2020 and compared them with the patients attended within the same period in 2019 before and after propensity score matching. All patients referred in 2020 wore a facemask. RESULTS: A total of 854 patients were included: 398 in the 2020 group and 456 in 2019. No significant differences in baseline characteristics of the patients were observed, with the exception of dyspnoea, which was nearly twice as high in 2020 as compared with 2019. Regarding the results of the tests, no differences were observed, with almost 80% of maximal tests, similar functional capacity and over a 20% of positive exercise tests in both groups. These results remained after propensity score matching. CONCLUSION: COVID-19 pandemic has not changed the clinical profile of patients referred to exercise testing. In addition, performing exercise testing wearing a facemask is feasible, with no influence in functional capacity and clinical results.

An analysis of tissue-specific alternative splicing at the protein level.

The role of alternative splicing is one of the great unanswered questions in cellular biology. There is strong evidence for alternative splicing at the transcript level, and transcriptomics experiments show that many splice events are tissue specific. It has been suggested that alternative splicing evolved in order to remodel tissue-specific protein-protein networks. Here we investigated the evidence for tissue-specific splicing among splice isoforms detected in a large-scale proteomics analysis. Although the data supporting alternative splicing is limited at the protein level, clear patterns emerged among the small numbers of alternative splice events that we could detect in the proteomics data. More than a third of these splice events were tissue-specific and most were ancient: over 95% of splice events that were tissue-specific in both proteomics and RNAseq analyses evolved prior to the ancestors of lobe-finned fish, at least 400 million years ago. By way of contrast, three in four alternative exons in the human gene set arose in the primate lineage, so our results cannot be extrapolated to the whole genome. Tissue-specific alternative protein forms in the proteomics analysis were particularly abundant in nervous and muscle tissues and their genes had roles related to the cytoskeleton and either the structure of muscle fibres or cell-cell connections. Our results suggest that this conserved tissue-specific alternative splicing may have played a role in the development of the vertebrate brain and heart.

Malignant prediction in paragangliomas: analysis for clinical risk factors.

INTRODUCTION: Paragangliomas are infrequent neuroendocrine tumours whose only criterion for malignancy is presence of metastases; thus, all paragangliomas show malignant potential. Actually, different risk factors have been analyzed to predict metastases but they remain unclear. PURPOSE: To analyze clinical, histological, and genetic factors to predict the occurrence of metastasis. PATIENTS AND METHOD: A multicentre retrospective observational analysis was performed between January 1990 and July 2019. Patients diagnosed with paraganglioma were selected. Clinical, histological, and genetic features were analyzed for the prediction of malignancy. RESULTS: A total of 83 patients diagnosed with paraganglioma were included, of which nine (10.8%) had malignant paraganglioma. Tumour size was greater in malignant tumours than in benign (6 cm vs. 4 cm, respectively; p = 0.027). The most frequent location of malignancy was the thorax-abdomen-pelvis area observed in six cases (p = 0.024). No differences were observed in histological differentiation, age, symptoms, and catecholaminergic production. The most frequent genetic mutation was SDHD followed by SDHB but no differences were observed between benign and malignant tumours. In the univariate analysis for predictive factors for malignancy, location, tumour size, and histological differentiation showed statistical significance (p = 0.025, p = 0.014, and p = 0.046, respectively); however, they were not confirmed as predictive factors for malignancy in the multivariate analysis. CONCLUSION: In this study, no risk factors for malignancy have been established; therefore, we recommend follow-up of all patients diagnosed with paraganglioma.

SanXoT: a modular and versatile package for the quantitative analysis of high-throughput proteomics experiments.

SUMMARY: Mass spectrometry-based proteomics has had a formidable development in recent years, increasing the amount of data handled and the complexity of the statistical resources needed. Here we present SanXoT, an open-source, standalone software package for the statistical analysis of high-throughput, quantitative proteomics experiments. SanXoT is based on our previously developed weighted spectrum, peptide and protein statistical model and has been specifically designed to be modular, scalable and user-configurable. SanXoT allows limitless workflows that adapt to most experimental setups, including quantitative protein analysis in multiple experiments, systems biology, quantification of post-translational modifications and comparison and merging of experimental data from technical or biological replicates. AVAILABILITY AND IMPLEMENTATION: Download links for the SanXoT Software Package, source code and documentation are available at https://wikis.cnic.es/proteomica/index.php/SSP. CONTACT: jvazquez@cnic.es or ebonzon@cnic.es. SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.

The SLC7A11: sperm mitochondrial function and non-canonical glutamate metabolism.

Spermatozoa are redox-regulated cells, and stallion spermatozoa, in particular, present an intense mitochondrial activity in which large amounts of reactive oxygen species (ROS) are produced. To maintain the redox potential under physiological conditions, sophisticated mechanisms ought to be present, particularly in the mitochondria. In the present study, we investigated the role of the SLC7A11 antiporter. This antiporter exchanges intracellular glutamate for extracellular cystine. In the spermatozoa, cystine is reduced to cysteine and used for GSH synthesis. The importance of the antiporter for mitochondrial functionality was studied using flow cytometry and UHPLC/MS/MS approaches. Intracellular GSH increased in the presence of cystine, but was reduced in the presence of Buthionine sulphoximine (BSO), a γ-glutamylcysteine synthetase inhibitor (P < 0.001). Inhibition of the SLC7A11 antiporter with sulfasalazine caused a dramatic drop in intracellular GSH (P < 0.001) and in the percentage of spermatozoa showing active mitochondria (P < 0.001). These findings suggest that proper functionality of this antiporter is required for the mitochondrial function of spermatozoa. We also describe that under some conditions, glutamate may be metabolized following non-conventional pathways, also contributing to sperm functionality. We provide evidences, that the stallion spermatozoa have important metabolic plasticity, and also of the relation between redox regulation and metabolic regulation. These findings may have important implications for the understanding of sperm biology and the development of new strategies for sperm conservation and treatment of male factor infertility.

APPRIS 2017: principal isoforms for multiple gene sets.

The APPRIS database (http://appris-tools.org) uses protein structural and functional features and information from cross-species conservation to annotate splice isoforms in protein-coding genes. APPRIS selects a single protein isoform, the 'principal' isoform, as the reference for each gene based on these annotations. A single main splice isoform reflects the biological reality for most protein coding genes and APPRIS principal isoforms are the best predictors of these main proteins isoforms. Here, we present the updates to the database, new developments that include the addition of three new species (chimpanzee, Drosophila melangaster and Caenorhabditis elegans), the expansion of APPRIS to cover the RefSeq gene set and the UniProtKB proteome for six species and refinements in the core methods that make up the annotation pipeline. In addition APPRIS now provides a measure of reliability for individual principal isoforms and updates with each release of the GENCODE/Ensembl and RefSeq reference sets. The individual GENCODE/Ensembl, RefSeq and UniProtKB reference gene sets for six organisms have been merged to produce common sets of splice variants.

Loose ends: almost one in five human genes still have unresolved coding status.

Seventeen years after the sequencing of the human genome, the human proteome is still under revision. One in eight of the 22 210 coding genes listed by the Ensembl/GENCODE, RefSeq and UniProtKB reference databases are annotated differently across the three sets. We have carried out an in-depth investigation on the 2764 genes classified as coding by one or more sets of manual curators and not coding by others. Data from large-scale genetic variation analyses suggests that most are not under protein-like purifying selection and so are unlikely to code for functional proteins. A further 1470 genes annotated as coding in all three reference sets have characteristics that are typical of non-coding genes or pseudogenes. These potential non-coding genes also appear to be undergoing neutral evolution and have considerably less supporting transcript and protein evidence than other coding genes. We believe that the three reference databases currently overestimate the number of human coding genes by at least 2000, complicating and adding noise to large-scale biomedical experiments. Determining which potential non-coding genes do not code for proteins is a difficult but vitally important task since the human reference proteome is a fundamental pillar of most basic research and supports almost all large-scale biomedical projects.