Pbp1 associates with Puf3 and promotes translation of its target mRNAs involved in mitochondrial biogenesis.

Pbp1 (poly(A)-binding protein-binding protein 1) is a cytoplasmic stress granule marker that is capable of forming condensates that function in the negative regulation of TORC1 signaling under respiratory conditions. Polyglutamine expansions in its mammalian ortholog ataxin-2 lead to spinocerebellar dysfunction due to toxic protein aggregation. Here, we show that loss of Pbp1 in S. cerevisiae leads to decreased amounts of mRNAs and mitochondrial proteins which are targets of Puf3, a member of the PUF (Pumilio and FBF) family of RNA-binding proteins. We found that Pbp1 supports the translation of Puf3-target mRNAs in respiratory conditions, such as those involved in the assembly of cytochrome c oxidase and subunits of mitochondrial ribosomes. We further show that Pbp1 and Puf3 interact through their respective low complexity domains, which is required for Puf3-target mRNA translation. Our findings reveal a key role for Pbp1-containing assemblies in enabling the translation of mRNAs critical for mitochondrial biogenesis and respiration. They may further explain prior associations of Pbp1/ataxin-2 with RNA, stress granule biology, mitochondrial function, and neuronal health.

Comparative Study of Ergonomics in Conventional and Robotic-Assisted Laparoscopic Surgery.

BACKGROUND: This study aims to implement a set of wearable technologies to record and analyze the surgeon's physiological and ergonomic parameters during the performance of conventional and robotic-assisted laparoscopic surgery, comparing the ergonomics and stress levels of surgeons during surgical procedures. METHODS: This study was organized in two different settings: simulator tasks and experimental model surgical procedures. The participating surgeons performed the tasks and surgical procedures in both laparoscopic and robotic-assisted surgery in a randomized fashion. Different wearable technologies were used to record the surgeons' posture, muscle activity, electrodermal activity and electrocardiography signal during the surgical practice. RESULTS: The simulator study involved six surgeons: three experienced (>100 laparoscopic procedures performed; 36.33 ± 13.65 years old) and three novices (<100 laparoscopic procedures; 29.33 ± 8.39 years old). Three surgeons of different surgical specialties with experience in laparoscopic surgery (>100 laparoscopic procedures performed; 37.00 ± 5.29 years old), but without experience in surgical robotics, participated in the experimental model study. The participating surgeons showed an increased level of stress during the robotic-assisted surgical procedures. Overall, improved surgeon posture was obtained during robotic-assisted surgery, with a reduction in localized muscle fatigue. CONCLUSIONS: A set of wearable technologies was implemented to measure and analyze surgeon physiological and ergonomic parameters. Robotic-assisted procedures showed better ergonomic outcomes for the surgeon compared to conventional laparoscopic surgery. Ergonomic analysis allows us to optimize surgeon performance and improve surgical training.

An MXD1-derived repressor peptide identifies noncoding mediators of MYC-driven cell proliferation.

MYC controls the transcription of large numbers of long noncoding RNAs (lncRNAs). Since MYC is a ubiquitous oncoprotein, some of these lncRNAs probably play a significant role in cancer. We applied CRISPR interference (CRISPRi) to the identification of MYC-regulated lncRNAs that are required for MYC-driven cell proliferation in the P493-6 and RAMOS human lymphoid cell lines. We identified 320 noncoding loci that play positive roles in cell growth. Transcriptional repression of any one of these lncRNAs reduces the proliferative capacity of the cells. Selected hits were validated by RT-qPCR and in CRISPRi competition assays with individual GFP-expressing sgRNA constructs. We also showed binding of MYC to the promoter of two candidate genes by chromatin immunoprecipitation. In the course of our studies, we discovered that the repressor domain SID (SIN3-interacting domain) derived from the MXD1 protein is highly effective in P493-6 and RAMOS cells in terms of the number of guides depleted in library screening and the extent of the induced transcriptional repression. In the cell lines used, SID is superior to the KRAB repressor domain, which serves routinely as a transcriptional repressor domain in CRISPRi. The SID transcriptional repressor domain is effective as a fusion to the MS2 aptamer binding protein MCP, allowing the construction of a doxycycline-regulatable CRISPRi system that allows controlled repression of targeted genes and will facilitate the functional analysis of growth-promoting lncRNAs.

Autonomous Underwater Vehicles: Identifying Critical Issues and Future Perspectives in Image Acquisition.

Underwater imaging has been present for many decades due to its relevance in vision and navigation systems. In recent years, advances in robotics have led to the availability of autonomous or unmanned underwater vehicles (AUVs, UUVs). Despite the rapid development of new studies and promising algorithms in this field, there is currently a lack of research toward standardized, general-approach proposals. This issue has been stated in the literature as a limiting factor to be addressed in the future. The key starting point of this work is to identify a synergistic effect between professional photography and scientific fields by analyzing image acquisition issues. Subsequently, we discuss underwater image enhancement and quality assessment, image mosaicking and algorithmic concerns as the last processing step. In this line, statistics about 120 AUV articles fro recent decades have been analyzed, with a special focus on state-of-the-art papers from recent years. Therefore, the aim of this paper is to identify critical issues in autonomous underwater vehicles encompassing the entire process, starting from optical issues in image sensing and ending with some issues related to algorithmic processing. In addition, a global underwater workflow is proposed, extracting future requirements, outcome effects and new perspectives in this context.

Near-infrared spectroscopy-based analysis to study sensory parameters on pork loins as affected by cooking methods and conditions.

BACKGROUND: The main objectives of this study were to evaluate the use of near infrared spectroscopy (NIRS) to classify pork loins under different methods and cooking conditions, and to predict sensory attributes of this product. RESULTS: Samples were oven cooked at two temperatures (150 and 180 °C) for different times (45, 60 and 75 min) and confit cooked for different times (120, 180 and 240 min). All cooked loin samples were subjected to a Quantitative Descriptive Analysis by a trained panel. For classification, principal component analysis was performed based on the NIRS database, showing a good discrimination between loins samples subjected to different cooking conditions. Regarding prediction, a data mining technique (multiple linear regression) was applied on a database constructed with data from NIRS and sensory analysis. CONCLUSION: The correlation coefficient and the mean absolute error obtained suggest that the calculated prediction equations of this study are valid to predict the changes in the sensory attributes depending on the cooking method and conditions used for pork loins. © 2018 Society of Chemical Industry.

Impaired urinary osteopontin excretion in Npt2a-/- mice.

Mutations in the renal sodium-dependent phosphate cotransporters NPT2a and NPT2c have been reported in patients with renal stone disease and nephrocalcinosis. Oral phosphate supplementation is currently thought to reduce risk by reversing the hypercalciuria, but the exact mechanism remains unclear and the relative contribution of modifiers of mineralization such as osteopontin (Opn) to the formation of renal mineral deposits in renal phosphate wasting disorders has not been studied. We observed a marked decrease of renal gene expression and urinary excretion of Opn in Npt2a-/- mice, a mouse model of these disorders, at baseline. Following supplementation with phosphate Opn gene expression was restored to wild-type levels in Npt2a-/- mice; however, urine excretion of the protein remained low. To further investigate the role of Opn, we used a double-knockout strategy, which provides evidence that loss of Opn worsens the nephrocalcinosis and nephrolithiasis observed in these mice on a high-phosphate diet. These studies suggest that impaired Opn gene expression and urinary excretion in Npt2a-/- mice may be an additional risk factor for nephrolithiasis, and normalizing urine Opn levels may improve the therapy of phosphaturic disorders.

Hypophosphatemia promotes lower rates of muscle ATP synthesis.

Hypophosphatemia can lead to muscle weakness and respiratory and heart failure, but the mechanism is unknown. To address this question, we noninvasively assessed rates of muscle ATP synthesis in hypophosphatemic mice by using in vivo saturation transfer [31P]-magnetic resonance spectroscopy. By using this approach, we found that basal and insulin-stimulated rates of muscle ATP synthetic flux (VATP) and plasma inorganic phosphate (Pi) were reduced by 50% in mice with diet-induced hypophosphatemia as well as in sodium-dependent Pi transporter solute carrier family 34, member 1 (NaPi2a)-knockout (NaPi2a-/-) mice compared with their wild-type littermate controls. Rates of VATP normalized in both hypophosphatemic groups after restoring plasma Pi concentrations. Furthermore, VATP was directly related to cellular and mitochondrial Pi uptake in L6 and RC13 rodent myocytes and isolated muscle mitochondria. Similar findings were observed in a patient with chronic hypophosphatemia as a result of a mutation in SLC34A3 who had a 50% reduction in both serum Pi content and muscle VATP After oral Pi repletion and normalization of serum Pi levels, muscle VATP completely normalized in the patient. Taken together, these data support the hypothesis that decreased muscle ATP synthesis, in part, may be caused by low blood Pi concentrations, which may explain some aspects of muscle weakness observed in patients with hypophosphatemia.-Pesta, D. H., Tsirigotis, D. N., Befroy, D. E., Caballero, D., Jurczak, M. J., Rahimi, Y., Cline, G. W., Dufour, S., Birkenfeld, A. L., Rothman, D. L., Carpenter, T. O., Insogna, K., Petersen, K. F., Bergwitz, C., Shulman, G. I. Hypophosphatemia promotes lower rates of muscle ATP synthesis.

Non-destructive analysis of sensory traits of dry-cured loins by MRI-computer vision techniques and data mining.

BACKGROUND: Magnetic resonance imaging (MRI) combined with computer vision techniques have been proposed as an alternative or complementary technique to determine the quality parameters of food in a non-destructive way. The aim of this work was to analyze the sensory attributes of dry-cured loins using this technique. For that, different MRI acquisition sequences (spin echo, gradient echo and turbo 3D), algorithms for MRI analysis (GLCM, NGLDM, GLRLM and GLCM-NGLDM-GLRLM) and predictive data mining techniques (multiple linear regression and isotonic regression) were tested. RESULTS: The correlation coefficient (R) and mean absolute error (MAE) were used to validate the prediction results. The combination of spin echo, GLCM and isotonic regression produced the most accurate results. In addition, the MRI data from dry-cured loins seems to be more suitable than the data from fresh loins. CONCLUSIONS: The application of predictive data mining techniques on computational texture features from the MRI data of loins enables the determination of the sensory traits of dry-cured loins in a non-destructive way. © 2016 Society of Chemical Industry.

Heuristic evaluation on mobile interfaces: a new checklist.

The rapid evolution and adoption of mobile devices raise new usability challenges, given their limitations (in screen size, battery life, etc.) as well as the specific requirements of this new interaction. Traditional evaluation techniques need to be adapted in order for these requirements to be met. Heuristic evaluation (HE), an Inspection Method based on evaluation conducted by experts over a real system or prototype, is based on checklists which are desktop-centred and do not adequately detect mobile-specific usability issues. In this paper, we propose a compilation of heuristic evaluation checklists taken from the existing bibliography but readapted to new mobile interfaces. Selecting and rearranging these heuristic guidelines offer a tool which works well not just for evaluation but also as a best-practices checklist. The result is a comprehensive checklist which is experimentally evaluated as a design tool. This experimental evaluation involved two software engineers without any specific knowledge about usability, a group of ten users who compared the usability of a first prototype designed without our heuristics, and a second one after applying the proposed checklist. The results of this experiment show the usefulness of the proposed checklist for avoiding usability gaps even with nontrained developers.

Applying artificial intelligence on EDA sensor data to predict stress on minimally invasive robotic-assisted surgery.

PURPOSE: This study aims predicting the stress level based on the ergonomic (kinematic) and physiological (electrodermal activity-EDA, blood pressure and body temperature) parameters of the surgeon from their records collected in the previously immediate situation of a minimally invasive robotic surgery activity. METHODS: For this purpose, data related to the surgeon's ergonomic and physiological parameters were collected during twenty-six robotic-assisted surgical sessions completed by eleven surgeons with different experience levels. Once the dataset was generated, two preprocessing techniques were applied (scaled and normalized), these two datasets were divided into two subsets: with 80% of data for training and cross-validation, and 20% of data for test. Three predictive techniques (multiple linear regression-MLR, support vector machine-SVM and multilayer perceptron-MLP) were applied on training dataset to generate predictive models. Finally, these models were validated on cross-validation and test datasets. After each session, surgeons were asked to complete a survey of their feeling of stress. These data were compared with those obtained using predictive models. RESULTS: The results showed that MLR combined with the scaled preprocessing achieved the highest R2 coefficient and the lowest error for each parameter analyzed. Additionally, the results for the surgeons' surveys were highly correlated to the results obtained by the predictive models (R2 = 0.8253). CONCLUSIONS: The linear models proposed in this study were successfully validated on cross-validation and test datasets. This fact demonstrates the possibility of predicting factors that help us to improve the surgeon's health during robotic surgery.

Intraoperative angiography with indocyanine green, an aid in the diagnosis and treatment of obscure digestive tract bleeding, a case report.

Lower digestive tract bleeding occurs distal to the angle of Treitz. While many cases remit spontaneously; some pose a diagnostic challenge for surgeons. We present the case of a 68-year-old man with unexplained digestive tract bleeding. Despite various diagnostic efforts, the source remained unknown. Faced with the challenge of persistent bleeding and hemodynamic instability, surgery became necessary. During the procedure, intraoperative angiography with indocyanine green was used to facilitate the identification of the bleeding site, revealing a gastrointestinal stromal tumor in the small bowel. Resection was performed with favorable outcomes. Indocyanine green staining has become popular for locating intestinal bleeding during emergency surgeries, aiding surgeons in making precise decisions.

Some key parameters in contextual fear conditioning and extinction in adult rats.

Contextual fear conditioning is a behavioral paradigm used to assess hippocampal-dependent memory in experimental animals. Perception of the context depends on activation of a distinct population of neurons in the hippocampus and in hippocampal-related areas that process discrete aspects of context perception. In the absence of any putatively associated cue, the context becomes the salient element that may warn of an upcoming aversive event; and in particular conditions, animals generalize this warning to any new or similar context. In this study we evaluated the effects of the number of sessions, the number of unconditioned stimuli per acquisition session and the distribution of extinction sessions to assess fear acquisition and extinction and determine under which conditions generalization occurred in adult, male rats. We observed that the organization and spacing of sessions were relevant factors in the acquisition and extinction of contextual fear memories. Extinction occurred with significantly greater robustness when sessions were spread over two days. Furthermore, results indicated that exposure to a single 0.3 mA, 0.5 s footshock in two different sessions could produce context-specific fear, while more acquisition sessions or more footshocks within a single session produced a generalization of the fear response to a new context. Notably, when generalization occurred, successive re-exposure to the generalized context produced extinction in a similar way to the paired exposure. Together, the present findings identify clear procedural and behavioral parameters amenable to neural systems analysis of three clinically relevant outcomes of contextual fear conditioning, i.e., memory acquisition, storage and extinction.

Modulation of contextual fear acquisition and extinction by acute and chronic relaxin-3 receptor (RXFP3) activation in the rat retrosplenial cortex.

The retrosplenial cortex (RSC) plays a central role in processing contextual fear conditioning. In addition to corticocortical and thalamocortical projections, the RSC receives subcortical inputs, including a substantial projection from the nucleus incertus in the pontine tegmentum. This GABAergic projection contains the neuropeptide, relaxin-3 (RLN3), which inhibits target neurons via its Gi/o-protein-coupled receptor, RXFP3. To assess this peptidergic system role in contextual fear conditioning, we bilaterally injected the RSC of adult rats with an adeno-associated-virus (AAV), expressing the chimeric RXFP3 agonist R3/I5 or a control AAV, and subjected them to contextual fear conditioning. The R3/I5 injected rats did not display any major differences to control-injected and naïve rats but displayed a significantly delayed extinction. Subsequently, we employed acute bilateral injections of the specific RXFP3 agonist peptide, RXFP3-Analogue 2 (A2), into RSC. While the administration of A2 before each extinction trial had no impact on the extinction process, treatment with A2 before each acquisition trial resulted in delayed extinction. In related anatomical studies, we detected an enrichment of RLN3-immunoreactive nerve fibers in deep layers of the RSC, and a higher level of co-localization of RXFP3 mRNA with vesicular GABA transporter (vGAT) mRNA than with vesicular glutamate transporter-1 (vGLUT1) mRNA across the RSC, consistent with an effect of RLN3/RXFP3 signalling on the intrinsic, inhibitory circuits within the RSC. These findings suggest that contextual conditioning processes in the RSC involve, in part, RLN3 afferent modulation of local inhibitory neurons that provides a stronger memory acquisition which, in turn, retards the extinction process.

Long Non-Coding RNAs as "MYC Facilitators".

In this article, we discuss a class of MYC-interacting lncRNAs (long non-coding RNAs) that share the following criteria: They are direct transcriptional targets of MYC. Their expression is coordinated with the expression of MYC. They are required for sustained MYC-driven cell proliferation, and they are not essential for cell survival. We refer to these lncRNAs as "MYC facilitators" and discuss two representative members of this class of lncRNAs, SNHG17 (small nuclear RNA host gene) and LNROP (long non-coding regulator of POU2F2). We also present a general hypothesis on the role of lncRNAs in MYC-mediated transcriptional regulation.

The MYC-regulated lncRNA LNROP (ENSG00000254887) enables MYC-driven cell proliferation by controlling the expression of OCT2.

MYC controls most of the non-coding genome. Several long noncoding transcripts were originally identified in the human B cell line P496-3 and then shown to be required for MYC-driven proliferation of Burkitt lymphoma-derived RAMOS cells. In this study, we used RAMOS cells exclusively as a representative of the human B cell lineage. One of the MYC-controlled lncRNAs required for RAMOS cell proliferation is ENSG00000254887 which we will term LNROP (long non-coding regulator of POU2F2). In the genome, LNROP is located in close proximity of POU2F2, the gene encoding OCT2. OCT2 is a transcription factor with important roles in sustaining the proliferation of human B cells. Here we show that LNROP is a nuclear RNA and a direct target of MYC. Downregulation of LNROP attenuates the expression of OCT2. This effect of LNROP on the expression of OCT2 is unidirectional as downregulation of OCT2 does not alter the expression of LNROP. Our data suggest that LNROP is a cis-acting regulator of OCT2. To illustrate the downstream reach of LNROP, we chose a prominent target of OCT2, the tyrosine phosphatase SHP-1. Downregulation of OCT2 elevates the expression of SHP-1. Our data suggest the following path of interactions: LNROP enables the proliferation of B cells by positively and unidirectionally regulating the growth-stimulatory transcription factor OCT2. In actively proliferating B cells, OCT2 attenuates the expression and anti-proliferative activity of SHP-1.

1H NMR to analyse the lipid profile in the glyceride fraction of different categories of Iberian dry-cured hams.

The extraordinary organoleptic qualities of Iberian ham derive from the singular producing pig breed and from the traditional rearing conditions, both of which define its lipid content and composition. In this work 1H NMR spectroscopy is used for the first time to analyse the lipid profile of Iberian hams as determinant of quality. Quantification of fatty acids is readily obtained from the spectra, with the monounsaturated fatty acids standing out, especially in the higher quality hams. Unprecedently, triacylglyceride hydrolysis products formed during the curing process can also be directly detected and quantified. Furthermore, chemometric analysis of the NMR data allows to classify Iberian hams according to the pig's crossbreed and feeding regime. Principal component analysis shows fatty acid unsaturation and triacylglyceride hydrolysis as discriminating variables. 1H NMR spectroscopy has thus revealed as a convenient and powerful tool for the lipid analysis and classification of Iberian hams and for detection of fraud.

Increased glycine contributes to synaptic dysfunction and early mortality in Nprl2 seizure model.

Targeted therapies for epilepsies associated with the mTORC1 signaling negative regulator GATOR1 are lacking. NPRL2 is a subunit of the GATOR1 complex and mutations in GATOR1 subunits, including NPRL2, are associated with epilepsy. To delineate the mechanisms underlying NPRL2-related epilepsies, we created a mouse (Mus musculus) model with neocortical loss of Nprl2. Mutant mice have increased mTORC1 signaling and exhibit spontaneous seizures. They also display abnormal synaptic function characterized by increased evoked and spontaneous EPSC and decreased evoked and spontaneous IPSC frequencies, respectively. Proteomic and metabolomics studies of Nprl2 mutants revealed alterations in known epilepsy-implicated proteins and metabolic pathways, including increases in the neurotransmitter, glycine. Furthermore, glycine actions on the NMDA receptor contribute to the electrophysiological and survival phenotypes of these mice. Taken together, in this neuronal Nprl2 model, we delineate underlying molecular, metabolic, and electrophysiological mechanisms contributing to mTORC1-related epilepsy, providing potential therapeutic targets for epilepsy.

Inosine triphosphate pyrophosphatase from Trypanosoma brucei cleanses cytosolic pools from deaminated nucleotides.

Inosine triphosphate pyrophosphatases (ITPases) are ubiquitous house-cleaning enzymes that specifically recognize deaminated purine nucleotides and catalyze their hydrolytic cleavage. In this work, we have characterized the Trypanosoma brucei ITPase ortholog (TbITPA). Recombinant TbITPA efficiently hydrolyzes (deoxy)ITP and XTP nucleotides into their respective monophosphate form. Immunolocalization analysis performed in bloodstream forms suggests that the primary role of TbITPA is the exclusion of deaminated purines from the cytosolic nucleoside triphosphate pools. Even though ITPA-knockout bloodstream parasites are viable, they are more sensitive to inhibition of IMP dehydrogenase with mycophenolic acid, likely due to an expansion of IMP, the ITP precursor. On the other hand, TbITPA can also hydrolyze the activated form of the antiviral ribavirin although in this case, the absence of ITPase activity in the cell confers protection against this nucleoside analog. This unexpected phenotype is dependant on purine availability and can be explained by the fact that ribavirin monophosphate, the reaction product generated by TbITPA, is a potent inhibitor of trypanosomal IMP dehydrogenase and GMP reductase. In summary, the present study constitutes the first report on a protozoan inosine triphosphate pyrophosphatase involved in the removal of harmful deaminated nucleotides from the cytosolic pool.

Optimization of the image acquisition procedure in low-field MRI for non-destructive analysis of loin using predictive models.

The use of low-field magnetic resonance imaging (LF-MRI) scanners has increased in recent years. The low economic cost in comparison to high-field (HF-MRI) scanners and the ease of maintenance make this type of scanner the best choice for nonmedical purposes. However, LF-MRI scanners produce low-quality images, which encourages the identification of optimization procedures to generate the best possible images. In this paper, optimization of the image acquisition procedure for an LF-MRI scanner is presented, and predictive models are developed. The MRI acquisition procedure was optimized to determine the physicochemical characteristics of pork loin in a nondestructive way using MRI, feature extraction algorithms and data processing methods. The most critical parameters (relaxation times, repetition time, and echo time) of the LF-MRI scanner were optimized, presenting a procedure that could be easily reproduced in other environments or for other purposes. In addition, two feature extraction algorithms (gray level co-occurrence matrix (GLCM) and one point fractal texture algorithm (OPFTA)) were evaluated. The optimization procedure was validated by using several evaluation metrics, achieving reliable and accurate results (r > 0.85; weighted absolute percentage error (WAPE) lower than 0.1%; root mean square error of prediction (RMSEP) lower than 0.1%; true standard deviation (TSTD) lower than 2; and mean absolute error (MAE) lower than 2). These results support the high degree of feasibility and accuracy of the optimized procedure of LF-MRI acquisition. No other papers present a procedure to optimize the image acquisition process in LF-MRI. Eventually, the optimization procedure could be applied to other LF-MRI systems.

Evaluation of fresh meat quality by Hyperspectral Imaging (HSI), Nuclear Magnetic Resonance (NMR) and Magnetic Resonance Imaging (MRI): A review.

The development of non-destructive methodologies based on Hyperspectral Imaging (HSI), Nuclear Magnetic Resonance (NMR) and Magnetic Resonance Imaging (MRI) techniques to determine quality characteristics of fresh meat has been reviewed in this study. It has been focused primarily on research published in the last decade, and has placed particular attention on the instrumentation, data acquisition and main applications of each technique, finding a wide variety of possibilities for systems and methodologies as well as evidence of accurate and promising results. Most samples analysed were pork and beef, followed by lamb and chicken, with few studies on fresh meat from rabbit and duck. The overall evaluation is that work has been performed primarily in an experimental way but generally still lacks real application in the meat industry. In that respect, these non-destructive techniques should be improved, especially regarding speed, price and influence of external factors.