Biology subjects

Silva, J.

Publications and source records attributed to Silva, J..

43 records · Page 3Linked to original sources

bioRxiv2020

Optimizing athlete assessment of maximal force and rate of development A comparison of the isometric squat and mid-thigh pull

This study compared force-time characteristics and muscle activity between the isometric squat (ISQ) and mid-thigh pull (IMTP) in both bilateral (ISQBI and IMTPBI) and unilateral (ISQUNI and IMTPUNI) stance. Peak force (PF), rate-of-force (RFD) (e.g. 0-300ms) and EMG of the multifidus, erector spinae (ES), gluteus maximus (GM), biceps femoris (BF), semitendinosus (ST), vastus medialis (VM), vastus lateralis (VL) and soleus were recorded in ten recreationally trained males. PF was significantly greater during the ISQBI vs. IMTPBI (p=0.016, ES=1.08) but not in the unilateral test mode although effects remained moderate (ES=0.62). A trend indicated heightened RFD300ms (p = 0.083; ES=0.81) during the IMTPBI vs. the ISQBI, but these effects were smaller in the unilateral test (ES = 0.51). Greater (p<0.0001) EMG for VL (ES=1.00-1.13) and VM were recorded during the ISQ compared to IMTP modes in both modes (ES = 0.97 - 1.18). Greater BF EMG (p = 0.030, ES = 0.31) was shown in IMTPBI vs. ISQBI and these effects were stronger in the unilateral modes (p = < 0.05; ES = 0.81 - 0.83). Significantly greater ST activation was shown in both IMTPUNI (p < 0.05; ES = 0.69-0.76) and IMTPBI (p < 0.001; ES = 1.08). These findings indicate that ISQ results in elevated PF, whereas, RFD is heightened during the IMTP and these differences are more pronounced in bilateral modes. Greater activation of the quadriceps and hamstring muscles are expected in ISQ and IMPT respectively.

physiology↗

bioRxiv2020

Ribo-ODDR: Ribo-seq focused Oligo Design pipeline for experiment-specific Depletion of Ribosomal RNAs

Ribosome profiling (Ribo-seq) has revolutionized the study of RNA translation by providing information on ribosome positions across all translated RNAs with nucleotide-resolution. Yet, several technical limitations restrict the sequencing depth of such experiments, the most common of which is the overabundance of ribosomal RNA (rRNA) fragments, which frequently make up more than 90% of sequencing reads if not depleted. Various strategies can be employed to tackle this issue, including the use of commercial rRNA depletion kits. However, as they are designed for more standardized RNAseq experiments, such kits may perform suboptimally in Ribo-seq. There is therefore potential to significantly increase the information that can be gleaned from Ribo-seq experiments. Here we show that a major confounding issue is that the rRNA fragments generated via Ribo-seq vary significantly with differing experimental conditions, suggesting that a "one-size-fits-all" approach may result in inefficient rRNA depletion. In order to overcome this, it is possible to use custom-designed biotinylated oligos complementary to the most abundant rRNA fragments, however currently no computational framework exists to aid the design of optimal oligos. We have developed Ribo-ODDR, an oligo design pipeline integrated with a user-friendly interface that assists in oligo selection for efficient experiment-specific rRNA depletion. Ribo-ODDR uses preliminary data to identify the most abundant rRNA fragments, and calculates the rRNA depletion efficiency of potential oligos. We show that Ribo-ODDR designed oligos lead to a significant increase in rRNA depletion, and increased sequencing depth as a result, providing substantial information that would otherwise have been lost. Ribo-ODDR is freely accessible at https://github.com/fallerlab/Ribo-ODDR

bioinformatics↗

bioRxiv2019

Glucocorticoids regulate cancer cell dormancy

The glucocorticoid receptor directly regulates thousands of genes across the human genome in a cell-type specific manner, governing various aspects of homeostasis. The influence of the glucocorticoid receptor is also seen in various pathologies, including cancer, where it has been linked to tumorigenesis, metastasis, apoptosis resistance, and therapy bypass. Nonetheless, the direct genetic and molecular underpinnings of glucocorticoid action in cancer remain elusive. Here, we dissected the glucocorticoid receptor signalling axis and uncovered the mechanism of glucocorticoid-mediated cancer cell dormancy. Upon glucocorticoid receptor activation cancer cells undergo quiescence, subserved by cell cycle arrest through CDKN1C and reprogramming of signalling orchestrated via FOXO1/IRS2. Strikingly, co-expression of these three genes, directly regulated by glucocorticoid-induced chromatin looping, correlates with a benign molecular phenotype across human cancers, whereas triple loss is associated with increased expression of proliferation/aggressiveness markers. Finally, we show that the glucocorticoid receptor signalling axis is inactivated by alterations of either the chromatin remodelling complex or TP53 in vitro and in vivo. Our results indicate that the activation of the glucocorticoid receptor leads to cancer cell dormancy, which has several implications in terms of glucocorticoid use in cancer therapy.

cancer biology↗

bioRxiv2019

Regulation of neuronal mRNA splicing and Tau isoform ratio by ATXN3 through deubiquitylation of splicing factors

The ubiquitylation/deubiquitylation balance in cells is maintained by deubiquitylating enzymes, including ATXN3. The precise role of this protein, mutated in spinocerebellar ataxia type 3 (SCA3), remains elusive, as few substrates for its deubiquitylating activity were identified. Here, we characterized the ubiquitome of neuronal cells lacking ATXN3, and found altered polyubiquitylation in a large proportion of proteins involved in RNA metabolism, including splicing factors. Using transcriptomic analysis and reporter minigenes we confirmed that splicing was globally altered in these cells. Among the candidate targets of ATXN3 was SRSF7 (9G8), a key regulator of MAPT (Tau) exon 10 splicing. Loss-of-function of ATXN3 led to reduced SRSF7 levels and a deregulation of MAPT exon 10 splicing, resulting in a decreased 4R/3R-Tau ratio. Similar alterations were found in cellular models of expanded polyQ ATXN3 and SCA3 patient brains, pointing to a relevant role of this mechanism in SCA3, and establishing a previously unsuspected link between two key proteins involved in different neurodegenerative disorders.

neuroscience↗

bioRxiv2018

MORPhA Scale: behavioral and electroencephalographic validation of a rodent anesthesia scale

Degree of anesthesia in laboratory rodents is normally evaluated by testing loss of reflexes. While these are useful endpoint assessments, they are of limited application to study induction/reversal kinetics or factors affecting individual susceptibility (e.g. sex or age). We developed and validated a grading system for a temporal follow up of anesthesia. The Minho Objective Rodent Phenotypical Anesthesia (MORPhA) scale was tested in mice and rats anaesthetized with a mixture of ketamine/dexmedetomidine (ket/dex - 3 doses). The scale comprises 12 behavioral readouts organized in 5 stages - (i) normal/(ii) hindered voluntary movement, elicited response to (iii) non-noxious/(iv) noxious stimuli and (v) absence of response - evaluated at regular time points. Progression across stages was monitored by electroencephalography (EEG) in rats during anesthesia induction and reversal (atipamezole) and during induction with a second anesthetic drug (pentobarbital). Higher anesthetic doses decreased the time to reach higher levels of anesthesia during progression, while increasing the time to regain waking behavior during reversal, in mice and in rats. A regular decrease in high frequencies (low and high gamma) power was observed as the MORPhA score increased during anesthesia induction, while the opposite pattern was observed during emergence from anesthesia through reversion of dex effect. The devised anesthetic scale is of simple application and provides a semi-quantifiable readout of anesthesia induction/reversal.

neuroscience↗

bioRxiv2018

Endo-lysosomal sorting and degradation of Tau mediates glucocorticoid-driven hippocampalmalfunction

Emerging studies implicate Tau as an essential mediator of neuronal atrophy and cognitive impairment in Alzheimers disease (AD), yet the factors that precipitate Tau dysfunction in AD are poorly understood. Chronic environmental stress and elevated glucocorticoids (GC), the major stress hormones, are associated with increased risk of AD, and have been shown to trigger intracellular Tau accumulation and downstream Tau-dependent neuronal dysfunction. However, the mechanisms through which stress and GC disrupt Tau clearance and degradation in neurons remain unclear. Here, we demonstrate that Tau undergoes degradation via endolysosomal sorting in a pathway requiring the small GTPase Rab35 and the endosomal sorting complex required for transport (ESCRT) machinery. Furthermore, we find that GC impair Tau degradation by decreasing Rab35 levels, and that AAV-mediated expression of Rab35 in the hippocampus rescues GC-induced Tau accumulation and related neurostructural deficits. These studies indicate that the Rab35/ESCRT pathway is essential for Tau clearance and part of the mechanism through which GC precipitate brain pathology.

neuroscience↗

bioRxiv2017

Immediate effects of psychosocial stress on attention depend on subjective experience and not directly on stress-related physiological changes

Acute psychosocial stress is associated with physiological, subjective and cognitive changes. In particular, attention, which is considered one of the main processes driving cognition, has been related to different stress outcomes, such as anxiety, cortisol levels and autonomic responses, individually. Nonetheless, their specific contributions to and association with attention is still not fully understood. To study this association, 42 male participants were asked to perform an attentional task just before and immediately after being exposed to either an experimental treatment designed to induce psychosocial stress using the Trier Social Stress Test (TSST) or a matching stress-free control condition. The salivary cortisol concentration, heart rate, and self-reported anxiety were measured to assess the physiological response to stress and the subjective experience during the protocol. As expected, psychosocial stress induced increases in heart rate, salivary cortisol levels and anxiety. The behavioral analysis revealed that members of the control group performed better on the attentional task after the protocol, while members of the TSST group showed no changes. Moreover, after dividing the stress group into sub-groups of participants with high and low anxiety, we observed that participants in the high-anxiety group not only failed to perform better but also performed worse. Finally, after testing several single-level mediation models, we found that anxiety is sufficient to explain the changes in attention and that it mediates the effects between heart rate and cortisol levels on attention. Our results suggest that the immediate effects of acute psychosocial stress on attention are highly dependent on the participants subjective experience, which, in turn, is affected and can mediate stress-related physiological changes.

neuroscience↗