Biology subjects

Gomes, B.

Publications and source records attributed to Gomes, B..

5 recordsLinked to original sources

bioRxiv2024

Peroxidasin expression is increased in intratumoural capillaries and in proximal tubular cells adjacent to clear cell renal cell carcinoma.

Peroxidasin (PXDN), is a heme peroxidase with a critical role in the crosslinking of type IV collagen, being essential for basement membrane integrity. In many cancers, PXDN overexpression has been linked with processes associated with poor disease outcomes, namely the impairment of endothelial functions, pathogenesis of vascular diseases, vascular remodelling, apoptosis, and tissue fibrosis. In RCC, almost nothing is so far known. In this work we characterized the expression of PXDN in tumour and non-neoplastic adjacent tissue from clear cell renal cell carcinoma (ccRCC) and renal oncocytoma by immunohistochemistry. Results showed a significant increase of PXDN expression in intratumoural capillaries of ccRCC in comparison with oncocytoma, and an increase in the proximal tubular epithelial cells of non-neoplastic adjacent parenchyma from ccRCC cases, in comparison with the same area from oncocytomas. Overall, our results suggest, for the first time, that PXDN may have a role in tumour angiogenesis that may favour metastases and tumour malignity, being also enrolled in the crosstalk between the tumour and adjacent tissue, that deserves further investigation. HighlightsO_LIPeroxidasin is increased in ccRCC microvasculature comparing to oncocytoma. C_LIO_LIPeroxidasin is increased in proximal tubules of ccRCC kidney adjacent parenchyma. C_LIO_LIIs Peroxidasin a modulator of tumour microenvironment promoting angiogenesis? C_LI

pathology↗

bioRxiv2023

Characterization of peroxidasin expression in histologically normal human adult and fetal kidney tissue

Peroxidasin (PXDN) is an enzyme of the peroxidase family that plays a critical role in extracellular matrix (ECM) formation and tissue development. In the kidney, very few studies using animal cells suggested that PXDN may have a role in the maintenance of the structural and functional integrity of the renal ECM. Still, the normal expression and (patho)physiological roles of PDXN in the mature and developing human kidney remain unknown. In this work we used fluorescent immunohistochemistry and advanced microscopy and image processing methodologies to perform a quantitative characterization of PXDN expression in the different anatomic compartments of histologically normal kidney tissue, obtained from adult nephrectomy specimens, and from postmortem fetal and neonatal kidney specimens (excluding death by kidney disease and genitourinary developmental anomalies). Results show that PXDN is expressed in all mature kidney compartments, but at significantly higher levels in tubular epithelial cells, particularly in the distal tubules. A similar PXDN expression pattern was observed in the developing kidney, as early as the in the comma-shaped-body stage. In the fetal kidney, PXDN was diffusely expressed in the branches of the ureteric bud but not in the cells of the metanephric blastema. This is the first demonstration that PXDN is differentially expressed in histologically normal human renal parenchyma, exhibiting a remarkably consistent pattern of predominant tubular expression since the early stages of metanephrogenesis This data suggests a relevant, compartment-specific, role of PXDN in nephrogenesis and in the kidney physiology, highlighting a main role in tubular functions, that is worth further investigation.

physiology↗

bioRxiv2023

Stimulus representations in visual cortex shaped by spatial attention and microsaccades

SUMMARY/ABSTRACTMicrosaccades (MSs) are commonly associated with spatially directed attention, but how they affect visual processing is still not clear. We studied MSs in a task in which the animal was randomly cued to attend to a target stimulus and ignore distractors, and it was rewarded for detecting a color change in the target. We found that the enhancement of firing rates normally found with attention to a cued stimulus was delayed until the first MS directed towards that stimulus. Once that MS occurred, attention to the target was engaged and there were persistent effects of attention on firing rates for the remainder of the trial. These effects were found in the superficial and deep layers of V4 as well as the lateral pulvinar and IT cortex. Although the tuning curves of V4 cells do not change depending on the locus of spatial attention, we found pronounced effects of MS direction on stimulus representations that persisted for the length of the trial in V4. In intervals following a MS towards the target in the RF, stimulus decoding from population activity was substantially better than in intervals following a MS away from the target. Likewise, turning curves of cells were substantially sharper following a MS towards the target in the RF. This sharpening appeared to result from both a "refreshing" of the initial transient sensory response to stimulus onset, and a magnification of the effects of attention in this condition. MSs to the target also enhanced the neuronal response to the behaviorally relevant target color change and led to faster reaction times. These results thus reveal a major link between spatial attention, object processing and its coordination with eye movements.

neuroscience↗

bioRxiv2022

Genomic Analysis of Two Phlebotomine Sand Fly Vectors of Leishmania from the New and Old World

Phlebotomine sand flies are of global significance as important vectors of human disease, transmitting bacterial, viral, and protozoan pathogens, including the devastating kinetoplastid parasites of the genus Leishmania, the causative agents of diseases collectively termed leishmaniasis. More than 40 pathogenic Leishmania species are transmitted to humans by approximately 35 sand fly species in 98 countries with hundreds of millions of people at risk around the world. As no approved efficacious vaccine exists, available drugs are expensive and/or toxic, and resistance is emerging, management of sand fly populations to break transmission is currently the most effective disease control strategy. To better understand the biology of sand flies, including the mechanisms involved in their vectorial capacity, insecticide resistance, and population structures we sequenced the genomes of two of the most important sand fly species: Phlebotomus papatasi, a cutaneous leishmaniasis vector, (distributed in the Middle East and North Africa) and Lutzomyia longipalpis, a visceral leishmaniasis vector (distributed across Central and South America). We categorized and curated genes involved in processes important to their roles as disease vectors, including chemosensation, blood feeding, circadian rhythm, immunity, and detoxification, as well as mobile genetic elements. We also defined gene orthology and observed micro-synteny among the genomes. Finally, we present the genetic diversity and population structure of these species in their respective geographical areas. These genomes will be a foundation on which to base future efforts to prevent vector-borne transmission of Leishmania parasites. Author SummaryThe leishmaniases are a group of neglected tropical diseases caused by protist parasites from the Genus Leishmania. Different Leishmania species present a wide clinical profile, ranging from mild, often self-resolving cutaneous lesions that can lead to protective immunity, to severe metastatic mucosal disease, to visceral disease that is ultimately fatal. Leishmania parasites are transmitted by the bites of sand flies, and as no approved vaccine exists, available drugs are toxic and/or expensive and resistance is emerging, new dual control strategies to combat these diseases must be developed, combining interventions on human infections and integrated sand fly population management. Effective vector control requires a good understanding of the biology of sand flies. To this end, we sequenced and annotated the genomes of two sand fly species that are important leishmaniasis vectors from the Old and New Worlds. These genomes allow us to better understand, at the genetic level, processes important in the vector biology of these species, such as finding hosts, blood-feeding, immunity, and detoxification. These genomic resources highlight the driving forces of evolution of two major Leishmania vectors and provide foundations for future research on how to better prevent leishmaniasis by control of the sand fly vectors.

genomics↗

bioRxiv2019

Exploring the Dynamics of Nonlinear Biochemical Systems using Control-Based Continuation

AO_SCPLOWBSTRACTC_SCPLOWMathematical modelling is routinely used in Systems Biology to understand the mechanisms causing nonlinear phenomena in gene expression, such as switch-like behaviours and temporal oscillations. The reliability of model predictions and bifurcation analysis depend on modelling assumptions and specific choices of model parameters; however, the identification of models is highly challenging due to the complexity of biochemical interactions and noise in experimental data. This paper numerically investigates the use of control-based continuation (CBC) for tracking dynamical features of biochemical systems and, in particular, the bistable dynamics of a gene regulating pluripotency in embryonic stem cells. CBC is a method that exploits feedback control and path following algorithms to explore the dynamic features of a nonlinear physical system directly during experimental tests. CBC applications have so far been limited to non-living (i.e. electro-mechanical) systems. Our numerical simulations show that, in principle, CBC could also be applied to biological experiments to characterise the switch-like dynamics of genes that are important for cell decision making.

systems biology↗