Biology subjects

Lopes, G.

Publications and source records attributed to Lopes, G..

10 recordsLinked to original sources

bioRxiv2026

Thalassoporum longitrichum sp. nov., a marine epizoic cyanobacterium with anti-inflammatory potential, and the taxonomic reassessment of Limnothrix Meffert

The strain LEGE 10371, isolated from the surface of a marine sponge at Praia da Memoria, Portugal, was characterized as a new Thalassoporum species (Pseudanabaenales) using a polyphasic approach that included 16S rRNA gene phylogenetic analysis (Maximum Likelihood and Bayesian Inference), 16S-23S ITS secondary structures, p-distance calculations, MALDI-TOF MS profiling, and morphological analysis by optical and scanning electron microscopy, as well as ecological and biochemical characterization. Phylogenetically, LEGE 10371 clustered within the Thalassoporum clade, however distant from the other existent species of the genus. The p-distance analysis revealed low sequence identity with other Thalassoporum species, with a maximum value of 97.2% to Th. komareki. The MALDI-TOF profile displayed high-intensity peaks at approximately 3,000, 4,000, 6,000 and 8,000 m/z, representing strong candidates for diagnostic markers of the new species. Morphologically, the new species differ from the other species of the genus by presenting trichomes with more than 10 cells and lack of aerotopes. Biocompatibility of the fractions was evaluated in HaCaT keratinocytes, showing no cytotoxic effects at most tested concentrations. PCR screening targeting mcyE, sxtG, anaC, and cyrA confirmed the absence of the genetic potential for the production of major cyanotoxins. Chemical characterization revealed a pigment-rich profile dominated by chlorophyll-a and carotenoids, including {beta}-carotene, zeaxanthin, lutein, and mixoxanthophyll. Bioactivity assays showed superoxide anion radical scavenging by the aqueous fraction (IC2 {approx} 0.042-0.045 mg mL-{superscript 1}), strong nitric oxide radical scavenging by the acetonic fraction (IC = 0.045 mg mL-{superscript 1}), and lipoxygenase inhibition ([~]41%, for a fraction concentration of 0.25 mg mL-), suggesting a potential contribution of these fractions to modulate inflammation-related pathways. Additionally to this results, the polyphasic analysis permitted to confirm previous data that Pseudanabaena and Limnothrix represent the same generic entity. Both genera clustered together, presented high 16S rRNA gene identity (up to 99.9%) and share the same morphological and ecological features. Consequently, we formally proposed the synonimization of Limnothrix into Pseudanabaena.

microbiology↗

bioRxiv2025

Aeon: an open-source platform to study the neural basis of ethological behaviours over naturalistic timescales

Ethological behaviours are a powerful tool for neuroscience since they leverage the robust neural computations shaped by the species evolution to study the neural basis of cognitive functions. However, such behaviours are often transitory and dependent on factors that vary over space, time and number of individuals, making them difficult to capture with standard laboratory tasks. Here we present Aeon, an open-source platform designed for continuous, long-term study of self-guided behaviours in multiple mice and simultaneous recording of brain activity within large, customizable habitats. By integrating specialized modules for navigation, nesting and sleeping, escaping, foraging, and social interaction, Aeon enables the expression of key ethological behaviours while achieving experimental control and multi-dimensional quantifications from sub-millisecond to month-long durations. Its software architecture ensures robust data acquisition via many synchronized data streams and delivers a new standardised, unified data format that yields seamless, integrated analysis pipelines. Using assays such as digging-to-threshold and social foraging, Aeon reveals how mice adapt strategies in a changing environment and in response to conspecifics. Aeon bridges ecological relevance with rigorous experimental control to advance our understanding of how neural circuit activity gives rise to a range of highly conserved and adaptive behaviours.

neuroscience↗

bioRxiv2025

Advancing Mobile Neuroscience: A Novel Wearable Backpack for Multi-Sensor Research in Urban Environments

The rapid global urbanisation has intensified the need to understand the complex interactions and impacts that city environments have on human physical or mental health and well-being. Traditional indoor laboratory-based approaches conduct experiments in well controlled settings but, while advantageous for their controlled conditions, they often lack ecological validity. To address this gap, we present the "eMOTIONAL Cities Walker Backpack" -- a wearable unit developed for synchronously collecting multi-modal data in dynamic real-world settings. Designed for both indoor and outdoor use, the backpack integrates environmental (for microclimate, air pollution and noise) and physiological sensors (including electroencephalography, eye-tracking and wrist-based biosensors for cardiovascular monitoring) to enable the study of human experience in naturalistic urban environments. In this paper, we describe the technical specifications and implementation of this technology during outdoor acquisitions across selected urban locations in the city of Lisbon. We also highlight its potential for methodological comparison with traditional lab-based tasks (particularly through the use of equivalent sensing technologies), and thus advancing the field of translational research in mental health and urban studies.

neuroscience↗

bioRxiv2023

A unified open-source platform for multimodal neural recording and perturbation during naturalistic behavior

Behavioral neuroscience faces two conflicting demands: long-duration recordings from large neural populations and unimpeded animal behavior. To meet this challenge, we developed ONIX, an open-source data acquisition system with high data throughput (2GB/sec) and low closed-loop latencies (<1ms) that uses a novel 0.3 mm thin tether to minimize behavioral impact. Head position and rotation are tracked in 3D and used to drive active commutation without torque measurements. ONIX can acquire from combinations of passive electrodes, Neuropixels probes, head-mounted microscopes, cameras, 3D-trackers, and other data sources. We used ONIX to perform uninterrupted, long ([~]7 hours) neural recordings in mice as they traversed complex 3-dimensional terrain. ONIX allowed exploration with similar mobility as non-implanted animals, in contrast to conventional tethered systems which restricted movement. By combining long recordings with full mobility, our technology will enable new progress on questions that require high-quality neural recordings during ethologically grounded behaviors.

neuroscience↗

bioRxiv2021

Biochemical and subcellular characterization of a squid hnRNPA/B-like protein in osmotic stress activated cells reflects molecular properties conserved in this protein family

In previous works, we characterized a novel, strongly basic, squid hnRNPA/B-like Protein 2 in presynaptic terminals of squid neurons. Here, we show that squid hnRNPA/B-like Protein 2 are exclusively nuclear localization and relocated to cytoplasmic granules containing hnRNPA1 and Poly-A binding protein-1 (PABP-1) when the cells are treated with sorbitol. Also, we show an interaction of hnRNPA/B like Protein 2 with squid RNA, its interfered with dynamic of formation of hnRNPA/B like Protein 2 dimers, whereas possibly involved disulfide bounds and postranslations modification in a distinct stage of dimers formation. An understanding of the molecular and biochemical mechanisms involved in the stability of the dimeric form, and the regulation of the transition between monomeric and dimeric forms may bring insights into evolution of several neurodegenerative diseases. HighlightsO_LIWe identified monomeric (p37) and dimeric (p65) forms of squid hnRNPA/B-like Protein 2 in squid optic lobes C_LIO_LIOur data indicate a conserved structure and cellular properties of squid hnRNPA/B-like Protein 2 and human hnRNPA1 protein colocalizing with PABP into stress granules (SGs) C_LIO_LIThe stability of hnRNPA/B-like dimers involved the squid RNAs and disulfide bonds to promote higher SDS-stable dimers formation C_LIO_LIAn understanding of the transition between monomeric and dimeric forms of squid hnRNPA/B-like Protein 2 may give clues to misfolding processes in neuropathologies C_LI

cell biology↗

bioRxiv2020

Real-time, low-latency closed-loop feedback using markerless posture tracking

The ability to control a behavioral task or stimulate neural activity based on animal behavior in real-time is an important tool for experimental neuroscientists. Ideally, such tools are noninvasive, low-latency, and provide interfaces to trigger external hardware based on posture. Recent advances in pose estimation with deep learning allows researchers to train deep neural networks to accurately quantify a wide variety of animal behaviors. Here we provide a new DeepLabCut-Live! package that achieves low-latency real-time pose estimation (within 15 ms, >100 FPS), with an additional forward-prediction module that achieves zero-latency feedback, and a dynamic-cropping mode that allows for higher inference speeds. We also provide three options for using this tool with ease: (1) a stand-alone GUI (called DLC-Live! GUI), and integration into (2) Bonsai and (3) AutoPilot. Lastly, we benchmarked performance on a wide range of systems so that experimentalists can easily decide what hardware is required for their needs.

neuroscience↗

bioRxiv2020

BonVision - an open-source software to create and control visual environments

Real-time rendering of closed-loop visual environments is necessary for next-generation understanding of brain function and behaviour, but is prohibitively difficult for non-experts to implement and is limited to few laboratories worldwide. We developed BonVision as an easy-to-use open-source software for the display of virtual or augmented reality, as well as standard visual stimuli. As the architecture is based on the open-source Bonsai graphical programming language, BonVision benefits from native integration with experimental hardware. BonVision therefore enables easy implementation of closed-loop experiments, including real-time interaction with deep neural networks and communication with behavioural and physiological measurement and manipulation devices.

neuroscience↗

bioRxiv2018

Recording from the same neuron with high-density CMOS probes and patch-clamp: a ground-truth dataset and an experiment in collaboration.

We built a rig to perform patch-clamp and extracellular recordings from the same neuron in vivo. In this setup, the axes of two micromanipulators are precisely aligned and their relative position tracked in real-time, allowing us to accurately target patch-clamp recordings to neurons near an extracellular probe. We used this setup to generate a publicly-available dataset where a cortical neurons spiking activity is recorded in patch-clamp next to a dense CMOS Neuropixels probe. "Ground-truth" datasets of this kind are rare but valuable to the neuroscience community, as they power the development and improvement of spike-sorting and analysis algorithms, tethering them to empirical observations. In this article, we describe our approach and report exploratory and descriptive analysis on the resulting dataset. We study the detectability of patch-clamp spikes on the extracellular probe, within-unit reliability of spike features and spatiotemporal dynamics of the action potential waveform. We open discussion and collaboration on this dataset through an online repository, with a view to producing follow-up publications. PrologueOur efforts to record from the same neuron in vivo using patch-clamp and dense extracellular probes have resulted in three outputs: a publicly-available dataset (http://bit.ly/paired_recs), a manuscript, and a code repository (http://bit.ly/paired_git). Together, these three components form the publication arising from the experiments we have performed. The role of the dataset is to be downloaded and re-used. The role of the manuscript is to describe the experimental methods through which we acquired the dataset, explain it and showcase which types of questions it can be used to address. The repository has two roles: first, promoting reproducibility and error correction. By making our analysis and figure-generation code freely-available, we wish to make our analysis procedures clear and enable the reader to reproduce our results from the raw data, alerting us to any potential mistakes. Second, the repository will form a living, dynamic and interactive component of the publication: a forum for open collaboration on this dataset. Any interested scientists can contribute to it, joining us in detailed exploration of these recordings with a view to producing follow-up publications in which they will be credited for their input. Why did we opt to publish this way? The first reason is that the very nature of the project we here describe - recording the same neuron with patch-clamp and extracellular probes - invites an open science and open source approach. This is because the primary use of this type of "ground truth" validation data is to aid the development of new sorting and analysis algorithms, as well as to benchmark and improve existing ones. The second reason is that despite being conceptually very simple, this project generated a large and complex dataset that can be tackled in many ways and used to address different types of question. Some of these questions are beyond the reach of our analytical expertise; others lie even beyond the scope of our scientific imagination. By releasing the dataset and providing a repository for scientific discussion and collaboration, we aim to maximise its scientific return to the community. Instead of having each interested research group work in isolation, we hope that by encouraging collaboration and discussion between peers we can foster synergy between them that will lead to work of greater scientific value. Although datasets like ours are exquisitely suited for such an approach, we believe this publication strategy needs to become more widely adopted in neuroscience. We were pleased to note recent publications spontaneously and independently using similar approaches1-4, in what may well be evidence of convergent thinking. Perhaps the time has come for new publication and collaboration paradigms. We will elaborate on this subject during the Epilogue. For now, let us get back to electrophysiological recordings, before we begin an experiment on scientific collaboration.

neuroscience↗

bioRxiv2018

Why not record from every channel with a CMOS scanning probe?

It is an uninformative truism to state that the brain operates at multiple spatial and temporal scales, each with each own set of emergent phenomena. More worthy of attention is the point that our current understanding of it cannot clearly indicate which of these phenomenological scales are the significant contributors to the brains function and primary output (i.e. behaviour). Apart from the sheer complexity of the problem, a major contributing factor to this state of affairs is the lack of instrumentation that can simultaneously address these multiple scales without causing function altering damages to the underlying tissue. One important facet of this problem is that standard neural recording devices normally require one output connection per electrode. This limits the number of electrodes that can fit along the thin shafts of implantable probes generating a limiting balance between density and spread. Sharing a single output connection between multiple electrodes relaxes this constraint and permits designs of ultra-high density probes. Here we report the design and in-vivo validation of such a device, a complementary metal-oxide-semiconductor (CMOS) scanning probe with 1344 electrodes; the outcome of the European research project NeuroSeeker. We show that this design targets both local and global spatial scales by allowing the simultaneous recording of more than 1000 neurons spanning 7 functional regions with a single shaft. The neurons show similar recording longevity and signal to noise ratio to passive probes of comparable size and no adverse effects in awake or anesthetized animals. Addressing the data management of this device we also present novel visualization and monitoring methods. Using the probe with freely moving animals we show how accessing a number of cortical and subcortical brain regions offers a novel perspective on how the brain operates around salient behavioural events. Finally, we compare this probe with lower density, non CMOS designs (which have to adhere to the one electrode per output line rule). We show that an increase in density results in capturing neural firing patterns, undetectable by lower density devices, which correlate to self-similar structures inherent in complex naturalistic behaviour. To help design electrode configurations for future, even higher density, CMOS probes, recordings from many different brain regions were obtained with an ultra-dense passive probe.

neuroscience↗

bioRxiv2018

Does impedance matter when recording spikes with polytrodes?

Extracellular microelectrodes have been widely used to measure brain activity, yet there are still basic questions about the requirements for a good extracellular microelectrode. One common source of confusion is how an electrodes impedance affects the amplitude of extracellular spikes and background noise.\n\nHere we discuss how an electrodes impedance affects data quality in extracellular recordings, which is crucial for both the detection of spikes and their assignment to the correct neurons. This study employs commercial polytrodes containing 32 electrodes (177 m2) arranged in a dense array. This allowed us to directly compare, side-by-side, the same extracellular signals measured by modified low impedance (~100 kOhm) microelectrodes with unmodified high impedance (~1 MOhm) microelectrodes. We begin with an evaluation of existing protocols to lower the impedance of the electrodes. The poly(3,4-ethylenedioxythiophene)-polystyrene sulfonate (PEDOT-PSS) electrodeposition protocol is a simple, stable, and reliable method for decreasing the impedance of a microelectrode up to tenfold. We next record in vivo using polytrodes that are modified in a chess board pattern, such that the signal of one neuron is detected by multiple coated and non-coated electrodes. The performance of the coated and non-coated electrodes is then compared on measures of background noise and amplitude of the detected action potentials.\n\nIf the proper recording system is used, then the impedance of a microelectrode within the range of standard polytrodes (~ 0.1 to 2 MOhm) does not significantly affect data quality and spike sorting. This study should encourage neuroscientists to stop worrying about one more unknown.

neuroscience↗