Adapting beyond borders: Insights from the 19th Student Council Symposium (SCS2023), the first hybrid ISCB Student Council global event.

Summary: The 19th ISCB Student Council Symposium (SCS2023) organized by ISCB-SC adopted a hybrid format for the first time, allowing participants to engage in-person in Lyon, France, and virtually via an interactive online platform. The symposium prioritized inclusivity, featuring on-site sessions, poster presentations, and social activities for in-person attendees, while virtual participants accessed live sessions, interactive Q&A, and a virtual exhibit hall. Attendee statistics revealed a global reach, with Europe as the major contributor. SCS2023's success in bridging in-person and virtual experiences sets a precedent for future events in Computational Biology and Bioinformatics. Availability and Implementation: The details of the symposium, speaker information, schedules, and accepted abstracts, are available in the program booklet (https://doi.org/10.5281/zenodo.8173977). For organizers interested in adopting a similar hybrid model, it would be beneficial to have access to details regarding the online platform used, the types of sessions offered, and the challenges faced. Future iterations of SCS can address these aspects to further enhance accessibility and inclusivity.

Brachymetatarsia.

Brachymetatarsia involves a reduction in length of one or more metatarsals. The affected metatarsal is shortened by 5 mm or more, altering the normal metatarsal parabola. In addition to being an aesthetic deformity, it can present with pain due to transfer metatarsalgia. A possible association with genetic disorders needs to be investigated during clinical evaluation. Surgical treatment may involve a one-stage lengthening procedure or progressive distraction, each having its advantages and limitations.

On the mechanical response of graphene-capped copper nanoparticles.

In this study, we investigated the mechanical behavior of pristine copper (Cu) nanoparticles (NPs) and Cu@graphene (Cu@G) hybrid NPs using molecular dynamics simulations. The longitudinal engineering strain was calculated as a measure of compression until reaching 25% of the initial size of the NPs. The stress-strain curves revealed the elastic-to-plastic transition in the Cu NPs at a longitudinal strain of 3.57% with a yield strength of 6.15 GPa. On the other hand, the Cu@G NPs exhibited a maximum average load point at a longitudinal strain of 6.81% with a yield strength of 8.26 GPa. The hybrid Cu@G NPs showed increased strength and resistance to plastic deformation compared to the pure Cu NPs, while the calculation of the elastic modulus indicated a higher load resistance provided by the graphene coverage for the Cu@G NPs. Furthermore, the analysis of atomic configurations, dislocations, and stress distribution demonstrated that the graphene flakes play a crucial role in preventing dislocation events and faceting in the Cu@G NPs by acting as a shock absorber, distributing the applied force on themselves, and producing a more homogeneous stress distribution on the Cu NPs; additionally, they prevent the movement of Cu atoms, reducing the occurrence of dislocations and surface faceting, thanks to their supportive effect. Overall, our findings highlight the potential of hybrid nanomaterials, such as Cu@G, for enhancing the mechanical properties of metallic NPs, which could have significant implications for the development of advanced nanomaterials with improved performance in a variety of applications.

1st ASCS: Expanding the ISCB Student Council Symposia to Asia.

Since 2004, the ISCB Student Council (ISCB-SC) has successfully organized Student Council Symposia across several continents, including North America, Latin America, Europe, and Africa, as well as local events led by more than 25 Regional Student Groups (RSG) across the world. The ISCB-SC Symposia provide students and early career researchers the chance to showcase their work at an international venue in a format that includes keynote talks, round table discussions, workshops, and more. After several efforts spanning several years to build enough critical mass in the region, we have successfully organized the first Asian Student Council Symposium (1st ASCS). This article discusses the organizational details of this unprecedented event, the challenges faced, and the lessons learned.

Can graphene improve the thermal conductivity of copper nanofluids?

Copper (Cu) nanofluids (NFs) have attracted attention due to their high thermal conductivity, which has conferred a wide variety of applications. However, their high reactivity favors oxidation, corrosion and aggregation, leading them to lose their properties of interest. Copper capped by graphene (Cu@G) core@shell nanoparticles (NPs) have also attracted interest from the medical and industrial sectors because graphene can shield the Cu NPs from undesired phenomena. Additionally, they share some properties that expand the range of applications of Cu NFs. In this work, new Morse potentials are reported to reproduce the behavior of Cu@G NPs through molecular dynamics. Coordination-dependent Morse parameters were fitted for C, H, and Cu based on density functional theory calculations. Then, these parameters were implemented to evaluate the thermal conductivity of Cu@G NFs employing the Green-Kubo formalism, with NPs from 1.5 to 6.1 nm at 100 to 800 K, varying the size, the number of layers and the orientation of the graphene flakes. It was found that Cu@G NFs are stable and have an improved thermal conductivity compared to the Cu NFs, being 3.7 to 18.2 times higher at 300 K with only one graphene layer and above 26.2 times higher for the graphene-trilayered NPs. These values can be higher for temperatures below 300 K. Oppositely, the size, homogeneity and orientations of the graphene flakes did not affect the thermal conductivity of the Cu@G NFs.

ISCB Student Council Symposium 2021, a virtual global venue: challenges and lessons learned.

Since 2004, the ISCB Student Council has been organizing different symposia worldwide, gathering together the community of young computational biologists. Due to the coronavirus disease 2019 (COVID-19) pandemic situation, the world scientific community was forced to cancel in-person meetings for almost two years, imposing the adoption of virtual formats instead. After the successful editions of our continental symposia in 2020 in the USA, Latin America, and Europe, we organized our flagship global event, the Student Council Symposium (SCS) 2021, trying to apply all previous lessons learned and to exploit the advantages that virtuality has to offer.

The Adsorption of P2X2 Receptors Interacting with IgG Antibodies Revealed by Combined AFM Imaging and Mechanical Simulation.

The adsorption of proteins onto surfaces significantly impacts biomaterials, medical devices, and biological processes. This study aims to provide insights into the irreversible adsorption process of multiprotein complexes, particularly focusing on the interaction between anti-His6 IgG antibodies and the His6-tagged P2X2 receptor. Traditional approaches to understanding protein adsorption have centered around kinetic and thermodynamic models, often examining individual proteins and surface coverage, typically through Molecular Dynamics (MD) simulations. In this research, we introduce a computational approach employing Autodesk Maya 3D software for the investigation of multiprotein complexes' adsorption behavior. Utilizing Atomic Force Microscopy (AFM) imaging and Maya 3D-based mechanical simulations, our study yields real-time structural and kinetic observations. Our combined experimental and computational findings reveal that the P2X2 receptor-IgG antibody complex likely undergoes absorption in an 'extended' configuration. Whereas the P2X2 receptor is less adsorbed once is complexed to the IgG antibody compared to its individual state, the opposite is observed for the antibody. This insight enhances our understanding of the role of protein-protein interactions in the process of protein adsorption.

6th European Student Council Symposium (ESCS): overcoming obstacles to enhance virtuality, connectivity, inclusivity and community engagement.

This editorial summarises the organisation, activities, and scientific content of the 6th European Student Council Symposium (ESCS) organised by the International Society for Computational Biology Student Council (ISCB-SC). The event was held on September 6, 2020, as a satellite event preceding the ISCB's  19th European Conference in Computational Biology. Both events were first planned to be held in-person in Sitges, Spain, but moved virtually as a strategy to face the SARS-CoV2 sanitary crisis. This completely unforeseen situation has posed several challenges that have been successfully addressed thanks to the robust ISCB Student Council community structure and the strong commitment of the organisers. Despite all the obstacles and challenges, we have found that virtuality has several advantages that can continue to be kept to improve in-person meetings in the future and make conferences more inclusive allowing a larger audience to participate.

Global network of computational biology communities: ISCB's Regional Student Groups breaking barriers.

Regional Student Groups (RSGs) of the International Society for Computational Biology Student Council (ISCB-SC) have been instrumental to connect computational biologists globally and to create more awareness about bioinformatics education. This article highlights the initiatives carried out by the RSGs both nationally and internationally to strengthen the present and future of the bioinformatics community. Moreover, we discuss the future directions the organization will take and the challenges to advance further in the ISCB-SC main mission: "Nurture the new generation of computational biologists".

Electrophysiological characterization of sleep/wake, activity and the response to caffeine in adult cynomolgus macaques.

Most preclinical sleep studies are conducted in nocturnal rodents that have fragmented sleep in comparison to humans who are primarily diurnal, typically with a consolidated sleep period. Consequently, we sought to define basal sleep characteristics, sleep/wake architecture and electroencephalographic (EEG) activity in a diurnal non-human primate (NHP) to evaluate the utility of this species for pharmacological manipulation of the sleep/wake cycle. Adult, 9-11 y.o. male cynomolgus macaques (n = 6) were implanted with telemetry transmitters to record EEG and electromyogram (EMG) activity and Acticals to assess locomotor activity under baseline conditions and following injections either with vehicle or the caffeine (CAF; 10 mg/kg, i.m.) prior to the 12 h dark phase. EEG/EMG recordings (12-36 h in duration) were analyzed for sleep/wake states and EEG spectral composition. Macaques exhibited a sleep state distribution and architecture similar to previous NHP and human sleep studies. Acute administration of CAF prior to light offset enhanced wakefulness nearly 4-fold during the dark phase with consequent reductions in both NREM and REM sleep, decreased slow wave activity during wakefulness, and increased higher EEG frequency activity during NREM sleep. Despite the large increase in wakefulness and profound reduction in sleep during the dark phase, no sleep rebound was observed during the 24 h light and dark phases following caffeine administration. Cynomolgus macaques show sleep characteristics, EEG spectral structure, and respond to CAF in a similar manner to humans. Consequently, monitoring EEG/EMG by telemetry in this species may be useful both for basic sleep/wake studies and for pre-clinical assessments of drug-induced effects on sleep/wake.

Trace amine-associated receptor 1 agonism promotes wakefulness without impairment of cognition in Cynomolgus macaques.

Trace amine-associated receptor 1 (TAAR1) is a G-protein coupled receptor with affinity for the trace amines. TAAR1 agonists have pro-cognitive, antidepressant-, and antipsychotic-like properties in both rodents and non-human primates (NHPs). TAAR1 agonism also increases wakefulness and suppresses rapid-eye movement (REM) sleep in mice and rats and reduces cataplexy in two mouse models of narcolepsy. We investigated the effects of TAAR1 agonism in Cynomolgus macaques, a diurnal species that exhibits consolidated night-time sleep, and evaluated the effects of TAAR1 agonists on cognition using a working memory (WM) paradigm in this species. Adult male Cynomolgus macaques (n = 6) were surgically implanted to record the electroencephalogram (EEG), electromyogram, and locomotor activity (LMA) and the efficacy of the TAAR1 partial agonist RO5263397 (0.1,1,10 mg/kg, p.o.) on sleep/wake, EEG spectra, and LMA was determined. In a second experiment, the acute effects of RO5263397 (0.1,1,10 mg/kg, p.o.) were assessed on a delayed-match-to-sample test of WM in adult male macaques (n = 7). RO5263397 (10 mg/kg) administered at lights off, when sleep pressure was high, promoted wakefulness and reduced both REM and non-REM sleep without inducing hyperlocomotion. RO5263397 (10 mg/kg) also increased delta/theta activity during all vigilance states. RO5263397 had no effect on WM at either short (2 sec) or long (10 sec) delay intervals. The wake-enhancing and REM-suppressing effects of R05263397 shown here in a diurnal primate are consistent with previous results in nocturnal rodents. These effects and the associated alterations in EEG spectra occurred without inducing hyperlocomotion or affecting WM, encouraging further study of TAAR1 agonists as potential narcolepsy therapeutics.

Nurturing tomorrow's leaders: The ISCB Student Council Symposia in 2018.

The Student Council of the International Society for Computational Biology (ISCB-SC) is a student-focused organization for researchers from all early career levels of training (undergraduates, masters, PhDs and postdocs) that organizes bioinformatics and computational biology activities across the globe. Among its activities, the ISCB-SC organizes several symposia in different continents, many times, with the help of the Regional Student Groups (RSGs) that are based on each region. In this editorial we highlight various key moments and learned lessons from the 14th Student Council Symposium (SCS, Chicago, USA), the 5th European Student Council Symposium (ESCS, Athens, Greece) and the 3rd Latin American Student Council Symposium (LA-SCS, Viña del Mar, Chile).

High resolution mass spectrometry-based screening reveals lipophilic toxins in multiple trophic levels from the North Sea.

Lipophilic marine biotoxins, which are mainly produced by small dinoflagellates, are increasingly detected in coastal waters across the globe. As these producers are consumed by zooplankton and shellfish, the toxins are introduced, bioaccumulated and possibly biomagnified throughout marine food chains. Recent research has demonstrated that ultra-high performance liquid chromatography coupled to high-resolution mass spectrometry (UHPLC-HRMS) is an excellent tool to detect marine toxins in algae and seafood. In this study, UHPLC-HRMS was used to screen lipophilic marine biotoxins in organisms from different trophic levels of the Belgian coastal zone ecosystem. A total of 20 tentatively identified lipophilic compounds was detected. Hereby, the trophic transfer of lipophilic marine biotoxins to the upper trophic level was considered to be rather limited. Furthermore, 36% of the compounds was clearly transferred between different organisms. A significant biotransformation of compounds from the okadaic acid and spirolide toxin groups was observed (64%), mainly in filter feeders. Through a multi-targeted approach, this study showed that marine organisms in the Belgian coastal zone are exposed to a multi-toxin mixture. Further research on both single compound and interactive toxic effects of the frequently detected lipophilic marine toxin ester metabolites throughout the food chain is therefore needed. As a future perspective, confirmatory identification of potential toxins by studying their fragmentation spectra (using new tools such as hybrid quadrupole Q-Exactive™ Orbitrap-MS) is designated.

Quantification and profiling of lipophilic marine toxins in microalgae by UHPLC coupled to high-resolution orbitrap mass spectrometry.

During the last decade, a significant increase in the occurrence of harmful algal blooms (HABs), linked to repetitive cases of shellfish contamination has become a public health concern and therefore, accurate methods to detect marine toxins in different matrices are required. In this study, we developed a method for profiling lipophilic marine microalgal toxins based on ultra-high-performance liquid chromatography coupled to high-resolution Orbitrap mass spectrometry (UHPLC-HR-Orbitrap MS). Extraction of selected toxins (okadaic acid (OA), dinophysistoxin-1 (DTX-1), pectenotoxin-2 (PTX-2), azaspiracid-1 (AZA-1), yessotoxin (YTX) and 13-desmethyl spirolide C (SPX-1)) was optimized using a Plackett-Burman design. Three key algal species, i.e., Prorocentrum lima, Protoceratium reticulatum and Alexandrium ostenfeldii were used to test the extraction efficiency of OA, YTXs and SPXs, respectively. Prorocentrum micans, fortified with certified reference solutions, was used for recovery studies. The quantitative and confirmatory performance of the method was evaluated according to CD 2002/657/EC. Limits of detection and quantification ranged between 0.006 and 0.050 ng mL(-1) and 0.018 to 0.227 ng mL(-1), respectively. The intra-laboratory reproducibility ranged from 6.8 to 11.7 %, repeatability from 6.41 to 11.5 % and mean corrected recoveries from 81.9 to 119.6 %. In addition, algae cultures were retrospectively screened for analogues and metabolites through a homemade database. Using the ToxID software programme, 18 toxin derivates were detected in the extract of three toxin producing microalgae species. In conclusion, the generic extraction and full-scan HRMS approach offers an excellent quantitative performance and simultaneously allows to profile analogues and metabolites of marine toxins in microalgae. Graphical Abstract Optimization of extraction, detection and quantification of lipophilic marine toxins in microalgae by UHPLC-HR Orbitrap MS.

Validation of a confirmatory method for lipophilic marine toxins in shellfish using UHPLC-HR-Orbitrap MS.

Lipophilic marine toxins are produced by harmful microalgae and can accumulate in edible filter feeders such as shellfish, leading to an introduction of toxins into the human food chain, causing different poisoning effects. During the last years, analytical methods, based on liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), have been consolidated by interlaboratory validations. However, the main drawback of LC-MS/MS methods remains the limited number of compounds that can be analyzed in a single run. Due to the targeted nature of these methods, only known toxins, previously considered during method optimization, will be detected. Therefore in this study, a method based on ultra-high-performance liquid chromatography coupled to high-resolution Orbitrap mass spectrometry (UHPLC-HR-Orbitrap MS) was developed. Its quantitative performance was evaluated for confirmatory analysis of regulated lipophilic marine toxins in shellfish flesh according to Commission Decision 2002/657/EC. Okadaic acid (OA), dinophysistoxin-1 (DTX-1), pectenotoxin-2 (PTX-2), azaspiracid-1 (AZA-1), yessotoxin (YTX), and 13-desmethyl spirolide C (SPX-1) were quantified using matrix-matched calibration curves (MMS). For all compounds, the reproducibility ranged from 2.9 to 4.9 %, repeatability from 2.9 to 4.9 %, and recoveries from 82.9 to 113 % at the three different spiked levels. In addition, confirmatory identification of the compounds was effectively performed by the presence of a second diagnostic ion ((13)C). In conclusion, UHPLC-HR-Orbitrap MS permitted more accurate and faster detection of the target toxins than previously described LC-MS/MS methods. Furthermore, HRMS allows to retrospectively screen for many analogues and metabolites using its full-scan capabilities but also untargeted screening through the use of metabolomics software.

Highlights from the 1st ISCB Latin American Student Council Symposium 2014. Introduction.

This report summarizes the scientific content and activities of the first edition of the Latin American Symposium organized by the Student Council of the International Society for Computational Biology (ISCB), held in conjunction with the Third Latin American conference from the International Society for Computational Biology (ISCB-LA 2014) in Belo Horizonte, Brazil, on October 27, 2014.

DNA barcoding and microsatellites help species delimitation and hybrid identification in endangered galaxiid fishes.

The conservation of data deficient species is often hampered by inaccurate species delimitation. The galaxiid fishes Aplochiton zebra and Aplochiton taeniatus are endemic to Patagonia (and for A. zebra the Falkland Islands), where they are threatened by invasive salmonids. Conservation of Aplochiton is complicated because species identification is hampered by the presence of resident as well as migratory ecotypes that may confound morphological discrimination. We used DNA barcoding (COI, cytochrome b) and a new developed set of microsatellite markers to investigate the relationships between A. zebra and A. taeniatus and to assess their distributions and relative abundances in Chilean Patagonia and the Falkland Islands. Results from both DNA markers were 100% congruent and revealed that phenotypic misidentification was widespread, size-dependent, and highly asymmetric. While all the genetically classified A. zebra were correctly identified as such, 74% of A. taeniatus were incorrectly identified as A. zebra, the former species being more widespread than previously thought. Our results reveal, for the first time, the presence in sympatry of both species, not only in Chilean Patagonia, but also in the Falkland Islands, where A. taeniatus had not been previously described. We also found evidence of asymmetric hybridisation between female A. taeniatus and male A. zebra in areas where invasive salmonids have become widespread. Given the potential consequences that species misidentification and hybridisation can have for the conservation of these endangered species, we advocate the use of molecular markers in order to reduce epistemic uncertainty.

[Long term consequences among children exposed to lead poisoning]. / Efectos clínicos a largo plazo en niños intoxicados con plomo en una región del sur de Chile.

BACKGROUND: In 1996 there was a massive lead poisoning in a southern rural community in Chile. The contamination source was a mill whose grinding stone was repaired with lead and contaminated the flour. AIM: To assess the presence of sequelae ten years later, among subjects that were exposed to lead on that occasion. MATERIAL AND METHODS: Cross sectional study of 77 individuals (47 males), aged 10 to 25 years, that were exposed to lead in 1996 and were treated with EDTA. RESULTS: Twenty one percent of subjects had a subnormal intelligence quotient (IQ). The risk of having a low IQ was significantly higher among those exposed before the age of six years. IQ was significantly lower among subjects that, immediately after the exposure, had a lead level over 48 microg/dl, compared with those that had a lead level below 43 microg/dl (86.7+/-7.3 and 93+/-11.6 respectively). No subjects with high blood pressure or evidences of nephrotoxicity were detected. CONCLUSIONS: Subjects aged less than six years at the moment of lead exposure had a lower IQ when assessed ten years later.

Efectos clínicos a largo plazo en niños intoxicados con plomo en una región del sur de Chile / Long term consequences among children exposed to lead poisoning

Background: In 1996 there was a massive lead poisoning in a southern rural community in Chile. The contamination source was a mill whose grinding stone was repaired with lead and contaminated the flour. Aim: To assess the presence of sequelae ten years later, among subjects that were exposed to lead on that occasion. Material and methods: Cross sectional study of 77 individuals (47 males), aged 10 to 25 years, that were exposed to lead in 1996 and were treated with EDTA. Results: Twenty one percent of subjects had a subnormal intellingence quotient (IQ). The risk of having a low IQ was significantly higher among those exposed before the age of six years. IQ was significantly lower among subjects that, immediately after the exposure, had a lead level over 48 fig/dl, compared with those that had a lead level below 43 fig/dl (86.7±7.3 and 93±11.6 respectively). No subjects with high blood pressure or evidences of nephrotoxicity were detected. Conclusions: Subjects aged ¡ess than six years at the moment of lead exposure had a lower IQ when assessed ten years later.