Ten simple rules for computational biologists collaborating with wet lab researchers.

Computational biologists are frequently engaged in collaborative data analysis with wet lab researchers. These interdisciplinary projects, as necessary as they are to the scientific endeavor, can be surprisingly challenging due to cultural differences in operations and values. In this Ten Simple Rules guide, we aim to help dry lab researchers identify sources of friction and provide actionable tools to facilitate respectful, open, transparent, and rewarding collaborations.

Point-of-Care Testing for the Detection of MicroRNAs: Towards Liquid Biopsy on a Chip.

Point-of-care (PoC) testing is revolutionizing the healthcare sector improving patient care in daily hospital practice and allowing reaching even remote geographical areas. In the frame of cancer management, the design and validation of PoC enabling the non-invasive, rapid detection of cancer markers is urgently required to implement liquid biopsy in clinical practice. Therefore, focusing on stable blood-based markers with high-specificity, such as microRNAs, is of crucial importance. In this work, we highlight the potential impact of circulating microRNAs detection on cancer management and the crucial role of PoC testing devices, especially for low-income countries. A detailed discussion about the challenges that should be faced to promote the technological transfer and clinical use of these tools has been added, to provide the readers with a complete overview of potentialities and current limitations.

Seminal cadmium affects human sperm motility through stable binding to the cell membrane.

Environmental pollutants are claimed to be major factors involved in the progressive decline of the fertility rate worldwide. Exposure to the heavy metal Cadmium (Cd) has been associated with reproductive toxicity due to its ionic mimicry. However, the possible direct accumulation of Cd in human sperm cells has been poorly investigated. In this study, we aimed to clarify the possible direct effect of Cd exposure on sperm function through the analysis of its cell accumulation. Semen samples from 30 male subjects residing in high environmental impact areas and adhering to the "Exposoma e Plurifocalità nella Prevenzione Oncologica" campaign for testis cancer prevention were compared with semen samples from 15 males residing in low exposure areas. Semen levels and cell Cd content were quantified by inductively coupled plasma (ICP) spectroscopy. Cell Cd distribution was assessed by scanning electron microscopy coupled with energy dispersive spectroscopy (SEM-EDS). The impact of Cd on sperm function was evaluated by the in vitro exposure to the heavy metal, whilst possible scavenging approaches/agents were assessed. In addition to higher values of semen Cd, exposed subjects showed a reduction in total motile sperm fraction compared to not-exposed controls (59.6% ± 13.6% vs. 66.3% ± 7.3%, p = 0.037). Semen Cd levels were also significantly correlated with SEM-EDS signals of Cd detected on the head and neck of sperm (respectively p = 0.738, p < 0.001 and ρ = 0.465, p < 0.001). A total of 2 h of in vitro exposure to 0.5 µM Cd was associated with a significant reduction of sperm progressive motility. Scavenging approaches with either hypo-osmotic swelling or 10 µM reduced glutathione were ineffective in blunting cell Cd and restoring motility. The reduction of exposure levels appears to be the main approach to reducing the reproductive issues associated with Cd.

Haem-mediated albumin biosensing: Towards voltammetric detection of PFOA.

The haem group is a promising redox probe for the design of albumin-based voltammetric sensors. Among the endogenous ligands carried by human serum albumin (hSA), haem is characterised by a reversible redox behaviour and its binding kinetics strongly depend on hSA's conformation, which, in turn, depends on the presence of other ligands. In this work, the potential applicability of haem, especially hemin, as a redox probe was first tested in a proof-of-concept study using perfluorooctanoic acid (PFOA) as model analyte. PFOA is known to bind hSA by occupying Sudlow's I site (FA7) which is spatially related to the haem-binding site (FA1). The latter undergoes a conformational change, which is expected to affect hemin's binding kinetics. To verify this hypothesis, hemin:albumin complexes in the presence/absence of PFOA were first screened by UV-Vis spectroscopy. Once the complex formation was verified, haem was further characterised via electrochemical methods to estimate its electron transfer kinetics. The hemin:albumin:PFOA system was studied in solution, with the aim of describing the multiple equilibria at stake and designing an electrochemical assay for PFOA monitoring. This latter could be integrated with protein-based bioremediation approaches for the treatment of per- and polyfluoroalkyl substances polluted waters. Overall, our preliminary results show how hemin can be applied as a redox probe in albumin-based voltammetric sensing strategies.

Pesticides monitoring in biological fluids: Mapping the gaps in analytical strategies.

Pesticides play a key-role in the development of the agrifood sector allowing controlling pest growth and, thus, improving the production rates. Pesticides chemical stability is responsible of their persistency in environmental matrices leading to bioaccumulation in animal tissues and hazardous several effects on living organisms. The studies regarding long-term effects of pesticides exposure and their toxicity are still limited to few studies focusing on over-exposed populations, but no extensive dataset is currently available. Pesticides biomonitoring relies mainly on chromatographic techniques coupled with mass spectrometry, whose large-scale application is often limited by feasibility constraints (costs, time, etc.). On the contrary, chemical sensors allow rapid, in-situ screening. Several sensors were designed for the detection of pesticides in environmental matrices, but their application in biological fluids needs to be further explored. Aiming at contributing to the implementation of pesticides biomonitoring methods, we mapped the main gaps between screening and chromatographic methods. Our overview focuses on the recent advances (2016-2021) in analytical methods for the determination of commercial pesticides in human biological fluids and provides guidelines for their application.

Investigation of the Interaction between Human Serum Albumin and Branched Short-Chain Perfluoroalkyl Compounds.

The current trend dealing with the production of per- and polyfluoroalkyl substances (PFASs) involves the shifting toward branched short-chain fluorinated compounds known as new-generation PFASs. A key aspect to be clarified, to address the adverse health effects associated with the exposure to PFASs, is their binding mode to human serum albumin (hSA), the most abundant protein in plasma. In this study, we investigated the interaction between hSA and two representative branched short-chain PFASs, namely, HPFO-DA and C6O4. In-solution studies revealed that both compounds bind hSA with affinities and stoichiometries lower than that of the legacy long-chain perfluoroalkyl compound PFOA. Competition experiments using hSA-binding drugs with known site-selectivity revealed that both HPFO-DA and C6O4 bound to pockets located in subdomain IIIA. The crystal structure of hSA in complex with HPFO-DA unveiled the presence of two binding sites. The characterization and direct comparison of hSA interactions with new-generation PFASs may be key elements for the understanding of the toxicological impact of these compounds.

Bicyclic peptide-based assay for uPA cancer biomarker.

The use of synthetic bioreceptors to develop biosensing platforms has been recently gaining momentum. This case study compares the performance of a biosensing platform for the human biomarker urokinase-type plasminogen activator (h-uPA) when using two bicyclic peptides (P1 and P2) with different affinities for the target protein. The bioreceptors P1 and P2 were immobilized on magnetic microbeads and tested within a sandwich-type affinity electrochemical assay. Apart from enabling h-uPA quantification at nanomolar levels (105.8 ng/mL for P1 and 32.5 ng/mL for P2), this case study showed the potential of synthetic bicyclic peptides applicability and how bioreceptor affinity can influence the performance of the final sensing platform.

Molecular analysis and therapeutic applications of human serum albumin-fatty acid interactions.

Human serum albumin (hSA) is the major carrier protein for fatty acids (FAs) in plasma. Its ability to bind multiple FA moieties with moderate to high affinity has inspired the use of FA conjugation as a safe and natural platform to generate long-lasting therapeutics with enhanced pharmacokinetic properties and superior efficacy. In this frame, the choice of the FA is crucial and a comprehensive elucidation of the molecular interactions of FAs with hSA cannot be left out of consideration. To this intent, we report here a comparative analysis of the binding mode of different FA moieties with hSA. The choice among different albumin-binding FAs and how this influence the pharmacokinetics properties of a broad spectrum of therapeutic molecules will be discussed including a critical description of some clinically relevant FA conjugated therapeutics.

How perfluoroalkyl substances modify fluorinated self-assembled monolayer architectures: An electrochemical and computational study.

There is an urgent need for sensing strategies to screen perfluoroalkyl substances (PFAS) in aqueous matrices. These strategies must be applicable in large-scale monitoring plans to face the ubiquitous use of PFAS, their wide global spread, and their fast evolution towards short-chain, branched molecules. To this aim, the changes in fluorinated self-assembled monolayers (SAM) with different architectures (pinholes/defects-free and with randomized pinholes/defects) were studied upon exposure to both long and short-chain PFAS. The applicability of fluorinated SAM in PFAS sensing was evaluated. Changes in the SAM structures were characterised combining electrochemical impedance spectroscopy and voltammetric techniques. The experimental data interpretation was supported by molecular dynamics simulations to gain a more in-depth understanding of the interaction mechanisms involved. Pinhole/defect-free fluorinated SAM were found to be applicable to long-chain PFAS screening within switch-on sensing strategy, while a switch-off sensing strategy was reported for screening of both short/long-chain PFAS. These strategies confirmed the possibility to play on fluorophilic interactions when designing PFAS screening methods.

Structural Analysis of Human Serum Albumin in Complex with the Fibrate Drug Gemfibrozil.

Gemfibrozil (GEM) is an orally administered lipid-regulating fibrate derivative drug sold under the brand name Lopid®, among others. Since its approval in the early 80s, GEM has been largely applied to treat hypertriglyceridemia and other disorders of lipid metabolism. Though generally well tolerated, GEM can alter the distribution and the free, active concentration of some co-administered drugs, leading to adverse effects. Most of them appear to be related to the ability of GEM to bind with high affinity human serum albumin (HSA), the major drug-carrier protein in blood plasma. Here, we report the crystal structure of HSA in complex with GEM. Two binding sites have been identified, namely Sudlow's binding sites I (FA7) and II (FA3-FA4). A comparison of the crystal structure of HSA in complex with GEM with those of other previously described HSA-drug complexes enabled us to appreciate the analogies and differences in their respective binding modes. The elucidation of the molecular interaction between GEM and HSA might offer the basis for the development of novel GEM derivatives that can be safely and synergistically co-administered with other drugs, enabling augmented therapeutic efficacies.

Imaging features and ultraearly hematoma growth in intracerebral hemorrhage associated with COVID-19.

PURPOSE: Intracerebral hemorrhage (ICH) is an uncommon but deadly event in patients with COVID-19 and its imaging features remain poorly characterized. We aimed to describe the clinical and imaging features of COVID-19-associated ICH. METHODS: Multicenter, retrospective, case-control analysis comparing ICH in COVID-19 patients (COV19 +) versus controls without COVID-19 (COV19 -). Clinical presentation, laboratory markers, and severity of COVID-19 disease were recorded. Non-contrast computed tomography (NCCT) markers (intrahematoma hypodensity, heterogeneous density, blend sign, irregular shape fluid level), ICH location, and hematoma volume (ABC/2 method) were analyzed. The outcome of interest was ultraearly hematoma growth (uHG) (defined as NCCT baseline ICH volume/onset-to-imaging time), whose predictors were explored with multivariable linear regression. RESULTS: A total of 33 COV19 + patients and 321 COV19 - controls with ICH were included. Demographic characteristics and vascular risk factors were similar in the two groups. Multifocal ICH and NCCT markers were significantly more common in the COV19 + population. uHG was significantly higher among COV19 + patients (median 6.2 mL/h vs 3.1 mL/h, p = 0.027), and this finding remained significant after adjustment for confounding factors (systolic blood pressure, antiplatelet and anticoagulant therapy), in linear regression (B(SE) = 0.31 (0.11), p = 0.005). This association remained consistent also after the exclusion of patients under anticoagulant treatment (B(SE) = 0.29 (0.13), p = 0.026). CONCLUSIONS: ICH in COV19 + patients has distinct NCCT imaging features and a higher speed of bleeding. This association is not mediated by antithrombotic therapy and deserves further research to characterize the underlying biological mechanisms.

The Role of Peptides in the Design of Electrochemical Biosensors for Clinical Diagnostics.

Peptides represent a promising class of biorecognition elements that can be coupled to electrochemical transducers. The benefits lie mainly in their stability and selectivity toward a target analyte. Furthermore, they can be synthesized rather easily and modified with specific functional groups, thus making them suitable for the development of novel architectures for biosensing platforms, as well as alternative labelling tools. Peptides have also been proposed as antibiofouling agents. Indeed, biofouling caused by the accumulation of biomolecules on electrode surfaces is one of the major issues and challenges to be addressed in the practical application of electrochemical biosensors. In this review, we summarise trends from the last three years in the design and development of electrochemical biosensors using synthetic peptides. The different roles of peptides in the design of electrochemical biosensors are described. The main procedures of selection and synthesis are discussed. Selected applications in clinical diagnostics are also described.

Chemical analysis and computed tomography of metallic inclusions in Roman glass to unveil ancient coloring methods.

This paper describes the analysis of two near-spherical metallic inclusions partially incorporated within two Roman raw glass slags in order to elucidate the process that induced their formation and to determine whether their presence was related to ancient glass colouring processes. The theory of metallic scraps or powder being used in Roman times for glass-making and colouring purposes is widely accepted by the archaeological scientific community, although the assumption has been mainly based on oral traditions and documented medieval practices of glass processing. The analysis of the two inclusions, carried out by X-ray computed tomography, electrochemical analyses, and scanning electron microscopy, revealed their material composition, corrosion and internal structure. Results indicate that the two metallic bodies originated when, during the melting phase of glass, metal scraps were added to colour the material: the colloidal metal-glass system reached then a supersaturation condition and the latter ultimately induced metal expulsion and agglomeration. According to the authors' knowledge, these two inclusions represent the first documented and studied finds directly associated with the ancient practise of adding metallic agents to colour glass, and their analysis provides clear insights into the use of metallic waste in the glass colouring process.

Differential regulation of ß-catenin-mediated transcription via N- and C-terminal co-factors governs identity of murine intestinal epithelial stem cells.

The homeostasis of the gut epithelium relies upon continuous renewal and proliferation of crypt-resident intestinal epithelial stem cells (IESCs). Wnt/ß-catenin signaling is required for IESC maintenance, however, it remains unclear how this pathway selectively governs the identity and proliferative decisions of IESCs. Here, we took advantage of knock-in mice harboring transgenic ß-catenin alleles with mutations that specifically impair the recruitment of N- or C-terminal transcriptional co-factors. We show that C-terminally-recruited transcriptional co-factors of ß-catenin act as all-or-nothing regulators of Wnt-target gene expression. Blocking their interactions with ß-catenin rapidly induces loss of IESCs and intestinal homeostasis. Conversely, N-terminally recruited co-factors fine-tune ß-catenin's transcriptional output to ensure proper self-renewal and proliferative behaviour of IESCs. Impairment of N-terminal interactions triggers transient hyperproliferation of IESCs, eventually resulting in exhaustion of the self-renewing stem cell pool. IESC mis-differentiation, accompanied by unfolded protein response stress and immune infiltration, results in a process resembling aberrant "villisation" of intestinal crypts. Our data suggest that IESC-specific Wnt/ß-catenin output requires selective modulation of gene expression by transcriptional co-factors.

Unveiling the binding mode of perfluorooctanoic acid to human serum albumin.

Perfluorooctanoic acid (PFOA) is a toxic compound that is absorbed and distributed throughout the body by noncovalent binding to serum proteins such as human serum albumin (hSA). Though the interaction between PFOA and hSA has been already assessed using various analytical techniques, a high resolution and detailed analysis of the binding mode is still lacking. We report here the crystal structure of hSA in complex with PFOA and a medium-chain saturated fatty acid (FA). A total of eight distinct binding sites, four occupied by PFOAs and four by FAs, have been identified. In solution binding studies confirmed the 4:1 PFOA-hSA stoichiometry and revealed the presence of one high and three low affinity binding sites. Competition experiments with known hSA-binding drugs allowed locating the high affinity binding site in sub-domain IIIA. The elucidation of the molecular basis of the interaction between PFOA and hSA might provide not only a better assessment of the absorption and elimination mechanisms of these compounds in vivo but also have implications for the development of novel molecular receptors for diagnostic and biotechnological applications.

Native mass spectrometry for the design and selection of protein bioreceptors for perfluorinated compounds.

Biosensing platforms are answering the increasing demand for analytical tools for environmental monitoring of small molecules, such as per- and polyfluoroalkyl substances (PFAS). By transferring toxicological findings in bioreceptor design we can develop innovative pathways for biosensor design. Indeed, toxicological studies provide fundamental information about PFAS-biomolecule complexes that can help evaluate the applicability of the latter as bioreceptors. The toolbox of native mass spectrometry (MS) can support this evaluation, as shown by the two case studies reported in this work. The analysis of model proteins' (i.e. albumin, haemoglobin, cytochrome c and neuroglobin) interactions with well-known PFAS, such as perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), demonstrated the potential of this native MS screening approach. In the first case study, untreated albumin and delipidated albumin were compared in the presence and absence of PFOA confirming that the delipidation step increases albumin affinity for PFOA without affecting protein stability. In the second case study, the applicability of our methodology to identify potential bioreceptors for PFOS/PFOA was extended to other proteins. Structurally related haemoglobin and neuroglobin revealed a 1 : 1 complex, whereas no binding was observed for cytochrome c. These studies have value as a proof-of-concept for a general application of native MS to identify bioreceptors for toxic compounds.

Bio- and Biomimetic Receptors for Electrochemical Sensing of Heavy Metal Ions.

Heavy metals ions (HMI), if not properly handled, used and disposed, are a hazard for the ecosystem and pose serious risks for human health. They are counted among the most common environmental pollutants, mainly originating from anthropogenic sources, such as agricultural, industrial and/or domestic effluents, atmospheric emissions, etc. To face this issue, it is necessary not only to determine the origin, distribution and the concentration of HMI but also to rapidly (possibly in real-time) monitor their concentration levels in situ. Therefore, portable, low-cost and high performing analytical tools are urgently needed. Even though in the last decades many analytical tools and methodologies have been designed to this aim, there are still several open challenges. Compared with the traditional analytical techniques, such as atomic absorption/emission spectroscopy, inductively coupled plasma mass spectrometry and/or high-performance liquid chromatography coupled with electrochemical or UV-VIS detectors, bio- and biomimetic electrochemical sensors provide high sensitivity, selectivity and rapid responses within portable and user-friendly devices. In this review, the advances in HMI sensing in the last five years (2016-2020) are addressed. Key examples of bio and biomimetic electrochemical, impedimetric and electrochemiluminescence-based sensors for Hg2+, Cu2+, Pb2+, Cd2+, Cr6+, Zn2+ and Tl+ are described and discussed.

Neurosurgery in times of a pandemic: a survey of neurosurgical services during the COVID-19 outbreak in the Veneto region in Italy.

OBJECTIVE: The purpose of this study was to analyze the effect of the coronavirus disease 2019 (COVID-19) outbreak and of the subsequent lockdown on the neurosurgical services of the Veneto region in Italy compared to the previous 4 years. METHODS: A survey was conducted in all 6 neurosurgical departments in the Veneto region to collect data about surgical, inpatient care and endovascular procedures during the month of March for each year from 2016 to 2020. Safety measures to avoid infection from SARS-CoV-2 and any COVID-19 cases reported among neurosurgical patients or staff members were considered. RESULTS: The mean number of neurosurgical admissions for the month of March over the 2016-2019 period was 663, whereas in March 2020 admissions decreased by 42%. Emergency admissions decreased by 23%. The average number of neurosurgical procedures was 697, and declined by 30% (range -10% to -51% in individual centers). Emergency procedures decreased in the same period by 23%. Subarachnoid hemorrhage and spontaneous intracerebral hemorrhage both decreased in Veneto-by 25% and 22%, respectively. Coiling for unruptured aneurysm, coiling for ruptured aneurysm, and surgery for ruptured aneurysm or arteriovenous malformation diminished by 49%, 27%, and 78%, respectively. Endovascular procedures for acute ischemic stroke (AIS) increased by 33% in 2020 (28 procedures in total). There was a slight decrease (8%) in brain tumor surgeries. Neurosurgical admissions decreased by 25% and 35% for head trauma and spinal trauma, respectively, while surgical procedures for head trauma diminished by 19% and procedures for spinal trauma declined by 26%. Admissions and surgical treatments for degenerative spine were halved. Eleven healthcare workers and 8 patients were infected in the acute phase of the pandemic. CONCLUSIONS: This multicenter study describes the effects of a COVID-19 outbreak on neurosurgical activities in a vast region in Italy. Remodulation of neurosurgical activities has resulted in a significant reduction of elective and emergency surgeries compared to previous years. Most likely this is a combined result of cancellation of elective and postponable surgeries, increase of conservative management, increase in social restrictions, and in patients' fear of accessing hospitals. Curiously, only endovascular procedures for AIS have increased, possibly due to reduced physical activity or increased thrombosis in SARS-CoV-2. The confounding effect of thrombectomy increase over time cannot be excluded. No conclusion can be drawn on AIS incidence. Active monitoring with nasopharyngeal swabs, wearing face masks, and using separate pathways for infected patients reduce the risk of infection.

Covalent immobilization of delipidated human serum albumin on poly(pyrrole-2-carboxylic) acid film for the impedimetric detection of perfluorooctanoic acid.

The immobilization of biomolecules at screen printed electrodes for biosensing applications is still an open challenge. To enrich the toolbox of bioelectrochemists, graphite screen printed electrodes (G-SPE) were modified with an electropolymerized film of pyrrole-2-carboxilic acid (Py-2-COOH), a pyrrole derivative rich in carboxylic acid functional groups. These functionalities are suitable for the covalent immobilization of biomolecular recognition layers. The electropolymerization was first optimized to obtain stable and conductive polymeric films, comparing two different electrolytes: sodium dodecyl sulphate (SDS) and sodium perchlorate. The G-SPE modified with Py-2-COOH in 0.1 M SDS solution showed the required properties and were further tested. A proof-of-concept study for the development of an impedimetric sensor for perfluorooctanoic acid (PFOA) was carried out using the delipidated human serum albumin (hSA) as bioreceptor. The data interpretation was supported by size exclusion chromatography and small-angle X-ray scattering (SEC-SAXS) analysis of the bioreceptor-target complex and the preliminary results suggest the possibility to further develop this biosensing strategy for toxicological and analytical studies.

Redesigning an Electrochemical MIP Sensor for PFOS: Practicalities and Pitfalls.

There is a growing interest in the technological transfer of highly performing electrochemical sensors within portable analytical devices for the in situ monitoring of environmental contaminants, such as perfluorooctanesulfonic acid (PFOS). In the redesign of biomimetic sensors, many parameters should be taken into account from the working conditions to the electrode surface roughness. A complete characterization of the surface modifiers can help to avoid time-consuming optimizations and better interpret the sensor responses. In the present study, a molecularly imprinted polymer electrochemical sensor (MIP) for PFOS optimized on gold disk electrodes was redesigned on commercial gold screen-printed electrodes. However, its performance investigated by differential pulse voltammetry was found to be poor. Before proceeding with further optimization, a morphological study of the bare and modified electrode surfaces was carried out by scanning electron microscopy-energy-dispersive X-ray spectrometry (SEM-EDS), atomic force microscopy (AFM) and profilometry revealing an heterogeneous distribution of the polymer strongly influenced by the electrode roughness. The high content of fluorine of the target-template molecule allowed to map the distribution of the molecularly imprinted polymer before the template removal and to define a characterization protocol. This case study shows the importance of a multi-analytical characterization approach and identify significant parameters to be considered in similar redesigning studies.