DNA Polymerase I Large Fragment from Deinococcus radiodurans, a Candidate for a Cutting-Edge Room-Temperature LAMP.

In recent years, the loop-mediated isothermal amplification (LAMP) technique, designed for microbial pathogen detection, has acquired fundamental importance in the biomedical field, providing rapid and precise responses. However, it still has some drawbacks, mainly due to the need for a thermostatic block, necessary to reach 63 °C, which is the BstI DNA polymerase working temperature. Here, we report the identification and characterization of the DNA polymerase I Large Fragment from Deinococcus radiodurans (DraLF-PolI) that functions at room temperature and is resistant to various environmental stress conditions. We demonstrated that DraLF-PolI displays efficient catalytic activity over a wide range of temperatures and pH, maintains its activity even after storage under various stress conditions, including desiccation, and retains its strand-displacement activity required for isothermal amplification technology. All of these characteristics make DraLF-PolI an excellent candidate for a cutting-edge room-temperature LAMP that promises to be very useful for the rapid and simple detection of pathogens at the point of care.

Crystal structures of Schistosoma mansoni histone deacetylase 8 reveal a novel binding site for allosteric inhibitors.

Parasitic diseases cause significant global morbidity and mortality particularly in the poorest regions of the world. Schistosomiasis, one of the most widespread neglected tropical diseases, affects more than 200 million people worldwide. Histone deacetylase (HDAC) inhibitors are prominent epigenetic drugs that are being investigated in the treatment of several diseases, including cancers and parasitic diseases. Schistosoma mansoni HDAC8 (SmHDAC8) is highly expressed in all life cycle stages of the parasite, and selective inhibition is required in order to avoid undesirable off-target effects in the host. Herein, by X-ray crystal structures of SmHDAC8-inhibitor complexes, biochemical and phenotypic studies, we found two schistosomicidal spiroindoline derivatives binding a novel site, next to Trp198, on the enzyme surface. We determined that by acting on this site, either by mutation of the Trp198 or by compound binding, a decrease in the activity of the enzyme is achieved. Remarkably, this allosteric site differs from the human counterpart; rather, it is conserved in all Schistosoma species, as well as Rhabidoptera and Trematoda classes, thus paving the way for the design of HDAC8-selective allosteric inhibitors with improved properties.

An All-Green Photo-Electrochemical Biosensor Using Microalgae Immobilized on Eco-Designed Lignin-Based Screen-Printed Electrodes to Detect Sustainable Nanoherbicides.

Herein, a novel completely green biosensor was designed exploiting both the biological and instrumental components made of eco-friendly materials for the detection of herbicides encapsulated into biodegradable nanoparticles for a sustainable agriculture. Similar nanocarriers, indeed, can deliver herbicides to the correct location, reducing the amount of active chemicals deposited in the plant, impacting the agricultural and food industries less. However, handling measurements of nanoherbicides is crucial to provide comprehensive information about their status in the agricultural fields to support farmers in decision-making. In detail, whole cells of the unicellular green photosynthetic alga Chlamydomonas reinhardtii UV180 mutant were immobilized by a green protocol on carbonized lignin screen-printed electrodes and integrated into a photo-electrochemical transductor for the detection of nanoformulated atrazine. Specifically, atrazine encapsulated into zein and chitosan doped poly-ε-caprolactone nanoparticles (atrazine-zein and atrazine-PCL-Ch) were analyzed following the current signals at a fixed applied potential of 0.8 V, in a range between 0.1 and 5 µM, indicating a linear relationship in the measured dose-response curves and a detection limit of 0.9 and 1.1 nM, respectively. Interference studies resulted in no interference from 10 ppb bisphenol A, 1 ppb paraoxon, 100 ppb arsenic, 20 ppb copper, 5 ppb cadmium, and 10 ppb lead at safety limits. Finally, no matrix effect was observed on the biosensor response from wastewater samples and satisfactory recovery values of 106 ± 8% and 93 ± 7% were obtained for atrazine-zein and atrazine-PCL-Ch, respectively. A working stability of 10 h was achieved.

Chlamydomonas reinhardtii: A Factory of Nutraceutical and Food Supplements for Human Health.

Chlamydomonas reinhardtii (C. reinhardtii) is one of the most well-studied microalgae organisms that revealed important information for the photosynthetic and metabolic processes of plants and eukaryotes. Numerous extensive studies have also underpinned its great potential as a biochemical factory, capable of producing various highly desired molecules with a direct impact on human health and longevity. Polysaccharides, lipids, functional proteins, pigments, hormones, vaccines, and antibodies are among the valuable biomolecules that are produced spontaneously or under well-defined conditions by C. reinhardtii and can be directly linked to human nutrition and diet. The aim of this review is to highlight the recent advances in the field focusing on the most relevant applications related to the production of important biomolecules for human health that are also linked with human nutrition and diet. The limitations and challenges are critically discussed along with the potential future applications of C. reinhardtii biomass and processed products in the field of nutraceuticals and food supplements. The increasing need for high-value and low-cost biomolecules produced in an environmentally and economy sustainable manner also underline the important role of C. reinhardtii.

The Finely Coordinated Action of SSB and NurA/HerA Complex Strictly Regulates the DNA End Resection Process in Saccharolobus solfataricus.

Generation of the 3' overhang is a critical step during homologous recombination (HR) and replication fork rescue processes. This event is usually performed by a series of DNA nucleases and/or helicases. The nuclease NurA and the ATPase HerA, together with the highly conserved MRE11/RAD50 proteins, play an important role in generating 3' single-stranded DNA during archaeal HR. Little is known, however, about HerA-NurA function and activation of this fundamental and complicated DNA repair process. Herein, we analyze the functional relationship among NurA, HerA and the single-strand binding protein SSB from Saccharolubus solfataricus. We demonstrate that SSB clearly inhibits NurA endonuclease activity and its exonuclease activities also when in combination with HerA. Moreover, we show that SSB binding to DNA is greatly stimulated by the presence of either NurA or NurA/HerA. In addition, if on the one hand NurA binding is not influenced, on the other hand, HerA binding is reduced when SSB is present in the reaction. In accordance with what has been observed, we have shown that HerA helicase activity is not stimulated by SSB. These data suggest that, in archaea, the DNA end resection process is governed by the strictly combined action of NurA, HerA and SSB.

A dual electro-optical biosensor based on Chlamydomonas reinhardtii immobilised on paper-based nanomodified screen-printed electrodes for herbicide monitoring.

The indiscriminate use of herbicides in agriculture contributes to soil and water pollution, with important endangering consequences on the ecosystems. Among the available analytical systems, algal biosensors have demonstrated to be valid tools thanks to their high sensitivity, cost-effectiveness, and eco-design. Herein, we report the development of a dual electro-optical biosensor for herbicide monitoring, based on Chlamydomonas reinhardtii whole cells immobilised on paper-based screen-printed electrodes modified with carbon black nanomaterials. To this aim, a systematic study was performed for the selection and characterisation of a collection among 28 different genetic variants of the alga with difference response behaviour towards diverse herbicide classes. Thus, CC125 strain was exploited as case study for the study of the analytical parameters. The biosensor was tested in standard solutions and real samples, providing high sensitivity (detection limit in the pico/nanomolar), high repeatability (RSD of 5% with n = 100), long lasting working (10 h) and storage stability (3 weeks), any interference in the presence of heavy metals and insecticides, and low matrix effect in drinking water and moderate effect in surface one.

The plastoquinol-plastoquinone exchange mechanism in photosystem II: insight from molecular dynamics simulations.

In the photosystem II (PSII) of oxygenic photosynthetic organisms, the reaction center (RC) core mediates the light-induced electron transfer leading to water splitting and production of reduced plastoquinone molecules. The reduction of plastoquinone to plastoquinol lowers PSII affinity for the latter and leads to its release. However, little is known about the role of protein dynamics in this process. Here, molecular dynamics simulations of the complete PSII complex embedded in a lipid bilayer have been used to investigate the plastoquinol release mechanism. A distinct dynamic behavior of PSII in the presence of plastoquinol is observed which, coupled to changes in charge distribution and electrostatic interactions, causes disruption of the interactions seen in the PSII-plastoquinone complex and leads to the "squeezing out" of plastoquinol from the binding pocket. Displacement of plastoquinol closes the second water channel, recently described in a 2.9 Å resolution PSII structure (Guskov et al. in Nat Struct Mol Biol 16:334-342, 2009), allowing to rule out the proposed "alternating" mechanism of plastoquinol-plastoquinone exchange, while giving support to the "single-channel" one. The performed simulations indicated a pivotal role of D1-Ser264 in modulating the dynamics of the plastoquinone binding pocket and plastoquinol-plastoquinone exchange via its interaction with D1-His252 residue. The effects of the disruption of this hydrogen bond network on the PSII redox reactions were experimentally assessed in the D1 site-directed mutant Ser264Lys.

Organophosphorous Pesticide Detection in Olive Oil by Using a Miniaturized, Easy-to-Use, and Cost-Effective Biosensor Combined with QuEChERS for Sample Clean-Up.

Herein, we report a portable electrochemical biosensor based on butyrylcholinesterase (BChE) immobilized on carbon black (CB)-modified screen-printed electrodes (SPEs) for the detection of organophosphorous pesticides in olive oil. The BChE/CB-SPE biosensor was developed to detect paraoxon in standard solutions as well as in olive oil samples previously treated with the QuEChERS method to extract pesticides from the whole fatty matrix. The biosensor shows a linear concentration range of between 20 and 100 ppb for paraoxon both in standard solutions (phosphate buffer 0.05 M) and in olive oil extracts, with a detection limit of 6 ppb in olive oil extract, corresponding to 10% of inhibition. The accuracy of this biosensor in olive oil samples was assessed with olive oil spiked with paraoxon, obtaining satisfactory recovery values.

A choline oxidase amperometric bioassay for the detection of mustard agents based on screen-printed electrodes modified with Prussian Blue nanoparticles.

In this work a novel bioassay for mustard agent detection was proposed. The bioassay is based on the capability of these compounds to inhibit the enzyme choline oxidase. The enzymatic activity, which is correlated to the mustard agents, was electrochemically monitored measuring the enzymatic product, hydrogen peroxide, by means of a screen-printed electrode modified with Prussian Blue nanoparticles. Prussian Blue nanoparticles are able to electrocatalyse the hydrogen peroxide concentration reduction at low applied potential (-50 mV vs. Ag/AgCl), thus allowing the detection of the mustard agents with no electrochemical interferences. The suitability of this novel bioassay was tested with the nitrogen mustard simulant bis(2-chloroethyl)amine and the sulfur mustard simulants 2-chloroethyl ethyl sulfide and 2-chloroethyl phenyl sulfide. The bioassay proposed in this work allowed the detection of mustard agent simulants with good sensitivity and fast response, which are excellent premises for the development of a miniaturised sensor well suited for an alarm system in case of terrorist attacks.

Design and biophysical characterization of atrazine-sensing peptides mimicking the Chlamydomonas reinhardtii plastoquinone binding niche.

The plastoquinone (Q(B)) binding niche of the Photosystem II (PSII) D1 protein is the subject of intense research due to its capability to bind also anthropogenic pollutants. In this work, the Chlamydomonas reinhardtii D1 primary structure was used as a template to computationally design novel peptides enabling the binding of the herbicide atrazine. Three biomimetic molecules, containing the Q(B)-binding site in a loop shaped by two α-helices, were reconstituted by automated protein synthesis, and their structural and functional features deeply analysed by biophysical techniques. Standing out among the others, the biomimetic mutant peptide, D1pepMut, showed high ability to mimic the D1 protein in binding both Q(B) and atrazine. Circular dichroism spectra suggested a typical properly-folded α-helical structure, while isothermal titration calorimetry (ITC) provided a complete thermodynamic characterization of the molecular interaction. Atrazine binds to the D1pepMut with a high affinity (Kd = 2.84 µM), and a favourable enthalpic contribution (ΔH = -11.9 kcal mol(-1)) driving the interaction. Fluorescence spectroscopy assays, in parallel to ITC data, provided hyperbolic titration curves indicating the occurrence of a single atrazine binding site. The binding resulted in structural stabilisation of the D1pepMut molecule, as suggested by atrazine-induced cooperative profiles for the fold-unfold transition. The interaction dynamics and the structural stability of the peptides in response to the ligand were particularly considered as mandatory parameters for biosensor/biochip development. These studies paved the way to the set-up of an array of synthetic mutant peptides with a wide range of affinity towards different classes of target analytes, for the development of optical nanosensing platforms for herbicide detection.

Last Trends in Point-of-Care (POC) Diagnostics for the Management of Hematological Indices in Home Care Patients.

Today, complete blood count (CBC) analyses are highly automated and allow for high throughput and accurate and reliable results. However, new analytical tools are in great demand to provide simple, rapid and cost-effective management of hematological indices in home care patients. Chronic disease monitoring at home has become a benefit for patients who are finding cost savings in programs designed to monitor/treat patients in offsite locations. This review reports the latest trends in point-of-care (POC) diagnostics useful for home testing of key hematological counts that may be affected during home therapy treatment.

A Proof-of-Concept Electrochemical Cytosensor Based on Chlamydomonas reinhardtii Functionalized Carbon Black Screen-Printed Electrodes: Detection of Escherichia coli in Wastewater as a Case Study.

Herein, we report a proof-of-concept algal cytosensor for the electrochemical quantification of bacteria in wastewater, exploiting the green photosynthetic alga Chlamydomonas reinhardtii immobilized on carbon black (CB) nanomodified screen-printed electrodes. The CB nanoparticles are used as nanomodifiers, as they are able to sense the oxygen produced by the algae and thus the current increases when algae are exposed to increasing concentrations of bacteria. The sensor was tested on both standard solutions and real wastewater samples for the detection Escherichia coli in a linear range of response from 100 to 2000 CFU/100 mL, showing a limit of detection of 92 CFU/100 mL, in agreement with the maximum E. coli concentration established by the Italian law for wastewater (less than 5000 CFU/100 mL). This bacterium was exploited as a case study target of the algal cytosensor to demonstrate its ability as an early warning analytical system to signal heavy loads of pathogens in waters leaving the wastewater treatment plants. Indeed, the cytosensor is not selective towards E. coli but it is capable of sensing all the bacteria that induce the algae oxygen evolution by exploiting the effect of their interaction. Other known toxicants, commonly present in wastewater, were also analyzed to test the cytosensor selectivity, with any significant effect, apart from atrazine, which is a specific target of the D1 protein of the Chlamydomonas photosystem II. However, the latter can also be detected by chlorophyll fluorescence simultaneously to the amperometric measurements. The matrix effect was evaluated, and the recovery values were calculated as 105 ± 8, 83 ± 7, and 88 ± 7% for 1000 CFU/100 mL of E. coli in Lignano, San Giorgio, and Pescara wastewater samples, respectively.

Isothermal amplification-assisted diagnostics for COVID-19.

The scenery of molecular diagnostics for infectious diseases is rapidly evolving to respond to the COVID-19 epidemic. The sensitivity and specificity of diagnostics, along with speed and accuracy, are crucial requirements for effective analytical tools to address the disease spreading around the world. Emerging diagnostic devices combine the latest trends in isothermal amplification methods for nucleic acids with state-of-the-art biosensing systems, intending to bypass roadblocks encountered in the last 2 years of the pandemic. Isothermal nucleic acid amplification is a simple procedure that quickly and efficiently accumulates nucleic acid sequences at a constant temperature, without the need for sophisticated equipment. The integration of isothermal amplification into portable biosensing devices confers high sensitivity and improves screening at the point of need in low-resource settings. This review reports the latest trends reached in this field with the latest examples of isothermal amplification-powered biosensors for detecting SARS-CoV-2, with different configurations, as well as their intrinsic advantages and disadvantages.

Photoautotrophs-Bacteria Co-Cultures: Advances, Challenges and Applications.

Photosynthetic microorganisms are among the fundamental living organisms exploited for millennia in many industrial applications, including the food chain, thanks to their adaptable behavior and intrinsic proprieties. The great multipotency of these photoautotroph microorganisms has been described through their attitude to become biofarm for the production of value-added compounds to develop functional foods and personalized drugs. Furthermore, such biological systems demonstrated their potential for green energy production (e.g., biofuel and green nanomaterials). In particular, the exploitation of photoautotrophs represents a concrete biorefinery system toward sustainability, currently a highly sought-after concept at the industrial level and for the environmental protection. However, technical and economic issues have been highlighted in the literature, and in particular, challenges and limitations have been identified. In this context, a new perspective has been recently considered to offer solutions and advances for the biomanufacturing of photosynthetic materials: the co-culture of photoautotrophs and bacteria. The rational of this review is to describe the recently released information regarding this microbial consortium, analyzing the critical issues, the strengths and the next challenges to be faced for the intentions attainment.

Quantum dots functionalised artificial peptides bioinspired to the D1 protein from the Photosystem II of Chlamydomonas reinhardtii for endocrine disruptor optosensing.

Herein we describe the design and synthesis of novel artificial peptides mimicking the plastoquinone binding niche of the D1 protein from the green photosynthetic alga Chlamydomonas reinhardtii, also able to bind herbicides. In particular, molecular dynamics (MD) simulations were performed to model in silico the behaviour of three peptides, D1Pep70-H, D1Pep70-S264K and D1Pep70-S268C, as genetic variants with different affinity towards the photosynthetic herbicide atrazine. Then the photosynthetic peptides were functionalised with quantum dots for the development of a hybrid optosensor for the detection of atrazine, one of the most employed herbicides for weed control in agriculture as well as considered as a putative endocrine disruptor case study. The excellent agreement between computational and experimental results self consistently shows resistance or super-sensitivity toward the atrazine target, with detection limits in the µg/L concentration range, meeting the requirements of E.U. legislation.

State of the Art on the SARS-CoV-2 Toolkit for Antigen Detection: One Year Later.

The recent global events of COVID-19 in 2020 have alerted the world to the risk of viruses and their impacts on human health, including their impacts in the social and economic sectors. Rapid tests are urgently required to enable antigen detection and thus to facilitate rapid and simple evaluations of contagious individuals, with the overriding goal to delimitate spread of the virus among the population. Many efforts have been achieved in recent months through the realization of novel diagnostic tools for rapid, affordable, and accurate analysis, thereby enabling prompt responses to the pandemic infection. This review reports the latest results on electrochemical and optical biosensors realized for the specific detection of SARS-CoV-2 antigens, thus providing an overview of the available diagnostics tested and marketed for SARS-CoV-2 antigens as well as their pros and cons.

Biotechnological Advances in the Design of Algae-Based Biosensors.

In addition to their use in biomass production and bioremediation, algae have been extensively exploited in biosensing applications. Algae-based biosensors have demonstrated potential for sensitive, sustainable, and multiplexed detection of analytes of agroenvironmental and security interest. Their advantages include the availability of different algal bioreceptors including whole cells and their photosynthetic subcomponents, their potential to be integrated into dual transduction miniaturized devices, and the opportunity for continuous environmental monitoring. Despite obstacles including limited stability and selectivity, algae-based biosensing is a realistic prospect that has some recent effective applications. Strategic exploitation of cutting-edge technologies including materials science, nanotechnology, microfluidics, and genome editing will help to achieve the full potential of algae-based sensors.

Reusable optical multi-plate sensing system for pesticide detection by using electrospun membranes as smart support for acetylcholinesterase immobilisation.

Herein we report a multiplated and biopolymeric-based optical bioassay for organophosphate detection based on the use of acetylcholinesterase (AChE) as biocomponent and biopolymeric electrospun fibrous mats as eco-designed supports for AChE immobilisation. The principle of the detection relays on the decrease of enzymatic activity due to the capability of the organophosphorus pesticides to irreversibly inhibit AChE, which is optically detected using Ellman colorimetric method. The proposed bioassay consists in a novel, cost-effective, and multiplex-based 96-well system, in combination with customised biopolymeric membranes modified with AChE, with the aim to deliver a sustainable analytical tool. Indeed, the designed set-up should provide and guarantee several advantages, including: i) the re-use of plastic multi-plate with the only replacement of polymer dishes in the case of inhibition absence; ii) the exploiting of the properties of the immobilised enzyme, i.e. multiple analysis using the same amount of enzyme, reducing the AChE amount for analysis. In detail, three different biopolymers (i.e. polylactic acid (PLA), polycaprolactone (PCL), and poly-hydroxybutyrate-co-hydroxyvalerate (PHBV)) were investigated and morphologically characterised, as supports for enzyme immobilisation, to identify the optimal one. Among them, PHBV was selected as the best support to immobilise AChE by cross-linking method. The analytical features of the bioassay were then assessed by measuring standard solutions of paraoxon in a range of concentrations between 10 and 100 ppb, achieving a linear range up to 60 ppb and a detection limit of 10 ppb. Thus, the suitability of this sustainable bioassay to detect organophosphate at ppb level was demonstrated.

High-Tech and Nature-Made Nanocomposites and Their Applications in the Field of Sensors and Biosensors for Gas Detection.

Gas sensors have been object of increasing attention by the scientific community in recent years. For the development of the sensing element, two major trends seem to have appeared. On one hand, the possibility of creating complex structures at the nanoscale level has given rise to ever more sensitive sensors based on metal oxides and metal-polymer combinations. On the other hand, gas biosensors have started to be developed, thanks to their intrinsic ability to be selective for the target analyte. In this review, we analyze the recent progress in both areas and underline their strength, current problems, and future perspectives.

Carbon black as an outstanding and affordable nanomaterial for electrochemical (bio)sensor design.

Advances in cutting-edge technologies including nanotechnology, microfluidics, electronic engineering, and material science have boosted a new era in the design of robust and sensitive biosensors. In recent years, carbon black has been re-discovered in the design of electrochemical (bio)sensors thanks to its interesting electroanalytical properties, absence of treatment requirement, cost-effectiveness (c.a. 1 €/Kg), and easiness in the preparation of stable dispersions. Herein, we present an overview of the literature on carbon black-based electrochemical (bio)sensors, highlighting current trends and possible challenges to this rapidly developing area, with a special focus on the fabrication of carbon black-based electrodes in the realisation of sensors and biosensors (e.g. enzymatic, immunosensors, and DNA-based).