Learning from virtual experiments to assist users of Small Angle Neutron Scattering in model selection.

In this work, we combine the advantages of virtual Small Angle Neutron Scattering (SANS) experiments carried out by Monte Carlo simulations with the recent advances in computer vision to generate a tool that can assist SANS users in small angle scattering model selection. We generate a dataset of almost 260.000 SANS virtual experiments of the SANS beamline KWS-1 at FRM-II, Germany, intended for Machine Learning purposes. Then, we train a recommendation system based on an ensemble of Convolutional Neural Networks to predict the SANS model from the two-dimensional scattering pattern measured at the position-sensitive detector of the beamline. The results show that the CNNs can learn the model prediction task, and that this recommendation system has a high accuracy in the classification task on 46 different SANS models. We also test the network with real data and explore the outcome. Finally, we discuss the reach of counting with the set of virtual experimental data presented here, and of such a recommendation system in the SANS user data analysis procedure.

RNA Sequencing Experimental Analysis Workflow Using Caenorhabditis elegans.

RNA sequencing is an approach to transcriptomic profiling that enables the detection of differentially expressed genes in response to genetic mutation or experimental treatment, among other uses. Here we describe a method for the use of a customizable, user-friendly bioinformatic pipeline to identify differentially expressed genes in RNA sequencing data obtained from C. elegans, with attention to the improvement in reproducibility and accuracy of results.

Perkinsus marinus in bioreactor: growth and a cost-reduced growth medium.

Perkinsus marinus (Perkinsea) is an osmotrophic facultative intracellular marine protozoan responsible for "Dermo" disease in the eastern oyster, Crassostrea virginica. In 1993 in vitro culture of P. marinus was developed in the absence of host cells. Compared to most intracellular protozoan parasites, the availability of P. marinus to grow in the absence of host cells has provided the basis to explore its use as a heterologous expression system. As the genetic toolbox is becoming available, there is also the need for larger-scale cultivation and lower-cost media formulations. Here, we took an industrial approach to scaled-up growth from a small culture flask to bioreactors, which required developing new cultivation parameters, including aeration, mixing, pH, temperature control, and media formulation. Our approach also enabled more real-time data collection on growth. The bioreactor cultivation method showed similar or accelerated growth rates of P. marinus compared to culture in T-flasks. Redox measurements indicated sufficient oxygen availability throughout the cultivation. Replacing fetal bovine serum with chicken serum showed no differences in the growth rate and a 60% reduction in the medium cost. This study opens the door to furthering P. marinus as a valid heterologous expression system by showing the ability to grow in bioreactors. ONE-SENTENCE SUMMARY: Perkinsus marinus, a microbial parasite of oysters that could be useful for developing vaccines for humans, has been shown to grow well in laboratory equipment that can be expanded to commercial scale using a less expensive growth formula than usual laboratory practice.

Survival and Detection of Bivalve Transmissible Neoplasia from the Soft-Shell Clam Mya arenaria (MarBTN) in Seawater.

Many pathogens can cause cancer, but cancer itself does not normally act as an infectious agent. However, transmissible cancers have been found in a few cases in nature: in Tasmanian devils, dogs, and several bivalve species. The transmissible cancers in dogs and devils are known to spread through direct physical contact, but the exact route of transmission of bivalve transmissible neoplasia (BTN) has not yet been confirmed. It has been hypothesized that cancer cells from bivalves could be released by diseased animals and spread through the water column to infect/engraft into other animals. To test the feasibility of this proposed mechanism of transmission, we tested the ability of BTN cells from the soft-shell clam (Mya arenaria BTN, or MarBTN) to survive in artificial seawater. We found that MarBTN cells are highly sensitive to salinity, with acute toxicity at salinity levels lower than those found in the native marine environment. BTN cells also survive longer at lower temperatures, with 50% of cells surviving greater than 12 days in seawater at 10 °C, and more than 19 days at 4 °C. With one clam donor, living cells were observed for more than eight weeks at 4 °C. We also used qPCR of environmental DNA (eDNA) to detect the presence of MarBTN-specific DNA in the environment. We observed release of MarBTN-specific DNA into the water of laboratory aquaria containing highly MarBTN-diseased clams, and we detected MarBTN-specific DNA in seawater samples collected from MarBTN-endemic areas in Maine, although the copy numbers detected in environmental samples were much lower than those found in aquaria. Overall, these data show that MarBTN cells can survive well in seawater, and they are released into the water by diseased animals. These findings support the hypothesis that BTN is spread from animal-to-animal by free cells through seawater.

CRISPR/Cas9 Ribonucleoprotein-Based Genome Editing Methodology in the Marine Protozoan Parasite Perkinsus marinus.

Perkinsus marinus (Perkinsozoa), a close relative of apicomplexans, is an osmotrophic facultative intracellular marine protozoan parasite responsible for "Dermo" disease in oysters and clams. Although there is no clinical evidence of this parasite infecting humans, HLA-DR40 transgenic mice studies strongly suggest the parasite as a natural adjuvant in oral vaccines. P. marinus is being developed as a heterologous gene expression platform for pathogens of medical and veterinary relevance and a novel platform for delivering vaccines. We previously reported the transient expression of two rodent malaria genes Plasmodium berghei HAP2 and MSP8. In this study, we optimized the original electroporation-based protocol to establish a stable heterologous expression method. Using 20 µg of pPmMOE[MOE1]:GFP and 25.0 × 106 P. marinus cells resulted in 98% GFP-positive cells. Furthermore, using the optimized protocol, we report for the first time the successful knock-in of GFP at the C-terminus of the PmMOE1 using ribonucleoprotein (RNP)-based CRISPR/Cas9 gene editing methodology. The GFP was expressed 18 h post-transfection, and expression was observed for 8 months post-transfection, making it a robust and stable knock-in system.

First characterization of chemical environments using energy dispersive inelastic x-ray scattering induced by an x-ray tube.

Energy Dispersive Inelastic X-ray Scattering (EDIXS) is a reliable technique for the discrimination and characterization of local chemical environments. By means of this methodology, the speciation of samples has been attained in a variety of samples and experimental conditions, such as total reflection, grazing incidence, and confocal setups. Until now, due to the requirement of a monochromatic and intense exciting beam, this tool had been applied using exclusively synchrotron radiation sources. We present, for the first time, results of test measurements using EDIXS for chemical characterization implemented in a conventional x-ray tube based laboratory. The results show good discrimination between different iron compounds under study, suggesting the real possibility of rutinary chemical state characterizations of samples by means of EDIXS using a conventional x-ray tube.

A compact high-resolution spectrometer based on a segmented conical crystal analyzer.

In this work, the design, fabrication, and evaluation of a compact, one-shot spectrometer based on a segmented conically bent crystal analyzer are described. The system is a "one-shot" wavelength dispersive spectrometer, which has a crystal analyzer with an innovative geometry. It reaches an energy resolution of around 8 eV for Mn Kα1 line, which is at least an order of magnitude better than the commonly used energy dispersive spectrometers for fluorescence, and is comparable to current wavelength dispersive spectrometers. The prototype spectrometer fabricated in this work avoids angle scans that most wavelength dispersive spectrometers require, has the advantage of a sample-detector distance of only 146 mm, and allows for the simultaneous measurement of approximately a 2 keV window. This system is suitable to be used at synchrotron radiation facilities and free electron lasers, and it can even be adapted to an x-ray tube in any conventional x-ray laboratory.

Genome to phenome tools: In vivo and in vitro transfection of Crassostrea virginica hemocytes.

The sequencing of the Crassostrea virginica genome has brought back the interest for gene delivery and editing methodologies. Here, we report the expression in oyster hemocytes of two heterologous expression vectors under the CMV promoter delivered with dendrimers. Expression was monitored using confocal microscopy, flow cytometry, and immunofluorescence assay. C. virginica hemocytes were able to express the green fluorescence protein and Crassostrea gigas vascular endothelial growth factor under CMV viral promoter both in vivo and in vitro. These results provide the bases for interrogating the genome and adapting genome editing methodologies.

Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

A qPCR-Based Survey of Haplosporidium nelsoni and Perkinsus spp. in the Eastern Oyster, Crassostrea virginica in Maine, USA.

Eastern oyster (Crassostrea virginica) aquaculture is increasingly playing a significant role in the state of Maine's (USA) coastal economy. Here, we conducted a qPCR-based survey for Haplosporidium nelsoni, Perkinsus marinus, and Perkinsus chesapeaki in C. virginica (n = 1440) from six Maine sites during the summer-fall of 2016 and 2017. In the absence of reported die-offs, our results indicated the continued presence of the three protozoan parasites in the six sites. The highest H. nelsoni qPCR-prevalence corresponded to Jack's Point and Prentiss Island (x=40 and 48% respectively), both located in the Damariscotta River Estuary. Jack's Point, Prentiss Island, New Meadows River, and Weskeag River recorded the highest qPCR-prevalence for P. marinus (32-39%). While the P. marinus qPCR-prevalence differed slightly for the years 2016 and 2017, P. chesapeaki qPCR-prevalence in 2016 was markedly lower than 2017 (<20% at all sites versus >60% at all sites for each of the years, respectively). Mean qPCR-prevalence values for P. chesapeaki over the two-year study were ≥40% for samples from Jack's Point (49%), Prentiss Island (44%), and New Meadows River (40%). This study highlights that large and sustained surveys for parasitic diseases are fundamental for decision making toward the management of the shellfish aquaculture industry, especially for having a baseline in the case that die-offs occur.

Genetic tool development in marine protists: emerging model organisms for experimental cell biology.

Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.

Uso de plasma rico en fibrina comparado con colágeno en el tratamiento de recesión gingival utilizando la técnica estenopéica. Ensayo clínico aleatorizado / Use of fibrin-rich plasma compared to collagen in the treatment of gingival recession using the stenopic technique. Randomized clinical trial

La recesión gingival (RG) es un problema de salud bucodental frecuente que aumenta con la edad, predispone a hipersensibilidad dentaria, caries radicular, inflamación gingival y efectos antiestéticos. El objetivo de este ensayo clínico aleatorizado fue evaluar comparativamente el efecto clínico del recubrimiento radicular utilizando la técnica estenopéica Pinhole con colágeno y la técnica estenopéica Pinhole modificada al incorporarle plasma rico en fibrina (PRF). Veintiséis participantes sistémicamente sanos, con diagnóstico de RG grado I de Miller, fueron reclutados y seguidos por 6 meses después de la cirugía. Los parámetros clínicos registrados fueron nivel de inserción clínica (NIC), RG y banda de encía queratinizada. Los participantes fueron asignados aleatoriamente a un grupo en quienes se utilizó PRF con 14 participantes, tratando 36 piezas dentales, y otro grupo en quienes se utilizó membrana de colágeno con 12 participantes, tratando 35 piezas dentales. Los resultados muestran un logro de ganancia en el NIC en ambos grupos, (M = 45.24 %, DE = 17.37 %) en el grupo PRF y (M = 47.37 %, DE = 15.67 %) en el grupo colágeno, diferencia que no fue significativa (p = .59). En ambos grupos existió un aumento significativo en la banda de encía queratinizada (p < .01). El uso de PRF como material de relleno al realizar la técnica estenopéica genera resultados similares al ser comparado con la técnica convencional que utiliza colágeno. Al presentar un menor costo el PRF aumenta las posibilidades que más personas tengan acceso al tratamiento.

Gingival recession (GR) is a frequent oral health disease that increases with age and may increase risk of dental hypersensitivity, root decay, gingival inflammation and aesthetic problems. The aim of this randomized clinical trial was to compare clinical parameters of dental root coverage using Pinhole technique with collagen and modi¬fied Pinhole technique using platelet-rich fibrin (PRF). Twenty-six participants, systemically healthy, with Miller class I GR diagnosis, were recruited and measured at baseline and after 6 months follow-up. Clinical parameters measured included clinical attachment level (ICL), GR and keratinized gingival width (KGW). All participants were randomly assigned to a group using PRF, with 14 participants and 36 teeth treated, and other group using collagen, with 12 participants and 35 teeth treated. Both PRF group and collagen group gained ICL, (M = 45.24 %, SD = 17.37 %) in PRF group and (M = 47.37 %, SD = 15.67 %) in collagen group, with no statistically significant difference (p = .59). Both groups gained KGW (p < .01). Use of PRF as filled material by using Pinhole technique resulted in similar clinical improvements compare to collagen as filled material. Considering that PRF is cheaper than collagen, it increases chances that people can have access to treatment.

Molecular Epizootiology of Toxoplasma gondii and Cryptosporidium parvum in the Eastern Oyster (Crassostrea virginica) from Maine (USA).

Shellfish are known as a potential source of Toxoplasma gondii (responsible for toxoplasmosis), and Cryptosporidium parvum, which is one of the major causes of gastroenteritis in the world. Here we performed a comprehensive qPCR-based monthly survey for T. gondii and C. parvum during 2016 and 2017 in oysters (Crassostrea virginica) (n = 1440) from all six sites along the coast of Maine (USA). Pooled samples (mantle, gills, and rectum) from individual oysters were used for DNA extraction and qPCR. Our study resulted in detections of qPCR positives oysters for T. gondii and C. parvum at each of the six sites sampled (in 31% and 10% of total oysters, respectively). The prevalence of T. gondii was low in 2016, and in September 2017 several sites peaked in prevalence with 100% of the samples testing positive. The prevalence of C. parvum was very low except in one estuarine location (Jack's Point) in June 2016 (58%), and in October of 2016, when both prevalence and density of C. parvum at most of the sampling sites were among the highest values detected. Statistical analysis of environmental data did not identify clear drivers of retention, but there were some notable statistically significant patterns including current direction and nitrate along with the T. gondii prevalence. The major C. parvum retention event (in October 2016) corresponded with the month of highest dissolved oxygen measurements as well as a shift in the current direction revealed by nearby instrumentation. This study may guide future research to locate any contributing parasite reservoirs and evaluate the potential risk to human consumption.

From the raw bar to the bench: Bivalves as models for human health.

Bivalves, from raw oysters to steamed clams, are popular choices among seafood lovers and once limited to the coastal areas. The rapid growth of the aquaculture industry and improvement in the preservation and transport of seafood have enabled them to be readily available anywhere in the world. Over the years, oysters, mussels, scallops, and clams have been the focus of research for improving the production, managing resources, and investigating basic biological and ecological questions. During this decade, an impressive amount of information using high-throughput genomic, transcriptomic and proteomic technologies has been produced in various classes of the Mollusca group, and it is anticipated that basic and applied research will significantly benefit from this resource. One aspect that is also taking momentum is the use of bivalves as a model system for human health. In this review, we highlight some of the aspects of the biology of bivalves that have direct implications in human health including the shell formation, stem cells and cell differentiation, the ability to fight opportunistic and specific pathogens in the absence of adaptive immunity, as source of alternative drugs, mucosal immunity and, microbiome turnover, toxicology, and cancer research. There is still a long way to go; however, the next time you order a dozen oysters at your favorite raw bar, think about a tasty model organism that will not only please your palate but also help unlock multiple aspects of molluscan biology and improve human health.

Energy-Dispersive Total-Reflection Resonant Inelastic X-ray Scattering as a Tool for Elemental Speciation in Contaminated Water.

This work presents a state-of the-art analytical methodology, by which chemical state information on metallic elements is obtained for liquid samples in a fast and simple manner. This method overcomes limitations of conventional X-ray techniques, such as X-ray absorption spectroscopy, by applying resonant inelastic X-ray scattering under total reflection geometry (TRIXS). TRIXS is particularly applicable for the analysis of small quantity of liquid samples deposited on polished reflectors. This feature is relevant for the chemical speciation of metallic trace elements contained in water samples, since the degree of their toxicity depends crucially on the concentration of specific chemical species included. The analytical merits of the proposed methodology were studied at Elettra Sincrotrone Trieste and at the Brazilian Synchrotron Light Laboratory. Contaminated water samples with low concentration of different chromium and manganese compounds were measured. Results prove the analytical potential of the TRIXS technique in characterizing different chemical species of metallic elements in water samples.

Transient Expression of Plasmodium berghei MSP8 and HAP2 in the Marine Protozoan Parasite Perkinsus marinus.

Perkinsus marinus is a protozoan parasite of molluscs that can be propagated in vitro in a defined culture medium, in the absence of host cells. We previously reported that P. marinus trophozoites can be transfected with high efficiency by electroporation using a plasmid based on MOE, a highly expressed gene, and proposed its potential use as a "pseudoparasite." This is a novel gene expression platform for parasites of medical relevance for which the choice of the surrogate organism is based on phylogenetic affinity to the parasite of interest, while taking advantage of the whole engineered surrogate organism as a vaccination adjuvant. Here we improved the original transfection plasmid by incorporating a multicloning site, an enterokinase recognition sequence upstream of GFP, and a His-tag and demonstrate its potential suitability for the heterologous expression of Plasmodium sp. genes relevant to the development of anti-malarial vaccines. Plasmodium berghei HAP2 and MSP8, currently considered candidate genes for a malaria vaccine, were cloned into p[MOE]:GFP, and the constructs were used to transfect P. marinus trophozoites. Within 48 hr of transfection we observed fluorescent cells indicating that the P. berghei genes fused to GFP were expressed. The expression appeared to be transient for both P. berghei genes, as florescence of the transfectants diminished gradually over time. Although this heterologous expression system will require optimization for integration and constitutive expression of Plasmodium genes, our results represent attainment of proof for the "pseudoparasite" concept we previously proposed, as we show that the engineered P. marinus system has the potential to become a surrogate system suitable for expression of Plasmodium spp. genes of interest, which could eventually be used as a malaria vaccine delivery platform. The aim of the present study was to test the ability of marine protozoan parasite P. marinus to express genes of P. berghei .

Open Source Drug Discovery with the Malaria Box Compound Collection for Neglected Diseases and Beyond.

A major cause of the paucity of new starting points for drug discovery is the lack of interaction between academia and industry. Much of the global resource in biology is present in universities, whereas the focus of medicinal chemistry is still largely within industry. Open source drug discovery, with sharing of information, is clearly a first step towards overcoming this gap. But the interface could especially be bridged through a scale-up of open sharing of physical compounds, which would accelerate the finding of new starting points for drug discovery. The Medicines for Malaria Venture Malaria Box is a collection of over 400 compounds representing families of structures identified in phenotypic screens of pharmaceutical and academic libraries against the Plasmodium falciparum malaria parasite. The set has now been distributed to almost 200 research groups globally in the last two years, with the only stipulation that information from the screens is deposited in the public domain. This paper reports for the first time on 236 screens that have been carried out against the Malaria Box and compares these results with 55 assays that were previously published, in a format that allows a meta-analysis of the combined dataset. The combined biochemical and cellular assays presented here suggest mechanisms of action for 135 (34%) of the compounds active in killing multiple life-cycle stages of the malaria parasite, including asexual blood, liver, gametocyte, gametes and insect ookinete stages. In addition, many compounds demonstrated activity against other pathogens, showing hits in assays with 16 protozoa, 7 helminths, 9 bacterial and mycobacterial species, the dengue fever mosquito vector, and the NCI60 human cancer cell line panel of 60 human tumor cell lines. Toxicological, pharmacokinetic and metabolic properties were collected on all the compounds, assisting in the selection of the most promising candidates for murine proof-of-concept experiments and medicinal chemistry programs. The data for all of these assays are presented and analyzed to show how outstanding leads for many indications can be selected. These results reveal the immense potential for translating the dispersed expertise in biological assays involving human pathogens into drug discovery starting points, by providing open access to new families of molecules, and emphasize how a small additional investment made to help acquire and distribute compounds, and sharing the data, can catalyze drug discovery for dozens of different indications. Another lesson is that when multiple screens from different groups are run on the same library, results can be integrated quickly to select the most valuable starting points for subsequent medicinal chemistry efforts.

An Agar-Based Method for Plating Marine Protozoan Parasites of the Genus Perkinsus.

The genus Perkinsus includes protozoan parasites of mollusks responsible for losses in the aquaculture industry and hampering the recovery of natural shellfish beds worldwide, and they are a key taxon for understanding intracellular parasitism adaptations. The ability to propagate the parasite in liquid media, in the absence of the host, has been crucial for improving understanding of its biology; however, alternative techniques to grow the parasite are needed to explore other basic aspects of the Perkinsus spp. biology. We optimized a DME: Ham's F12-5% FBS- containing solid agar medium for plating Perkinsus marinus. This solid medium supported trophozoite propagation both by binary fission and schizogony. Colonies were visible to the naked eye 17 days after plating. We tested the suitability of this method for several applications, including the following: 1) Subcloning P. marinus isolates: single discrete P. marinus colonies were obtained from DME: Ham's F12-5% FBS- 0.75% agar plates, which could be further propagated in liquid medium; 2) Subcloning engineered Perkinsus mediterraneus MOE[MOE]: GFP by streaking cultures on plates; 3) Chemical susceptibility: Infusing the DME: Ham's F12-5% FBS- 0.75% agar plates with triclosan resulted in inhibition of the parasite propagation in a dose-dependent manner. Altogether, our plating method has the potential for becoming a key tool for investigating diverse aspects of Perkinsus spp. biology, developing new molecular tools, and for biotechnological applications.

Titanium diffusion in shinbone of rats with osseointegrated implants.

Dental implants are composed of commercially pure Ti (which is actually an alloy of titanium, and minor or trace components such as aluminium and vanadium). When the implant is inserted, its surface undergoes a number of chemical and mechanical processes, releasing particles of titanium to the medium. The metabolism of free ions of titanium is uncertain; the uptaking processes in the body are not well known, nor their toxic dose. In addition, physical properties of newly formed bone, such as diffusivity and activation energy, are scarce and rarely studied. In this study, we analysed the diffusion of titanium in the titanium-implanted shinbones of six adult male Wistar rats by spatially resolved micro x-ray fluorescence. The measurements were carried out at the microfluorescence station of the x-ray fluorescence (XRF) beamline of the Brazilian synchrotron facility LNLS (from Portuguese 'Laboratorio Nacional de Luz Sincrotron'). For each sample, XRF spectra were taken by linear scanning in area near the new bone formed around the Ti implant. The scanning line shows a clear effect of titanium diffusion whereas calcium intensity presents a different behaviour. Moreover, a clear correlation among the different structures of bones is observed in the Ti and Ca intensities. The results obtained in these measurements may allow determining quantitatively the parameters of diffusion rates and other physical properties of new bone like diffusion coefficients.