Reconstructing Viral Genomes from the Environment Using Fosmid Clones: The Case of Haloviruses

Background: Metaviriomes, the viral genomes present in an environment, have been studied by direct sequencing of the viral DNA or by cloning in small insert libraries. The short reads generated by both approaches make it very difficult to assemble and annotate such flexible genomic entities. Many environmental viruses belong to unknown groups or prey on uncultured and little known cellular lineages, and hence might not be present in databases. Methodology and Principal Findings: Here we have used a different approach, the cloning of viral DNA into fosmids before sequencing, to obtain natural contigs that are close to the size of a viral genome. We have studied a relatively low diversity extreme environment: saturated NaCl brines, which simplifies the analysis and interpretation of the data. Forty-two different viral genomes were retrieved, and some of these were almost complete, and could be tentatively identified as head-tail phages (Caudovirales). Conclusions and Significance: We found a cluster of phage genomes that most likely infect Haloquadratum walsbyi, the square archaeon and major component of the community in these hypersaline habitats. The identity of the prey could be confirmed by the presence of CRISPR spacer sequences shared by the virus and one of the available strain genomes. Other viral clusters detected appeared to prey on the Nanohaloarchaea and on the bacterium Salinibacter ruber, covering most of the diversity of microbes found in this type of environment. This approach appears then as a viable alternative to describe metaviriomes in a much more detailed and reliable way than by the more common approaches based on direct sequencing. An example of transfer of a CRISPR cluster including repeats and spacers was accidentally found supporting the dynamic nature and frequent transfer of this peculiar prokaryotic mechanism of cell protection.This work was supported by projects MAGYK (BIO2008-02444), MICROGEN (Programa CONSOLIDERINGENIO 2010 CDS2009-00006), CGL2'09-12651-C02-01 from the Spanish Ministerio de Ciencia e Innovación, DIMEGEN (PROMETEO/2010/089) and ACOMP/2009/155 from the Generalitat Valenciana. FEDER funds supported this project. IG-H was supported by MAGYK from Ministerio de Ciencia e Innovación. A-BM-C was supported by CONSOLIDER-INGENIO 2010

Pilot Study to Assess the Effectiveness of the Sustainable Culturally adaptive Nutrition Program (Scan) to Improve adherence to the National Diabetes Prevention Program

PURPOSE: The Sustainable Culturally Adapted Nutrition Program (SCAN) is a novel adaptation to the National Diabetes Prevention Program (NDPP) that aims to improve attendance and effectiveness. This paper presents its feasibility and impact through the initial 6-month outcomes. DESIGN: A pragmatic quasi-experimental pilot study with intervention (DPP plus SCAN) and control (DPP only) groups. SAMPLES AND INCLUSION CRITERIA: Sustainable Culturally Adapted Nutrition Program participants were recruited from federally qualified health center (FQHC) clinic patients enrolled in a NDPP in Houston, Texas. Participants needed to be (1) ≥18 years old, (2) body mass index \u3e25, (3) no prior diagnosis of diabetes, and (4) not pregnant. INTERVENTION: Sustainable Culturally Adapted Nutrition Program cooking classes were designed to teach skills to prepare fresh produce, and utilized Motivational Interviewing (MI) techniques to encourage participants to adapt these skills for foods that were culturally important to them. OUTCOME MEASURES: (1) National Diabetes Prevention Program attendance, (2) BMI and (3) percent weight loss. ANALYSIS: We used linear mixed models to test the association between weights and NDPP attendance. RESULTS: 22 intervention and 15 control participants completed the program to the 6-month point. Intervention participants had increased DPP attendance over controls (7.14 vs 6.87 session). Intervention participants also demonstrated on average, 1.5% weight loss for each additional SCAN class attended ( CONCLUSIONS: The SCAN adaptation shows promising results for effectively increasing both NDPP attendance and weight loss

The AEROARMS Project: Aerial Robots with Advanced Manipulation Capabilities for Inspection and Maintenance

This article summarizes new aerial robotic manipulation technologies and methods—aerial robotic manipulators with dual arms and multidirectional thrusters—developed in the AEROARMS project for outdoor industrial inspection and maintenance (I&M). Our report deals with the control systems, including the control of the interaction forces and the compliance the teleoperation, which uses passivity to tackle the tradeoff between stability and performance the perception methods for localization, mapping, and inspection the planning methods, including a new control-aware approach for aerial manipulation. Finally, we describe a novel industrial platform with multidirectional thrusters and a new arm design to increase the robustness in industrial contact inspections. In addition, the lessons learned in applying the platform to outdoor aerial manipulation for I&M are pointed out

Local piezoresponse and polarization switching in nucleobase thymine microcrystals

Thymine (2-oxy-4-oxy-5 methyl pyrimidine) is one of the four nucleobases of deoxyribonucleic acid (DNA). In the DNA molecule, thymine binds to adenine via two hydrogen bonds, thus stabilizing the nucleic acid structure and is involved in pairing and replication. Here, we show that synthetic thymine microcrystals grown from the solution exhibit local piezoelectricity and apparent ferroelectricity, as evidenced by nanoscale electromechanical measurements via Piezoresponse Force Microscopy. Our experimental results demonstrate significant electromechanical activity and polarization switchability of thymine, thus opening a pathway for piezoelectric and ferroelectric-based applications of thymine and, perhaps, of other DNA nucleobase materials. The results are supported by molecular modeling of polarization switching under an external electric field. (C) 2015 AIP Publishing LLC

Dyskeratosis congenita: natural history of the disease through the study of a cohort of patients diagnosed in childhood

BackgroundDyskeratosis congenita (DC) is a multisystem and ultra-rare hereditary disease characterized by somatic involvement, bone marrow failure, and predisposition to cancer. The main objective of this study is to describe the natural history of DC through a cohort of patients diagnosed in childhood and followed up for a long period of time.Material and methodsMulticenter, retrospective, longitudinal study conducted in patients followed up to 24 years since being diagnosed in childhood (between 1998 and 2020).ResultsFourteen patients were diagnosed with DC between the ages of 3 and 17 years (median, 8.5 years). They all had hematologic manifestations at diagnosis, and nine developed mucocutaneous manifestations during the first decade of life. Seven presented severe DC variants. All developed non-hematologic manifestations during follow-up. Mutations were identified in 12 patients. Thirteen progressed to bone marrow failure at a median age of 8 years [range, 3–18 years], and eight received a hematopoietic stem cell transplant. Median follow-up time was 9 years [range, 2–24 years]. Six patients died, the median age was 13 years [range, 6–24 years]. As of November 2022, eight patients were still alive, with a median age of 18 years [range, 6–32 years]. None of them have developed myeloblastic syndrome or cancer.ConclusionsDC was associated with high morbidity and mortality in our series. Hematologic manifestations appeared early and consistently. Non-hematologic manifestations developed progressively. No patient developed cancer possibly due to their young age. Due to the complexity of the disease multidisciplinary follow-up and adequate transition to adult care are essential

Pan-Atlantic analysis of the overlap of a highly migratory species, the leatherback turtle, with pelagic longline fisheries

Large oceanic migrants play important roles in ecosystems, yet many species are of conservation concern as a result of anthropogenic threats, of which incidental capture by fisheries is frequently identified. The last large populations of the leatherback turtle, Dermochelys coriacea, occur in the Atlantic Ocean, but interactions with industrial fisheries could jeopardize recent positive population trends, making bycatch mitigation a priority. Here, we perform the first pan-Atlantic analysis of spatio-temporal distribution of the leatherback turtle and ascertain overlap with longline fishing effort. Data suggest that the Atlantic probably consists of two regional management units: northern and southern (the latter including turtles breeding in South Africa). Although turtles and fisheries show highly diverse distributions, we highlight nine areas of high susceptibility to potential bycatch (four in the northern Atlantic and five in the southern/equatorial Atlantic) that are worthy of further targeted investigation and mitigation. These are reinforced by reports of leatherback bycatch at eight of these sites. International collaborative efforts are needed, especially from nations hosting regions where susceptibility to bycatch is likely to be high within their exclusive economic zone (northern Atlantic: Cape Verde, Gambia, Guinea Bissau, Mauritania, Senegal, Spain, USA and Western Sahara; southern Atlantic: Angola, Brazil, Namibia and UK) and from nations fishing in these high-susceptibility areas, including those located in international waters

ANTIMICROBIAL EFFECT OF VANCOMYCIN ELECTRO-TRANSFERRED WATER AGAINST METHICILLIN-RESISTANT STAPHYLOCOCCUS AUREUS VARIANT

Background: There is a number of alternative and complementary therapeutics that are unproven or have not been properly tested. For past twenty years, the transfer of bio-energetic information has been recognized as a novel scientific approach capable of contributing to improved therapy in the management of several diseases through the so-called bio-resonance therapy (BRT). Although BRT was discovered in the late 1980s, it is still poorly studied. The aim of this study was to evaluate the antibacterial effect of water samples transferred with electronic information of vancomycin, a well known drug against methicillin-resistant Staphylococcus aureus (MRSA), by using a BRT device on bacterial cultures. Material and Methods: MRSA cultures were treated with vancomycin electro-transferred water samples, vancomycin (4.0 and 8.0 µg/mL), sham electro-transferred (water to water) and non-transferred water samples (medium alone). Growth inhibition was evaluated in liquid and solid culture medium, spectrophotometrically and by CFU determination respectively. Results: The obtained data showed that by transferring vancomycin (4.0 and 8.0 µg/mL) information to water samples, the growth of cultured MRSA was significantly (p< 0.05) inhibited (up to 35%), compared with those cultures treated with electro-transferred water to water or cultured in medium alone (0% growth inhibition). Conclusion: This in vitro study suggests that water samples that are electronically transferred with vibration sustained information of vancomycin are capable of inhibiting growth of axenically cultured methicillin resistant S. aureus

Search for Neutral Higgs Bosons in Events with Multiple Bottom Quarks at the Tevatron

The combination of searches performed by the CDF and D0 collaborations at the Fermilab Tevatron Collider for neutral Higgs bosons produced in association with b quarks is reported. The data, corresponding to 2.6 fb-1 of integrated luminosity at CDF and 5.2 fb-1 at D0, have been collected in final states containing three or more b jets. Upper limits are set on the cross section multiplied by the branching ratio varying between 44 pb and 0.7 pb in the Higgs boson mass range 90 to 300 GeV, assuming production of a narrow scalar boson. Significant enhancements to the production of Higgs bosons can be found in theories beyond the standard model, for example in supersymmetry. The results are interpreted as upper limits in the parameter space of the minimal supersymmetric standard model in a benchmark scenario favoring this decay mode.Comment: 10 pages, 2 figure

Search for the standard model Higgs boson decaying to a bbˉb\bar{b} pair in events with no charged leptons and large missing transverse energy using the full CDF data set

We report on a search for the standard model Higgs boson produced in association with a vector boson in the full data set of proton-antiproton collisions at $\sqrt{s} = 1.96$ TeV recorded by the CDF II detector at the Tevatron, corresponding to an integrated luminosity of 9.45 fb$^{-1}$. We consider events having no identified charged lepton, a transverse energy imbalance, and two or three jets, of which at least one is consistent with originating from the decay of a $b$ quark. We place 95% credibility level upper limits on the production cross section times standard model branching fraction for several mass hypotheses between 90 and $150 \mathrm{GeV}/c^2$. For a Higgs boson mass of $125 \mathrm{GeV}/c^2$, the observed (expected) limit is 6.7 (3.6) times the standard model prediction.Comment: Accepted by Phys. Rev. Let