X-chromosome terminal deletion in a female with premature ovarian failure: Haploinsufficiency of X-linked genes as a possible explanation

<p>Abstract</p> <p>Background</p> <p>Premature ovarian failure (POF) has repeatedly been associated to X-chromosome deletions. <it>FMR1 </it>gene premutation allele's carrier women have an increased risk for POF. We intent to determine the cause of POF in a 29 year old female, evaluating both of these situations.</p> <p>Methods</p> <p>Concomitant analysis of <it>FMR1 </it>gene CGG repeat number and karyotype revealed an X-chromosome terminal deletion. Fluorescence <it>in situ </it>further characterized the breakpoint. A methylation assay for <it>FMR1 </it>gene allowed to determine its methylation status, and hence, the methylation status of the normal X-chromosome.</p> <p>Results</p> <p>We report a POF patient with a 46,X,del(X)(q26) karyotype and with skewed X-chromosome inactivation of the structural abnormal X-chromosome.</p> <p>Conclusions</p> <p>Despite the hemizygosity of <it>FMR1 </it>gene, the patient does not present Fragile X syndrome features, since the normal X-chromosome is not subject to methylation. The described deletion supports the hypothesis that haploinsufficiency of X-linked genes can be on the basis of POF, and special attention should be paid to X-linked genes in region Xq28 since they escape inactivation and might have a role in this disorder. A full clinical and cytogenetic characterization of all POF cases is important to highlight a pattern and help to understand which genes are crucial for normal ovarian development.</p

Characterization of a new Staphylococcus aureus Kayvirus harboring a lysin active against biofilms

Staphylococcus aureus is one of the most relevant opportunistic pathogens involved in many biofilm-associated diseases, and is a major cause of nosocomial infections, mainly due to the increasing prevalence of multidrug-resistant strains. Consequently, alternative methods to eradicate the pathogen are urgent. It has been previously shown that polyvalent staphylococcal kayviruses and their derived endolysins are excellent candidates for therapy. Here we present the characterization of a new bacteriophage: vB_SauM-LM12 (LM12). LM12 has a broad host range (>90%; 56 strains tested), and is active against several MRSA strains. The genome of LM12 is composed of a dsDNA molecule with 143,625 bp, with average GC content of 30.25% and codes for 227 Coding Sequences (CDSs). Bioinformatics analysis did not identify any gene encoding virulence factors, toxins, or antibiotic resistance determinants. Antibiofilm assays have shown that this phage significantly reduced the number of viable cells (less than one order of magnitude). Moreover, the encoded endolysin also showed activity against biofilms, with a consistent biomass reduction during prolonged periods of treatment (of about one order of magnitude). Interestingly, the endolysin was shown to be much more active against stationary-phase cells and suspended biofilm cells than against intact and scraped biofilms, suggesting that cellular aggregates protected by the biofilm matrix reduced protein activity. Both phage LM12 and its endolysin seem to have a strong antimicrobial effect and broad host range against S. aureus, suggesting their potential to treat S. aureus biofilm infections.This study was supported by Lisando GmbH and by the Portuguese Foundation for Science and Technology (FCT), under the scope of the scope of the project the Project PTDC/BBB-BSS/6471/2014 (POCI-01-0145-FEDER-016678), the strategic funding of UID/BIO/04469/2013 unit, COMPETE 2020 (POCI-01-0145-FEDER-006684), and BioTecNorte operation (NORTE-01-0145-FEDER-000004), funded by the European Regional Development Fund under the scope of Norte2020—Programa Operacional Regional do Norte. Ana Brandão and Ergun Akturk acknowledge FCT for grants SFRH/BD/133193/2017 and PD/BD/13524/2017, respectively. The authors declare that they have no competing financial interests.info:eu-repo/semantics/publishedVersio

EPS and aggregates changes on activated sludge under atrazine exposure

Extracellular polymeric substances (EPS) play a vital role in biological wastewater treatment systems, affecting their performance in aggregates settling, structure and arrangement, and interacting with micropollutants present in wastewater. In this study, the effects of herbicide atrazine (ATZ) on the EPS yield and composition and aggregates structure were investigated on activated sludge (AS) in a sequencing batch reactor (SBR). The results demonstrated that TB-EPS and LB-EPS increased under ATZ exposure, indicating that microorganisms release EPS as a self-mechanism of defense against environmental changes. Above 5.5 mg L-1 of ATZ aggregates become larger. Principal component analysis (PCA) was useful in highlighting biomass changes during the experimental phases, and Pearson correlation revealed that TB-EPS content correlate well with large aggregates (0.996).The authors thank the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UIDB/04469/2020 unit, and by LABBELS – Associate Laboratory in Biotechnology, Bioengineering and Microelectromechanical Systems, LA/P/0029/2020. The authors also acknowledge the financial support to A. Melo through the grant 240-20170220 provided by Instituto Federal de Educação, Ciência e Tecnologia de Pernambuco (IFPE). D.P. Mesquita and C. Quintelas acknowledge FCT funding under DL57/2016 Transitory Norm Programme.info:eu-repo/semantics/publishedVersio

Efficacy studies of phage phiIBB-Sep1 against S. epidermidis cells under different metabolic states

Staphylococcus epidermidis has recently become known as a usual cause of nosocomial infections, predominantly in patients with indwelling medical devices. Although, S. epidermidis infections only rarely develop into life-threatening diseases, they are very frequent and difficult to treat due to the ability of this bacterium to adhere to the surfaces of indwelling medical devices and form biofilms. When S. epidermidis cells are in a biofilm they are more resistant to antibiotics and to the immune system. The importance of biofilms in the pathogenesis of the S. epidermidis infections is becoming more understandable, consequently several studies are needed, in order to develop effective methods for biofilm control. The use of bacteriophages (phages) to eradicate biofilms can be seen as a potentially valuable approach. Phages are virus that infect bacteria and are the most abundant organisms on Earth. They are generally very efficient antibacterial agents and possess many advantages over antibiotics. Our aim is to search for virulent phages with broad host range for S. epidermidis biofilm therapy. Using wastewater treatment plants raw effluents we were able to isolate 5 phages. Their lytic activity was screened against 40 clinical S. epidermidis isolates with different genetic profiles and it was found to be different ranging from 46% to 95% of positive results. Further morphologic and genetic characterization of these isolated phages is now being performed. Efficacy studies results show that phage phiIBB-Sep1 is able to cause a 6 Log CFU/ml reduction of the cell titre in <2h for some of the clinical strains at exponential phase and in <4h for stationary phase cells (using a MOI of 1). This phage has also the capacity of reducing by up to 2 Log CFU/ml 24h biofilm cells and in some strains it was observed 50% cell reduction on biofilms. Besides CFU counting, all the cell counts were confirmed by flow cytometry assays. Additionally, flow cytometry allow the observation that this phage kill cells under different metabolic states from the biofilm. Work developed with non biofilm forming strains showed that possibly PNAG might be the cell receptor of the phage. The high amounts of PNAG on biofilms, might the lower activity of this phage on biofilms. These are promising results, since phage phiIBB-Se1 presents a broad host range and ability to control S. epidermidis under different metabolic states. Ongoing studies are being performed with 4 other phages, with the purpose of developing a phage cocktail to be used against S. epidermidis biofilm infections

Ion Energy Measurements in Plasma Immersion Ion Implantation

This thesis investigates ion energy distributions (IEDs) during plasma immersion ion implantation (PIII). PIII is a surface modification technique where an object is placed in a plasma and pulse biased with large negative voltages. The energy distribution of implanted ions is important in determining the extent of surface modifications. IED measurements were made during PIII using a pulse biased retarding field energy analyser (RFEA) in a capacitive RF plasma. Experimental results were compared with those obtained from a two dimensional numerical simulation to help explain the origins of features in the IEDs. Time resolved IED measurements were made during PIII of metal and insulator materials and investigated the effects of the use of a metal mesh over the surface and the effects of insulator surface charging. When the pulse was applied to the RFEA, the ion flux rapidly increased above the pulse-off value and then slowly decreased during the pulse. The ion density during the pulse decreased below values measured when no pulse was applied to the RFEA. This indicates that the depletion of ions by the pulsed RFEA is greater than the generation of ions in the plasma. IEDs measured during pulse biasing showed a peak close to the maximum sheath potential energy and a spread of ions with energies between zero and the maximum ion energy. Simulations showed that the peak is produced by ions from the sheath edge directly above the RFEA inlet and that the spread of ions is produced by ions which collide in the sheath and/or arrive at the RFEA with trajectories not perpendicular to the RFEA front surface. The RFEA discriminates ions based only on the component of their velocity perpendicular to the RFEA front surface. To minimise the effects of surface charging during PIII of an insulator, a metal mesh can be placed over the insulator and pulse biased together with the object. Measurements were made with metal mesh cylinders fixed to the metal RFEA front surface. The use of a mesh gave a larger ion flux compared to the use of no mesh. The larger ion flux is attributed to the larger plasma-sheath surface area around the mesh. The measured IEDs showed a low, medium and high energy peak. Simulation results show that the high energy peak is produced by ions from the sheath above the mesh top. The low energy peak is produced by ions trapped by the space charge potential hump which forms inside the mesh. The medium energy peak is produced by ions from the sheath above the mesh corners. Simulations showed that the IED is dependent on measurement position under the mesh. To investigate the effects of insulator surface charging during PIII, IED measurements were made through an orifice cut into a Mylar insulator on the RFEA front surface. With no mesh, during the pulse, an increasing number of lower energy ions were measured. Simulation results show that this is due to the increase in the curvature of the sheath over the orifice region as the insulator potential increases due to surface charging. The surface charging observed at the insulator would reduce the average energy of ions implanted into the insulator during the pulse. Compared to the case with no mesh, the use of a mesh increases the total ion flux and the ion flux during the early stages of the pulse but does not eliminate surface charging. During the pulse, compared to the no mesh case, a larger number of lower energy ions are measured. Simulation results show that this is caused by the potential in the mesh region which affects the trajectories of ions from the sheaths above the mesh top and corners and results in more ions being measured with trajectories less than ninety degrees to the RFEA front surface

Genomic characterization of the Staphylococcus epidermidis-specific bacteriophage SEP1 and evaluation of its lytic activity against bacterial under different metabolic states

Staphylococcus epidermidis is one of the most frequent causative agents of nosocomial infections, predominantly in patients with indwelling medical devices. This microrganism may form biofilms which are microbial structures very tolerant to the host immune defenses and to antibiotherapy. Therefore, studies are needed in order to develop effective methods for biofilm control. Currently, bacteriophages (phages) are seen as an important tool to combat pathogenic organisms. These bacteria-specific viruses are generally very efficient antibacterial agents and possess many advantages over antibiotics. The present study concerns the search for virulent phages with broad host range for S. epidermidis biofilm therapy. Using wastewater treatment plant raw effluents, a novel phage was isolated and characterized. This virus was named phiIBB-SEP1 and TEM micrographs suggested that it belonged to the Twortlikevirus genus. Phage phiIBB-SEP1 is able to infect 41 S. epidermidis clinical isolates used in this study, and contrarily to other polyvalent viruses of the Twortlikevirus genus, phiIBB-SEP1 is highly specific for S. epidermidis strains. The genome of this phage was fully sequenced and presents the typical structure of a member of the Twortlikevirus. However, when compared to other staphylococcal members of this genus, it showed DNA sequence identities no greater than 58.2%, suggesting that phiIBB-SEP1 is a new species within this subfamily. Efficacy studies results showed that phage phiIBB-SEP1 is able to cause a 6 Log CFU per ml reduction of the cell titre in less than 2h for some of the clinical strains in exponential phase; and, in less than 4h for stationary phase cells (using a multiplicity of infection of 1). This phage has also the capacity of reducing, by up to 2 Log CFU per ml, 24h scraped biofilm cells, and in some strains it was observed 50% cell reduction. Besides CFU counting, this cell reduction was confirmed by flow cytometry counting. Additionally, live/death flow cytometry staining allowed the observation that this phage kills biofilms bacteria in different metabolic states. These are promising results, since phage phiIBB-SEP1 presents a broad host strain range and the ability to control S. epidermidis bacteria in different metabolic states. Keywords: bacteriophage, Twortlikevirus, S. epidermidis, staphylococci, biofilm

A Social Assessment of Forest Degradation in the "Cacheu Mangroves Natural Park", Guinea-Bissau

The Cacheu Mangroves Natural Park (PNTC) was established in the year 2000 with the objective of protecting the coastal forests of Northern Guinea-Bissau, which have been subject to deforestation and are at risk. Concomitantly, the need to find sustainable financial revenues to support forest conservation motivated the development of projects that explore avoidance of deforestation and forest degradation (REDD+) as a potential income possibility. The 886,150 ha of forest in the PNTC include a mosaic of different villages where communities with different cultural and socio-economic habits reside. In addition to the uncontrolled expansion of subsistence agriculture with the associated shortening of fallow periods, forests may have also been subject to degradation from selective logging, fuel wood collection, and charcoal production. To contribute to a forest degradation baseline forest uses for household fuel consumption (wood and charcoal) were surveyed using questionnaires, interviews and focus groups. The data were collected from a representative sample of circa 200 households within a 2 km buffer of the PNTC. These data are analyzed and the results are discussed according to a scenario of ethnic diversity, i.e., a diversity of approaches relating to forest conservation. Even though the results indicate that fuel wood is the main (and almost sole) source of energy for cooking, they also show that the average daily fuel consumption per capita (1.21 kg) is well below the sub-Saharan average and that fuel is obtained from downed dead wood or dead trees. Therefore, it is concluded that reported forest degradation in PNTC cannot be attributed to fuel wood consumption by local populations

Enzymatic Potential of Filamentous Fungi as a Biological Pretreatment for Acidogenic Fermentation of Coffee Waste

This work was developed within the scope of the project CICECO-Aveiro Institute of Materials (UIDB/50011/2020, UIDP/50011/2020, and LA/P/0006/2020), and the Associate Laboratory for Green Chemistry-LAQV (UIDB/50006/2020 and UIDP/50006/2020). It was financed by national funds through the FCT/MCTES (PIDDAC) and, when appropriate, co-financed by FEDER under the PT2020 Partnership Agreement. Paulo C. Lemos acknowledges the support of FCT/MCTES for contract IF/01054/2014/CP1224/CT0005 and Joana Pereira thanks FCT/MCTES for her Ph.D. grant SFRH/BD/130003/2017.Spent coffee grounds (SCGs) are a promising substrate that can be valorized by biotechnological processes, such as for short-chain organic acid (SCOA) production, but their complex structure implies the application of a pretreatment step to increase their biodegradability. Physicochemical pretreatments are widely studied but have multiple drawbacks. An alternative is the application of biological pretreatments that include using fungi Trametes versicolor and Paecilomyces variotii that naturally can degrade complex substrates such as SCGs. This study intended to compare acidic and basic hydrolysis and supercritical CO 2 extraction with the application of these fungi. The highest concentration of SCOAs, 2.52 gCOD/L, was achieved after the acidification of SCGs pretreated with acid hydrolysis, but a very similar result, 2.44 gCOD/L, was obtained after submerged fermentation of SCGs by T. versicolor. This pretreatment also resulted in the best acidification degree, 48%, a very promising result compared to the 13% obtained with the control, untreated SCGs, highlighting the potential of biological pretreatments.publishersversionpublishe