Genome-wide discovery and development of polymorphic microsatellites from Leishmania panamensis parasites circulating in central Panama

The parasite Leishmania panamensis is the main cause of leishmaniasis in Panama. The disease is largely uncontrolled, with a rising incidence and no appropriate control measures. While microsatellites are considered some of the best genetic markers to study population genetics and molecular epidemiology in these and other parasites, none has been developed for L. panamensisThe parasite Leishmania panamensis is the main cause of leishmaniasis in Panama. The disease is largely uncontrolled, with a rising incidence and no appropriate control measures. While microsatellites are considered some of the best genetic markers to study population genetics and molecular epidemiology in these and other parasites, none has been developed for L. panamensi

Betacoronavirus genomes: How genomic information has been used to deal with past outbreaks and the COVID-19 pandemic

In the 21st century, three highly pathogenic betacoronaviruses have emerged, with an alarming rate of human morbidity and case fatality. Genomic information has been widely used to understand the pathogenesis, animal origin and mode of transmission of betacoronaviruses in the aftermath of the 2002-03 severe acute respiratory syndrome (SARS) and 2012 Middle East respiratory syndrome (MERS) outbreaks. Furthermore, genome sequencing and bioinformatic analysis have had an unprecedented relevance in the battle against the 2019-20 coronavirus disease 2019 (COVID-19) pandemic, the newest and most devastating outbreak caused by a coronavirus in the history of mankind, allowing the follow up of disease spread and transmission dynamics in near real time. Here, we review how genomic information has been used to tackle outbreaks caused by emerging, highly pathogenic, betacoronavirus strains, emphasizing on SARS-CoV, MERS-CoV and SARS-CoV-2.In the 21st century, three highly pathogenic betacoronaviruses have emerged, with an alarming rate of human morbidity and case fatality. Genomic information has been widely used to understand the pathogenesis, animal origin and mode of transmission of betacoronaviruses in the aftermath of the 2002-03 severe acute respiratory syndrome (SARS) and 2012 Middle East respiratory syndrome (MERS) outbreaks. Furthermore, genome sequencing and bioinformatic analysis have had an unprecedented relevance in the battle against the 2019-20 coronavirus disease 2019 (COVID-19) pandemic, the newest and most devastating outbreak caused by a coronavirus in the history of mankind, allowing the follow up of disease spread and transmission dynamics in near real time. Here, we review how genomic information has been used to tackle outbreaks caused by emerging, highly pathogenic, betacoronavirus strains, emphasizing on SARS-CoV, MERS-CoV and SARS-CoV-2

DNA Repair Mechanisms as Drug Targets in Prokaryotes

Nowadays, a great amount of pathogenic bacteria has been identified such as Mycobacterium sp. and Helicobacter pylori and have become a serious health problem around the world. These bacteria have developed several DNA repair mechanisms as a strategy to neutralize the effect of the exposure to endogenous and exogenous agents that will lead to two different kinds of DNA damage: single strand breaks (SSBs) and double strand breaks (DSBs). For SSBs repair, bacteria use the base excision repair (BER) and nucleotide excision repair (NER) mechanisms, which fix the damaged strand replacing the damaged base or nucleotide. DSBs repair in bacteria is performed by homologous recombination repair (HRR) and non-homologous end-joining (NHEJ). HRR uses the homologous sequence to fix the two damaged strand, while NHEJ repair does not require the use of its homologous sequence. The use of unspecific antibiotics to treat bacterial infections has caused a great deal of multiple resistant strains making less effective the current therapies with antibiotics. In this review, we emphasized the mechanisms mentioned above to identify molecular targets that can be used to develop novel and more efficient drugs in future.Nowadays, a great amount of pathogenic bacteria has been identified such as Mycobacterium sp. and Helicobacter pylori and have become a serious health problem around the world. These bacteria have developed several DNA repair mechanisms as a strategy to neutralize the effect of the exposure to endogenous and exogenous agents that will lead to two different kinds of DNA damage: single strand breaks (SSBs) and double strand breaks (DSBs). For SSBs repair, bacteria use the base excision repair (BER) and nucleotide excision repair (NER) mechanisms, which fix the damaged strand replacing the damaged base or nucleotide. DSBs repair in bacteria is performed by homologous recombination repair (HRR) and non-homologous end-joining (NHEJ). HRR uses the homologous sequence to fix the two damaged strand, while NHEJ repair does not require the use of its homologous sequence. The use of unspecific antibiotics to treat bacterial infections has caused a great deal of multiple resistant strains making less effective the current therapies with antibiotics. In this review, we emphasized the mechanisms mentioned above to identify molecular targets that can be used to develop novel and more efficient drugs in future

Identificación de portadoras de distrofia muscular de Duchenne y Becker (DMD/DMB) mediante análisis de dosis génica y polimorfismos de ADN

Seven carrier and 15 non-carrier women from 16 families affected by Duchenne and Becker muscular dystrophy (DMD/DMB) were identified by quantitative PCR multiplex gene dosage. DMD/DMB patients showed 31.25% deletions and their mother carrier status was established by quantitative PCR multiplex and gene dosage analysis; no carriers of duplications were observed. X chromosome haplotypes were constructed on the maternal female relatives from both deletion and no deletion patients with dinucleotide intragenic polymorphisms D45 and SKI2 analysis; 63% of the women tested were informative in this study. After this molecular approach genetic counseling was given. thus contributing to their knowledge of risks and DMD/DMB prevention methods.Se identificaron 7 mujeres portadoras y 15 no portadoras de deleción en 16 familias con distrofia muscular de Duchenne o de Becker (DMDIDMB) mediante PCR multiplex cuantitativa y análisis de dosis génica. Los afectados con DMDIDMB mostraron deleciones en 31.25% de los casos y el estado materno de portadora se estableció por PCR multiplex cuantitativa y análisis de dosis génica. En este estudio no se observó ninguna portadora de duplicación. Tanto las mujeres portadoras de deleción como las no portadoras de 23 familias con DMD/DMB se estudiaron con los polimorfismos intragénicos dinucleotidicos D45 y SK12, para construir haplotipos del cromosoma X; 63% de las mujeres analizadas fueron 'informativas' (heterocigotas) en este estudio. Se brindó asesoramiento genético después del análisis molecular descrito, dándoles a conocer los riesgos y los métodos de prevención de la DMD/DMB

Valorization of passion fruit stalk by the preparation of cellulose nanofibers and immobilization of trypsin

Fibers from passion fruit stalks were first recovered with a pulping and bleaching process. Two mechanical treatments were further applied to the fibers, homogenization (with and without ultrasound), and blender application. The effect of those treatments on fibers was evaluated. The chemical composition of the different stages of fibers undergoing treatment were measured according to TAPPI standards and were also analyzed by SEM, FTIR, and XRD. Trypsin was immobilized by adsorption and by covalent binding. The biocatalyst support-trypsin was evaluated in terms of immobilization yield, retention, and enzymatic activity. The experimental results demonstrated that the final cellulose concentration in the fibers was 44 % higher than that in the raw stalks. The cellulose nanofibers obtained by homogenization presented a size distribution between 20200 nm, and the application of ultrasound did not show a significant effect on size (between 50 to 300 nm). Trypsin immobilized using glycidol presented an immobilization yield of 67 % and presented higher retention and enzymatic activity (1.17±0.05 U/mg protein and 44.0±2.0 %, respectively). These results show that passion fruit stalks can be successfully used as a source of cellulose nanofibers and also can be used as carriers for the immobilization of trypsin.The authors acknowledge the financial support of Universidad Nacional de Colombia (Hermes code project 34573), COLCIENCIAS call 727-2015 National Doctorates. FONTAGRO (ATN/RF-16111-RG Productividad y Competitividad Frutícola Andina), and Erasmus+Programme Key Action 1. This work was also supported by the Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of the UID/BIO/04469/2020 unit and by the BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020 - Programa Operacional Regional do Norte.info:eu-repo/semantics/publishedVersio

Linear and nonlinear optical absorption coefficients in GaAs/Ga1−xAlxAs concentric double quantum rings : Effects of hydrostatic pressure and aluminum concentration

ABSTRACT: The linear and nonlinear intra-band optical absorption coefficients in GaAs/Ga1−xAlxAs two-dimensional concentric double quantum rings are investigated. Taking into account the combined effects of hydrostatic pressure and aluminum concentration the energies of the ground and the first excited state have been found using the effective mass approximation and the transfer matrix formalism. The energies of these states and the corresponding threshold energy of the intra-band optical transitions are examined as a function of hydrostatic pressure and aluminum concentration for different sizes of the structure. We also investigated the dependencies of the linear, nonlinear, and total optical absorption coefficients as functions of the incident photon energy for different values of hydrostatic pressure, aluminum concentration, sizes of the structure, and incident optical intensity. Its is found that the effects of the hydrostatic pressure and the aluminum concentration lead to a shifting of the resonant peaks of the intra-band optical spectrum

Diversidad genética de aislados de pseudomonas aeruginosa multirresistentes portadores de los genes blavim-2 y blakpc-2 que se propagan en diferentes entornos genéticos en colombia

Pseudomonas aeruginosa es un patógeno Gram negativo oportunista con un aumento de la frecuencia de infecciones causadas por cepas multirresistentes (MDR) y extremadamente resistentes (XDR), lo que limita las opciones terapéuticas disponibles. La resistencia más problemática es la adquisición y producción de carbapenemasas, como las metalo-β-lactamasas codificadas por integrones de Verona (VIM), las más frecuentes y extendidas, y las carbapenemasas de Klebsiella pneumoniae (KPC), que no han dejado de propagarse en la última década. Su diseminación está ligada a su localización en elementos genéticos móviles (EGM). En Colombia, VIM y KPC han venido aumentando en su frecuencia mostrando una importante diseminación exitosa. En este artículo, caracterizamos molecularmente y analizamos el contexto genético de blaVIM y blaKPC en aislamientos de P. aeruginosa resistente a carbapenemasas (CRPA) provenientes de pacientes infectados y colonizados en dos hospitales de tercer nivel de atención, uno en Medellín y el otro en un municipio cercano a Medellín, ambas zonas con alta endemicidad de carbapenemasas en Colombia (2013-2015). Usando secuenciación del genoma completo (WGS), identificamos una notable variedad de antecedentes genéticos en estos aislados de P. aeruginosa MDR portadores de blaKPC-2 y blaVIM-2. Se observó una diversidad de integradores de clase 1 en los aislados de P. aeruginosa MDR. Hubo diversidad de integrones de clase 1 y variaciones en los casetes génicos asociados a blaVIM-2, así como un posible evento de diseminación de blaKPC-2 mediado por un plásmido que contenía parte de Tn4401b en un caso de infección. La diseminación de blaVIM-2 y blaKPC-2 en P. aeruginosa en esta área en Colombia ha estado fuertemente influenciada por clones internacionales exitosos, portadores de estos genes y determinantes adicionales de resistencia en MGEs, acompañados de reordenamiento génico bajo una presión de selección antimicrobiana. Estos hallazgos enfatizan la necesidad de implementar estrategias de control basadas en el uso racional de antibióticos.Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen with an increase in the frequency of infections caused by multidrug resistant (MDR) and extensively drug resistant (XDR) strains, limiting the available therapeutic options. The most troublesome resistance is the acquisition and production of carbapenemases such as Verona integron-encoded metallo-β-lactamases (VIM), the most frequent and widespread, and the Klebsiella pneumoniae carbapenemases (KPC), which has continuously spread in the last decade. Its dissemination is linked to their location on mobile genetic elements (MGEs). In Colombia, VIM and KPC have been increasing in its frequency showing major successful dissemination. In this article, we molecularly characterized and analyzed the genetic context of blaVIM and blaKPC in carbapenem-resistant P. aeruginosa (CRPA) isolates from infected and colonized patients in two tertiary-care hospitals, one in Medellín and the other in a municipality close to Medellín, both areas with high carbapenemase endemicity in Colombia (2013–2015). Using whole-genome sequencing (WGS), we identified a remarkable variety of genetic backgrounds in these MDR P. aeruginosa isolates carrying blaKPC–2 and blaVIM–2. There were a diversity of class 1 integron and variations in the gene cassettes associated to blaVIM–2, as well as a possible event of spread of blaKPC–2 mediated by a plasmid that contained part of Tn4401b in one infection case. The dissemination of blaVIM–2 and blaKPC–2 in P. aeruginosa in this area in Colombia has been strongly influenced by successful international clones, carrying these genes and additional determinants of resistance on MGEs, accompanied by gene rearrangement under an antimicrobial selection pressure. These findings emphasize the need to implement control strategies based on rational antibiotic us

Frequency of Toxoplasma gondii and Risk Factors Associated with the Infection in Stray Dogs and Cats of Panama

Stray animals such as dogs and cats have an important role in maintaining the transmission cycles and dissemination of Toxoplasma gondii. Therefore, the objective of this study was to evaluate the frequency of T. gondii in stray dogs and cats in six different regions of Panama and determine risk factors associated with the dynamics of infection in each of the studied regions. Data were obtained using serological tests for the detection of anti-T. gondii IgG and IgM antibodies. The results of this study revealed an overall infection frequency of 23.73%. The infection frequencies found in dog and cat populations were 25.70% and 21.93% respectively, showing no statistically significant difference. Risk factor correlations suggested different infection dynamics depending on the region analyzed. The San Miguelito, North and West regions were more associated with positive cases in dogs with an age range greater than 13 months. Conversely, the Metro, Central and East regions were more associated with negative cases in cats with age ranging between 0 and 5 months. Infection of the parasite in stray animals can be influenced by intrinsic characteristics of each region, which can potentiate different risk factors associated with the different routes of transmission.Stray animals such as dogs and cats have an important role in maintaining the transmission cycles and dissemination of Toxoplasma gondii. Therefore, the objective of this study was to evaluate the frequency of T. gondii in stray dogs and cats in six different regions of Panama and determine risk factors associated with the dynamics of infection in each of the studied regions. Data were obtained using serological tests for the detection of anti-T. gondii IgG and IgM antibodies. The results of this study revealed an overall infection frequency of 23.73%. The infection frequencies found in dog and cat populations were 25.70% and 21.93% respectively, showing no statistically significant difference. Risk factor correlations suggested different infection dynamics depending on the region analyzed. The San Miguelito, North and West regions were more associated with positive cases in dogs with an age range greater than 13 months. Conversely, the Metro, Central and East regions were more associated with negative cases in cats with age ranging between 0 and 5 months. Infection of the parasite in stray animals can be influenced by intrinsic characteristics of each region, which can potentiate different risk factors associated with the different routes of transmission

Dynamics of animal performance, and estimation of carbon footprint of two breeding herds grazing native neotropical savannas in eastern Colombia

The savannas of eastern Colombia located in the Orinoco river basin represent 18% of the Latin American neotropical savannas, and those areas that are tillable and closer to markets are subject to considerable anthropic pressure in the quest for intensification. Historically, and even today, beef cattle production constitutes the main land use, and much of it is subjected to extensive management. This paper describes for the first time, the use of cattle grazing experiments to assess methane (CH4) emissions from neotropical savanna-based beef breeding systems, and with the support of published research conducted next to them, estimates of the carbon (C) footprint in carbon dioxide equivalents (CO2-eq) for the whole system. Over 5 years and covering complete reproductive cycles, a conventional weaning (CW) herd system was compared to an early weaning (EW) herd system, that represented a modest degree of more intensive savanna management. Differences were found between the two management practices in total CH4 emissions, emission intensities [kg CH4 kg –1 calf born and kg CH4 kg –1 liveweight gain (LWG)] and emission efficiencies (kg CO2-eq kg –1 calf born and kg CH4 kg –1 LWG), that mostly associated with the different lactation lengths. When both herd systems were carried over until calves, later yearlings, reached to 25 months of age, the differences in favor of EW breeding herd system were diminished. The calculated C footprint in (CO2-eq) of both management practices was near neutral subjected to a number of assumptions and the use of limited published information on savanna C stocks and CH4 and nitrous oxide (N2O) emissions from soil, and it is posited that both herd systems were nearly in equilibrium. The available data and results show the need for further information on the neotropical savanna C stocks and C sequestration potential of soils of the Orinoco river basin. More reliable datasets regarding below-ground C inputs and CH4 and N2O emissions from soil are needed to provide a useful basal benchmark for, and approach to, future analyses of environmental impact of more intensive beef herd systems in the region

Renal volume of five-year-old preterm children are not different than full-term controls

Objective: In previous studies, smaller renal volumes were reported in prematurely born infants, however, these renal volumes were not corrected for body surface area, the main determinant of renal size. Given the rapid growth of the renal cortex after premature birth, the authors hypothesized that corrected volumes would not differ from healthy controls. Methods: Ambispective cohort study with prospective follow-up of prematurely born babies in a large specialized center and retrospectively recruited healthy control group. Children were assessed for renal length and renal volumes at age 5 by three independent ultrasonographers. Detailed anthropometry, blood pressure and renal function were also obtained. Age independent z-scores were calculated for all parameters and compared using descriptive statistics. Results: Eighty-nine premature study participants (median 32 weeks gestational age) and 33 healthy controls (median 38 weeks gestational age) were studied. Study participants did not differ in age, sex, Afro-Colombian descent, height, blood pressure, serum creatinine, or new Schwartz eGFR. Premature study participants had a significantly lower weight (17.65 ± 2.93 kg) than controls (19.05 ± 2.81 kg, p = 0.0072) and lower body surface area. The right renal volumes were significantly smaller (39.4 vs 43.4 mL), but after correction for body surface area, the renal volume and renal length z-scores were identical for both kidneys (mean right kidney -0.707 vs -0.507; mean left kidney -0.498 vs -0.524, respectively). Conclusion: Renal volumes need to be corrected to body surface area. After correction for body surface area, 5-year-old healthy and prematurely born children have comparable renal volumes