31 research outputs found
Steps and Tools for PCR-Based Technique Design
The identity and clonal differences within bacterial populations have been broadly explored through PCR-based techniques. Thus, bacterial identification and elucidation of DNA fingerprinting have provided insights regarding their phenotypic and genotypic variations. Indeed, some diversity of rates may reflect changes among subpopulations that have their own ecological dynamic and individual traits on coexisting genotypes. Therefore, identification of polymorphic regions from nucleic acid sequences is based on the identification of both conserved and variable regions. Advantages of PCR-based methods are high sensitivity, specificity, speed, cost-effectiveness, and the opportunity for simultaneous detection of many microbial agents or variants. Fingerprint information might allow the tracking of certain outbreaks globally in several reference databases containing valuable genotyping information. In this chapter, we will review applications from Web resources and computational tools online for the designing of PCR-based methods to identify bacterial species. We will also focus on lab applications and key conditions for technique standardization
Design of a molecular method for subspecies specific identification of Klebsiella pneumoniae by using the 16S ribosomal subunit gene
Introduction: Rhinoscleroma is caused by Klebsiella pneumoniae rhinoscleromatis and the ozena infections caused by K. pneumoniae ozaenae, both infections affect the upper respiratory tract. In the first clinical phases the symptoms are unspecific, and the disease can be misdiagnosed as a common cold, therefore antimicrobial therapy cannot reach effective results and patients must be following up for several years since the infection became chronic
Diseño de un método molecular para la identificación específica de Klebsiella pneumoniae a nivel de subespecie, usando el gen que codifica para la subunidad ribosomal 16S
Introduction: Rhinoscleroma is caused by Klebsiella pneumoniae rhinoscleromatis and the ozena infections caused by
K. pneumoniae ozaenae, both infections affect the upper respiratory tract. In the first clinical phases the symptoms are
unspecific, and the disease can be misdiagnosed as a common cold, therefore antimicrobial therapy cannot reach effective
results and patients must be following up for several years since the infection became chronic.
Objective: To identify Klebsiella subspecies using a specific assay based on amplicons restriction of a gene which
encodes 16S subunit ribosomal (rDNA16S).
Methodology: Specific restriction patterns were generated; using reported sequences from rDNA16S gene and bioinformatics
programs MACAW, PFE, GENEDOC and GENE RUNNER. Amplification and restriction assays were standardized.
Results: Predictions in silico allowed to propose an algorithm for Klebsiella species and subspecies identification. Two
reference strains were included and two clinical isolates which were biotyped and identified by the proposed method. rDNA16S
gene restriction patterns showed differences regarding the initially identified species for conventional methods. Additionally
two patterns of bands were observed for K. pneumoniae rhinoscleromatis, indicating the polymorphisms presence in the
rDNA16S gene.
Conclusions: It was confirmed the difficulty to identify K. pneumoniae subspecies by conventional methods. Implementation
of this technique could allow an accurate and rapid differentiation among K. pneumoniae ozaenae and K. pneumoniae
rhinoscleromatis aetiological agents of two frequently misdiagnosed infections. Antimicrobial therapy usually could be
ineffective, especially in chronic patients. Finally it is considered very important to enlarge the study by using more clinical
and reference strains. Introducción: El rinoescleroma es causado por Klebsiella pneumoniae rhinoscleromatis y la ocena por Klebsiella
pneumoniae ozaenae respectivamente. Estas infecciones se presentan sobre todo en el tracto respiratorio superior y tienen
una sintomatología inespecífica en sus fases iniciales por lo cual se pueden confundir con el catarro común. Las dificultades
de establecer un diagnóstico oportuno tienen repercusiones negativas en la terapia antimicrobiana, porque puede no ser
efectiva y hacer que la enfermedad evolucione a una fase crónica cuyo seguimiento puede implicar muchos años.
Objetivo: Diseñar un ensayo molecular para la identificación a nivel de subespecie de bacterias del género Klebsiella
basado en restricción de amplicones del gen que codifica para la subunidad ribosomal 16S (ADNr 16S).
Metodología: Se generaron patrones de restricción específicos, utilizando secuencias informadas del gen ADNr 16S y
los programas bioinformáticos MACAW, PFE, GENEDOC y GENE RUNNER. Se estandarizaron las condiciones para la amplificación y restricción para el ensayo experimental.
Resultados: Las predicciones in silico permitieron proponer
un algoritmo para la identificación a nivel de especie y
subespecie de las especies del género Klebsiella. Se incluyeron
dos cepas de referencia y dos aislados clínicos, que se
biotipificaron e identificaron por el método propuesto; los
patrones de restricción obtenidos del gen ADNr 16S evidenciaron
diferencias con respecto a la especie inicialmente
identificada por métodos convencionales. Además se encontraron
dos patrones de bandas en Klebsiella pneumoniae
rhinoscleromatis, indicando la presencia de polimorfismos
en el gen ADNr 16S para esta subespecie.
Conclusiones: Se confirmó la dificultad para identificar
Klebsiella pneumoniae a nivel de subespecie por métodos
convencionales. La implementación de esta técnica podría
permitir la diferenciación temprana entre Klebsiella
pneumoniae ozaenae y Klebsiella pneumoniae rhinoscleromatis
que causan dos infecciones tratadas por lo general
de forma empírica y como consecuencia de esto, la terapia
antimicrobiana suele no ser efectiva, en especial en pacientes
crónicos. Se requiere ampliar los estudios con un número
mayor de cepas de referencia y aislados clínicos
Klebsiella pneumoniae subsp. rhinoscleromatis; Klebsiella pneumoniae subsp. ozaenae; Klebsiella pneumoniae subsp. pneumoniae; Diagnosis
Introduction: Rhinoscleroma is caused by Klebsiella pneumoniae subsp. rhinoscleromatis and the ozena infections
caused by K. pneumoniae subsp. ozaenae, both infections affect the upper respiratory tract. In the first clinical phases the
symptoms are unspecific, and the disease can be misdiagnosed as a common cold, therefore antimicrobial therapy cannot
reach effective results and patients must be following up for several years since the infection became chronic.
Objective: To identify Klebsiella subspecies using a specific assay based on amplicons restriction of a gene which
encodes 16S subunit ribosomal (rDNA16S).
Methodology: Specific restriction patterns were generated; using reported sequences from rDNA16S gene and
bioinformatics programs MACAW, PFE, GENEDOC and GENE RUNNER. Amplification and restriction assays were
standardized.
Results: Predictions in silico allowed us to propose an algorithm for Klebsiella species and subspecies identification.
Two reference strains were included and two clinical isolates which were biotyped and identified by the proposed method.
rDNA16S gene restriction patterns showed differences regarding the initially identified species for conventional methods.
Additionally two patterns of bands were observed for K. pneumoniae subsp. rhinoscleromatis, indicating the polymorphisms
presence in the rDNA16S gene.
Conclusions: We confirmed the difficulty to identify K. pneumoniae subspecies by conventional methods. Implementation
of this technique could allow accurate and rapid differentiation among K. pneumoniae subsp. ozaenae and K. pneumoniae
subsp. rhinoscleromatis the aetiological agents of two frequently misdiagnosed infections. Antimicrobial therapy usually
could be ineffective, especially in chronic patients. Finally we consider very important to enlarge the study by using more
clinical and reference strains. Introducción: El rinoescleroma es causado por Klebsiella pneumoniae subsp. rhinoscleromatis y la ocena por K.
pneumoniae subsp. ozaenae, respectivamente. Estas infecciones se presentan sobre todo en el tracto respiratorio superior
y originan una sintomatología inespecífica en sus fases iniciales por lo cual se pueden confundir con el catarro común. Las
dificultades para establecer un diagnóstico oportuno tienen repercusiones negativas en la terapia antimicrobiana, que puede
no ser efectiva y hacer que la enfermedad evolucione a una fase crónica cuyo seguimiento en el paciente puede necesitar
muchos años. Objetivo: Diseñar un ensayo molecular para la identificación
a nivel de subespecie de bacterias del género Klebsiella
basado en restricción de amplicones del gen que codifica
para la subunidad ribosomal 16S (ADNr 16S).
Metodología: Se generaron patrones de restricción específicos,
con secuencias informadas del gen ADNr 16S y
los programas bioinformáticos MACAW, PFE, GENEDOC
y GENE RUNNER. Se estandarizaron las condiciones para
la amplificación y restricción del ensayo experimental.
Resultados: Las predicciones in silico permitieron proponer
un algoritmo para identificar a nivel de especie y
subespecie los miembros del género Klebsiella. Se incluyeron
dos cepas de referencia y dos aislamientos clínicos, que
fueron biotipificados e identificados por el método propuesto;
los patrones de restricción obtenidos del gen ADNr 16S
evidenciaron diferencias respecto a la especie inicialmente
identificada por métodos convencionales. Además, se encontraron
dos patrones de bandas en K. pneumoniae.
rhinoscleromatis, que indican la presencia de polimorfismos
en el gen ADNr 16S para esta subespecie.
Conclusiones: Se confirmó la dificultad para identificar
K. pneumoniae a nivel de subespecie por métodos convencionales.
La implementación de esta técnica podría permitir
la diferenciación temprana entre K. pneumoniae. ozaenae y
K. pneumoniae. rhinoscleromatis que causan dos infecciones
tratadas por lo general de forma empírica y como
consecuencia de lo anterior, la terapia antimicrobiana suele
no ser efectiva, especialmente en enfermos crónicos. Se
requiere ampliar los estudios con un número mayor de cepas
de referencia y aislamientos clínicos
Constructivism and strategies for learning
Es innegable que la educación debe ser preocupación de cualquier sociedad democrática, justamente por ello el estudio de las prácticas educativas y la concepción de aprendizaje, mediación y didáctica, así como el papel de la educación en la sociedad ha sido preocupación de muchos pensadores a lo largo de la historia.It is undeniable that education should be the concern of any democratic society, precisely for this reason the study of educational practices and the conception of learning, mediation and didactics, as well as the role of education in society has been the concern of many thinkers along the way. throughout history
Pervasive gaps in Amazonian ecological research
Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear un derstanding of how ecological communities respond to environmental change across time and space.3,4
While the increasing availability of global databases on ecological communities has advanced our knowledge
of biodiversity sensitivity to environmental changes,5–7 vast areas of the tropics remain understudied.8–11 In
the American tropics, Amazonia stands out as the world’s most diverse rainforest and the primary source of
Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepre sented in biodiversity databases.13–15 To worsen this situation, human-induced modifications16,17 may elim inate pieces of the Amazon’s biodiversity puzzle before we can use them to understand how ecological com munities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus
crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced
environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple or ganism groups in a machine learning model framework to map the research probability across the Brazilian
Amazonia, while identifying the region’s vulnerability to environmental change. 15%–18% of the most ne glected areas in ecological research are expected to experience severe climate or land use changes by
2050. This means that unless we take immediate action, we will not be able to establish their current status,
much less monitor how it is changing and what is being lostinfo:eu-repo/semantics/publishedVersio
Pervasive gaps in Amazonian ecological research
Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost
Pervasive gaps in Amazonian ecological research
Biodiversity loss is one of the main challenges of our time,1,2 and attempts to address it require a clear understanding of how ecological communities respond to environmental change across time and space.3,4 While the increasing availability of global databases on ecological communities has advanced our knowledge of biodiversity sensitivity to environmental changes,5,6,7 vast areas of the tropics remain understudied.8,9,10,11 In the American tropics, Amazonia stands out as the world's most diverse rainforest and the primary source of Neotropical biodiversity,12 but it remains among the least known forests in America and is often underrepresented in biodiversity databases.13,14,15 To worsen this situation, human-induced modifications16,17 may eliminate pieces of the Amazon's biodiversity puzzle before we can use them to understand how ecological communities are responding. To increase generalization and applicability of biodiversity knowledge,18,19 it is thus crucial to reduce biases in ecological research, particularly in regions projected to face the most pronounced environmental changes. We integrate ecological community metadata of 7,694 sampling sites for multiple organism groups in a machine learning model framework to map the research probability across the Brazilian Amazonia, while identifying the region's vulnerability to environmental change. 15%–18% of the most neglected areas in ecological research are expected to experience severe climate or land use changes by 2050. This means that unless we take immediate action, we will not be able to establish their current status, much less monitor how it is changing and what is being lost
Daño colateral en abejas por la exposición a pesticidas de uso agrícola
El uso de pesticidas es una práctica común en la industria agrícola para erradicar plagas. El objetivo de esta revisión fue documentar el efec to de los pesticidas en la relación ecológica de las abejas con el medio ambiente y los sistemas de producción agropecuaria. Se revisaron las publicaciones científicas y académicas en Science-Direct, Scielo, JSTOR, Springerlink y Google académico. Se encontró que las abejas proveen de servicios ecosistémicos poco valorados a nivel productivo y económico y, de acuerdo con estimaciones globales sus pobla ciones se encuentran en declive. Las abejas exhiben hipersensibilidad a la mayoría de diferentes pesticidas (especialmente insecticidas). Además, padecen diferentes alteraciones fisiológicas a nivel del sistema nervioso, respecto a su ciclo reproductivo e inmunosupresión. En conclusión, existe evidencia respecto a los efectos tóxicos de los pesticidas que alteran colateralmente las cosechas, específicamente en el proceso de polinización mediada por abejas