Salvaging Affymetrix probes after probe-level re-annotation

Background: Affymetrix GeneChips can be re-annotated at the probe-level by breaking up the original probe-sets and recomposing new probe-sets based on up-to-date genomic knowledge, such as available in Entrez Gene. This results in custom Chip Description Files (CDF). Using these custom CDFs improves the quality of the data and thus the results of related gene expression studies. However, 44-71% of the probes on a GeneChip are lost in this re-annotation process. Although generally aimed at less known genes, losing these probes obviously means a substantial loss of expensive experiment data. Biologists are therefore very reluctant to adopt this approach. Findings: We aimed to re-introduce the non-affected Affymetrix probe-sets after these re-annotation procedures. For this, we developed an algorithm (CDF-Merger) and applied it to standard Affymetrix CDFs and custom Brainarray CDFs to obtain Hybrid CDFs. Thus, salvaging lost Affymetrix probes with our CDF-Merger restored probe content up to 94%. Because the salvaged probes (up to 54% of the probe content on the arrays) represent less-reliable probe-sets, we made the origin of all probe-set definitions traceable, so biologists can choose at any time in their analyses, which subset of probe-sets they want to use. Conclusion: The availability of up-to-date Hybrid CDFs plus R environment allows for easy implementation of our approach

Single cell transcriptomics of neighboring hyphae of Aspergillus niger

Single cell profiling was performed to assess differences in RNA accumulation in neighboring hyphae of the fungus Aspergillus niger. A protocol was developed to isolate and amplify RNA from single hyphae or parts thereof. Microarray analysis resulted in a present call for 4 to 7% of the A. niger genes, of which 12% showed heterogeneous RNA levels. These genes belonged to a wide range of gene categories

The core genome of the anaerobic oral pathogenic bacterium Porphyromonas gingivalis

<p>Abstract</p> <p>Background</p> <p>The Gram negative anaerobic bacterium <it>Porphyromonas gingivalis </it>has long been recognized as a causative agent of periodontitis. Periodontitis is a chronic infectious disease of the tooth supporting tissues eventually leading to tooth-loss. Capsular polysaccharide (CPS) of <it>P. gingivalis </it>has been shown to be an important virulence determinant. Seven capsular serotypes have been described. Here, we used micro-array based comparative genomic hybridization analysis (CGH) to analyze a representative of each of the capsular serotypes and a non-encapsulated strain against the highly virulent and sequenced W83 strain. We defined absent calls using <it>Arabidopsis thaliana </it>negative control probes, with the aim to distinguish between aberrations due to mutations and gene gain/loss.</p> <p>Results</p> <p>Our analyses allowed us to call aberrant genes, absent genes and divergent regions in each of the test strains. A conserved core <it>P. gingivalis </it>genome was described, which consists of 80% of the analyzed genes from the sequenced W83 strain. The percentage of aberrant genes between the test strains and control strain W83 was 8.2% to 13.7%. Among the aberrant genes many CPS biosynthesis genes were found. Most other virulence related genes could be found in the conserved core genome. Comparing highly virulent strains with less virulent strains indicates that <it>hmuS, </it>a putative CobN/Mg chelatase involved in heme uptake, may be a more relevant virulence determinant than previously expected. Furthermore, the description of the 39 W83-specific genes could give more insight in why this strain is more virulent than others.</p> <p>Conclusion</p> <p>Analyses of the genetic content of the <it>P. gingivalis </it>capsular serotypes allowed the description of a <it>P. gingivalis </it>core genome. The high resolution data from three types of analysis of triplicate hybridization experiments may explain the higher divergence between <it>P. gingivalis </it>strains than previously recognized.</p

AAV-p40 Bioengineering Platform for Variant Selection Based on Transgene Expression

The power of AAV directed evolution for identifying novel vector variants with improved properties is well established, as evidenced by numerous publications reporting novel AAV variants. However, most capsid variants reported to date have been identified using either replication-competent selection platforms or PCR-based capsid DNA recovery methods, which can bias the selection towards efficient replication or unproductive intracellular trafficking, respectively. A central objective of this study was to validate a functional transduction (FT)-based method for rapid identification of novel AAV variants based on AAV capsid mRNA expression in target cells. We performed a comparison of the FT platform to existing replication competent strategies. Based on the selection kinetics and function of novel capsids identified in an in vivo screen in a xenograft model of human hepatocytes, we identified the mRNA-based FT selection as the most optimal AAV selection method. Lastly, to gain insight into the mRNA-based selection mechanism driven by the native AAV-p40 promoter, we studied its activity in a range of in vitro and in vivo targets. We found AAV-p40 to be a ubiquitously active promoter that can be modified for cell type-specific expression by incorporating binding sites for silencing transcription factors, allowing for cell-type-specific library selection

Embracing the variety of sustainable business models: Social entrepreneurship, corporate intrapreneurship, creativity, innovation, and other approaches to sustainability challenges

status: publishe

Concepción de un plan de negocios para la creación de una agencia de representación de nuevos músicos: modelo de aplicación basado en el género pop- rock

Al realizar un plan de negocio a partir de la idea de creación de una agencia de representación de artistas musicales, se analizaron los distintos factores que intervienen en el mismo, para de esta manera evaluar si la idea de negocio es factible o no y así mismo aplicar los conocimiento adquiridos en la maestría al emplearlos en un caso aplicativo que es el de IOSSA, un músico italiano con gran potencial. En el capítulo II, se realizó un análisis general del mercado en el cuál se determinó la oferta y la demanda de la música grabada y en streaming, para así poder determinar el tipo de estrategias a realizar. En el capítulo III, se realizó un estudio de la competencia y de acuerdo al análisis, realizó también un plan de marketing con las estrategias a realizar, seguido por una descripción de la estructura organizacional de la Agencia de Representación. Adicionalmente, se realizó un estudio de factibilidad económica y financiera para medir la factibilidad de la idea de negocio. Por último se realizó un caso aplicativo en el cuál se muestra cómo trabajará la Agencia de representación de artistas musicales. Líneas de investigación y desarrollo futuras: La información que se ha considerado necesaria presentar va desde la situación general del mercado, para luego realizar un estudio de la competencia y finalmente realizar un análisis de factibilidad del plan de negocios internacional. Así el proyecto pueda ser entendido, aceptado y también podría ser útil para solicitar créditos o buscar inversores o socios si el caso lo amerite.Facultad de Ciencias Económica

Development of a mobile application for detection of adolescent mental health problems and feasibility assessment with primary health care workers

INTRODUCTION : There has been a sharp increase in the use of digital health interventions in global health, particularly mobile health applications, in recent years. The extreme shortage of health care providers trained in mental health screening and intervention in low- and middle-income countries raises questions about the applicability of mobile applications to deliver these services due to their accessibility and availability. This exploratory paper describes the development and feasibility assessment of a mobile screening application for the detection of mental disorders among adolescents in Zambia and South Africa. METHODS : Eighty-two health care workers (HCW) working in primary care evaluated the acceptability and practicality of the mobile screening application after receiving brief training. The evaluation included questions from the Mobile Application Rating Scale (MARS) as well as open-ended questions. RESULTS : The acceptability of the screening app was high and study participants were positive about using the app in routine care. Problems with internet connectivity, and time and staff constraints were perceived as the main barriers to regular use. CONCLUSION : HCW in primary care were able and willing to use a mobile screening app for the detection of mental health problems among treatment-seeking adolescents. Implementation in clinical practice needs to be further evaluated.Erasmus + Capacity Building.https://www.tandfonline.com/loi/imhn20hj2023Psychiatr

Design and development process of a youth depression screening m-health application for primary health care workers in South Africa and Zambia : an overview of the MEGA project

Literature indicates a high prevalence and burden of mental illness in youths world-wide, which may be even higher in low- and middle-income countries (LMIC), such as South Africa and Zambia. Additionally, there is a lack of knowledge regarding youth depression amongst many primary health care (PHC) practitioners. The principal goal of the MEGA project is to provide youth with better access to mental health services and appropriate care, by developing a mental health screening mobile application tool to be used in PHC settings in South Africa and Zambia. In this study, we will use a mixed methods multi-center study design. In phase one, we will investigate the mental health literacy of PHC practitioners to identify areas in need of development. Based on the needs identified, we will develop and test a mobile health application to screen for common youth mental health problems in phase two. In phase three, we will implement and evaluate a tiered education and training program in the use of the m-health application. In the final phase, we will evaluate the acceptability and feasibility of the m-health application in PHC centres across South Africa and Zambia. Evidence suggests that PHC practitioners should routinely consider mental illness when assessing youth. However, common psychiatric disorders remain largely undetected and untreated in PHC settings. By identifying limitations in PHC workers knowledge with regard to youth mental health, we aspire to improve the depression care provided to youth in Southern Africa and Zambia by developing and implementing a locally relevant m-health application.http://www.tandfonline.com/loi/imhn20hj2020Psychiatr

Contribution of Eat1 and Other Alcohol Acyltransferases to Ester Production in Saccharomyces cerevisiae

Esters are essential for the flavor and aroma of fermented products, and are mainly produced by alcohol acyl transferases (AATs). A recently discovered AAT family named Eat (Ethanol acetyltransferase) contributes to ethyl acetate synthesis in yeast. However, its effect on the synthesis of other esters is unknown. In this study, the role of the Eat family in ester synthesis was compared to that of other Saccharomyces cerevisiae AATs (Atf1p, Atf2p, Eht1p, and Eeb1p) in silico and in vivo. A genomic study in a collection of industrial S. cerevisiae strains showed that variation of the primary sequence of the AATs did not correlate with ester production. Fifteen members of the EAT family from nine yeast species were overexpressed in S. cerevisiae CEN.PK2-1D and were able to increase the production of acetate and propanoate esters. The role of Eat1p was then studied in more detail in S. cerevisiae CEN.PK2-1D by deleting EAT1 in various combinations with other known S. cerevisiae AATs. Between 6 and 11 esters were produced under three cultivation conditions. Contrary to our expectations, a strain where all known AATs were disrupted could still produce, e.g., ethyl acetate and isoamyl acetate. This study has expanded our understanding of ester synthesis in yeast but also showed that some unknown ester-producing mechanisms still exist