Critical factors for the performance of chip array-based electrical detection of DNA for analysis of pathogenic bacteria

Different factors influencing chip array-based electrical detection of DNA for analysis of pathogenic bacteria were examined. Both rehydration of capture probe layer of functionalized chip arrays and efficient hybridization of targets irrespective of their length resulted in signal enhancement when high-ionic phosphate-buffered saline (i.e., 600 mM sodium chloride and 40 mM disodium hydrogen phosphate) was used. Similarly, placement of two adjacent capture and detection probe-binding sites at a terminal part of the target strand resulted in significant signal increase. Moreover, 10-min ultrasonic fragmentation of targets amplified the signals up to twofold for longer DNA strands (i.e., >300 bp). No obvious effects on signals were visible for shorter than 400-bp PCR amplicons subjected to ultrasonication. For DNA strands of all sizes, more than 10 min ultrasonication diminished the specific electrical responses. Our results also demonstrate that target analytes are detected with discrimination against mismatches even for single nucleotide sequence alteration. The mismatch detection appeared in order of ease of recognition as follows: triple random > quintuple middle > triple middle > single middle mismatch. Among the three variants of one-base mismatches, a sequence variation was most remarkable for adenine. On the other hand, no benefits in assay sensitivity were recognized by the use of longer capture probe linkers as the 6-C linker

Temperature limited fed-batch technique for control of proteolysis in Pichia pastoris bioreactor cultures

BACKGROUND: A temperature limited fed-batch (TLFB) technique is described and used for Pichia pastoris Mut(+ )strain cultures and compared with the traditional methanol limited fed-batch (MLFB) technique. A recombinant fusion protein composed of a cellulose-binding module (CBM) from Neocallimastix patriciarum cellulase 6A and lipase B from Candida antarctica (CALB), was produced and secreted by this strain. RESULTS: A protein concentration of about 1 g L(-1 )was produced in the MLFB process. However, this product was considerably degraded by protease(s). By applying the TLFB process, the yield was increased to 2 g L(-1 )full-length product and no proteolytic degradation was observed. Flow cytometry analysis showed that the percentage of dead cells increased rapidly during the initial methanol feed phase in the MLFB process and reached a maximum of about 12% after about 40–70 hours of methanol feeding. In the TLFB process, cell death rate was low and constant and reached 4% dead cells at the end of cultivation (about 150 hours methanol feeding time). The lower cell death rate in the TLFB correlated with a lower protease activity in the culture supernatant. The specific alcohol oxidase (AOX) activity in the TLFB process was 3.5 times higher than in the MLFB process. CONCLUSION: Three mechanisms that may contribute to the much higher accumulation of product in the TLFB process are: 1) reduced proteolysis due to lower temperature, 2) reduced proteolysis due to lower cell death and protease release to the medium, 3) increased synthesis rate due to higher AOX activity

Identification of pathogenic microbial cells and spores by electrochemical detection on a biochip

BACKGROUND: Bacillus cereus constitutes a significant cause of acute food poisoning in humans. Despite the recent development of different detection methods, new effective control measures and better diagnostic tools are required for quick and reliable detection of pathogenic micro-organisms. Thus, the objective of this study was to determine a simple method for rapid identification of enterotoxic Bacillus strains. Here, a special attention is given to an electrochemical biosensor since it meets the requirements of minimal size, lower costs and decreased power consumption. RESULTS: A bead-based sandwich hybridization system was employed in conjugation with electric chips for detection of vegetative cells and spores of Bacillus strains based on their toxin-encoding genes. The system consists of a silicon chip based potentiometric cell, and utilizes paramagnetic beads as solid carriers of the DNA probes. The specific signals from 20 amol of bacterial cell or spore DNA were achieved in less than 4 h. The method was also successful when applied directly to unpurified spore and cell extract samples. The assay for the haemolytic enterotoxin genes resulted in reproducible signals from B. cereus and B. thuringiensis while haemolysin-negative B. subtilis strain did not yield any signal. CONCLUSIONS: The sensitivity, convenience and specificity of the system have shown its potential. In this respect an electrochemical detection on a chip enabling a fast characterization and monitoring of pathogens in food is of interest. This system can offer a contribution in the rapid identification of bacteria based on the presence of specific genes without preceding nucleic acid amplification

Proprietes hydriques des sols dans deux zones a ecosystemes contrastes au Sahel

Les sécheresses répétées du Sahel et la pression de la population ont eu un impact négatif sur l’environnement ont conduit à la dégradation des ressources naturelles. Mais depuis ces deux dernières décennies, l’état des ressources au Sahel est mitigé. C’est ainsi que, dans certaines zones, on parle de la perte de certaines fonctions du sol. Cette étude menée dans le Sahel et dans deux zones à écosystèmes contrastés a porté sur la détermination des propriétés hydrodynamiques et la caractérisation des sols en fonction de l’occupation des terres afin de déterminer la capacité du sol à soutenir certaines fonctions. Elle analyse l’influence de l’occupation des terres sur les propriétés hydriques des sols. Elle a utilisé un échantillonnage de sol, des mesures de densité apparente, d’humidité et l’infiltrométrie à succion contrôlée à trois niveaux de tensions en fonction de l’occupation des terres. L’analyse statistique donne des différences significatives en ce qui concerne la variation de l’argile avec la profondeur, très significatives pour l’analyse texturale en fonction de l’occupation des terres. Pour les propriétés hydriques, seule la conductivité hydraulique à la tension (-5) et la taille des pores par sites donnent une différence significative. Les résultats montrent une dégradation de la texture qui induit celle de la porosité texturale et de forte valeur de conductibilité hydraulique à Koalma.Mots clés : Conductivité hydraulique ; texture du sol ; occupation des terres ; dégradation ; Sahe

Studying the complexity of change: toward an analytical framework for understanding deliberate social-ecological transformations

Faced with numerous seemingly intractable social and environmental challenges, many scholars and practitioners are increasingly interested in understanding how to actively engage and transform the existing systems holding such problems in place. Although a variety of analytical models have emerged in recent years, most emphasize either the social or ecological elements of such transformations rather than their coupled nature. To address this, first we have presented a definition of the core elements of a social-ecological system (SES) that could potentially be altered in a transformation. Second, we drew on insights about transformation from three branches of literature focused on radical change, i.e., social movements, socio-technical transitions, and social innovation, and gave consideration to the similarities and differences with the current studies by resilience scholars. Drawing on these findings, we have proposed a framework that outlines the process and phases of transformative change in an SES. Future research will be able to utilize the framework as a tool for analyzing the alteration of social-ecological feedbacks, identifying critical barriers and leverage points and assessing the outcome of social-ecological transformations

Confirmative electric DNA array-based test for food poisoning Bacillus cereus

Detection of the full set of toxin encoding genes involved in gastrointestinal diseases caused by B. cereus was performed. Eight genes determining the B. cereus pathogenicity, which results in diarrhea or emesis, were simultaneously evaluated on a 16-position electrical chip microarray. The DNA analyte preparation procedure comprising first 5 min of ultrasonic treatment, DNA extraction, and afterwards an additional 10 min sonication, was established as the most effective way of sample processing. No DNA amplification step prior to the analysis was included. The programmed assay was carried out within 30 min, once theDNAanalyte from 108 bacterial cells, corresponding to one agar colony, was subjected to the assay. In general, this work represents a mature analytical way for DNA review. It can be used under conditions that require almost immediate results

IMPACT OF PROJECTED CLIMATE CHANGE ON AGRICULTURAL PRODUCTION IN SEMI-ARID AREAS OF TANZANIA: A CASE OF SAME DISTRICT

Sub-Saharan Africa is one of the most vulnerable regions in the World to climate change because of widespread poverty and limited adaptive capacity. The future climate change is likely to present an additional challenge to the agricultural sector. Therefore, the effects of climate change on the current agronomic management practices were investigated using Same District, Tanzania as a case study area. APSIM software was used to investigate the response of maize ( Zea mays ) yield to different agronomic management practices using current and future (2046 - 2065) climate data. The climate change projections data from global climate models were downscaled using self-organising maps technique. Under the conventional practices, results show that during long rainy season (from March to May) there is yield decline of 13% for cultivar Situka, no change for cultivar Kito and increase of 10% and 15% for cultivars Sc401 and TMV1, respectively. Under the recommended practices, cultivars TMV1 and Sc401 are projected to register a 10% yield increase whereas cultivars Situka and Kito are projected to register a decrease of 10% and 45%, respectively. Also, under both conventional and recommended management practices, results showed that during short rainy season (from october to December/January) all cultivars are projected to register between 75% and 146% increase in maize yields. This implies that future climate change is going to have positive effects on current management practices during short rainy seasons and it will have negligible impact during long rainy seasons.L\u2019Afrique subsaharienne est une des r\ue9gions plus vuln\ue9rables au changement climatique au monde suite \ue0 la pauvret\ue9 g\ue9n\ue9ralis\ue9e et la capacit\ue9 d\u2019adaptation limit\ue9e. Dans l\u2019avenir, le changement climatique pr\ue9sentera probablement des d\ue9fis additionnels au secteur agricole. Pour ce faire, les effets du changement climatique sur les pratiques courantes de gestion agronomiques \ue9taient \ue9tudi\ue9s dans le district de Same en Tanzanie. Le logiciel APSIM \ue9tait utilis\ue9 en exploitant les donn\ue9es climatiques actuelles et futures (2046-2065), afin d\u2019\ue9valuer les effets des diff\ue9rentes pratiques agronomiques de gestion sur le rendement du ma\uefs ( Zea mays ). La projection des donn\ue9es de changement climatique \ue0 partir des mod\ue8les climatiques au niveau plan\ue9taire a \ue9t\ue9 r\ue9duite \ue0 l\u2019\ue9chelle \ue0 l\u2019aide de la technique d\u2019auto-organisation des cartes. Sous les pratiques conventionnelles, les r\ue9sultats montrent que durant la longue saison de pluie (du Mars au Mai) il ya eu diminution de 13% du rendement du cultivar Situka, augmentation 10% et 15% du rendement des cultivars Sc401 et TMV1, respectivement. Le cultivar Kito n\u2019a connu aucun changement de rendement. Sous les pratiques recommand\ue9es, les projections montrent que les cultivars TMV1 et Sc401 connaitront une augmentation de 10% de rendement pendant que les cultivars Situka et Kito enregistreront une baisse de rendement de 10% et 45%, respectivement. Aussi, sous les deux pratiques de gestion conventionnelles et recommand\ue9es, les r\ue9sultats de projections montrent que durant la courte saison de pluie (d\u2019octobre \ue0 D\ue9cembre/Janvier) tous les cultivars enregistreront une augmentation de rendements d\u2019entre 75% et 146%. Ceci impliquent des effets positifs du future changement climatique sur les pratiques courantes de gestion durant la courte saison de pluie et un effet n\ue9gligeable pendant la longue saison pluvieuse

Microbial population heterogeneity versus bioreactor heterogeneity: evaluation of Redox Sensor Green as an exogenous metabolic biosensor

peer reviewe