Book Reviews

Book Review

Binary control of enzymatic cleavage of DNA origami by structural antideterminants

Controlling DNA nanostructure interaction with protein is essential in developing nanodevices with programmable function, reactivity, and stability for biological and medical applications. Here, we show that the sequence-specific action of restriction endonucleases towards sharp triangular or rectangular DNA origami exhibits a novel, binary 'on/off' behaviour, as canonical recognition sites are either essentially fully reactive, or strongly resistant to enzymatic cutting. Moreover, introduction of structural defects in the sharp triangle can activate an otherwise unreactive site, with a site-to-defect distance of ∼50 nm. We argue that site reactivity is dependent upon programmable, mechanical coupling in the two-dimensional DNA origami, with specific structural elements, including DNA nicks and branches proximal to the sites that can function as negative(anti) determinants of reactivity. Empirically modelling the constraints to DNA degrees of freedom associated with each recognition site in the sharp triangle can rationalize the pattern of suppressed reactivity towards nine restriction endonucleases, in substantial agreement with the experimental results. These results provide a basis for a predictive understanding of structure-reactivity correlates of specific DNA nanostructures, which will allow a better understanding of the behaviour of nucleic acids under nanoscale confinement, as well as in the rational design of functional nanodevices based on self-assembling nucleic acids

Neuroprotective efficacy of P7C3 compounds in primate hippocampus.

There is a critical need for translating basic science discoveries into new therapeutics for patients suffering from difficult to treat neuropsychiatric and neurodegenerative conditions. Previously, a target-agnostic in vivo screen in mice identified P7C3 aminopropyl carbazole as capable of enhancing the net magnitude of postnatal neurogenesis by protecting young neurons from death. Subsequently, neuroprotective efficacy of P7C3 compounds in a broad spectrum of preclinical rodent models has also been observed. An important next step in translating this work to patients is to determine whether P7C3 compounds exhibit similar efficacy in primates. Adult male rhesus monkeys received daily oral P7C3-A20 or vehicle for 38 weeks. During weeks 2-11, monkeys received weekly injection of 5'-bromo-2-deoxyuridine (BrdU) to label newborn cells, the majority of which would normally die over the following 27 weeks. BrdU+ cells were quantified using unbiased stereology. Separately in mice, the proneurogenic efficacy of P7C3-A20 was compared to that of NSI-189, a proneurogenic drug currently in clinical trials for patients with major depression. Orally-administered P7C3-A20 provided sustained plasma exposure, was well-tolerated, and elevated the survival of hippocampal BrdU+ cells in nonhuman primates without adverse central or peripheral tissue effects. In mice, NSI-189 was shown to be pro-proliferative, and P7C3-A20 elevated the net magnitude of hippocampal neurogenesis to a greater degree than NSI-189 through its distinct mechanism of promoting neuronal survival. This pilot study provides evidence that P7C3-A20 safely protects neurons in nonhuman primates, suggesting that the neuroprotective efficacy of P7C3 compounds is likely to translate to humans as well

Gastric Tube Placement in Children 1-215 Months Old

poster abstractFeeding by a nasogastric/orogastric (NG/OG) tube is preferred when the gastrointestinal system is functional and the need for assisted feeding is expected to be short-term. Preliminary studies in children show that between 21% and 44% of these tubes are placed incorrectly. When tubes are out of place, children can be seriously harmed, causing increased morbidity and occasionally death. The aims of this study were to determine the best method to predict the insertion distance for placing NG/OG tubes and to determine the best clinical methods of testing the location of NG/OG tubes once they were inserted. A randomized clinical trial was conducted. The three insertion-distance prediction methods tested were nose-ear-xiphoid (NEX); nose-ear-mid-umbilicus (NEMU); and age-related, height-based (ARHB). An abdominal radiograph was obtained immediately following tube insertion to determine the internal location of the tube tip and orifice(s). Based on data from 95 children age 1-220 months (M = 51.8, SD = 54.9, median = 33.4), both the ARHB and NEMU methods were superior to NEX in placing the tube in the stomach (p = .0064). ARHB and NEMU were not significantly different from each other. NEX was frequently too short (41.93% of tube insertions) leaving the tube tip and/or orifices in the esophagus. The three clinical methods of testing tube location were CO2 monitoring and measuring pH and bilirubin in tube aspirate. Measuring pH of tube aspirate was the superior clinical method of determining tube location. Aspirate was available for testing in 84 children (88.42%). Based on a pH cutoff of 5 (recommended by Metheny in fasting adults), the sensitivity was 26.67 (low), specificity was 80.60 (high), positive predictive value was 23.53 (low), and negative predictive value was 83.08 (high). Measuring the NEX distance is the method most commonly used by nurses in practice; therefore, based on the results of this study and studies of other researchers, a practice change to either ARHB or NEMU should improve the safety of enteral feeding in children. Because of the low sensitivity in predicting misplaced tubes using pH, the superior clinical method, obtaining an abdominal x-ray to ensure placement in the stomach at the time of tube insertion is recommended

Whole genome methylation profiles as independent markers of survival in stage IIIc melanoma patients

Background: The clinical course of cutaneous melanoma (CM) can differ significantly for patients with identical stages of disease, defined clinico-pathologically, and no molecular markers differentiate patients with such a diverse prognosis. This study aimed to define the prognostic value of whole genome DNA methylation profiles in stage III CM.Methods: Genome-wide methylation profiles were evaluated by the Illumina Human Methylation 27 BeadChip assay in short-term neoplastic cell cultures from 45 stage IIIC CM patients. Unsupervised K-means partitioning clustering was exploited to sort patients into 2 groups based on their methylation profiles. Methylation patterns related to the discovered groups were determined using the nearest shrunken centroid classification algorithm. The impact of genome-wide methylation patterns on overall survival (OS) was assessed using Cox regression and Kaplan-Meier analyses.Results: Unsupervised K-means partitioning by whole genome methylation profiles identified classes with significantly different OS in stage IIIC CM patients. Patients with a " favorable" methylation profile had increased OS (P = 0.001, log-rank = 10.2) by Kaplan-Meier analysis. Median OS of stage IIIC patients with a " favorable" vs. " unfavorable" methylation profile were 31.5 and 10.4 months, respectively. The 5 year OS for stage IIIC patients with a " favorable" methylation profile was 41.2% as compared to 0% for patients with an " unfavorable" methylation profile. Among the variables examined by multivariate Cox regression analysis, classification defined by methylation profile was the only predictor of OS (Hazard Ratio = 2.41, for " unfavorable" methylation profile; 95% Confidence Interval: 1.02-5.70; P = 0.045). A 17 gene methylation signature able to correctly assign prognosis (overall error rate = 0) in stage IIIC patients on the basis of distinct methylation-defined groups was also identified.Conclusions: A discrete whole-genome methylation signature has been identified as molecular marker of prognosis for stage IIIC CM patients. Its use in daily practice is foreseeable, and promises to refine the comprehensive clinical management of stage III CM patients. © 2012 Sigalotti et al.; licensee BioMed Central Ltd

Composición de ácidos grasos y astaxantina de dos especies comestibles de acociles nativos de México, Cambarellus (C.) montezumae y Procambarus (M.) bouvieri

The content and composition of the fatty acids (FAs) and astaxanthin (AST) in the edible forms of crayfish: the whole animal of Cambarellus (C.) montezumae, and the tail meat (TM) of Procambarus (M.) bouvieri were determined by GC and HPLC. The exoskeleton (EXK) of P. (M.) bouvieri was also studied. Unsaturated FAs, and mostly oleic acid (C18:1 n-9), were predominant in both edible forms. The contents of the polyunsaturated eicosapentaenoic (C20:5 n-3, EPA), arachidonic (C20:4 n-6, ARA) and docosahexaenoic acid (C22:6 n-3, DHA), were higher in the TM of P. (M.) bouvieri than in the complete C. (C.) montezumae (p 79.50%). AST esters were enriched with saturated FAs in C. (C.) montezumae and with PUFAs in EXK of P. (M.) bouvieri. We conclude that both C. (C.) montezumae and the TM of P. (M.) bouvieri are traditional foods rich in n-3 PUFAs and C. (C.) montezumae in AST. The EXK of P. (M.) bouvieri is a rich potential source of AST, n-3 PUFAs, and the combination AST-DHA.Se determinó por GC y HPLC el contenido y composición de ácidos grasos (AGs) y astaxantina (AST), en dos formas comestibles de acocil: el animal completo de Cambarellus (C.) montezumae, y el músculo de la cola (MC) de Procambarus (M.) bouvieri. Adicionalmente, se estudió el exosqueleto (EXK) de P. (M.) bouvieri. En ambas formas comestibles predominaron los AGs insaturados. Los contenidos de ácido eicosapentaenoico (C20:5 n-3, EPA), araquidónico (C20:4 n-6, ARA) y docosahexaenoico (C22: 6 n-3, DHA), fueron mayores en el MC que en C. (C) montezumae (p 79.50%). Los ésteres de AST en C. (C.) montezumae fueron enriquecidos con AGs saturados mientras que los del EXK de P. (M.) bouvieri con AGs poliinsaturados. Se concluyó que tanto C. (C.) montezumae como el MC de P. (M.) bouvieri, son alimentos tradicionales ricos en PUFAs n-3, y C. (C.) montezumae en AST. El EXK de P. (M.) bouvieri abunda en AST, PUFAs n-3, y en la combinación AST-DHA

Construção de alternativas agroflorestais no Assentamento Tarumã-Mirim, zona rural de Manaus (AM).

Neste trabalho são apresentadas as atividades centrais de um projeto agroflorestal, em andamento, coordenado pela Embrapa Amazônia Ocidental com o objetivo de viabilizar sistemas de uso da terra sustentáveis. O projeto utiliza abordagem participativa com comunidades da zona rural de Manaus (Amazonas), em área com forte pressão antrópica, altos índices de pobreza e extrema relevância ecológica. São discutidos os princípios básicos do planejamento e a importância da pesquisa que caminha na direção da transformação de uma realidade, implicada diretamente na participação dos sujeitos que estão envolvidos no processo. A comunicação no processo de mobilização é dialógica, na medida em que não é transferência do saber, mas um encontro de sujeitos e interlocutores, o que torna o ser humano capaz de transformar sua realidade, sem imposições unilaterais

Utilization of low-molecular-weight organic compounds by the filterable fraction of a lotic microbiome

[EN] Filterable microorganisms participate in dissolved organic carbon (DOC) cycling in freshwater systems, however their exact functional role remains unknown. We determined the taxonomic identity and community dynamics of prokaryotic microbiomes in the 0.22 µm-filtered fraction and unfiltered freshwater from the Conwy River (North Wales, UK) in microcosms and, using targeted metabolomics and 14C-labelling, examined their role in the utilization of amino acids, organic acids and sugars spiked at environmentally-relevant (nanomolar) concentrations. To identify changes in community structure, we used 16S rRNA amplicon and shotgun sequencing. Unlike the unfiltered water samples where the consumption of DOC was rapid, the filtered fraction showed a 3-day lag phase before the consumption started. Analysis of functional categories of clusters of orthologous groups of proteins (COGs) showed that COGs associated with energy production increased in number in both fractions with substrate addition. The filtered fraction utilized low-molecular-weight (LMW) DOC at much slower rates than the whole community. Addition of nanomolar concentrations of LMW DOC did not measurably influence the composition of the microbial community nor the rate of consumption across all substrate types in either fraction. We conclude that due to their low activity, filterable microorganisms play a minor role in LMW DOC processing within a short residence time of lotic freshwater systems.This work was carried out under the DOMAINE project, which is funded by the UK Natural Environment Research Council (NERC) (large grant NE/K010689/1). D.L.J., O.V.G. and P.N.G. acknowledge the support of the Centre for Environmental Biotechnology Project funded by the European Regional Development Fund (ERDF) through the Welsh Government. D.L.J. and P.N.G. thank Natural Environment Research Council (NERC) for funding the project ‘Plastic Vectors’ (NE/S004548/1). 16S rRNA sequencing and thework of A.A.K.was supported by a grant from Ministry of Science and Higher Education of Russian Federation allocated to the Kurchatov Center for Genome Research (grant 075–15-2019–1659). The work of S.V.T. was supported by Ministry of Science and Higher Education within the State assignment of FRC ‘Fundamentals of Biotechnology’ RAS