A graph-based approach to defend agro-ecological systems against water vole outbreaks

The cyclic spread of montane water vole populations in the grasslands of the Jura plateaus causes severe economic, ecological, and public-health problems. Since this phenomenon cannot be managed by massive use of the anticoagulant rodenticide bromadiolone, the challenge is to limit it by reducing regional-level connectivity through landscaping and agro-environmental interventions such as planting hedgerows, ploughing, and cultivating cereals. We used landscape graphs – a spatial modelling approach based on graph theory – to represent the grassland network and identify key areas for intervention. Several strategies were compared in terms of their capacity to fulfil operational requirements by interchanging patches and meta-patches as nodes of the graph, and least-cost distances and resistance distances to weight links. The combination of meta-patches and resistance distances provides a relevant basis on which to design concrete action to decrease regional-level connectivity of grasslands. The results also indicate that the usual removal method applied to the links of the graph would benefit from data on the statistical distribution of cost values along the shortest paths. More broadly, this suggests the modelling approach should be better matched the actual field interventions if the connectivity analysis is to be operational.     

Green pathways: Metabolic network analysis of plant systems

Metabolic engineering of plants with enhanced crop yield and value-added compositional traits is particularly challenging as they probably exhibit the highest metabolic network complexity of all living organisms. Therefore, approaches of plant metabolic network analysis, which can provide systems-level understanding of plant physiology, appear valuable as guidance for plant metabolic engineers. Strongly supported by the sequencing of plant genomes, a number of different experimental and computational methods have emerged in recent years to study plant systems at various levels: from heterotrophic cell cultures to autotrophic entire plants. The present review presents a state-of-the-art toolbox for plant metabolic network analysis. Among the described approaches are different in silico modeling techniques, including flux balance analysis, elementary flux mode analysis and kinetic flux profiling, as well as different variants of experiments with plant systems which use radioactive and stable isotopes to determine in vivo plant metabolic fluxes. The fundamental principles of these techniques, the required data input and the obtained flux information are enriched by technical advices, specific to plants. In addition, pioneering and high-impacting findings of plant metabolic network analysis highlight the potential of the field.     

The impact of a knowledge translation intervention employing educational outreach and a point-of-care reminder tool vs standard lay health worker training on tuberculosis treatment completion rates: study protocol for a cluster randomized controlled trial

BackgroundDespite availability of effective treatment, tuberculosis (TB) remains an important cause of morbidity and mortality globally, with low- and middle-income countries most affected. In many such settings, including Malawi, the high burden of disease and severe shortage of skilled healthcare workers has led to task-shifting of outpatient TB care to lay health workers (LHWs). LHWs improve access to healthcare and some outcomes, including TB completion rates, but lack of training and supervision limit their impact. The goals of this study are to improve TB care provided by LHWs in Malawi by refining, implementing, and evaluating a knowledge translation strategy designed to address a recognized gap in LHWs’ TB and job-specific knowledge and, through this, to improve patient outcomes.Methods/designWe are employing a mixed-methods design that includes a pragmatic cluster randomized controlled trial and a process evaluation using qualitative methods. Trial participants will include all health centers providing TB care in four districts in the South East Zone of Malawi. The intervention employs educational outreach, a point-of-care reminder tool, and a peer support network. The primary outcome is proportion of treatment successes, defined as the total of TB patients cured or completing treatment, with outcomes taken from Ministry of Health treatment records. With an alpha of 0.05, power of 0.80, a baseline treatment success of 0.80, intraclass correlation coefficient of 0.1 based on our pilot study, and an estimated 100 clusters (health centers providing TB care), a minimum of 6 patients per cluster is required to detect a clinically significant 0.10 increase in the proportion of treatment successes. Our process evaluation will include interviews with LHWs and patients, and a document analysis of LHW training logs, quarterly peer trainer meetings, and mentorship meeting notes. An estimated 10–15 LHWs and 10–15 patients will be required to reach saturation in each of 2 planned interview periods, for a total of 40–60 interview participants.DiscussionThis study will directly inform the efforts of knowledge users within TB care and, through extension of the approach, other areas of care provided by LHWs in Malawi and other low- and middle-income countries.

Trial registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT02533089","term_id":"NCT02533089"}}NCT02533089. Registered 20 August 2015. Protocol Date/Version 29 May 2016/Version 2.

Electronic supplementary material

The online version of this article (doi:10.1186/s13063-016-1563-2) contains supplementary material, which is available to authorized users.     

General stress proteins in Bacillus subtilis

Abstract Bacillus cells frequently faced with various adverse environmental factors in nature have evolved different adaptational strategies. The induction of stress proteins is an essential component of this adaptational network. In Bacillus subtilis there are two groups of stress proteins. The first group is factor specific, whereas the second group is induced by growth restrictive conditions in general. The relationship between the stringent response and the induction of stress proteins is discussed.     

The control of pacemaker modulations for social communication in the weakly electric fish Sternopygus

Summary Nearly sinusoidal electric organ discharges (EODs) of the weakly electric fish Sternopygus, occur at a regular rate within a range from 50 to 200 Hz and are commanded by a medullary pacemaker nucleus (Pn). During courtship and aggression, the rate of EODs is modulated as smooth EOD-frequency rises or brief EOD-interruptions (Hopkins 1974b). The present study examines the control of such modulations. Rises were elicited by L-glutamate stimulation of the diencephalic prepacemaker nucleus, the only previously known source of input to the Pn. We demonstrate an additional input to the Pn, the sublemniscal prepacemaker nucleus (SPPn). L-glutamate stimulation of this area caused EOD-interruptions.The Pn contains electrotonically coupled pacemaker cells which generate the rhythm of the EODs, as well as relay cells which transmit the command pulse to the spinal motor neurons that innervate the electric organ. Pacemaker cells recorded intracellularly during EOD-interruptions continued firing at their regular frequency but with slightly increased jitter. Relay cells, on the other hand, were strongly depolarized and fired spikelets at a greatly increased frequency during EOD-interruptions. Thus EOD-interruptions were caused by SPPn input to relay cells that caused their massive depolarization, blocking the normal input from pacemaker cells without greatly affecting pacemaker cell firing characteristics.Application to the Pn of an antagonist to NMDA-type glutamate receptors blocked EOD-frequency rises and EOD-interruptions. Antagonists to quisqualate/ kainate receptor-types were ineffective.Abbreviations EOD Electric Organ Discharge - JAR Jamming Avoidance Response - Pn pacemaker nucleus - PPn diencephalic prepacemaker nucleus - SPPn sublemniscal prepacemaker nucleus     

Periclinal penetration of potassium permanganate into mature cuticular membranes ofAgave andClivia leaves: new implications for plant cuticle development

Staining cuticular membranes ofAgave americana andClivia miniata en bloc with potassium permanganate results in a strong contrast in the interior cuticular layer while the exterior part remains unstained. This is not caused by a selective chemical reaction with the interior part but by the unidirectional penetration of the reagent from the interior side, the outside being protected by the cuticle proper. In transverse cryosections of the cuticular membrane, permanganate penetrates nearly as easily into the exterior cuticular layer as into the interior one giving the same contrast. However, compared with the periclinal penetration into the cuticle proper this penetration is accelerated five-to tenfold by the polysaccharide network within the cuticular layer which serves as a distribution-channel system. Periclinal penetration into the cuticle proper occurs independently in each cutin penetration unit included between two obvious lucent lamellae and further divided into subunits.     

Anti-colorectal cancer targets of resveratrol and biological molecular mechanism: Analyses of network pharmacology,human and experimental data

In this study, colorectal cancer (CRC)-diseased targets and resveratrol (Res)-associated targets were combined and constructed by the use of grouped databases for identification of the predicted targets. After production of target-functional protein interaction network of Res anti-CRC, the topological analysis was used to create the core targets of Res anti-CRC. All core targets performed the analyses of biological function and pathway enrichment to optimize the biological processes and key signaling pathways of Res anti-CRC. The resultant five core therapeutic targets of Res anti-CRC were identified as protein kinase B1 (AKT1), interleukin 6 (IL6), Tumor protein p53 (TP53), vascular endothelial growth factor, and mitogen-activated protein kinase 1, respectively. Biological processes of Res anti-CRC were predominantly associated with regulating apoptosis, immune response, cellular communication, signal transduction, and metabolism of the nuclide. In addition, the top 10 key signaling pathways were identified, respectively. In human CRC sample assays, CRC histologic sections showed elevated expression of AKT1 and IL6 proteins, accompanied with abnormal changes in blood molecules. In pharmacological experiments of Res anti-CRC in vitro, Res-treated HCT116 cells showed inhibited cell growth, induced cell death. In addition, downregulation of intracellular AKT1 and IL6 expression were checked in Res-treated HCT116 cells. Taken together, these bioinformatic findings and preliminary validated data uncovered pharmacological molecular mechanisms associated with Res anti-CRC, and further identified top five core therapeutic targets. Beneficially, these five predicted targets might serve as potential biomolecules for anti-CRC treatment.     

Transformation of trans-Golgi Network During the Cell Cycle in a Green Alga, Botryococcus braunii

trans -Golgi network (TGN), and the changes in its structure and behavior throughout the cell cycle of a unicellular green alga, Botryococcus braunii, were examined with deep-etching replicas and in cryo-fixed/freeze-substituted specimens. In interphase cells, the TGN consisted of a hemispherically shaped cisterna (TGN-cisterna) with regularly distributed pores on the surface and a tubular network (TGN-tubules) with clathrin-coated vesicles. The TGNs changed their structure drastically throughout the cell cycle. The TGN-cisterna disappeared from the beginning of nuclear division to the completion of the cell wall, in contrast that TGN-tubules with the clathrin-coated vesicles were always observed. The TGN-tubules produced at least five other kinds of vesicles depending on the stage of the cell cycle: 200-nm vesicles with fibrillar substances and multivesicular bodies in interphase, 180–240 nm vesicles during cell division, and 400–450 nm vesicles containing fibrils and small masses of electron-dense substances, and 200-nm vesicles containing electron-dense spherical substances just after cell division. During cell wall formation, TGN-tubules were small and had only a few clathrin-coated vesicles. After cell wall formation, TGN-tubules grew and a TGN-cisterna with pores appeared again. Received 19 October 1998/ Accepted in revised form 1 March 1999     

Characterization of Leaf-Inspired Microfluidic Chips for Pumpless Fluid Transport

Microfluidic networks are extensively used in miniaturized lab-on-a-chip systems. However, most of the existing micro- channels are simply designed and the corresponding microfluidic systems commonly require external pumps to achieve effec- tive fluid transport. Here we employed microfabrication techniques to replicate naturally-optimized leaf venations into synthetic hydrogels for the fabrication of pumpless microfluidic chips. The unique properties of leaf-inspired microfluidic network in convectively transporting fluid were characterized at different inclination angles. Flow velocity inside these microfluidic net- works was quantitatively measured with Particle Image Velocimetry （PIV）. Mass diffusion from biomimetic microfluidic network to surrounding bulk hydrogels was investigated. The results demonstrate that the leaf-inspired microfluidic network can not only effectively transport fluid without the use of external pumps, but also facilitate rapid mass diffusion within bulk hy- drogel chips. These leaf-inspired microfluidic networks could be potentially used to engineer complex pumpless or- gan-on-a-chip systems.