Restoring riparian ecosystems: The challenge of accommodating variability and designing restoration trajectories

Flood disturbance processes play a key role in the functioning of riparian ecosystems and in the maintenance of biodiversity along river corridors. As a result, riparian ecosystems can be described as mobile habitat mosaics characterized by variability and unpredictability. Any river restoration initiative should aim to mimic these attributes. This paper suggests that there needs to be an increased institutional capacity to accept some levels of both variability and unpredictability in the ecological outcomes of river restoration projects. Restoration projects have frequently used some form of historical or contemporary reference system to define objectives and to help in the evaluation process. Using these reference systems can give a false sense of the predictability of ecological outcomes. We suggest that reference systems need to be used with caution for six reasons: (1) there are often no appropriate reference systems to use, (2) many catchment parameters have changed since the times of chosen historic reference systems, (3) climate change has been continuous throughout the Holocene, (4) projected climate change is of uncertain magnitude, (5) alien species cannot be avoided, and (6) landscape context changes through time. As well as defining short-term objectives, we suggest that river restoration projects should also formulate longer-term (decadel) restoration trajectories that are less predictable but more representative of real system attributes. Restoration trajectories could be defined using a range of ecological outcomes to accommodate interannual variability. The challenges of defining what levels of variability are important for restoring European floodplain forests are used to demonstrate the difficulties of broadening approaches and creating trajectories. In particular, the changing significance of variability at different spatial and temporal scales is discussed. An account is given of a restoration project at Wicken Fen in the United Kingdom in which nondeterministic approaches to goal setting have been initiated

Identification of the promoter of amidase gene for expression of useful mycobacterial genes

The genetics of mycobacteria has lagged behind because of several reasons. Mycobacteria grow very slowly. their generation time ranging anywhere between 12-24 hrs. Mycobacteria are rather hydrophobic and tend to grow in clusters and there is difficulty in purifying individual cells for genetic analysis. Very few genetic markers have been found in mycobacteria because there is no known naturally occurring genetic exchange in mycobacteria. With the creation of genomic libraries of M. tuberculosis more than 50 genes have been characterised. Many of them are not expressed efficiently in Escherichia coli (E.coli) under the control of their own promoters, since very few mycobacterial promoters are recognised by the E. coli transcription machinery. This clearly shows that mycobacteria use a different system of gene regulation. Understanding the gene regulation of mycobacteria might throw light on the slow growth rate, about their persistence in a resting phase and also about their intracellular survival. Besides this if inducible or strong promoters are identified they can be used in over expression of genes coding for proteins useful in diagnosis and protection

Non-HLA gene polymorphism in pulmonary tuberculosis

BCG vaccination has been shown to give protection against tuberculosis. However, South Indian (Chingleput) Trial of BCG vaccination did not give any protection against bacillary forms of tuberculosis. A number of hypotheses and possibilities were put forward for this failure (1). One of the possibilities suggested was the genetics of the people (Host genetics) living in that region. Pulmonary tuberculosis is a granulomatous lung disease caused by Mycobactrium tuberculosis. Susceptibility to tuberculosis has been suggested to be multifactorial. Though environmental and socio-economic factors are primarily related, numerous studies have emphasised the importance of host resistance and hereditary susceptibility (2,3)

Determination of Arsenic, Mercury and Barium in herbarium mount paper using dynamic ultrasound-assisted extraction prior to atomic fluorescence and absorption spectrometry

A dynamic ultrasound-assisted extraction method using Atomic Absorption and Atomic Flourescence spectrometers as detectors was developed to analyse mercury, arsenic and barium from herbarium mount paper originating from the herbarium collection of the National Museum of Wales. The variables influencing extraction were optimised by a multivariate approach. The optimal conditions were found to be 1% HNO3 extractant solution used at a flow rate of 1 mL min-1. The duty cycle and amplitude of the ultrasonic probe was found to be 50% in both cases with an ultrasound power of 400 W. The optimal distance between the probe and the top face of the extraction chamber was found to be 0 cm. Under these conditions the time required for complete extraction of the three analytes was 25 min. Cold vapour and hydride generation coupled to atomic fluorescence spectrometry was utilized to determine mercury and arsenic, respectively. The chemical and instrumental conditions were optimized to provide detection limits of 0.01ng g-1 and 1.25 ng g-1 for mercury and arsenic, respectively. Barium was determined by graphite-furnace atomic absorption spectrometry, with a detection limit of 25 ng g-1. By using 0.5 g of sample, the concentrations of the target analytes varied for the different types of paper and ranged between 0.4–2.55 µg g-1 for Ba, 0.035–10.47 µg g-1 for As and 0.0046–2.37 µg g-1 for Hg

Metabolic maturation in the first 2 years of life in resource-constrained settings and its association with postnatal growths

Funding Information: The Etiology, Risk Factors, and Interactions of Enteric Infections and Malnutrition and the Consequences for Child Health and Development Project (MAL-ED) is carried out as a collaborative project supported by the Bill & Melinda Gates Foundation (BMGF 47075), the Foundation for the National Institutes of Health, and the National Institutes of Health, Fogarty International Center, while additional support was obtained from BMGF for the examination of host innate factors on enteric disease risk and enteropathy (grants OPP1066146 and OPP1152146 to M.N.K.). Additional funding was obtained from the Sherrilyn and Ken Fisher Center for Environmental Infectious Diseases of the Johns Hopkins School of Medicine (to M.N.K.). Publisher Copyright: Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY).Peer reviewedPublisher PD

Development of an automated DNA purification module using a micro-fabricated pillar chip

We present a fully automated DNA purification module comprised of a micro-fabricated chip and sequential injection analysis system that is designed for use within autonomous instruments that continuously monitor the environment for the presence of biological threat agents. The chip has an elliptical flow channel containing a bed (3.5 &times; 3.5 mm) of silica-coated pillars with height, width and center-to-center spacing of 200, 15, and 30 &micro;m, respectively, which provides a relatively large surface area (ca. 3 cm2) for DNA capture in the presence of chaotropic agents. We have characterized the effect of various fluidic parameters on extraction performance, including sample input volume, capture flow rate, and elution volume. The flow-through design made the pillar chip completely reusable; carryover was eliminated by flushing lines with sodium hypochlorite and deionized water between assays. A mass balance was conducted to determine the fate of input DNA not recovered in the eluent. The device was capable of purifying and recovering Bacillus anthracis genomic DNA (input masses from 0.32 to 320 pg) from spiked environmental aerosol samples, for subsequent analysis using polymerase chain reaction-based assays.<br /

Persistent low-level variants in a subset of viral genes are highly predictive of poor outcome in immunocompromised patients with cytomegalovirus infection

ABSTRACT Background Human cytomegalovirus is the most common and serious opportunistic infection after solid organ and haematopoietic stem cell transplantation. In this study, we used whole-genome cytomegalovirus data to investigate viral factors associated with the clinical outcome. Methods We sequenced cytomegalovirus samples from 16 immunocompromised paediatric patients with persistent viraemia. 8/16 patients died of complications due to cytomegalovirus infection. We also sequenced samples from 35 infected solid organ adult recipients of whom one died with cytomegalovirus infection. Results We showed that samples from both groups have fixed variants at resistance sites and mixed infections. NGS sequencing also revealed non-fixed variants at resistance sites in most of the patients who died (6/9). A machine learning approach identified 10 genes with non-fixed variants in these patients. These genes formed a viral signature which discriminated patients with cytomegalovirus infection who died from those that survived with high accuracy (AUC=0.96). Lymphocyte numbers for a subset of patients showed no recovery post-transplant in the patients who died. Conclusions We hypothesise that the viral signature identified in this study may be a useful biomarker for poor response to antiviral drug treatment and indirectly for poor T cell function, potentially identifying early, those patients requiring non-pharmacological interventions

The emerging field of venom-microbiomics for exploring venom as a microenvironment, and the corresponding Initiative for Venom Associated Microbes and Parasites (iVAMP)

Venom is a known source of novel antimicrobial natural products. The substantial, increasing number of these discoveries have unintentionally culminated in the misconception that venom and venom-producing glands are largely sterile environments. Culture-dependent and -independent studies on the microbial communities in venom microenvironments reveal the presence of archaea, algae, bacteria, endoparasites, fungi, protozoa, and viruses. Venom-centric microbiome studies are relatively sparse to date and the adaptive advantages that venom-associated microbes might offer to their hosts, or that hosts might provide to venom-associated microbes, remain unknown. We highlight the potential for the discovery of venom-microbiomes within the adaptive landscape of venom systems. The considerable number of known, convergently evolved venomous animals juxtaposed with the comparatively few studies to identify microbial communities in venom provides new possibilities for both biodiversity and therapeutic discoveries. We present an evidence-based argument for integrating microbiology as part of venomics to which we refer to as venom-microbiomics. We also introduce iVAMP, the Initiative for Venom Associated Microbes and Parasites (https://ivamp-consortium.github.io/), as a growing consortium for interested parties to contribute and collaborate within this subdiscipline. Our consortium seeks to support diversity, inclusion and scientific collaboration among all researchers interested in this subdiscipline