Characterization of a functional endothelial super-enhancer that regulates ADAMTS18 and angiogenesis

Super-enhancers are clusters of enhancers associated with cell lineage. They can be powerful gene-regulators and may be useful in cell-type specific viral-vector development. Here, we have screened for endothelial super-enhancers and identified an enhancer from within a cluster that conferred 5–70-fold increase in transgene expression. Importantly, CRISPR/Cas9 deletion of enhancers demonstrated regulation of ADAMTS18, corresponding to evidence of chromatin contacts between these genomic regions. Cell division-related pathways were primarily affected by the enhancer deletions, which correlated with significant reduction in cell proliferation. Furthermore, we observed changes in angiogenesis-related genes consistent with the endothelial specificity of this SE. Indeed, deletion of the enhancers affected tube formation, resulting in reduced or shortened sprouts. The super-enhancer angiogenic role is at least partly due to its regulation of ADAMTS18, as siRNA knockdown of ADAMTS18 resulted in significantly shortened endothelial sprouts. Hence, functional characterization of a novel endothelial super-enhancer has revealed substantial downstream effects from single enhancer deletions and led to the discovery of the cis-target gene ADAMTS18 and its role in endothelial function.     

High occurrence of jellyfish predation by black‐browed and Campbell albatross identified by DNA metabarcoding

Gelatinous zooplankton are a large component of the animal biomass in all marine environments, but are considered to be uncommon in the diet of most marine top predators. However, the diets of key predator groups like seabirds have conventionally been assessed from stomach content analyses, which cannot detect most gelatinous prey. As marine top predators are used to identify changes in the overall species composition of marine ecosystems, such biases in dietary assessment may impact our detection of important ecosystem regime shifts. We investigated albatross diet using DNA metabarcoding of scats to assess the prevalence of gelatinous zooplankton consumption by two albatross species, one of which is used as an indicator species for ecosystem monitoring. Black‐browed and Campbell albatross scats were collected from eight breeding colonies covering the circumpolar range of these birds over two consecutive breeding seasons. Fish was the main dietary item at most sites; however, cnidarian DNA, primarily from scyphozoan jellyfish, was present in 42% of samples overall and up to 80% of samples at some sites. Jellyfish was detected during all breeding stages and consumed by adults and chicks. Trawl fishery catches of jellyfish near the Falkland Islands indicate a similar frequency of jellyfish occurrence in albatross diets in years of high and low jellyfish availability, suggesting jellyfish consumption may be selective rather than opportunistic. Warmer oceans and overfishing of finfish are predicted to favour jellyfish population increases, and we demonstrate here that dietary DNA metabarcoding enables measurements of the contribution of gelatinous zooplankton to the diet of marine predators.     

Modelling facilitation or competition within a root system: importance of the overlap of root depletion and accumulation zones

Background and aims

Relevant soil properties and nutrient distributions influencing crop root growth might be different under no-till (NT) and mouldboard plough (MP) management. The possible different root systems within different managements might have key impact on crop nutrient uptake and consequently crop production. Our objective was to assess the long-term combined effects of tillage and phosphorus (P) fertilization on corn (Zea mays L.) root distribution and morphology.

Methods

Corn root and soil samples were collected during the silking stage at five depths (0–5, 5–10, 10–20, 20–30 and 30–40 cm) and three horizontal distances perpendicular to the corn row (5, 15 and 25 cm) under MP and NT with three P fertilizations (0, 17.5, and 35 kg P ha^?1) for a long-term (22 years) experiment in eastern Canada. Root morphology and soil properties were determined.

Results

NT practice decreased corn root biomass by ?26 % compared to MP, mainly by decreasing the primary and secondary roots. Additionally, corn roots in NT tend to be more expansive on the surface layer with higher root length and surface densities for the depth of 0–5 cm at two sampling distances of 15 and 25 cm. The 35 kg P ha^?1 rate increased the root biomass by 26 and 41 % compared to the 0 and 17.5 kg P ha^?1 rates.

Conclusions

No-tillage practice and low rates of P fertilization reduce corn roots. This is probably caused by the weed competition in NT and the continued downward P status with low P rates over 22 years.

     

Stratégies biologiques à l’heure de l’Assistance Médicale à la Procréation chez le blessé médullaire

Most men with spinal cord injury (SCI) men have fertility problems caused by anejaculation and decreased fertility of the ejaculate. There are two main causes for the impaired reproductive potential in SCI men: ejaculatory dysfunction and poor quality semen. However, current treatment techniques allow a large number of SCI males to achieve ejaculation (rectal electro-stimulation, penile vibrator stimulation). Firstly, masturbation and/or penile vibrator are used at home allowing the couple to perform insemination themselves. The semen of men with spinal cord injuries has commonly been characterised by small volume, abnormal count (low or high), decreased sperm mobility, increased formation of reactive oxygen species, sperm autoimmunity, necrospermia. This impairment is thought to be due to insufficient drainage, genitourinary infections and raised scrotal temperature. Testicular biopsy reveals varying degrees of tubule degeneration and decreased spermatogenetic activity. Semen could be used for various assisted reproductive technologies such as intrauterine insemination,in vitro fertilisation (IVF) and microinsemination (ICSI). The literature reports pregnancy rates by intrauterine insemination of about 15 to 20% per couple. Clinical pregnancy rates after IVF and ICSI techniques are 30% per cycle and these results are comparable to the clinical pregnancy rates when these techniques are performed for female infertility. However, semen must be frozen as soon as possible after the injury and the patient must be informed about the various available assisted reproductive technologies.     

An Italian functional genomic resource for <Emphasis Type="Italic">Medicago truncatula</Emphasis>

Background

Medicago truncatula is a model species for legumes. Its functional genomics have been considerably boosted in recent years due to initiatives based both in Europe and US. Collections of mutants are becoming increasingly available and this will help unravel the genetic control of important traits for many species of legumes.

Findings

Our report is on the production of three complementary mutant collections of the model species Medicago truncatula produced in Italy in the frame of a national genomic initiative. Well established strategies were used: Tnt1 mutagenesis, TILLING and activation tagging. Both forward and reverse genetics screenings proved the efficiency of the mutagenesis approaches adopted, enabling the isolation of interesting mutants which are in course of characterization. We anticipate that the reported collections will be complementary to the recently established functional genomics tools developed for Medicago truncatula both in Europe and in the United States.

     

Aquatic Plants Stimulate the Growth of and Biofilm Formation by Mycobacterium ulcerans in Axenic Culture and Harbor These Bacteria in the Environment

Mycobacterium ulcerans is the causative agent of Buruli ulcer, one of the most common mycobacterial diseases of humans. Recent studies have implicated aquatic insects in the transmission of this pathogen, but the contributions of other elements of the environment remain largely unknown. We report here that crude extracts from two green algae added to the BACTEC 7H12B culture medium halved the doubling time of M. ulcerans and promoted biofilm formation. Using the 7H12B medium, modified by the addition of the algal extract, and immunomagnetic separation, we also demonstrate that M. ulcerans is associated with aquatic plants in an area of the Ivory Coast where Buruli ulcer is endemic. Genotype analysis showed that plant-associated M. ulcerans had the same profile as isolates recovered in the same region from both aquatic insects and clinical specimens. These observations implicate aquatic plants as a reservoir of M. ulcerans and add a new potential link in the chain of transmission of M. ulcerans to humans.     

Controlled disassembly of peptide amphiphile fibres.

In this paper, the introduction of both a methionine residue and a nitrobenzyl derivative as a labile linker between the peptide part and the hydrophobic alkyl chain of a peptide amphiphile are presented. These modifications are shown not to inhibit the formation of structured assemblies that analogous peptide amphiphiles lacking the linkers are able to form. Moreover, the introduction of either labile linker allows removal of the peptide amphiphile's stabilizing hydrophobic moieties to initiate a controlled disassembly of fibre aggregates. This is achieved by either treatment with CNBr or UV irradiation, respectively. These disassembly mechanisms could be the starting point for methodology that allows further manipulation of self-assembled peptide amphiphile architectures.     

Seven Decades of Change in the Zooplankton (s.l.) of the Nile Delta Lakes (Egypt), with Particular Reference to Lake Borullus

Around the 1930s, the zooplankton (and benthos) of the Nile delta lakes, and Lake Borullus in particular, had a mixed, eutrophic facies, with marine and mesohaline elements dominant for about eight months per year, and freshwater species taking over during the four months of the Nile flood. After the Aswan dam became operational, this regime changed: a steady supply of agricultural drainage water of Nilotic origin consistently freshened the delta. Thus, except in the immediate vicinity of their outlet to the sea, the lakes became almost fresh. Only during the rare and short‐lived (one‐three weeks) occasions when Aswan closes in winter, marine water is sucked in, and along with it, a saline fauna temporarily becomes re‐established in the east and centre of lake Borullus, and presumably of the other delta lakes as well. This marine fauna remained the same over 70+ years of observations. The freshwater component, in contrast, partly nilotic, partly mediterranean, changed deeply over time. First, the fraction of species from temporary waters disappeared, as well as (among copepods and cladocerans) all large‐bodied species. Several cladocerans and copepods with a euro‐mediterranean range appeared and diluted the pre‐existing Afrotropical fauna. The abundance of small cladocerans and, especially, rotifers increased by a factor ten or more. This latter change is believed to reflect two pressures. In a first phase, a re‐arrangement of the lake's fish fauna (a top down force) occurred. Freshwater fish replaced marine diadromic species, and their predation pressure on the zooplankton preferentially removed large‐bodied prey. In a second phase, increased agricultural drainage caused eutrophication (a bottom‐up force) and larger filtrators (cladocerans, some copepods) began to be replaced by small filtrators (rotifers). (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)