Identification of large-scale human-specific copy number differences by inter-species array comparative genomic hybridization

Copy number differences (CNDs), and the concomitant differences in gene number, have contributed significantly to the genomic divergence between humans and other primates. To assess its relative importance, the genomes of human, common chimpanzee, bonobo, gorilla, orangutan and macaque were compared by comparative genomic hybridization using a high-resolution human BAC array (aCGH). In an attempt to avoid potential interference from frequent intra-species polymorphism, pooled DNA samples were used from each species. A total of 322 sites of large-scale inter-species CND were identified. Most CNDs were lineage-specific but frequencies differed considerably between the lineages; the highest CND frequency among hominoids was observed in gorilla. The conserved nature of the orangutan genome has already been noted by karyotypic studies and our findings suggest that this degree of conservation may extend to the sub-microscopic level. Of the 322 CND sites identified, 14 human lineage-specific gains were observed. Most of these human-specific copy number gains span regions previously identified as segmental duplications (SDs) and our study demonstrates that SDs are major sites of CND between the genomes of humans and other primates. Four of the human-specific CNDs detected by aCGH map close to the breakpoints of human-specific karyotypic changes [e.g., the human-specific inversion of chromosome 1 and the polymorphic inversion inv(2)(p11.2q13)], suggesting that human-specific duplications may have predisposed to chromosomal rearrangement. The association of human-specific copy number gains with chromosomal breakpoints emphasizes their potential importance in mediating karyotypic evolution as well as in promoting human genomic diversity. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

The role of below-ground competition during early stages of secondary succession: the case of 3-year-old Scots pine (Pinus sylvestris L.) seedlings in an abandoned grassland

In abandoned or extensively managed grasslands, the mechanisms involved in pioneer tree species success are not fully explained. Resource competition among plants and microclimate modifications have been emphasised as possible mechanisms to explain variation of survivorship and growth. In this study, we evaluated a number of mechanisms that may lead to successful survival and growth of seedlings of a pioneer tree species (Pinus sylvestris) in a grass-dominated grassland. Three-year-old Scots pines were planted in an extensively managed grassland of the French Massif Central and for 2 years were either maintained in bare soil or subjected to aerial and below-ground interactions induced by grass vegetation. Soil temperatures were slightly higher in bare soil than under the grass vegetation, but not to an extent explaining pine growth differences. The tall grass canopy reduced light transmission by 77% at ground level and by 20% in the upper part of Scots pine seedlings. Grass vegetation presence also significantly decreased soil volumetric water content (Hv) and soil nitrate in spring and in summer. In these conditions, the average tree height was reduced by 5% compared to trees grown in bare soil, and plant biomass was reduced by 85%. Scots pine intrinsic water-use efficiency (A/g), measured by leaf gas-exchange, increased when Hv decreased owing to a rapid decline of stomatal conductance (g). This result was also confirmed by δ ¹³C analyses of needles. A summer ¹⁵N labelling of seedlings and grass vegetation confirmed the higher NO₃ capture capacity of grass vegetation in comparison with Scots pine seedlings. Our results provide evidence that the seedlings' success was linked to tolerance of below-ground resource depletion (particularly water) induced by grass vegetation based on morphological and physiological plasticity as well as to resource conservation.     

A synthetic de-greening gene circuit provides a reporting system that is remotely detectable and has a re-set capacity

Plants have evolved elegant mechanisms to continuously sense and respond to their environment, suggesting that these properties can be adapted to make inexpensive and widely used biological monitors, or sentinels, for human threats. For a plant to be a sentinel, a reporting system is needed for large areas and widespread monitoring. The reporter or readout mechanism must be easily detectable, allow remote monitoring and provide a re-set capacity; all current gene reporting technologies fall short of these requirements. Chlorophyll is one of the best-recognized plant pigments with an already well-developed remote imaging technology. However, chlorophyll is very abundant, with levels regulated by both genetic and environmental factors. We designed a synthetic de-greening circuit that produced rapid chlorophyll loss on perception of a specific input. With induction of the de-greening circuit, changes were remotely detected within 2 h. Analyses of multiple de-greening circuits suggested that the de-greening circuit functioned, in part, via light-dependent damage to photosystem cores and the production of reactive oxygen species. Within 24–48 h of induction, an easily recognized white phenotype resulted. Microarray analysis showed that the synthetic de-greening initiated a process largely distinct from normal chlorophyll loss in senescence. Remarkably, synthetically de-greened white plants re-greened after removal of the inducer, providing the first easily re-settable reporter system for plants and the capacity to make re-settable biosensors. Our results showed that the de-greening circuit allowed chlorophyll to be employed as a simple but powerful reporter system useful for widespread areas.     

An old enzyme for current needs: adenosine deaminase and a dendritic cell vaccine for HIV

After nearly three decades of searching for a vaccine against HIV, a cure for this pandemic disease still remains elusive. The low immunogenicity of the surface proteins and the huge variability of the virus, together with the immunocompromised status of the host, have made developing an HIV vaccine an uphill battle. Over the past few years, both immunogen design and immunization strategies have improved, providing hope for future, although the anti-HIV responses achieved still remain modest. As developing a prophylactic vaccine seems unlikely nowadays, efforts have focused on alternative therapeutic immunization approaches, although these still need to be further optimized. Using an immunomodulator capable of restoring immune function in the context of infection, thereby boosting cell-mediated and humoral responses, could be critical in effectively improving current therapeutic approaches. Adenosine deaminase, a protein with a pivotal role in T-cell co-stimulation, has been shown to robustly enhance specific T-cell responses against HIV in vitro. Although its role in humoral responses has not yet been assessed, genetic defects in this enzyme are associated with impaired cellular and humoral responses. Importantly, this molecule is already commercially available pharmaceutically and, therefore, it fulfils all the requirements to be assayed as an anti-HIV vaccine adjuvant.     

Effect of ghrelin on glucose regulation in mice

Improvement of glucose metabolism after bariatric surgery appears to be from the composite effect of the alterations in multiple circulating gut hormone concentrations. However, their individual effect on glucose metabolism during different conditions is not clear. The objective of this study was to determine whether ghrelin has an impact on glycogenolysis, gluconeogenesis, and insulin sensitivity (using a mice model). Rate of appearance of glucose, glycogenolysis, and gluconeogenesis were measured in wild-type (WT), ghrelin knockout (ghrelin(-/-)), and growth hormone secretagogue receptor knockout (Ghsr(-/-)) mice in the postabsorptive state. The physiological nature of the fasting condition was ascertained by a short-term fast commenced immediately at the end of the dark cycle. Concentrations of glucose and insulin were measured, and insulin resistance and hepatic insulin sensitivity were calculated. Glucose concentrations were not different among the groups during the food-deprived period. However, plasma insulin concentrations were lower in the ghrelin(-/-) and Ghsr(-/-) than WT mice. The rates of gluconeogenesis, glycogenolysis, and indexes of insulin sensitivity were higher in the ghrelin(-/-) and Ghsr(-/-) than WT mice during the postabsorptive state. Insulin receptor substrate 1 and glucose transporter 2 gene expressions in hepatic tissues of the ghrelin(-/-) and Ghsr(-/-) were higher compared with that in WT mice. This study demonstrates that gluconeogenesis and glycogenolysis are increased and insulin sensitivity is improved by the ablation of the ghrelin or growth hormone secretagogue receptor in mice.     

Ablation of ghrelin receptor in leptin-deficient ob/ob mice has paradoxical effects on glucose homeostasis when compared with ablation of ghrelin in ob/ob mice

The orexigenic hormone ghrelin is important in diabetes because it has an inhibitory effect on insulin secretion. Ghrelin ablation in leptin-deficient ob/ob (Ghrelin(-/-):ob/ob) mice increases insulin secretion and improves hyperglycemia. The physiologically relevant ghrelin receptor is the growth hormone secretagogue receptor (GHS-R), and GHS-R antagonists are thought to be an effective strategy for treating diabetes. However, since some of ghrelin's effects are independent of GHS-R, we have utilized genetic approaches to determine whether ghrelin's effect on insulin secretion is mediated through GHS-R and whether GHS-R antagonism indeed inhibits insulin secretion. We investigated the effects of GHS-R on glucose homeostasis in Ghsr-ablated ob/ob mice (Ghsr(-/-):ob/ob). Ghsr ablation did not rescue the hyperphagia, obesity, or insulin resistance of ob/ob mice. Surprisingly, Ghsr ablation worsened the hyperglycemia, decreased insulin, and impaired glucose tolerance. Consistently, Ghsr ablation in ob/ob mice upregulated negative β-cell regulators (such as UCP-2, SREBP-1c, ChREBP, and MIF-1) and downregulated positive β-cell regulators (such as HIF-1α, FGF-21, and PDX-1) in whole pancreas; this suggests that Ghsr ablation impairs pancreatic β-cell function in leptin deficiency. Of note, Ghsr ablation in ob/ob mice did not affect the islet size; the average islet size of Ghsr(-/-):ob/ob mice is similar to that of ob/ob mice. In summary, because Ghsr ablation in leptin deficiency impairs insulin secretion and worsens hyperglycemia, this suggests that GHS-R antagonists may actually aggravate diabetes under certain conditions. The paradoxical effects of ghrelin ablation and Ghsr ablation in ob/ob mice highlight the complexity of the ghrelin-signaling pathway.     

Identification of Novel Imidazo[1,2-a]pyridine Inhibitors Targeting M. tuberculosis QcrB

Mycobacterium tuberculosis is a major human pathogen and the causative agent for the pulmonary disease, tuberculosis (TB). Current treatment programs to combat TB are under threat due to the emergence of multi-drug and extensively-drug resistant TB. Through the use of high throughput whole cell screening of an extensive compound library a number of imidazo[1,2-a]pyridine (IP) compounds were obtained as potent lead molecules active against M. tuberculosis and Mycobacterium bovis BCG. The IP inhibitors (1–4) demonstrated minimum inhibitory concentrations (MICs) in the range of 0.03 to 5 µM against a panel of M. tuberculosis strains. M. bovis BCG spontaneous resistant mutants were generated against IP 1, 3, and 4 at 5× MIC and subsequent whole genome sequencing identified a single nucleotide polymorphism ⁹³⁷ACC>⁹³⁷GCC (T313A) in qcrB, which encodes the b subunit of the electron transport ubiquinol cytochrome C reductase. This mutation also conferred cross-resistance against IP 1, 3 and 4 demonstrating a common target. Gene dosage experiments confirmed M. bovis BCG QcrB as the target where over-expression in M. bovis BCG led to an increase in MIC from 0.5 to >8 µM for IP 3. An acute murine model of TB infection established bacteriostatic activity of the IP series, which await further detailed characterization.     

Inhibition of Angiotensin-Converting Enzyme Activity by Flavonoids: Structure-Activity Relationship Studies

Previous studies have demonstrated that certain flavonoids can have an inhibitory effect on angiotensin-converting enzyme (ACE) activity, which plays a key role in the regulation of arterial blood pressure. In the present study, 17 flavonoids belonging to five structural subtypes were evaluated in vitro for their ability to inhibit ACE in order to establish the structural basis of their bioactivity. The ACE inhibitory (ACEI) activity of these 17 flavonoids was determined by fluorimetric method at two concentrations (500 µM and 100 µM). Their inhibitory potencies ranged from 17 to 95% at 500 µM and from 0 to 57% at 100 µM. In both cases, the highest ACEI activity was obtained for luteolin. Following the determination of ACEI activity, the flavonoids with higher ACEI activity (i.e., ACEI >60% at 500 µM) were selected for further IC₅₀ determination. The IC₅₀ values for luteolin, quercetin, rutin, kaempferol, rhoifolin and apigenin K were 23, 43, 64, 178, 183 and 196 µM, respectively. Our results suggest that flavonoids are an excellent source of functional antihypertensive products. Furthermore, our structure-activity relationship studies show that the combination of sub-structures on the flavonoid skeleton that increase ACEI activity is made up of the following elements: (a) the catechol group in the B-ring, (b) the double bond between C2 and C3 at the C-ring, and (c) the cetone group in C4 at the C-ring. Protein-ligand docking studies are used to understand the molecular basis for these results.     

More and more generalists: two decades of changes in the European avifauna

Biotic homogenization (BH) is a process whereby some species (losers) are systematically replaced by others (winners). While this process has been related to the effects of anthropogenic activities, whether and how BH is occurring across regions and the role of native species as a driver of BH has hardly been investigated. Here, we examine the trend in the community specialization index (CSI) for 234 native species of breeding birds at 10 111 sites in six European countries from 1990 to 2008. Unlike many BH studies, CSI uses abundance information to estimate the balance between generalist and specialist species in local assemblages. We show that bird communities are more and more composed of native generalist species across regions, revealing a strong, ongoing BH process. Our result suggests a rapid and non-random change in community composition at a continental scale is occurring, most likely driven by anthropogenic activities.