HU histone-like DNA-binding protein from <Emphasis Type="Italic">Thermus thermophilus</Emphasis>: structural and evolutionary analyses

The histone-like DNA-binding proteins (HU) serve as model molecules for protein thermostability studies, as they function in different bacteria that grow in a wide range of temperatures and show sequence diversity under a common fold. In this work, we report the cloning of the hutth gene from Thermus thermophilus, the purification and crystallization of the recombinant HUTth protein, as well as its X-ray structure determination at 1.7 Å. Detailed structural and thermodynamic analyses were performed towards the understanding of the thermostability mechanism. The interaction of HUTth protein with plasmid DNA in solution has been determined for the first time with MST. Sequence conservation of an exclusively thermophilic order like Thermales, when compared to a predominantly mesophilic order (Deinococcales), should be subject, to some extent, to thermostability-related evolutionary pressure. This hypothesis was used to guide our bioinformatics and evolutionary studies. We discuss the impact of thermostability adaptation on the structure of HU proteins, based on the detailed evolutionary analysis of the Deinococcus–Thermus phylum, where HUTth belongs. Furthermore, we propose a novel method of engineering thermostable proteins, by combining consensus-based design with ancestral sequence reconstruction. Finally, through the structure of HUTth, we are able to examine the validity of these predictions. Our approach represents a significant advancement, as it explores for the first time the potential of ancestral sequence reconstruction in the divergence between a thermophilic and a mainly mesophilic taxon, combined with consensus-based engineering.     

Facilitation between woody and herbaceous plants that associate with arbuscular mycorrhizal fungi in temperate European forests

In late‐successional environments, low in available nutrient such as the forest understory, herbaceous plant individuals depend strongly on their mycorrhizal associates for survival. We tested whether in temperate European forests arbuscular mycorrhizal (AM) woody plants might facilitate the establishment of AM herbaceous plants in agreement with the mycorrhizal mediation hypothesis. We used a dataset spanning over 400 vegetation plots in the Weser‐Elbe region (northwest Germany). Mycorrhizal status information was obtained from published resources, and Ellenberg indicator values were used to infer environmental data. We carried out tests for both relative richness and relative abundance of herbaceous plants. We found that the subset of herbaceous individuals that associated with AM profited when there was a high cover of AM woody plants. These relationships were retained when we accounted for environmental filtering effects using path analysis. Our findings build on the existing literature highlighting the prominent role of mycorrhiza as a coexistence mechanism in plant communities. From a nature conservation point of view, it may be possible to promote functional diversity in the forest understory through introducing AM woody trees in stands when absent.     

Human leptin induces angiogenesis in vivo

Leptin is an adipocyte-produced peptide, which plays a crucial role in the regulation of body weight. There is also evidence that leptin stimulates endothelial cell proliferation and the formation of capillary-like tubes in vitro. The disc angiogenesis system was used to measure the angiogenic effect of leptin in vivo. Discs containing 25, 50, 100 and 250 ng/ml of leptin were implanted subcutaneously in Wistar rats, removed after a growth period of 7 and 14 days, and compared with spontaneous growth controls and with positive controls containing equivalent doses of vascular endothelial growth factor (VEGF). Discs were examined morphologically for stroma and vessel development and by immunohistochemistry for quantitative evaluation of angiogenesis. The specificity of the angiogenic effect of leptin was tested by blocking leptin with a polyclonal anti-leptin antibody. Leptin induced a significant level of angiogenesis in a dose-dependent manner both at 7 and 14 days, with a peak at the dose of 100 ng/ml. The angiogenic activity of leptin was completely abolished by the anti-leptin neutralizing antibody. VEGF also induced significant dose-dependent angiogenesis at the same time points with a peak observed at a concentration of 100 ng/ml. The angiogenic response to leptin was significantly higher at 7 days compared with VEGF but not at the 14-day time point. In conclusion, leptin has a specific angiogenic effect in vivo, which is dose- and time-dependent in a concentration range of 25–250 ng/ml. This effect is equivalent to the angiogenic effect of VEGF but is evident earlier compared with VEGF.     

Complex dynamics of microbial competition in the gradostat

We examine the conditions necessary for the emergence of complex dynamic behavior in systems of microbial competition. In particular, we study the effect of spatial heterogeneity and substrate-inhibition on the dynamics of such a system. This is accomplished through the study of a mathematical model of two microbial populations competing for a single nutrient in a configuration of two interconnected chemostats. Microbial growth is assumed to follow substrate-inhibited kinetics for both species. Such a system with sterile feed has been shown in a previous work to exhibit stable periodic states. In the present work we study the system for the case of non-sterile feed, i.e., when the two species are present in the feed of the chemostats. The analysis is done by numerical bifurcation theory methods. We demonstrate that, in addition to periodic states, the system possesses stable quasi-periodic states resulting from Neimark-Sacker bifurcations of limit cycles. Also, periodic states may undergo successive period doublings leading to periodic states of increasing period and indicating that chaotic states might be possible. Multistability is also observed, consisting in the coexistence of several stable steady states and possibly stable periodic or quasi-periodic states for given operating conditions. It appears that substrate-inhibition, spatial heterogeneity and presence of microorganisms in the inflow are all necessary conditions for complex dynamics to arise in a microbial system of pure and simple competition.     

Spatially distinct functions of PAX6 and NKX2.2 during gliogenesis in the ventral spinal cord

During ventral spinal cord (vSC) development, the p3 and pMN progenitor domain boundary is thought to be maintained by cross-repressive interactions between NKX2.2 and PAX6. Using loss-of-function analysis during the neuron-glial fate switch we show that the identity of the p3 domain is not maintained by the repressive function of NKX2.2 on Pax6 expression, even in the absence of NKX2.9. We further show that NKX2.2 is necessary to induce the expression of Slit1 and Sulfatase 1 (Sulf1) in the vSC in a PAX6-independent manner. Conversely, we show that PAX6 regulates Sulf1/Slit1 expression in the vSC in an NKX2.2/NKX6.1-independent manner. Consequently, deregulation of Sulf1 expression in Pax6-mutant embryos has stage-specific implications on neural patterning, associated with enhancement of Sonic Hedgehog activity. On the other hand, deregulation of Slit1 expression in gliogenic neural progenitors leads to changes in Astrocyte subtype identity. These data provide important insights into specific functions of PAX6 and NKX2.2 during glial cell specification that have so far remained largely unexplored.     

Generation of an ABCG2 transgenic line - A tool to study ABCG2 expression in mice

The ATP-binding cassette (ABC) transporter 2 (ABCG2) is expressed by stem cells in many organs and in stem cells of solid tumors. These cells are isolated based on the side population (SP) phenotype, a Hoechst 3342 dye efflux property believed to be conferred by ABCG2. Because of the limitations of this approach we generated transgenic mice that express Nuclear GFP (GFPn) coupled to the Puromycin-resistance gene, under the control of ABCG2 promoter/enhancer sequences. We show that ABCG2 is expressed in neural progenitors of the developing forebrain and spinal cord and in embryonic and adult endothelial cells of the brain. Using the neurosphere assay, we isolated tripotent ABCG2-expressing neural stem cells from embryonic mouse brain. This transgenic line is a powerful tool for studying the expression of ABCG2 in many tissues and for performing functional studies in different experimental settings.     

Hyaluronan Mediates Ozone-induced Airway Hyperresponsiveness in Mice

Ozone is a common urban environmental air pollutant and significantly contributes to hospitalizations for respiratory illness. The mechanisms, which regulate ozone-induced bronchoconstriction, remain poorly understood. Hyaluronan was recently shown to play a central role in the response to noninfectious lung injury. Therefore, we hypothesized that hyaluronan contributes to airway hyperreactivity (AHR) after exposure to ambient ozone. Using an established model of ozone-induced airways disease, we characterized the role of hyaluronan in airway hyperresponsiveness. The role of hyaluronan in response to ozone was determined by using therapeutic blockade, genetically modified animals, and direct challenge to hyaluronan. Ozone-exposed mice demonstrate enhanced AHR associated with elevated hyaluronan levels in the lavage fluid. Mice deficient in either CD44 (the major receptor for hyaluronan) or inter-α-trypsin inhibitor (molecule that facilitates hyaluronan binding) show similar elevations in hyaluronan but are protected from ozone-induced AHR. Mice pretreated with hyaluronan-binding peptide are protected from the development of ozone-induced AHR. Overexpression of hyaluronan enhances the airway response to ozone. Intratracheal instillation of endotoxin-free low molecular weight hyaluronan induces AHR dependent on CD44, whereas instillation of high molecular weight hyaluronan protects against ozone-induced AHR. In conclusion, we demonstrate that hyaluronan mediates ozone-induced AHR, which is dependent on the fragment size and both CD44 and inter-α-trypsin inhibitor. These data support the conclusion that pulmonary matrix can contribute to the development of airway hyperresponsiveness.Ozone is a commonly encountered urban air pollutant that significantly contributes to increased morbidity (1–4) and can lead to a significant economic burden. It has been estimated that each year inhalation of ambient ozone contributes to 800 premature deaths, 4,500 hospital admissions, 900,000 school absences, and more than 1 million restricted activity days with an estimated $5 billion annual economic burden (5). Population-based studies suggest that for each 10 ppb increase in 1-h daily maximum level of ozone there is an increase in mortality risk of 0.39–0.87%, especially in individuals with pre-existing respiratory disease (2, 3, 6, 7). However, the biological mechanisms, which regulate the response to ambient ozone exposure, remain poorly understood.Hyaluronan is an abundant extracellular matrix component, which has been recently shown to play a significant role in the response to noninfectious lung injury. Short fragment hyaluronan (sHA)² is released in the lung after sterile injury such as bleomycin instillation (8) or high tidal volume ventilation (9) and can modify the tissue response to injury. Furthermore, hyaluronan has been identified in airway secretions from asthmatics (10), and high molecular weight hyaluronan can attenuate the bronchoconstrictive response in exercise-induced asthma (11). We therefore hypothesized that hyaluronan may contribute to the biological response to airway injury after exposure to ozone.In this study, we provide evidence that hyaluronan mediates ozone-induced AHR. Mice exposed to ozone demonstrate elevated lung lavage fluid levels of hyaluronan, which is of low molecular weight. We observed that animals deficient in either CD44 (a hyaluronan surface receptor) or inter-α-trypsin inhibitor (IaI, which facilitates hyaluronan binding) are protected from ozone-induced AHR. Overexpression of hyaluronan by airway epithelia enhances ozone-induced AHR. Furthermore, pretreatment of mice with hyaluronan-binding peptide or high molecular weight hyaluronan protects animals from the development of ozone-induced AHR. Direct instillation of low molecular weight, but not high molecular weight, hyaluronan alone induces AHR. Our observations support a critical role for short fragment hyaluronan in the development of airway hyperresponsiveness after exposure to ozone.     

How Many 3D Structures Do We Need to Train a Predictor？

It has been shown that the progress in the determination of membrane protein structure grows exponentially, with approximately the same growth rate as that of the water-soluble proteins. In order to investigate the effect of this, on the performance of prediction algorithms for both α-helical and β-barrel membrane proteins, we conducted a prospective study based on historical records. We trained separate hidden Markov models with different sized training sets and evaluated their performance on topology pred...     

Lifestyle Intervention Favorably Affects Weight Loss and Maintenance Following Obesity Surgery

The present study was designed to evaluate the 3 year effects of a lifestyle intervention on weight loss and maintenance, dietary, and physical activity habits and eating behavior of patients following vertical banded gastroplasty (VBG). Thirty severely obese female volunteers were included in the study and they were randomly assigned to one of two intervention groups: usual care (UC) or lifestyle intervention (LS) group. Patients were followed for 3 years postoperatively. Outcome measures included weight loss, dietary habits, physical activity level (PAL), and eating behavior changes. Weight was significantly lower in the LS group after 12 months (84.4 ± 3.9 kg vs. 98.4 ± 4.4 kg, P < 0.05), 24 months (83.0 ± 3.3 vs. 101.9 ± 5.3 kg, P < 0.05), and 36 months following surgery (84.2 ± 3.3 vs. 102.5 ± 3.5 kg, P < 0.05). Repeated measures ANOVA revealed significant differences between the two groups overall and at specific time points for the PAL and TV viewing. With regard to eating behavior, the LS group scored significantly better in total Dutch Eating Behavior Questionnaire (DEBQ), Restraint Eating and External Eating scales at all postoperative time points. Similarly, significant differences were found between the two groups in dietary intake. These findings outline the importance of lifestyle intervention on weight loss and maintenance following bariatric surgery. The favorable effects of lifestyle intervention may be through adoption of healthier eating behaviors and increased physical activity.     

DNA damage and senescence in osteoprogenitors expressing Osx1 may cause their decrease with age

Age‐related bone loss in mice results from a decrease in bone formation and an increase in cortical bone resorption. The former is accounted by a decrease in the number of postmitotic osteoblasts which synthesize the bone matrix and is thought to be the consequence of age‐dependent changes in mesenchymal osteoblast progenitors. However, there are no specific markers for these progenitors, and conclusions rely on results from in vitro cultures of mixed cell populations. Moreover, the culprits of such changes remain unknown. Here, we have used Osx1‐Cre;TdRFP mice in which osteoprogenitors express the TdRFP fluorescent protein. We report that the number of TdRFP‐Osx1 cells, freshly isolated from the bone marrow, declines by more than 50% between 6 and 24 months of age in both female and male mice. Moreover, TdRFP‐Osx1 cells from old mice exhibited markers of DNA damage and senescence, such as γH2AX foci, G1 cell cycle arrest, phosphorylation of p53, increased p21^CIP1 levels, as well as increased levels of GATA4 and activation of NF‐κB – two major stimulators of the senescence‐associated secretory phenotype (SASP). Bone marrow stromal cells from old mice also exhibited elevated expression of SASP genes, including several pro‐osteoclastogenic cytokines, and increased capacity to support osteoclast formation. These changes were greatly attenuated by the senolytic drug ABT263. Together, these findings suggest that the decline in bone mass with age is the result of intrinsic defects in osteoprogenitor cells, leading to decreased osteoblast numbers and increased support of osteoclast formation.