Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis

Enzymes are basically composed of 20 naturally occurring amino acids, yet they catalyse a dizzying array of chemical reactions, with regiospecificity and stereospecificity and under physiological conditions. In this review, we attempt to gain some understanding of these complex proteins, from the chemical versatility of the catalytic toolkit, including the use of cofactors (both metal ions and organic molecules), to the complex mapping of reactions to proteins (which is rarely one-to-one), and finally the structural complexity of enzymes and their active sites, often involving multidomain or multisubunit assemblies. This work highlights how the enzymes that we see today reflect millions of years of evolution, involving de novo design followed by exquisite regulation and modulation to create optimal fitness for life.     

Understorey plant community assemblage of Australian Eucalyptus woodlands under elevated CO2 is modulated by water and phosphorus availability

水分和磷调控的澳大利亚桉树林林下植物群落组合对二氧化碳浓度升高的响应 鉴于林下植物群落具有的关键性功能作用和全球范围内巨大的森林覆盖面积,研究林下群落对 CO₂浓度升高(eCO₂)的响应以及土壤资源在这些响应中的作用,对于了解CO₂浓度升高对森林生态系统造成的影响非常重要。本研究评估了在澳大利亚东部磷有限的桉树林林下群落中,两种限制性的资源(即水分和磷)在发芽、物候、覆盖率、群落组成和叶片性状等方面对eCO₂响应的作用。我们收集了含有当地土壤种子库的土壤,在温室条件下种植实验性的林下植物群落。研究结果表明,添加磷提高了植物的总体覆盖率,特别是在生长期的最初4 周以及水分含量高的条件下,而且该响应是由植物群落中的类禾本科植物所驱动。然而,随着实验的进行,不同处理方法之间的差异逐渐减小,所有处理在大约11周后均达到了80%左右的植物覆盖率。相反,植物覆盖率并未受到eCO₂ 的影响。多元分析结果反映出植物群落组成随时间的变化,盆栽从以裸土为主变为以高覆盖率的多样化群落为主。但是在实验过程中,磷的添加以及水分可利用性和CO₂之间的相互作用都对植物群落随时间的变化轨迹有所影响。CO₂浓度的升高也增加了群落水平的比叶面积,这表明植物群落对eCO₂的功能适应可能发生在成分响应开始之前。鉴于我们用种子库培育的林下群落对eCO₂ 的响应随着时间的推移而有 所变化,并且受到与磷和水分可利用性的相互作用的调节。我们的结果表明,在水分含量有限的系统中, 特别是在土壤养分可利用性低所导致的生产力响应受限的情况下,CO₂浓度的升高在塑造植物群落方面作用有限。     

Tamarindus indica L. leaf is a source of allelopathic substance

The allelopathic potential of the Tamarindus indica L. leaf was investigated through bioassay guided studies using several weed and edible crop species. Both radicle and hypocotyl growth of all the plant species tested was strongly inhibited by the tamarind leaf using a sandwich method. The growth of weed species was reduced more than that of edible crop species. Among the weed species, barnyard grass followed by white clover, and in the edible crop species, lettuce followed by radish ranked top in terms of growth inhibition. Different concentrations of tamarind leaf crude water-soluble extract exhibited a strong inhibition in all the plant species tested and, by contrast, the magnitude of inhibition in the weed species was higher than in edible crop species and ranged from 30–75%. The 10% concentration of the tamarind leaf crude water-soluble extract was most potent against growth of seedlings. The concentrations of the nutrient components were linearly correlated with an increase in the concentration of tamarind leaf crude water-soluble extract. No significant changes in either pH or EC were found in the variations of different concentrations of tamarind leaf crude water-soluble extracts. As compared to control, growth of both radicle and hypocotyl in weed (barnyard grass and white clover) and in edible crop (lettuce and radish) species were significantly reduced when blended tamarind leaves at different concentrations were incorporated into the growth medium. The inhibitory magnitude increased with an increase in the concentration of the tamarind leaf. In terms of growth inhibition, among these tested plants, weed species particularly barnyard grass were most sensitive to the allelochemicals exuded from blended tamarind leaves. When the blended tamarind leaves were removed from the growth medium, all the seedlings grew quickly and the percentage of recovery was between 76–97% of the corresponding controls. Reduction in the fresh and dry weight of these 4 plant species was observed under the experimental conditions, and ranged between 33–42% and 40–53% in the radicle and hypocotyl, respectively. The fresh and dry weight, and total chlorophyll content declined significantly in the incorporated tamarind leaf treatments. Compared to the control, the highest drop in the chlorophyll content of 60% in barnyard grass was observed with the 10% concentration of the leaf treatment. These results clearly indicate that the tamarind leaf contains one or more strong biologically active allelochemical(s) that function as true growth regulator(s) and is involved in plant growth regulation, particularly in weed species.     

The design and discovery of novel amide CCR5 antagonists

The synthesis of a range of novel amine-containing structures and their primary potency as inhibitors of HIV-1 fusion via blocking of the CCR5 receptor is described. The development of the medicinal chemistry strategy and SAR’s which led to the identification of the piperidine amide compounds 33 and 36 as excellent leads for further evaluation is described, along with key physicochemical data which highlighted their lead potential.     

Microparticle Shedding from Neural Progenitor Cells and Vascular Compartment Cells Is Increased in Ischemic Stroke

Purpose

Ischemic stroke has shown to induce platelet and endothelial microparticle shedding, but whether stroke induces microparticle shedding from additional blood and vascular compartment cells is unclear. Neural precursor cells have been shown to replace dying neurons at sites of brain injury; however, if neural precursor cell activation is associated to microparticle shedding, and whether this activation is maintained at long term and associates to stroke type and severity remains unknown. We analyzed neural precursor cells and blood and vascular compartment cells microparticle shedding after an acute ischemic stroke.

Methods

Forty-four patients were included in the study within the first 48h after the onset of stroke. The cerebral lesion size was evaluated at 3–7 days of the stroke. Circulating microparticles from neural precursor cells and blood and vascular compartment cells (platelets, endothelial cells, erythrocytes, leukocytes, lymphocytes, monocytes and smooth muscle cells) were analyzed by flow cytometry at the onset of stroke and at 7 and 90 days. Forty-four age-matched high cardiovascular risk subjects without documented vascular disease were used as controls.

Results

Compared to high cardiovascular risk controls, patients showed higher number of neural precursor cell- and all blood and vascular compartment cell-derived microparticles at the onset of stroke, and after 7 and 90 days. At 90 days, neural precursor cell-derived microparticles decreased and smooth muscle cell-derived microparticles increased compared to levels at the onset of stroke, but only in those patients with the highest stroke-induced cerebral lesions.

Conclusions

Stroke increases blood and vascular compartment cell and neural precursor cell microparticle shedding, an effect that is chronically maintained up to 90 days after the ischemic event. These results show that stroke induces a generalized blood and vascular cell activation and the initiation of neuronal cell repair process after stroke. Larger cerebral lesions associate with deeper vessel injury affecting vascular smooth muscle cells.     

A Computational Model of Lipopolysaccharide-Induced Nuclear Factor Kappa B Activation: A Key Signalling Pathway in Infection-Induced Preterm Labour

Preterm birth is the single biggest cause of significant neonatal morbidity and mortality, and the incidence is rising. Development of new therapies to treat and prevent preterm labour is seriously hampered by incomplete understanding of the molecular mechanisms that initiate labour at term and preterm. Computational modelling provides a new opportunity to improve this understanding. It is a useful tool in (i) identifying gaps in knowledge and informing future research, and (ii) providing the basis for an in silico model of parturition in which novel drugs to prevent or treat preterm labour can be “tested”. Despite their merits, computational models are rarely used to study the molecular events initiating labour. Here, we present the first attempt to generate a dynamic kinetic model that has relevance to the molecular mechanisms of preterm labour. Using published data, we model an important candidate signalling pathway in infection-induced preterm labour: that of lipopolysaccharide (LPS) -induced activation of Nuclear Factor kappa B. This is the first model of this pathway to explicitly include molecular interactions upstream of Nuclear Factor kappa B activation. We produced a formalised graphical depiction of the pathway and built a kinetic model based on ordinary differential equations. The kinetic model accurately reproduced published in vitro time course plots of Lipopolysaccharide-induced Nuclear Factor kappa B activation in mouse embryo fibroblasts. In this preliminary work we have provided proof of concept that it is possible to build computational models of signalling pathways that are relevant to the regulation of labour, and suggest that models that are validated with wet-lab experiments have the potential to greatly benefit the field.     

Assessing the effectiveness of a community intervention for monkeypox prevention in the Congo basin

Background

In areas where health resources are limited, community participation in the recognition and reporting of disease hazards is critical for the identification of outbreaks. This is particularly true for zoonotic diseases such as monkeypox that principally affect people living in remote areas with few health services. Here we report the findings of an evaluation measuring the effectiveness of a film-based community outreach program designed to improve the understanding of monkeypox symptoms, transmission and prevention, by residents of the Republic of the Congo (ROC) who are at risk for disease acquisition.

Methodology/Principal Findings

During 90 days, monkeypox outreach was conducted for ∼23,860 people in northern ROC. Two hundred seventy-one attendees (selected via a structured sample) were interviewed before and after participating in a small-group outreach session. The proportion of interviewees demonstrating monkeypox-specific knowledge before and after was compared. Significant gains were measured in areas of disease recognition, transmission, and mitigation of risk. The ability to recognize at least one disease symptom and a willingness to take a family member with monkeypox to the hospital increased from 49 and 45% to 95 and 87%, respectively (p<0.001, both). Willingness to deter behaviors associated with zoonotic risk, such as eating the carcass of a primate found dead in the forest, remained fundamentally unchanged however, suggesting additional messaging may be needed.

Conclusions/Significance

These results suggest that our current program of film-based educational activities is effective in improving disease-specific knowledge and may encourage individuals to seek out the advice of health workers when monkeypox is suspected.     

Rab9 GTPase regulates late endosome size and requires effector interaction for its stability

Rab9 GTPase resides in a late endosome microdomain together with mannose 6-phosphate receptors (MPRs) and the tail-interacting protein of 47 kDa (TIP47). To explore the importance of Rab9 for microdomain establishment, we depleted the protein from cultured cells. Rab9 depletion decreased late endosome size and reduced the numbers of multilamellar and dense-tubule-containing late endosomes/lysosomes, but not multivesicular endosomes. The remaining late endosomes and lysosomes were more tightly clustered near the nucleus, implicating Rab9 in endosome localization. Cells displayed increased surface MPRs and lysosome-associated membrane protein 1. In addition, cells showed increased MPR synthesis in conjunction with MPR missorting to the lysosome. Surprisingly, Rab9 stability on late endosomes required interaction with TIP47. Rabs are thought of as independent, prenylated entities that reside either on membranes or in cytosol, bound to GDP dissociation inhibitor. These data show that Rab9 stability is strongly influenced by a specific effector interaction. Moreover, Rab9 and the proteins with which it interacts seem critical for the maintenance of specific late endocytic compartments and endosome/lysosome localization.