Discovery and structural characterization of an allosteric inhibitor of bacterial cis‐prenyltransferase

Undecaprenyl pyrophosphate synthase (UPPs) is an essential enzyme in a key bacterial cell wall synthesis pathway. It catalyzes the consecutive condensations of isopentenyl pyrophosphate (IPP) groups on to a trans-farnesyl pyrophosphate (FPP) to produce a C55 isoprenoid, undecaprenyl pyrophosphate (UPP). Here we report the discovery and co-crystal structures of a drug-like UPPs inhibitor in complex with Streptococcus pneumoniae UPPs, with and without substrate FPP, at resolutions of 2.2 and 2.1 Å, respectively. The UPPs inhibitor has a low molecular weight (355 Da), but displays potent inhibition of UPP synthesis in vitro (IC₅₀ 50 nM) that translates into excellent whole cell antimicrobial activity against pathogenic strains of Streptococcal species (MIC₉₀ 0.4 µg mL⁻¹). Interestingly, the inhibitor does not compete with the substrates but rather binds at a site adjacent to the FPP binding site and interacts with the tail of the substrate. Based on the structures, an allosteric inhibition mechanism of UPPs is proposed for this inhibitor. This inhibition mechanism is supported by biochemical and biophysical experiments, and provides a basis for the development of novel antibiotics targeting Streptococcus pneumoniae.     

Functional analyses of recombinant mouse hepcidin-1 in cell culture and animal model

Hepcidin is a peptide hormone that plays an important role in iron metabolism. We have produced a recombinant mouse hepcidin-1 by using baculovirus expression system. Its expression yield was 25 μg/ml when cell culture media were supplemented with a protease inhibitor cocktail. The recombinant mouse hepcidin-1 and synthetic human hepcidin-25 had similar effects on reducing ferroportin expression in J774A cell line and in peritoneal macrophages. However, synthetic human hepcidin-25 was more efficient than recombinant mouse hepcidin-1 in reducing iron concentration in blood circulation (p < 0.01).     

Human amniotic epithelial cells inhibit activation and pro-inflammatory cytokines production of naive CD4+ T cells from women with unexplained recurrent spontaneous abortion

Unexplained recurrent spontaneous abortion (URSA) has been assumed to be caused by a defect in maternal immunological tolerance to the fetus. Human amniotic epithelial cells (hAECs) have stem cell-like features and the ability to modulate the innate and adoptive immune responses. This study aimed to investigate whether hAECs have immunomodulatory effects on naive CD4+ T cells from URSA patients. hAECs were obtained from 15 healthy pregnant women and phenotypic profile of hAECs was determined by flow cytometry. Naive CD4+ T cells were isolated from 25 URSA patients using an immunomagnetic separation method. Naive T cells were stimulated with anti-CD3/anti-CD28 antibodies and co-cultured with different numbers of hAECs for 3 and 6 days. Immunomodulatory effect of hAECs on activation of stimulated T cell was assessed by flow cytometry and Enzyme-linked immunoasorbent assay (ELISA). The hAECs effect on pro-inflammatory cytokines production of activated T cells was also measured by ELISA. Our results indicated that hAECs significantly inhibited the activation of naive T cells in a dose-dependent manner (p?<?0.0001–0.05). They significantly reduced the production of transforming growth factor-beta1 (TGF-β1) of stimulated CD4+T cells (p?<?0.0001–0.05). Moreover, hAECs had potent immunomodulatory effects on the production of interferon-gamma (IFN-γ) and interleukin-17A (IL-17A) of activated T cells (p?<?0.0001–0.01). These findings suggest that hAECs may be a suitable cell source to modulate abnormal immune responses in women with URSA.     

DETERMINATION OF PREGNANCY STATUS FROM BLUBBER SAMPLES IN MINKE WHALES (BALAENOPTERA ACUTOROSTRATA)

Measurement of progesterone concentration in blubber was developed as a method to detect pregnancy in minke whales. Progesterone was extracted and quantified from blubber samples of minke whale carcasses by radioimmunoassay. Results showed a highly significant difference (almost 60-fold) between blubber progesterone concentrations of anatomically determined pregnant females versus non-pregnant female or male carcasses. The results of the study suggest that the blubber progesterone concentrations might be used to determine pregnancy status in free-ranging whales.     

Social life cycle assessment for material selection: a case study of building materials

Purpose

Sustainability of a material-based product mainly depends on the materials used for the product itself or during its lifetime. A material selection decision should not only capture the functional performance required but should also consider the economical, social, and environmental impacts originated during the product life cycle. There is a need to assess social impacts of materials along the full life cycle, not only to be able to address the “social dimension” in sustainable material selection but also for potentially improving the circumstances of affected stakeholders. This paper presents the method and a case study of social life cycle assessment (S-LCA) specialized for comparative studies. Although the authors’ focus is on material selection, the proposed methodology can be used for comparative assessment of products in general.

Methods

The method is based on UNEP/SETAC “guidelines for social life-cycle assessment of products” and includes four main phases: goal and scope definition, life cycle inventory analysis, life cycle impact assessment, and life cycle interpretation. However, some special features are presented to adjust the framework for materials comparison purpose. In life cycle inventory analysis phase, a hot spot assessment is carried out using material flow analysis and stakeholder and experts’ interviews. Based on the results of that, a pairwise comparison method is proposed for life cycle impact assessment applying analytic hierarchy process. A case study was conducted to perform a comparative assessment of the social and socio-economic impacts in life cycle of concrete and steel as building materials in Iran. For hot spot analysis, generic and national level data were gathered, and for impact assessment phase, site-specific data were used.

Result and discussion

The unique feature of the proposed method compared with other works in S-LCA is its specialty to materials and products comparison. This leads to some differences in methodological issues of S-LCA that are explained in the paper in detail. The case study results assert that “steel/iron” in the north of Iran generally has the better social performance than “concrete/cement.” However, steel is associated with many negative social effects in some subcategories, e.g., freedom of association, fair salary, and occupational health in extraction phase. Against, social profile of concrete and cement industry is damaged mainly due to the negative impact of cement production on safe and healthy living condition. The case study presented in this article shows that the evaluation of social impacts is possible, even if the assessment is always affected by subjective value systems.

Conclusions

Application of the UNEP/SETAC guidelines in comparative studies can be encouraged based on the results of this paper. It enables a hotspot assessment of the social and socio-economic impacts in life cycle of alternative materials. This research showed that the development of a specialized S-LCA approach for materials and products comparison is well underway although many challenges still persist. Particularly characterization method in life cycle impact assessment phase is challenging. The findings of this case study pointed out that social impacts are primarily connected to the conduct of companies and less with processes and materials in general. These findings confirm the results of Dreyer et al. (Int J Life Cycle Assess 11(2):88–97, 2006). The proposed approach aims not only to identify the best socially sustainable alternative but also to reveal product/process improvement potentials to facilitate companies to act socially compatible. It will be interesting to apply the UNEP/SETAC approach of S-LCA to other materials and products; materials with a more complex life cycle will be a special challenge. As with any new method, getting experience on data collection and evaluation, building a data base, integrating the method in software tools, and finding ways for effective communication of results are important steps until integrating S-LCA in routine decision support.     

Effect of landscape features on genetic structure of the goitered gazelle (<Emphasis Type="Italic">Gazella subgutturosa</Emphasis>) in Central Iran

The populations of goitered gazelle suffered significant decline due to natural and anthropogenic factors over the last century. Investigating the effects of barriers on gene flow among the remaining populations is vital for conservation planning. Here we adopted a landscape genetics approach to evaluate the genetic structure of the goitered gazelle in Central Iran and the effects of landscape features on gene flow using 15 polymorphic microsatellite loci. Spatial autocorrelation, isolation by distance (IBD) and isolation by resistance (IBR) models were used to elucidate the effects of landscape features on the genetic structure. Ecological modeling was used to construct landscape permeability and resistance map using 12 ecogeographical variables. Bayesian algorithms revealed three genetically homogeneous groups and restricted dispersal pattern in the six populations. The IBD and spatial autocorrelation revealed a pattern of decreasing relatedness with increasing distance. The distribution of potential habitats was strongly correlated with bioclimatic factors, vegetation type, and elevation. Resistance distances and graph theory were significantly related with variation in genetic structure, suggesting that gazelles are affected by landscape composition. The IBD showed greater impact on genetic structure than IBR. The Mantel and partial Mantel tests indicated low but non-significant effects of anthropogenic barriers on observed genetic structure. We concluded that a combination of geographic distance, landscape resistance, and anthropogenic factors are affecting the genetic structure and gene flow of populations. Future road construction might impede connectivity and gene exchange of populations. Conservation measures on this vulnerable species should consider some isolated population as separate management units.     

Understanding the Underlying Mechanism of HA-Subtyping in the Level of Physic-Chemical Characteristics of Protein

The evolution of the influenza A virus to increase its host range is a major concern worldwide. Molecular mechanisms of increasing host range are largely unknown. Influenza surface proteins play determining roles in reorganization of host-sialic acid receptors and host range. In an attempt to uncover the physic-chemical attributes which govern HA subtyping, we performed a large scale functional analysis of over 7000 sequences of 16 different HA subtypes. Large number (896) of physic-chemical protein characteristics were calculated for each HA sequence. Then, 10 different attribute weighting algorithms were used to find the key characteristics distinguishing HA subtypes. Furthermore, to discover machine leaning models which can predict HA subtypes, various Decision Tree, Support Vector Machine, Naïve Bayes, and Neural Network models were trained on calculated protein characteristics dataset as well as 10 trimmed datasets generated by attribute weighting algorithms. The prediction accuracies of the machine learning methods were evaluated by 10-fold cross validation. The results highlighted the frequency of Gln (selected by 80% of attribute weighting algorithms), percentage/frequency of Tyr, percentage of Cys, and frequencies of Try and Glu (selected by 70% of attribute weighting algorithms) as the key features that are associated with HA subtyping. Random Forest tree induction algorithm and RBF kernel function of SVM (scaled by grid search) showed high accuracy of 98% in clustering and predicting HA subtypes based on protein attributes. Decision tree models were successful in monitoring the short mutation/reassortment paths by which influenza virus can gain the key protein structure of another HA subtype and increase its host range in a short period of time with less energy consumption. Extracting and mining a large number of amino acid attributes of HA subtypes of influenza A virus through supervised algorithms represent a new avenue for understanding and predicting possible future structure of influenza pandemics.     

Phytoextraction of high value elements and contaminants from mining and mineral wastes: opportunities and limitations

Plant and Soil - Phytoextraction is an in situ technique that can be applied to minerals and mining wastes using hyperaccumulator plants to purposely bio-concentrate high levels of metals or...     

Characterization of Polar and Non‐Polar Compounds of House Edible Bird's Nest (EBN) from Johor,Malaysia

This work investigated the polar (PC: protein, amino acid and metabolite) and non‐polar (NPC: fatty acid) compounds and bioactivity characteristics of the EBN harvested from the state of Johor in Malaysia. The electrophoretic gels exhibited 15 protein bands (16–173 kD) with unique protein profile. Amino acids analysis by AccQ?Tag method revealed 18 types of amino acids in EBN. Metabolite profiling was performed using High‐Performance Liquid Chromatography coupled with Quadrupole Time‐of‐Flight Mass Spectrometer (HPLC‐QTOF/MS) technique and a total of 54 compounds belonging to different groups were detected and identified. These findings help to uncover the relation of therapeutic activity of EBN. The EBN was further extracted with AcOEt and BuOH. The AcOEt extract was fractionated into three fractions (F₁?F₃), and the high triglyceride content in F₂ was verified by gC‐FID. The three groups of fatty acids discovered in EBN are 48.43 % of poly‐unsaturated (PUFA), 25.35 % of saturated fatty acids (SFA) and 24.74 % of mono‐unsaturated fat (MUFA). This is the first time to report results ofEBN, BuOH, and AcOEt extracts and of fraction F₂ (TEBN) on their analysis for their antioxidant activities by DPPH, ABTS and catalase assay and for their paraoxonase and anti‐tyrosinase activities. The results showed that TEBN exhibited the significant bioactivity in all assays. These findings suggest that TEBN is a good source for natural bioactive compounds in promoting body vigor. Current work widened the content of EBN especially on the triglyceride and also marked the content of specific location (Johor, Malaysia) of EBN origin.