Kinetic model of phosphofructokinase-1 from Escherichia coli

This paper presents a kinetic model of phosphofructokinase-1 from Escherichia coli. A complete catalytic cycle has been reconstructed based on available information on the oligomeric structure of the enzyme and kinetic mechanism of its monomer. Applying the generalization of the Monod-Wyman-Changeux approach proposed by Popova and Sel'kov(35-37) to the reconstructed catalytic cycle rate equation has been derived. Dependence of the reaction rate on pH, magnesium, and effectors has been taken into account. Kinetic parameters have been estimated via fitting the rate equation against experimentally measured dependencies of initial rate on substrates, products, effectors, and pH available from the literature. The model of phosphofructokinase-1 predicts (1) cooperativity of binding both fructose-6-phosphate and ATPMg(2-), (2) significant inhibition of the enzyme resulting from an increase in total concentration of ATP under the condition of fixed concentration of Mg(2+) ions, and (3) dual effect of ADP consisting of allosteric activation and product inhibition of the enzyme. Moreover, the model developed can be used in the kinetic modeling of biochemical pathways containing phosphofructokinase-1.     

Bone morphogenetic protein (BMP)1-3 enhances bone repair

Members of the astacin family of metalloproteinases such as human bone morphogenetic protein 1 (BMP-1) regulate morphogenesis by processing precursors to mature functional extracellular matrix (ECM) proteins and several growth factors including TGFβ, BMP2, BMP4 and GFD8. We have recently discovered that BMP1-3 isoform of the Bmp-1 gene circulates in the human plasma and is significantly increased in patients with acute bone fracture. We hypothesized that circulating BMP1-3 might have an important role in bone repair and serve as a novel bone biomarker. When administered systemically to rats with a long bone fracture and locally to rabbits with a critical size defect of the ulna, recombinant human BMP1-3 enhanced bone healing. In contrast, neutralization of the endogenous BMP1-3 by a specific polyclonal antibody delayed the bone union. Invitro BMP1-3 increased the expression of collagen type I and osteocalcin in MC3T3-E₁ osteoblast like cells, and enhanced the formation of mineralized bone nodules from bone marrow mesenchymal stem cells. We suggest that BMP1-3 is a novel systemic regulator of bone repair.     

Morphology and Phylogeny of Calyptospora paranaidji n. sp. (Eimeriorina: Calyptosporidae), an Apicomplexan Parasite of the Hepatic Tissue of Cichla piquiti Kullander & Ferreira, 2006, From a Reservoir in the Brazilian Amazon Region

The coccidians of the family Calyptosporidae are parasites of the tissue and organs of fish and aquatic invertebrates, in particular in the tropical region. In contrast with other apicomplexans of the suborder Eimeriorina, the diversity and ecology of the species of the genus Calyptospora have been poorly investigated, resulting in a lacuna that restricts the understanding of the distribution and prevalence of this group of eukaryote microparasites in the Amazon region. In the present study, the integrated comparative analysis of morphological characteristics, histological and structural traits, and the sequences of a fragment of the 18S rRNA gene, provides support for the identification of a new species of Calyptospora, found parasitizing the hepatic tissue of the piscivorous blue peacock bass, Cichla piquiti, captured in the reservoir of the Estreito hydroelectric dam on the middle Tocantins River in northern Brazil. This new species was named Calyptospora paranaidji n. sp.     

An Enhanced Adaptive Management Approach for Remediation of Legacy Mercury in the South River

Uncertainties about future conditions and the effects of chosen actions, as well as increasing resource scarcity, have been driving forces in the utilization of adaptive management strategies. However, many applications of adaptive management have been criticized for a number of shortcomings, including a limited ability to learn from actions and a lack of consideration of stakeholder objectives. To address these criticisms, we supplement existing adaptive management approaches with a decision-analytical approach that first informs the initial selection of management alternatives and then allows for periodic re-evaluation or phased implementation of management alternatives based on monitoring information and incorporation of stakeholder values. We describe the application of this enhanced adaptive management (EAM) framework to compare remedial alternatives for mercury in the South River, based on an understanding of the loading and behavior of mercury in the South River near Waynesboro, VA. The outcomes show that the ranking of remedial alternatives is influenced by uncertainty in the mercury loading model, by the relative importance placed on different criteria, and by cost estimates. The process itself demonstrates that a decision model can link project performance criteria, decision-maker preferences, environmental models, and short- and long-term monitoring information with management choices to help shape a remediation approach that provides useful information for adaptive, incremental implementation.     

DNA polymerase lambda from calf thymus preferentially replicates damaged DNA

A new gene (POLL), has been identified encoding the novel DNA polymerase lambda and mapped to mouse chromosome 19 and at human chromosome 10. DNA polymerase lambda contains all the critical residues involved in DNA binding, nucleotide binding, nucleotide selection, and catalysis of DNA polymerization and has been assigned to family X based on sequence homology with polymerase beta, lambda, mu, and terminal deoxynucleotidyltransferase. Here we describe a purification of DNA polymerase lambda from calf thymus that preferentially can replicate damaged DNA. By testing polymerase activity on non-damaged and damaged DNA, DNA polymerase lambda was purified trough five chromatographic steps to near homogeneity and identified as a 67-kDa polypeptide that cross-reacted with monoclonal antibodies against DNA polymerase beta and polyclonal antibodies against DNA polymerase lambda. DNA polymerase lambda had no detectable nuclease activities and, in contrast to DNA polymerase beta, was aphidicolin-sensitive. DNA polymerase lambda was a 6-fold more accurate enzyme in an M13mp2 forward mutation assay and 5-fold more accurate in an M13mp2T90 reversion system than human recombinant DNA polymerase beta. The biochemical properties of the calf thymus DNA polymerase lambda, described here for the first time, are discussed in relationship to the proposed role for this DNA polymerase in vivo.     

Ten simple rules for establishing a mentorship programme

In recent years, a wide variety of mentorship programmes targeting issues that cannot be addressed through traditional teaching and learning methods alone have been developed. Mentoring plays significant roles in the growth and development of both mentors and mentees, and the positive impacts of mentoring have been well documented. Mentorship programmes are therefore increasingly being implemented in a wide variety of fields by organisations, academic institutes, businesses, and governments. While there is a growing body of literature on mentoring and mentorship programmes, gaining a clear overview of the field is often challenging. In this article, we therefore provide a concise summary of recommendations to consider when designing and establishing mentorship programmes. These recommendations are based on the collective knowledge and experiences of 4 different emerging and established mentorship programmes and can be adapted across various mentorship settings or contexts.     

A multi-criteria decision-making model for classifying wood products with respect to their impact on environment

Background, aim and scope  

Although life cycle assessment is frequently used in scientific studies of product comparison, many practitioners are looking for improvements in the normalisation, grouping and weighting of life cycle inventory results. Local conditions, which are well known to local experts, are very important to these steps. The goal of this work was to develop a computer-based decision support system for classifying wood products according to their influence on the environment in their whole life cycle. The model specifically addresses local conditions in the Republic of Slovenia and was developed by Slovenian experts.     

Hen egg white lysozyme fibrillation: a deep‐UV resonance Raman spectroscopic study

Amyloid fibrils are associated with numerous degenerative diseases. The molecular mechanism of the structural transformation of native protein to the highly ordered cross‐β structure, the key feature of amyloid fibrils, is under active investigation. Conventional biophysical methods have limited application in addressing the problem because of the heterogeneous nature of the system. In this study, we demonstrated that deep‐UV resonance Raman (DUVRR) spectroscopy in combination with circular dichroism (CD) and intrinsic tryptophan fluorescence allowed for quantitative characterization of protein structural evolution at all stages of hen egg white lysozyme fibrillation in vitro. DUVRR spectroscopy was found to be complimentary to the far‐UV CD because it is (i) more sensitive to β ‐sheet than to α ‐helix, and (ii) capable of characterizing quantitatively inhomogeneous and highly light‐scattering samples. In addition, phenylalanine, a natural DUVRR spectroscopic biomarker of protein structural rearrangements, exhibited substantial changes in the Raman cross section of the 1000‐cm^–1 band at various stages of fibrillation. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)