Characterization of membrane-bound dehydrogenases of Gluconobacter oxydans 621H using a new system for their functional expression

Acetic acid bacteria are used in biotechnology due to their ability to incompletely oxidize a great variety of carbohydrates, alcohols, and related compounds in a regio- and stereo-selective manner. These reactions are catalyzed by membrane-bound dehydrogenases (mDHs), often with a broad substrate spectrum. In this study, the promoters of six mDHs of Gluconobacter oxydans 621H were characterized. The constitutive promoter of the alcohol dehydrogenase and the glucose-repressed promoter of the inositol dehydrogenase were used to construct a shuttle vector system for the fully functional expression of mDHs in the multi-deletion strain G. oxydans BP.9 that lacks its mDHs. This system was used to express each mDH of G. oxydans 621H, in order to individually characterize the substrates, they oxidize. From 55 tested compounds, the alcohol dehydrogenase oxidized 30 substrates and the polyol dehydrogenase 25. The substrate spectrum of alcohol dehydrogenase overlapped largely with the aldehyde dehydrogenase and partially with polyol dehydrogenase. Thus, we were able to resolve the overlapping substrate spectra of the main mDHs of G. oxydans 621H. The described approach could also be used for the expression and detailed characterization of substrates used by mDHs from other acetic acid bacteria or a metagenome.

     

The concurrent use of novel soil surface microclimate measurements to evaluate CO<Subscript>2</Subscript> pulses in biocrusted interspaces in a cool desert ecosystem

Carbon cycling associated with biological soil crusts, which occupy interspaces between vascular plants in drylands globally, may be an important part of the coupled climate-carbon cycle of the Earth system. A major challenge to understanding CO₂ fluxes in these systems is that much of the biotic and biogeochemical activity occurs in the upper few mm of the soil surface layer (i.e., the ‘mantle of fertility’), which exhibits highly dynamic and difficult to measure temperature and moisture fluctuations. Here, we report a multi-sensor approach to simultaneously measuring temperature and moisture of this biocrust surface layer (0–2 mm), and the deeper soil profile, concurrent with automated measurement of surface soil CO₂ effluxes. Our results illuminate robust relationships between biocrust water content and field CO₂ pulses that have previously been difficult to detect and explain. All observed CO₂ pulses over the measurement period corresponded to surface wetting events, including when the wetting events did not penetrate into the soil below the biocrust layer (0–2 mm). The variability of temperature and moisture of the biocrust surface layer was much greater than even in the 0–5 cm layer of the soil beneath the biocrust, or deeper in the soil profile. We therefore suggest that coupling surface measurements of biocrust moisture and temperature to automated CO₂ flux measurements may greatly improve our understanding of the climatic sensitivity of carbon cycling in biocrusted interspaces in our study region, and that this method may be globally relevant and applicable.     

A possible correlation between the basal ganglia motor function and the inverse kinematics calculation

The main hypothesis of this study, based on experimental data showing the relations between the BG activities and kinematic variables, is that BG are involved in computing inverse kinematics (IK) as a part of planning and decision-making. Indeed, it is assumed that based on the desired kinematic variables (such as velocity) of a limb in the workspace, angular kinematic variables in the joint configuration space are calculated. Therefore, in this paper, a system-level computational model of BG is proposed based on geometrical rules, which is able to compute IK. Next, the functionality of each part in the presented model is interpreted as a function of a nucleus or a pathway of BG. Moreover, to overcome existing redundancy in possible trajectories, an optimization problem minimizing energy consumption is defined and solved to select an optimal movement trajectory among an infinite number of possible ones. The validity of the model is checked by simulating it to control a three-segment manipulator with rotational joints in a plane. The performance of the model is studied for different types of movement including different reaching movements, a continuous circular movement and a sequence of tracking movements. Furthermore, to demonstrate the physiological similarity of the presented model to the BG structure, the neuronal activity of each part of the model considered as a BG nucleus is verified. Some changes in model parameters, inspired by the dopamine deficiency, also allow simulating some symptoms of Parkinson’s disease such as bradykinesia and akinesia.     

Molecular and cellular dynamics of early embryonic cell divisions in Volvox carteri

Cell division is fundamental to all organisms and the green alga used here exhibits both key animal and plant functions. Specifically, we analyzed the molecular and cellular dynamics of early embryonic divisions of the multicellular green alga Volvox carteri (Chlamydomonadales). Relevant proteins related to mitosis and cytokinesis were identified in silico, the corresponding genes were cloned, fused to yfp, and stably expressed in Volvox, and the tagged proteins were studied by live-cell imaging. We reveal rearrangements of the microtubule cytoskeleton during centrosome separation, spindle formation, establishment of the phycoplast, and generation of previously unknown structures. The centrosomes participate in initiation of spindle formation and determination of spindle orientation. Although the nuclear envelope does not break down during early mitosis, intermixing of cytoplasm and nucleoplasm results in loss of nuclear identity. Finally, we present a model for mitosis in Volvox. Our study reveals enormous dynamics, clarifies spatio-temporal relationships of subcellular structures, and provides insight into the evolution of cell division.

Analysis of cell divisions of the microalga Volvox reveals enormous dynamics of cytoskeletal and membranous structures with coordination of intranuclear spindle formation by cytosolic centrosomes.

IN A NUTSHELLBackground: Mitosis, a type of cell division, is fundamental to all eukaryotic life and must be carried out very accurately. Even though the process of mitosis itself is highly conserved among eukaryotes, there are significant differences between animals, fungi, plants, and algae. From an evolutionary point of view, the green alga Volvox carteri used here possesses both key animal and plant functions and it exhibits important features of the last common eukaryotic ancestor that have been lost in other lineages. Prior to our work, a comprehensive in vivo analysis of the entire process of cell division in green algae was lacking.Question: How exactly does cell division work in green algae? How do the cytosolic centrosomes deal with the persistent nuclear envelope in this process? What is the relationship between different microtubular structures?Findings: Our study reveals enormous dynamics during mitosis, clarifies spatio-temporal relationships of subcellular structures, and provides insights into evolution of cell division. Although the nuclear envelope does not break down during early mitosis of Volvox, it becomes permeable and the nucleus temporarily loses its identity. Two microtubule-organizing centers, the centrosomes, located immediately outside the nuclear envelope participate in initiation of the mitotic spindle formation inside the nuclear envelope. This process also defines the orientation of the mitotic spindle. In cytokinesis, an algae-specific microtubule structure, the phycoplast, replaces the spindle. The microtubules of the phycoplast may play a direct role in promoting the cell membrane invagination of the cleavage furrow.Next steps: How are the massive rearrangements of subcellular structures regulated? What happens at the nuclear pores when the nuclear envelope becomes permeable at the onset of mitosis? What determines in later embryogenesis which cells then divide asymmetrically rather than symmetrically?     

Genomic organization of the HSET locus and the possible association of HLA-linked genes with immotile cilia syndrome (ICS)

 The kinesin-related protein (HSET) gene belongs to the kinesin superfamily, the members of which are involved in cellular transport processes. The HSET gene product was previously characterized by partial cDNA sequencing. The gene is located on the short arm of human Chromosome 6 (6p21.3), at the centromeric end of the major histocompatibility complex. Here, we report the genomic structure of the complete HSET gene together with its flanking loci. Sequence analysis of the 40 kilobase (kb) cosmid clone containing the HSET gene also revealed the presence of several new genes not related to the kinesin superfamily. These include a 60S ribosomal protein L35A-like pseudogene (rPL35A-like) on the telomeric side and a polycomb-like gene (PHF1), a copper tolerance-like gene (CUTA1) and the 5' part of the synaptic ras-GTPase-activating protein (SynGAP) gene centromeric of HSET. In addition, a complete 60S ribosomal protein L12-like (rPL12L) gene in intron 3 of the HSET gene was identified which appears to have an open reading frame. The possible involvement of the HSET gene and a β-tubulin gene (TUBB) in the pathogenesis of immotile cilia syndrome (ICS) was studied by screening two unrelated ICS families with microtubular defects and suspected HLA linkage for mutations within the HSET gene and the TUBB gene. Four single base substitutions were detected in the HSET gene, and none in the TUBB gene. On the basis of these data, a role of the HSET and TUBB products in the pathogenesis of ICS in the two families is unlikely. Received: 22 October / Revised: 15 February 1999     

The Chicken Pan-Genome Reveals Gene Content Variation and a Promoter Region Deletion in IGF2BP1 Affecting Body Size

Domestication and breeding have reshaped the genomic architecture of chicken, but the retention and loss of genomic elements during these evolutionary processes remain unclear. We present the first chicken pan-genome constructed using 664 individuals, which identified an additional approximately 66.5-Mb sequences that are absent from the reference genome (GRCg6a). The constructed pan-genome encoded 20,491 predicated protein-coding genes, of which higher expression levels are observed in conserved genes relative to dispensable genes. Presence/absence variation (PAV) analyses demonstrated that gene PAV in chicken was shaped by selection, genetic drift, and hybridization. PAV-based genome-wide association studies identified numerous candidate mutations related to growth, carcass composition, meat quality, or physiological traits. Among them, a deletion in the promoter region of IGF2BP1 affecting chicken body size is reported, which is supported by functional studies and extra samples. This is the first time to report the causal variant of chicken body size quantitative trait locus located at chromosome 27 which was repeatedly reported. Therefore, the chicken pan-genome is a useful resource for biological discovery and breeding. It improves our understanding of chicken genome diversity and provides materials to unveil the evolution history of chicken domestication.     

Quantitative modeling of triacylglycerol homeostasis in yeast--metabolic requirement for lipolysis to promote membrane lipid synthesis and cellular growth

Triacylglycerol metabolism in Saccharomyces cerevisiae was analyzed quantitatively using a systems biological approach. Cellular growth, glucose uptake and ethanol secretion were measured as a function of time and used as input for a dynamic flux-balance model. By combining dynamic mass balances for key metabolites with a detailed steady-state analysis, we trained a model network and simulated the time-dependent degradation of cellular triacylglycerol and its interaction with fatty acid and membrane lipid synthesis. This approach described precisely, both qualitatively and quantitatively, the time evolution of various key metabolites in a consistent and self-contained manner, and the predictions were found to be in excellent agreement with experimental data. We showed that, during pre-logarithmic growth, lipolysis of triacylglycerol allows for the rapid synthesis of membrane lipids, whereas de novo fatty acid synthesis plays only a minor role during this growth phase. Progress in triacylglycerol hydrolysis directly correlates with an increase in cell size, demonstrating the importance of lipolysis for supporting efficient growth initiation.     

Repetitive measurements of pulmonary mechanics to inhaled cholinergic challenge in spontaneously breathing mice.

Precise and repeatable measurements of pulmonary function in intact mice are becoming increasingly important for experimental investigations on various respiratory disorders including asthma. Here, we present validation of a novel in vivo method that, for the first time, combines direct and repetitive recordings of standard pulmonary mechanics with cholinergic aerosol challenges in anesthetized, orotracheally intubated, spontaneously breathing mice. We demonstrate that, in several groups of nonsensitized BALB/c mice, dose-related increases in pulmonary resistance and dynamic compliance to aerosolized methacholine are reproducible over short and extended intervals without causing detectable cytological alterations in the bronchoalveolar lavage or relevant histological changes in the proximal trachea and larynx regardless of the number of orotracheal intubations. Moreover, as further validation, we confirm that allergic mice, sensitized and challenged with Aspergillus fumigatus, were significantly more responsive to cholinergic challenge (P < 0.01) and exhibited marked eosinophilia and lymphocytosis in bronchoalveolar lavage fluids as well as significant pathological alterations in laryngotracheal histology compared with nonsensitized mice. We suggest that this approach will provide useful and necessary information on pulmonary mechanics in studies of various respiratory disorders in mice, including experimental models of asthma and chronic obstructive pulmonary disorder, investigations of pulmonary pharmacology, or more general investigations of the genetic determinants of lung function.     

Electrochemistry and spectroelectrochemistry of a linear triiron cluster

This work reports electrochemical and spectroelectrochemical studies of a unique linear triiron cluster carbonyl complex, Fe₃(CO)₇L₂, where L is a -diazothioketone. Oxidation and reduction reactions have been observed in non-aqueous media over the temperature range −40 to 20 °C by differential pulse voltammetry, cyclic voltammetry, thin-layer, UV-Vis spectroelectrochemistry and ESR spectrometry. The sequence of the individual electron-transfer steps comprising the overall redox process is described, and a comparison between the electrochemistry of different non-linear ironcarbonyl complexes is discussed. A single one electron reduction produces the radical anion, [Fe₃(CO)₇L₂]-, which decomposes at temperatures greater than −10 °C to species which are reduced at a more negative potential, an ECE mechanism. A single one-electron oxidation produces the radical cation, [Fe₃(CO)₇L₂]⁺, which is unstable, decomposing completely at room temperature, an EC mechanism. Spectroscopic evidence indicates that in non-bonding solvents, the Fe₃(CO)₇L₂ framework remains intact at low temperatures for both the anion and cation radical produced electrochemically with radical stability higher than might be expected for a linear structure. Observations indicate only strongly bonding solvents disrupt the structure. Low temperature stability occurs at relatively high temperatures, with the cation radical less than stable and vulnerable to strongly bonding solvents.