Role of the pentose phosphate pathway and the Entner–Doudoroff pathway in glucose metabolism of Gluconobacter oxydans 621H

Glucose catabolism by the obligatory aerobic acetic acid bacterium Gluconobacter oxydans 621H proceeds in two phases comprising rapid periplasmic oxidation of glucose to gluconate (phase I) and oxidation of gluconate to 2-ketogluconate or 5-ketogluconate (phase II). Only a small amount of glucose and part of the gluconate is taken up into the cells. To determine the roles of the pentose phosphate pathway (PPP) and the Entner–Doudoroff pathway (EDP) for intracellular glucose and gluconate catabolism, mutants defective in either the PPP (Δgnd, Δgnd zwf*) or the EDP (Δedd–eda) were characterized under defined conditions of pH 6 and 15 % dissolved oxygen. In the presence of yeast extract, neither of the two pathways was essential for growth with glucose. However, the PPP mutants showed a reduced growth rate in phase I and completely lacked growth in phase II. In contrast, the EDP mutant showed the same growth behavior as the reference strain. These results demonstrate that the PPP is of major importance for cytoplasmic glucose and gluconate catabolism, whereas the EDP is dispensable. Reasons for this difference are discussed.     

Behavioural Responses of European Roe Deer to Temporal Variation in Predation Risk

In natural environments, predation risk varies over time. The risk allocation hypothesis predicts that prey is expected to adjust key anti‐predator behaviours such as vigilance to temporal variation in risk. We tested the predictions of the risk allocation hypothesis in a natural environment where both a species‐rich natural predator community and human hunters are abundant and where the differences in seasonal and circadian activity between natural and anthropogenic predators provided a unique opportunity to quantify the contributions of different predator classes to anti‐predator behaviour. Whereas natural predators were expected to show similar levels of activity throughout the seasons, hunter activity was high during the daytime during a clearly defined hunting season. According to the risk allocation hypothesis, vigilance should then be higher during the hunting season and during daytime hours than during the non‐hunting season and night‐time hours. Roe deer (Capreolus capreolus) on the edge of Bia?owie?a Primeval Forest in Eastern Poland displayed vigilance behaviour consistent with these predictions. The behavioural response of roe deer to temporarily varying predation risks emphasises the behavioural plasticity of this species and suggests that future studies of anti‐predator behaviour need to incorporate circadian variation in predation pressure as well as risk gradients of both natural and anthropogenic predators.     

Balancing redox cofactor generation and ATP synthesis: Key microaerobic responses in thermophilic fermentations

Geobacillus thermoglucosidasius is a Gram‐positive, thermophilic bacterium capable of ethanologenic fermentation of both C5 and C6 sugars and may have possible use for commercial bioethanol production [Tang et al., 2009; Taylor et al. (2009) Trends Biotechnol 27(7): 398–405]. Little is known about the physiological changes that accompany a switch from aerobic (high redox) to microaerobic/fermentative (low redox) conditions in thermophilic organisms. The changes in the central metabolic pathways in response to a switch in redox potential were analyzed using quantitative real‐time PCR and proteomics. During low redox (fermentative) states, results indicated that glycolysis was uniformly up‐regulated, the Krebs (tricarboxylic acid or TCA) cycle non‐uniformly down‐regulated and that there was little to no change in the pentose phosphate pathway. Acetate accumulation was accounted for by strong down‐regulation of the acetate CoA ligase gene (acs) in addition to up‐regulation of the pta and ackA genes (involved in acetate production), thus conserving ATP while reducing flux through the TCA cycle. Substitution of an NADH dehydrogenase (down‐regulated) by an up‐regulated NADH:FAD oxidoreductase and up‐regulation of an ATP synthase subunit, alongside the observed shifts in the TCA cycle, suggested that an oxygen‐scavenging electron transport chain likely remained active during low redox conditions. Together with the observed up‐regulation of a glyoxalase and down‐regulation of superoxide dismutase, thought to provide protection against the accumulation of toxic phosphorylated glycolytic intermediates and reactive oxygen species, respectively, the changes observed in G. thermoglucosidasius NCIMB 11955 under conditions of aerobic‐to‐microaerobic switching were consistent with responses to low pO₂ stress. Biotechnol. Bioeng. 2013; 110: 1057–1065. © 2012 Wiley Periodicals, Inc.     

TRADE‐OFFS,SPATIAL HETEROGENEITY,AND THE MAINTENANCE OF MICROBIAL DIVERSITY

Specialization and concomitant trade‐offs are assumed to underlie the non‐neutral coexistence of lineages. Trade‐offs across heterogeneous environments can promote diversity by preventing competitive exclusion. However, the importance of trade‐offs in maintaining diversity in natural microbial assemblages is unclear, as trade‐offs are frequently not detected in artificial evolution experiments. Stressful conditions associated with patches of heavy‐metal enriched serpentine soils provide excellent opportunities for examining how heterogeneity may foster genetic diversity. Using a spatially replicated design, we demonstrate that rhizobium bacteria symbiotic with legumes inhabiting contrasting serpentine and nonserpentine soils exhibit a trade‐off between a genotype's nickel tolerance and its ability to replicate rapidly. Furthermore, we detected adaptive divergence in rhizobial assemblages across soil type heterogeneity at multiple sites, suggesting that this trade‐off may promote the coexistence of phenotypically distinct bacterial lineages. Trade‐offs and adaptive divergence may be important factors maintaining the tremendous diversity within natural assemblages of bacteria.     

Guidance of Cell Migration by Substrate Dimension

There is increasing evidence to suggest that physical parameters, including substrate rigidity, topography, and cell geometry, play an important role in cell migration. As there are significant differences in cell behavior when cultured in 1D, 2D, or 3D environments, we hypothesize that migrating cells are also able to sense the dimension of the environment as a guidance cue. NIH 3T3 fibroblasts were cultured on micropatterned substrates where the path of migration alternates between 1D lines and 2D rectangles. We found that 3T3 cells had a clear preference to stay on 2D rather than 1D substrates. Cells on 2D surfaces generated stronger traction stress than did those on 1D surfaces, but inhibition of myosin II caused cells to lose their sensitivity to substrate dimension, suggesting that myosin-II-dependent traction forces are the determining factor for dimension sensing. Furthermore, oncogene-transformed fibroblasts are defective in mechanosensing while generating similar traction forces on 1D and 2D surfaces. Dimension sensing may be involved in guiding cell migration for both physiological functions and tissue engineering, and for maintaining normal cells in their home tissue.     

Dual factor delivery of CXCL12 and Exendin‐4 for improved survival and function of encapsulated beta cells under hypoxic conditions

A bioartifical pancreas (BAP) remains a promising approach for treating insulin‐dependent diabetes. Several obstacles to the clinical implementation of a BAP remain, including hypoxia following implantation. Within native pancreatic islets, CXCL12 and glucagon‐like peptide‐1 (GLP‐1) act in a paracrine fashion to promote the survival, function, and proliferation of β‐cells. This work sought to investigate if the presentation of CXCL12 and delivery of a GLP‐1 receptor analog, Exendin‐4 (Ex‐4), alone and in combination, conferred pro‐survival and insulinotropic effects on an encapsulated β‐cell line, βTC‐tet, cultured under hypoxic conditions of 7.6 mmHg O₂. Our findings indicate that presentation of CXCL12 in the encapsulation matrix completely abrogated apoptosis under hypoxic conditions. Delivery of Ex‐4 increased insulin secretion rate under both normoxic and hypoxic conditions, and additionally reduced apoptosis under hypoxic conditions. Furthermore, presentation of CXCL12 combined with Ex‐4 delivery significantly increased insulin secretion rate under hypoxic conditions compared to delivery of Ex‐4 alone. These findings demonstrate that the presentation of CXCL12 combined with the delivery of Ex‐4 may constitute a promising strategy for supporting β‐cell function and survival following transplantation. Biotechnol. Bioeng. 2013; 110: 2292–2300. © 2013 Wiley Periodicals, Inc.     

Dynamic compressive loading differentially regulates chondrocyte anabolic and catabolic activity with age

Dynamic loading has emerged as an important part of cartilage tissue engineering strategies for enhancing tissue production and producing cartilage with functionally competent mechanical properties. As patients in need of cartilage span a range of age groups, questions arise as to the role of age in a cell's ability to respond to dynamic loading. Therefore, this study's goal was to characterize age‐related anabolic and catabolic responses of chondrocytes to dynamic compressive loading. Bovine chondrocytes isolated from juvenile (3‐week‐old) and adult (2‐ to 3‐year‐old) donors were encapsulated in poly(ethylene glycol) hydrogels and subjected to dynamic loading applied intermittently in a sinusoidal waveform at 1 or 0.3 Hz with 5 or 10% amplitude strain up to 2 weeks. Loading significantly enhanced total sulfated glycosaminoglycan (sGAG) production by 220% for juvenile chondrocytes with 0.3 Hz/5% loading and by 88% for adult chondrocytes with 1 Hz/5% loading, while all other loading regimes did not affect or inhibited total sGAG production. Contrarily, deposition of larger matrix molecules of aggrecan and collagen II was either not affected or inhibited by loading. Collagen VI deposition was significantly upregulated by loading but only in adult chondrocytes and under different loading regimes (1 Hz/10% and 0.3 Hz/5%) when compared to total sGAGs. Both cell populations displayed catabolic activity, which appeared to be stimulated by loading. Taken together, findings from this study suggest that loading differentially regulates matrix synthesis and the response is highly dependent on donor age. Biotechnol. Bioeng. 2013; 110: 2046–2057. © 2013 Wiley Periodicals, Inc.     

Exome Sequencing Identifies Mutations in CCDC114 as a Cause of Primary Ciliary Dyskinesia

Primary ciliary dyskinesia (PCD) is a genetically heterogeneous, autosomal-recessive disorder, characterized by oto-sino-pulmonary disease and situs abnormalities. PCD-causing mutations have been identified in 14 genes, but they collectively account for only ∼60% of all PCD. To identify mutations that cause PCD, we performed exome sequencing on six unrelated probands with ciliary outer dynein arm (ODA) defects. Mutations in CCDC114, an ortholog of the Chlamydomonas reinhardtii motility gene DCC2, were identified in a family with two affected siblings. Sanger sequencing of 67 additional individuals with PCD with ODA defects from 58 families revealed CCDC114 mutations in 4 individuals in 3 families. All 6 individuals with CCDC114 mutations had characteristic oto-sino-pulmonary disease, but none had situs abnormalities. In the remaining 5 individuals with PCD who underwent exome sequencing, we identified mutations in two genes (DNAI2, DNAH5) known to cause PCD, including an Ashkenazi Jewish founder mutation in DNAI2. These results revealed that mutations in CCDC114 are a cause of ciliary dysmotility and PCD and further demonstrate the utility of exome sequencing to identify genetic causes in heterogeneous recessive disorders.     

Metamerism,morphogenesis, and the expression of carabelli and other dental traits in humans

The patterning cascade model of tooth morphogenesis has emerged as a useful tool in explaining how tooth shape develops and how tooth evolution may occur. Enamel knots, specialized areas of dental epithelium where cusps initiate, act as signaling centers that direct the growth of surrounding tissues. For a new cusp to form, an enamel knot must form beyond the inhibition fields of other enamel knots. The model predicts that the number and size of cusps depends on the spacing between enamel knots, reflected in the spacing between cusps. Recently, work by our group demonstrated that the model predicted Carabelli trait expression in human first molars. Here we test whether differences in Carabelli trait expression along the molar row can also be predicted by the model. Crown areas and intercusp distances were measured from dental casts of 316 individuals with a digital microscope. Although absolute cusp spacing is similar in first and second molars, the smaller size and more triangular shape of second molars results in larger cusp spacing relative to size and, likely, less opportunity for the Carabelli trait to form. The presence and size of the hypocone (HY) and a range of small accessory cusps in a larger sample of 340 individuals were also found to covary with the Carabelli trait in a complex way. The results of this study lend further support to the view that the dentition develops, varies, and evolves as a single functional complex. Am J Phys Anthropol, 2013. © 2013 Wiley Periodicals, Inc.