The ABCs of membrane transporters in health and disease (SLC series): introduction

The field of transport biology has steadily grown over the past decade and is now recognized as playing an important role in manifestation and treatment of disease. The SLC (solute carrier) gene series has grown to now include 52 families and 395 transporter genes in the human genome. A list of these genes can be found at the HUGO Gene Nomenclature Committee (HGNC) website (see www.genenames.org/genefamilies/SLC). This special issue features mini-reviews for each of these SLC families written by the experts in each field. The existing online resource for solute carriers, the Bioparadigms SLC Tables (www.bioparadigms.org), has been updated and significantly extended with additional information and cross-links to other relevant databases, and the nomenclature used in this database has been validated and approved by the HGNC. In addition, the Bioparadigms SLC Tables functionality has been improved to allow easier access by the scientific community. This introduction includes: an overview of all known SLC and "non-SLC" transporter genes; a list of transporters of water soluble vitamins; a summary of recent progress in the structure determination of transporters (including GLUT1/SLC2A1); roles of transporters in human diseases and roles in drug approval and pharmaceutical perspectives.

Can jatropha improve the energy supply of rural households in Africa?

There is still discussion regarding whether liquid biofuels can contribute to rural energy security in the global South. We argue that transitioning to a village energy supply based on jatropha hedges around smallholder plots is possible, but requires collective effort for the acquisition and maintenance of processing equipment and for the running of village generators. The use of jatropha oil for lighting in rural households is affordable and technically possible, but not ideal if more efficient electric solutions exist. Cooking with jatropha oil or press cake is also possible, but quantities produced in hedges can only substitute a small part of the firewood used by rural households.

Microgram-Level Radiocarbon Determination of Carbonaceous Particles in Firn and Ice Samples: Pretreatment and Oc/Ec Separation

Carbonaceous particles that comprise organic carbon (OC) and elemental carbon (EC) are of increasing interest in climate research because of their influence on the radiation balance of the Earth. The radiocarbon determination of particulate OC and EC extracted from ice cores provides a powerful tool to reconstruct the long-term natural and anthropogenic emissions of carbonaceous particles. However, this C-14-based source apportionment method has not been applied for the firn section, which is the uppermost part of Alpine glaciers with a typical thickness of up to 50 m. In contrast to glacier ice, firn samples are more easily contaminated through drilling and handling operations. In this study, an alternative decontamination method for firn samples consisting of chiselling off the outer parts instead of rinsing them was developed and verified. The obtained procedural blank of 2.8 +/- 0.8 mu g C for OC is a factor of 2 higher compared to the rinsing method used for ice, but still relatively low compared to the typical OC concentration in firn samples from Alpine glaciers. The EC blank of 0.3 +/- 0.1 mu g C is similar for both methods. For separation of OC and EC for subsequent C-14 analysis, a thermal-optical method instead of the purely thermal method was applied for the first time to firn and ice samples, resulting in a reduced uncertainty of both the mass and C-14 determination. OC and EC concentrations as well as their corresponding fraction of modern for firn and ice samples from Fiescherhorn and Jungfraujoch agree well with published results, validating the new method.

ANALYSIS OF β8 INTEGRIN IN NEUROGENESIS AND NEUROVASCULAR HOMEOSTASIS

Neurogenesis in the adult mouse brain occurs within the subventricular zone (SVZ) of the lateral ventricle. In the SVZ, neural stem cells (NSC) reside in a specialized microenvironment, or vascular niche, consisting of blood vessels and their basement membranes. Most NSCs in the SVZ differentiate into progenitor cells, which further differentiate to generate neuroblasts, which then migrate from the SVZ to the olfactory bulbs (OB) along the rostral migratory stream (RMS). ECM-mediated adhesion and signaling within the vascular niche likely contribute to proper NSC self-renewal, survival, differentiation and neuroblast motility. The mechanisms that control these events are poorly understood. Previous studies from our group and others have shown that loss of the ECM receptor, αvβ8 integrin, in NSCs in the embryonic mouse brain leads to severe developmental vascular defects and premature death. Here, the functions of αvβ8 integrin in the adult brain have been examined using mice that have been genetically manipulated to lack a functional β8 integrin gene. This study reveals that loss of β8 integrin leads to widespread defects in homeostasis of the neurovascular unit, including increased intracerebral blood vessels with enhanced perivascular astrogliosis. Additionally, β8 integrin dependent defects in NSC proliferation, survival, and differentiation, as well as neuroblast migration in the RMS were observed both in vivo and in vitro. The defects correlated, in part, with diminished integrin-mediated activation of TGFβ, an ECM ligand of β8 integrin. Collectively, these data identify important adhesion and signaling functions for β8 integrin in the regulation of neural stem and progenitor cells in the SVZ as well as in neuroblast migration along the RMS in the adult brain.

In search of epigenetic marks in testes and sperm cells of differentially fed boars

In search of transmittable epigenetic marks we investigated gene expression in testes and sperm cells of differentially fed F0 boars from a three generation pig feeding experiment that showed phenotypic differences in the F2 generation. RNA samples from 8 testes of boars that received either a diet enriched in methylating micronutrients or a control diet were analyzed by microarray analysis. We found moderate differential expression between testes of differentially fed boars with a high FDR of 0.82 indicating that most of the differentially expressed genes were false positives. Nevertheless, we performed a pathway analysis and found disparate pathway maps of development_A2B receptor: action via G-protein alpha s, cell adhesion_Tight junctions and cell adhesion_Endothelial cell contacts by junctional mechanisms which show inconclusive relation to epigenetic inheritance. Four RNA samples from sperm cells of these differentially fed boars were analyzed by RNA-Seq methodology. We found no differential gene expression in sperm cells of the two groups (adjusted P-value>0.05). Nevertheless, we also explored gene expression in sperm by a pathway analysis showing that genes were enriched for the pathway maps of bacterial infections in cystic fibrosis (CF) airways, glycolysis and gluconeogenesis p.3 and cell cycle_Initiation of mitosis. Again, these pathway maps are miscellaneous without an obvious relationship to epigenetic inheritance. It is concluded that the methylating micronutrients moderately if at all affects RNA expression in testes of differentially fed boars. Furthermore, gene expression in sperm cells is not significantly affected by extensive supplementation of methylating micronutrients and thus RNA molecules could not be established as the epigenetic mark in this feeding experiment.

The relationship between the field-shifting phenomenon and representational coherence of place cells in CA1 and CA3 in a cue-altered environment.

Subfields of the hippocampus display differential dynamics in processing a spatial environment, especially when changes are introduced to the environment. Specifically, when familiar cues in the environment are spatially rearranged, place cells in the CA3 subfield tend to rotate with a particular set of cues (e.g., proximal cues), maintaining a coherent spatial representation. Place cells in CA1, in contrast, display discordant behaviors (e.g., rotating with different sets of cues or remapping) in the same condition. In addition, on average, CA3 place cells shift their firing locations (measured by the center of mass, or COM) backward over time when the animal encounters the changed environment for the first time, but not after that first experience. However, CA1 displays an opposite pattern, in which place cells exhibit the backward COM-shift only from the second day of experience, but not on the first day. Here, we examined the relationship between the environment-representing behavior (i.e., rotation vs. remapping) and the COM-shift of place fields in CA1 and CA3. Both in CA1 and CA3, the backward (as well as forward) COM-shift phenomena occurred regardless of the rotating versus remapping of the place cell. The differential, daily time course of the onset/offset of backward COM-shift in the cue-altered environment in CA1 and CA3 (on day 1 in CA1 and from day 2 onward in CA3) stems from different population dynamics between the subfields. The results suggest that heterogeneous, complex plasticity mechanisms underlie the environment-representating behavior (i.e., rotate/remap) and the COM-shifting behavior of the place cell.

An Examination of Treatment Fidelity in an Intensive Family Preservation Program

Most models of intensive family preservation services are based on providing flexible services to reduce risk and keep families together. This study examined 40 cases served by a public agency Family Preservation Unit in 1992-1993, in order to assess the provision of hard, soft and enabling services in the program and whether their provision matched the program model. The relationships of these services to program outcomes, in terms of child removal, new reports of abuse or neglect, and family gains in resources and strengths, are also assessed.

Molecular analysis of TNF sensitivity in normal and Ha-{\it ras\/} transformed murine fibroblasts

Tumor necrosis factor (TNF) is known to have antiproliferative effects on a wide variety of tumor cells but proliferative effects on normal cells. However, the molecular basis for such differences in the action of TNF are unknown. The overall objectives of my research are to investigate the role of oncogenes in TNF sensitivity and delineate some of the molecular mechanisms involved in TNF sensitivity and resistance. To accomplish these objectives, I transfected TNF-resistant C3H mouse embryo fibroblasts (10T1/2) with an activated Ha-ras oncogene and determined whether these cells exhibit altered sensitivity to TNF. The results indicated that 10T1/2 cells transfected with an activated Ha-ras oncogene (10T-EJ) not only produced tumors in nude mice but also exhibited extreme sensitivity to cytolysis by TNF. In contrast, 10T1/2 cells transfected with the pSV2-neo gene alone were resistant to the cytotoxic effects of TNF. I also found that TNF-induced cell death was mediated through apoptosis. The differential sensitivity of 10T1/2 and 10T-EJ cell lines to TNF was not due to differences in the number of TNF receptors on their cell surface. In addition, TNF-resistant revertants isolated from Ha-ras-transformed, TNF-sensitive cells still expressed the same amount of p21 as TNF-sensitive cells and were still tumorigenic, suggesting that Ha-ras-induced transformation and TNF sensitivity may follow different pathways. Interestingly, TNF-resistant but not sensitive cells expressed higher levels of bcl-2, c-myc, and manganese superoxide dismutase (MnSOD) mRNA following exposure to TNF. However, TNF treatment resulted in a marginal induction of p53 mRNA in both TNF-sensitive and resistant cells. Based on these results I can conclude that (i) Ha-ras oncogene induces both transformation and TNF sensitivity, (ii) TNF-induced cytotoxicity involves apoptosis, and (iii) TNF-induced upregulation of bcl-2, c-myc, and MnSOD genes is associated with TNF resistance in C3H mouse embryo fibroblasts. ^

Estimation of male-to-female ratios of mutation rate in primates and rodents

Haldane (1935) developed a method for estimating the male-to-female ratio of mutation rate ($\alpha$) by using sex-linked recessive genetic disease, but in six different studies using hemophilia A data the estimates of $\alpha$ varied from 1.2 to 29.3. Direct genomic sequencing is a better approach, but it is laborious and not readily applicable to non-human organisms. To study the sex ratios of mutation rate in various mammals, I used an indirect method proposed by Miyata et al. (1987). This method takes advantage of the fact that different chromosomes segregate differently between males and females, and uses the ratios of mutation rate in sequences on different chromosomes to estimate the male-to-female ratio of mutation rate. I sequenced the last intron of ZFX and ZFY genes in 6 species of primates and 2 species of rodents; I also sequenced the partial genomic sequence of the Ube1x and Ube1y genes of mice and rats. The purposes of my study in addition to estimation of $\alpha$'s in different mammalian species, are to test the hypothesis that most mutations are replication dependent and to examine the generation-time effect on $\alpha$. The $\alpha$ value estimated from the ZFX and ZFY introns of the six primate specise is ${\sim}$6. This estimate is the same as an earlier estimate using only 4 species of primates, but the 95% confidence interval has been reduced from (2, 84) to (2, 33). The estimate of $\alpha$ in the rodents obtained from Zfx and Zfy introns is ${\sim}$1.9, and that deriving from Ube1x and Ube1y introns is ${\sim}$2. Both estimates have a 95% confidence interval from 1 to 3. These two estimates are very close to each other, but are only one-third of that of the primates, suggesting a generation-time effect on $\alpha$. An $\alpha$ of 6 in primates and 2 in rodents are close to the estimates of the male-to-female ratio of the number of germ-cell divisions per generation in humans and mice, which are 6 and 2, respectively, assuming the generation time in humans is 20 years and that in mice is 5 months. These findings suggest that errors during germ-cell DNA replication are the primary source of mutation and that $\alpha$ decreases with decreasing length of generation time. ^

An application of combinatorial optimization in the printing industry

Offset printing is a common method to produce large amounts of printed matter. We consider a real-world offset printing process that is used to imprint customer-specific designs on napkin pouches. The print- ing technology used yields a number of specific constraints. The planning problem consists of allocating designs to printing-plate slots such that the given customer demand for each design is fulfilled, all technologi- cal and organizational constraints are met and the total overproduction and setup costs are minimized. We formulate this planning problem as a mixed-binary linear program, and we develop a multi-pass matching-based savings heuristic. We report computational results for a set of problem instances devised from real-world data.

Identification of Clostridium chauvoei in cultures and clinical material from blackleg using PCR.

An identification system for Clostridium chauvoei, using PCR amplification of the 16S rRNA gene (rrs) with specific oligonucleotide primers and subsequent restriction digestion of the amplification product is described. The specific oligonucleotide primers were designed based on the rrs gene sequences of C. chauvoei by comparing it to the DNA sequences of the rrs genes of its most closely related species Clostridium septicum and Clostridium carnis. A subsequent restriction digestion of the 960 bp amplification product was used in order to unambiguously identify C. chauvoei. The developed identification system was evaluated on clinical material during a recent outbreak of blackleg in cattle. Thereby, C. chauvoei was identified as the etiologic agent of the outbreak either directly from clinical samples of muscle, liver, spleen and kidney or from primary cultures made with this material. A comparison of the newly developed method with standard diagnostic tools for C. chauvoei showed that it has advantages over the immunofluorescence and is, therefore, a useful option to it. Moreover, the assay is a valuable tool for the phylogenetic identification of C. chauvoei which can assist to substitute the fastidious traditional identification methods and replace laboratory animal testing currently used.

Immunoblotting for the serodiagnosis of alveolar echinococcosis in alive and dead Eurasian beavers (Castor fiber)

A novel species-specific anti-beaver-IgG-alkaline-phosphatase conjugate was synthesized for the development of a new serological test for echinococcosis in beavers. Two different ELISAs conventionally used for human Echinococcus multilocularis serology (Em18-ELISA and Em2-ELISA) yielded diagnostic sensitivities of 0% and 46%, respectively. In contrast, the subsequently developed immunoblotting assay gave an 85% diagnostic sensitivity (11 out of 13 beavers with alveolar echinococcosis were immunoblotting-positive, i.e. showed reactivity with a specific 21 Mr band), and maximal specificity. In conclusion, this immunoblotting assay should be the method of choice for use in serological studies on E. multilocularis in Eurasian beavers, and the test proved suitable to investigate both animals alive and post-mortem.

Gender, Professional Networks, and Subjective Career Success within Early Academic Science Careers: The Role of Gender Composition in Inside and Outside Departmental Support Networks

The present study analyzed (a) gender differences in the gender composition (i.e., the proportion of male to female contacts) of professional support networks inside and outside an individual’s academic department and (b) how these differences in gender composition relate to subjective career success (i.e., perceived career success and perceived external marketability). Results showed that the networks’ gender composition is associated with subjective career success. Men’s networks consist of a higher proportion of male to female supporters, which, in turn, was positively related to subjective career success. Additional analyses revealed that the findings could not be accounted for by alternative factors, such as network size, networking behaviors, and career ambition.