Degradation and Fate of Carbon Tetrachloride in Unadapted Methanogenic Granular Sludge

The potential of granular sludge from upflow anaerobic sludge blanket (UASB) reactors for bioremediation of chlorinated pollutants was evaluated by using carbon tetrachloride (CT) as a model compound. Granular sludges cultivated in UASB reactors on methanol, a volatile fatty acid mixture, or sucrose readily degraded CT supplied at a concentration of 1,500 nmol/batch (approximately 10 μM) without any prior exposure to organohalogens. The maximum degradation rate was 1.9 μmol of CT g of volatile suspended solids⁻¹ day⁻¹. The main end products of CT degradation were CO₂ and Cl⁻, and the yields of these end products were 44 and 68%, respectively, of the initial amounts of [¹⁴C]CT and CT-Cl. Lower chlorinated methanes accumulated in minor amounts temporarily. Autoclaved (dead) sludges were capable of degrading CT at rates two- to threefold lower than those for living sludges, indicating that abiotic processes (mediated by cofactors or other sludge components) played an important role in the degradation observed. Reduced components in the autoclaved sludge were vital for CT degradation. A major part (51%) of the CT was converted abiotically to CS₂. The amount of CO₂ produced (23%) was lower and the amount of Cl⁻ produced (86%) was slightly higher with autoclaved sludge than with living sludge. Both living and autoclaved sludges could degrade chloroform. However, only living sludge degraded dichloromethane and methylchloride. These results indicate that reductive dehalogenation, which was mediated better by living sludge than by autoclaved sludge, is only a minor pathway for CT degradation. The main pathway involves substitutive and oxidative dechlorination reactions that lead to the formation of CO₂. Granular sludge, therefore, has outstanding potential for gratuitous dechlorination of CT to safe end products.     

Phylogenetic analysis based on spectral methods

Whole-genome or multiple gene phylogenetic analysis is of interest since single gene analysis often results in poorly resolved trees. Here, the use of spectral techniques for analyzing multigene data sets is explored. The protein sequences are treated as categorical time series, and a measure of similarity between a pair of sequences, the spectral covariance, is based on the common periodicity between these two sequences. Unlike the other methods, the spectral covariance method focuses on the relationship between the sites of genetic sequences. By properly scaling the dissimilarity measures derived from different genes between a pair of species, we can use the mean of these scaled dissimilarity measures as a summary statistic to measure the taxonomic distances across multiple genes. The methods are applied to three different data sets, one noncontroversial and two with some dispute over the correct placement of the taxa in the tree. Trees are constructed using two distance-based methods, BIONJ and FITCH. A variation of block bootstrap sampling method is used for inference. The methods are able to recover all major clades in the corresponding reference trees with moderate to high bootstrap support. Through simulations, we show that the covariance-based methods effectively capture phylogenetic signal even when structural information is not fully retained. Comparisons of simulation results with the bootstrap permutation results indicate that the covariance-based methods are fairly robust under perturbations in sequence similarity but more sensitive to perturbations in structural similarity.     

Determination of Chinese hamster ovary cell line stability and recombinant antibody expression during long-term culture

Chinese hamster ovary (CHO) cell lines are frequently used as hosts for the production of recombinant therapeutics, such as monoclonal antibodies, due to their ability to perform correct post-translational modifications. A potential issue when utilizing CHO cells for therapeutic protein production is the selection of cell lines that do not retain stable protein expression during long-term culture (LTC). Instability of expression impairs process yields, effective usage of time and money, and regulatory approval for the desired therapeutic. In this study, we investigated a model unstable GS-CHO cell line over a continuous period of approximately 100 generations to determine markers of mechanisms that underlie instability. In this cell line, stability of expression was retained for 40-50 generations after which time a 40% loss in antibody production was detected. The instability observed within the cell line was not due to a loss in recombinant gene copy number or decreased expression of mRNA encoding for recombinant antibody H or L chain, but was associated with lower cumulative cell time values and an apparent increased sensitivity to cellular stress (exemplified by increased mRNA expression of the stress-inducible gene GADD153). Changes were also noted in cellular metabolism during LTC (alterations to extracellular alanine accumulation, and enhanced rates of glucose and lactate utilization, during the exponential and decline phase of batch culture, respectively). Our data indicates the breadth of changes that may occur to recombinant CHO cells during LTC ranging from instability of recombinant target production at a post-mRNA level to metabolic events. Definition of the mechanisms, regulatory events, and linkages underpinning cellular phenotype changes require further detailed analysis at a molecular level.     

Molecular evolution of voltage-sensitive ion channel genes: on the origins of electrical excitability

We have analyzed nucleic acid and amino acid sequence alignments of a variety of voltage-sensitive ion channels, using several methods for phylogenetic tree reconstruction. Ancient duplications within this family gave rise to three distantly related groups, one consisting of the Na+ and Ca++ channels, another the K+ channels, and a third including the cyclic nucleotide-binding channels. A series of gene duplications produced at least seven mammalian homologues of the Drosophila Shaker K+ channel; clones of only three of these genes are available from all three mammalian species examined (mouse, rat, and human), pointing to specific genes that have yet to be recovered in one or another of these species. The Shaw-related K+ channels and the Na+ channel family have also undergone considerable expansion in mammals, relative to flies. These expansions presumably reflect the needs of the high degree of physiological and neuronal complexity of mammals. Analysis of the separate domains of the four-domain channels (Ca++ and Na+) supports their having evolved by two sequential gene duplications and implies the historical existence of a functional two-domain channel.      

A conserved proline-rich region of the Saccharomyces cerevisiae cyclase-associated protein binds SH3 domains and modulates cytoskeletal localization.

Saccharomyces cerevisiae cyclase-associated protein (CAP or Srv2p) is multifunctional. The N-terminal third of CAP binds to adenylyl cyclase and has been implicated in adenylyl cyclase activation in vivo. The widely conserved C-terminal domain of CAP binds to monomeric actin and serves an important cytoskeletal regulatory function in vivo. In addition, all CAP homologs contain a centrally located proline-rich region which has no previously identified function. Recently, SH3 (Src homology 3) domains were shown to bind to proline-rich regions of proteins. Here we report that the proline-rich region of CAP is recognized by the SH3 domains of several proteins, including the yeast actin-associated protein Abp1p. Immunolocalization experiments demonstrate that CAP colocalizes with cortical actin-containing structures in vivo and that a region of CAP containing the SH3 domain binding site is required for this localization. We also demonstrate that the SH3 domain of yeast Abp1p and that of the yeast RAS protein guanine nucleotide exchange factor Cdc25p complex with adenylyl cyclase in vitro. Interestingly, the binding of the Cdc25p SH3 domain is not mediated by CAP and therefore may involve direct binding to adenylyl cyclase or to an unidentified protein which complexes with adenylyl cyclase. We also found that CAP homologous from Schizosaccharomyces pombe and humans bind SH3 domains. The human protein binds most strongly to the SH3 domain from the abl proto-oncogene. These observations identify CAP as an SH3 domain-binding protein and suggest that CAP mediates interactions between SH3 domain proteins and monomeric actin.     

Evolutionary stability and the rarity of grandmothering

The provision of intergenerational care, via the Grandmother Hypothesis, has been implicated in the evolution of postfertile longevity, particularly in humans. However, if grandmothering does provide fitness benefits, a key question is why has it evolved so infrequently? We investigate this question with a combination of life‐history and evolutionary game theory. We derive simple eligibility and stability thresholds, both of which must be satisfied if intergenerational care is first to evolve and then to persist in a population. As one threshold becomes easier to fulfill, the other becomes more difficult, revealing a conflict between the two. As such, we suggest that, in fact, we should expect the evolution of grandmothering to be rare.     

Abnormal immune responses in fa/fa Zucker rats and effects of feeding conjugated linoleic acid

Objective: The objective of this study was to characterize immune function in the fa/fa Zucker rat, and to determine the effects of feeding conjugated linoleic acid (CLA) isomers on immune function. Methods and Procedures: Lean and fa/fa Zucker rats were fed for 8 weeks nutritionally complete diets with different CLA isomers (%wt/wt): control (0%), c9t11 (0.4%), t10c12 (0.4%), or MIX (0.4% c9t11 + 0.4% t10c12). Isolated splenocytes were used to determine phospholipid (PL) fatty acid composition and cell phenotypes, or stimulated with mitogen to determine their ability to produce cytokines, immunoglobulins (Ig), and nitric oxide (NO). Results: Splenocyte PL of fa/fa rats had a higher proportion of total monounsaturated fatty acids and n ?3 polyunsaturated fatty acids (PUFA), and lower n ?6 PUFA and n ?6‐to‐n ?3 PUFA ratio (P < 0.05). Feeding CLA increased the content of CLA isomers into PL, but there were lower proportions of each CLA isomer in fa/fa rats. Splenocytes of fa/fa rats produced more amounts of IgA, IgG, and IgM, NO, and interleukin‐1β (IL‐1β), IL‐6, and tumor necrosis factor‐α (TNF‐α) (P < 0.05). Obese rats fed the t10c12 diet produced less TNF‐α and IL‐1β (lippopolysaccharide (LPS), P < 0.05). Splenocytes of fa/fa rats produced less concanavalin A (ConA)‐stimulated IL‐2 (P < 0.0001) than lean rats, except fa/fa rats fed the c9t11 diet (P < 0.05). Discussion: The c9t11 and t10c12 CLA isomers were incorporated into the membrane PL of the fa/fa Zucker rat, but to a lesser extent than lean rats. Splenocytes of obese rats responded in a proinflammatory manner and had reduced T‐cell function and feeding the t10c12 and c9t11 CLA isomers may improve some of these abnormalities by distinct methods.