Regional differences in awareness and attitudes regarding genetic testing for disease risk and ancestry

Little is known about the lay public’s awareness and attitudes concerning genetic testing and what factors influence their perspectives. The existing literature focuses mainly on ethnic and socioeconomic differences; however, here we focus on how awareness and attitudes regarding genetic testing differ by geographical regions in the US. We compared awareness and attitudes concerning genetic testing for disease risk and ancestry among 452 adults (41% Black and 67% female) in four major US cities, Norman, OK; Cincinnati, OH; Harlem, NY; and Washington, DC; prior to their participation in genetic ancestry testing. The OK participants reported more detail about their personal ancestries (p = 0.02) and valued ancestry testing over disease testing more than all other sites (p < 0.01). The NY participants were more likely than other sites to seek genetic testing for disease (p = 0.01) and to see benefit in finding out more about one’s ancestry (p = 0.02), while the DC participants reported reading and hearing more about genetic testing for African ancestry than all other sites (p < 0.01). These site differences were not better accounted for by sex, age, education, self-reported ethnicity, religion, or previous experience with genetic testing/counseling. Regional differences in awareness and attitudes transcend traditional demographic predictors, such as ethnicity, age and education. Local sociocultural factors, more than ethnicity and socioeconomic status, may influence the public’s awareness and belief systems, particularly with respect to genetics.     

Comparative genomics identifies new alpha class genes within the avian glutathione S-transferase gene cluster

Glutathione S-transferases (GSTs: EC2.5.1.18) are a superfamily of multifunctional dimeric enzymes that catalyze the conjugation of glutathione (GSH) to electrophilic chemicals. In most animals and in humans, GSTs are the principal enzymes responsible for detoxifying the mycotoxin aflatoxin B₁ (AFB₁) and GST dysfunction is a known risk factor for susceptibility towards AFB₁. Turkeys are one of the most susceptible animals known to AFB₁, which is a common contaminant of poultry feeds. The extreme susceptibility of turkeys is associated with hepatic GSTs unable to detoxify the highly reactive and electrophilic metabolite exo-AFB₁-8,9-epoxide (AFBO). In this study, comparative genomic approaches were used to amplify and identify the α-class tGST genes (tGSTA1.1, tGSTA1.2, tGSTA1.3, tGSTA2, tGSTA3 and tGSTA4) from turkey liver. The conserved GST domains and four α-class signature motifs in turkey GSTs (with the exception of tGSTA1.1 which lacked one motif) confirm the presence of hepatic α-class GSTs in the turkey. Four signature motifs and conserved residues found in α-class tGSTs are (1) xMExxxWLLAAAGVE, (2) YGKDxKERAxIDMYVxG, (3) PVxEKVLKxHGxxxL and (4) PxIKKFLXPGSxxKPxxx. A BAC clone containing the α-class GST gene cluster was isolated and sequenced. The turkey α-class GTS genes genetically map to chromosome MGA2 with synteny between turkey and human α-class GSTs and flanking genes. This study identifies the α-class tGST gene cluster and genetic markers (SNPs, single nucleotide polymorphisms) that can be used to further examine AFB₁ susceptibility and resistance in turkeys. Functional characterization of heterologously expressed proteins from these genes is currently underway.     

Evolution: like any other science it is predictable

Evolutionary biology rejoices in the diversity of life, but this comes at a cost: other than working in the common framework of neo-Darwinian evolution, specialists in, for example, diatoms and mammals have little to say to each other. Accordingly, their research tends to track the particularities and peculiarities of a given group and seldom enquires whether there are any wider or deeper sets of explanations. Here, I present evidence in support of the heterodox idea that evolution might look to a general theory that does more than serve as a tautology (‘evolution explains evolution’). Specifically, I argue that far from its myriad of products being fortuitous and accidental, evolution is remarkably predictable. Thus, I urge a move away from the continuing obsession with Darwinian mechanisms, which are entirely uncontroversial. Rather, I emphasize why we should seek explanations for ubiquitous evolutionary convergence, as well as the emergence of complex integrated systems. At present, evolutionary theory seems to be akin to nineteenth-century physics, blissfully unaware of the imminent arrival of quantum mechanics and general relativity. Physics had its Newton, biology its Darwin: evolutionary biology now awaits its Einstein.     

Implications of climate change for the reproductive capacity and survival of New World silversides (family Atherinopsidae)

The New World silversides (family Atherinopsidae) are found in marine, estuarine and inland waters of North, Central and South America, where they are ecologically important as forage fishes and sometimes economically important for commercial and recreational fisheries. This report reviews the knowledge of the reproductive attributes of temperate and subtropical atherinopsids in relation to temperature and discusses the potential effects of climate change on their reproduction and adaptive responses. Their reproductive cycles are primarily entrained by photoperiod with high temperature acting as a limiting factor. They are generally multiple spawners which release successive batches of eggs in spring, but some species can spawn also in autumn and even summer when temperatures do not increase excessively. The decoupling of temperature patterns and photoperiod with further global warming and associated asymmetric thermal fluctuations could lead to spawning at times or temperatures that are unsuitable for larval development and growth. Many members of this family show temperature-dependent sex determination (TSD), where the phenotypic sex of an individual is determined partly or wholly by the temperature experienced during gonadal sex differentiation, and high-temperature induced germ cell degeneration and decreased fertility. The predicted short-term reproductive responses of atherinopsids to climate change therefore include acceleration, shortening or overall disruption of spawning activity, and also more subtle, but nonetheless equally population-threatening, dysfunctions such as highly skewed sex ratios and partial or total loss of fertility. In the case of species with TSD, asymmetric thermal fluctuations could also cause larvae to encounter temperatures lower than normal during early development and be feminized. Such dysfunctions have been documented already in natural populations but are confined so far to landlocked, inland water habitats, perhaps because they impose more severe thermal fluctuations and limitations to migration and dispersal. The severity and recurrence of these dysfunctions with further climate change will depend both on the magnitude, speed and pattern of change and on how much (or how fast) physiological and behavioural traits can evolve to match the new conditions imposed by the climate, which is largely unknown. In this regard, compelling evidence is shown that numerous traits, including the sex determination system, are capable of rapid evolution and could mitigate the negative effects of temperature increases on population viability in atherinopsids.     

Characterization of N-Linked Protein Glycosylation in Helicobacter pullorum

The first bacterial N-linked glycosylation system was discovered in Campylobacter jejuni, and the key enzyme involved in the coupling of glycan to asparagine residues within the acceptor sequon of the glycoprotein is the oligosaccharyltransferase PglB. Emerging genome sequence data have revealed that pglB orthologues are present in a subset of species from the Deltaproteobacteria and Epsilonproteobacteria, including three Helicobacter species: H. pullorum, H. canadensis, and H. winghamensis. In contrast to C. jejuni, in which a single pglB gene is located within a larger gene cluster encoding the enzymes required for the biosynthesis of the N-linked glycan, these Helicobacter species contain two unrelated pglB genes (pglB1 and pglB2), neither of which is located within a larger locus involved in protein glycosylation. In complementation experiments, the H. pullorum PglB1 protein, but not PglB2, was able to transfer C. jejuni N-linked glycan onto an acceptor protein in Escherichia coli. Analysis of the characterized C. jejuni N-glycosylation system with an in vitro oligosaccharyltransferase assay followed by matrix-assisted laser desorption ionization (MALDI) mass spectrometry demonstrated the utility of this approach, and when applied to H. pullorum, PglB1-dependent N glycosylation with a linear pentasaccharide was observed. This reaction required an acidic residue at the −2 position of the N-glycosylation sequon, as for C. jejuni. Attempted insertional knockout mutagenesis of the H. pullorum pglB2 gene was unsuccessful, suggesting that it is essential. These first data on N-linked glycosylation in a second bacterial species demonstrate the similarities to, and fundamental differences from, the well-studied C. jejuni system.Glycosylation is one of the most common protein modifications, and eukaryotes glycosylate many of their secreted proteins with asparagine or N-linked glycans. This process is thought to have diverse roles in protein folding, quality control, protein secretion, and sorting (13). Eukaryotic glycosylation takes place at the luminal side of the endoplasmic reticulum (ER) membrane, where a preassembled oligosaccharide is transferred from a lipid carrier to asparagine residues within an N-X-S/T consensus sequence, where X can be any amino acid except proline (19). The coupling of glycan to the protein takes place cotranslationally as nascent polypeptide chains cross the ER membrane via a translocon apparatus (5). This reaction involves a protein complex of at least eight subunits (49), with the STT3 protein (50, 52) apparently acting as the central enzyme in the process of N-linked protein glycosylation (29, 48). The STT3 protein consists of an amino terminus with multiple membrane-spanning domains and a carboxy-terminal region containing the highly conserved WWDYG amino acid sequence motif (15).The first prokaryotic glycoproteins were described for archaeal species over 30 years ago (26), and for some time it was thought that protein glycosylation was a eukaryotic and archaeal, but not a bacterial, trait. However, there are now many examples of protein glycosylation in species from the domain Bacteria. For example, general O-linked protein glycosylation systems in which functionally diverse sets of proteins are glycosylated via a single pathway have recently been identified in Neisseria and Bacteroides spp. (8, 21, 44). The most-well-characterized bacterial species with respect to protein glycosylation is the enteropathogen Campylobacter jejuni, which encodes an O-linked system that glycosylates the flagellin protein of the flagellar filament along with the first described bacterial N-linked glycosylation system (39).The C. jejuni N-linked glycosylation pathway is encoded by genes from a single protein glycosylation, or pgl, locus (38). The glycosylation reaction is thought to occur at the periplasmic face of the bacterial inner membrane mediated by the product of the STT3 orthologue pglB (46). The C. jejuni heptasaccharide glycan is assembled on a lipid carrier in the cytoplasm through the action of glycosyltransferases encoded by the pglA, pglC, pglH, pglJ, and pglI genes (11, 12, 24, 31). This lipid-linked oligosaccharide (LLO) is then “flipped” into the periplasm by the pglK gene product, or “flippase” (1), and transferred by PglB onto an asparagine residue within an extended D/E-X-N-X-S/T sequon (19). Many C. jejuni periplasmic and surface proteins of diverse function are N glycosylated (51), yet the function of glycosylation remains elusive. Unlike in eukaryotes, this process occurs posttranslationally, and the surface location of the sequon in folded proteins appears to be required for glycosylation (20).The C. jejuni pgl gene locus can be transferred into Escherichia coli, and the corresponding gene products will function to transfer the heptasaccharide onto asparagine residues of coexpressed C. jejuni glycoproteins as well as non-C. jejuni proteins containing the appropriately located acceptor sequon (19, 46). When alternative lipid-linked glycans are present, such as those involved in lipopolysaccharide biosynthesis, glycans with diverse structure can also be transferred onto proteins (7). Although there are limitations, particularly with regard to the apparent structural requirement for an acetamido group on the C-2 carbon of the reducing end sugar (7, 47), this is still a significant advance toward tractable in vivo systems for glycoconjugate synthesis. The identification and characterization of further bacterial PglB proteins with potentially diverse properties would considerably expand the utility of such systems. Data from genome sequencing indicate that pglB orthologues are found in species closely related to C. jejuni, such as Campylobacter coli, Campylobacter lari, and Campylobacter upsaliensis (40), as well as in the more distantly related species Wolinella succinogenes (2). These species are members of the phylogenetic grouping known as the epsilon subdivision of the Proteobacteria, or Epsilonproteobacteria, consisting of the well-established genera Campylobacter, Helicobacter, Arcobacter, and Wolinella, which are often associated with human and animal hosts, as well as a number of newly recognized groupings of environmental bacteria often found in sulfidic environments (3). However, not all species of Epsilonproteobacteria contain pglB orthologues, and until recently, all characterized Helicobacter species lacked pglB genes.Given the considerable interest in exploiting bacterial protein glycosylation, especially the C. jejuni N-linked glycosylation system, for generating glycoconjugates of biotechnological and therapeutic potential, the functional characterization of newly discovered pglB orthologues is a priority. In this report we describe the application of an in vitro oligosaccharyltransferase assay to investigate N-linked glycosylation initially in C. jejuni, where the utility of this approach was demonstrated, and then in Helicobacter pullorum, demonstrating that one of the two H. pullorum PglB enzymes is responsible for N-linked protein glycosylation with a pentasaccharide glycan.     

Hyperparasitism has wide-ranging implications for studies on the invertebrate phase of myxosporean (Myxozoa) life cycles

All of the actinospore releasing oligochaetes collected in an environmental sample were found to be infected with the microsporidian Neoflabelliforma aurantiae n. gen. n. sp. Ultrastructural and phylogenetic studies on this microsporidian indicated similarities with Flabelliforma magnivora but not with the type species Flabelliforma montana, necessitating the formation of a new genus Neoflabelliforma and reassignment of F. magnivora as Neoflabelliforma magnivora n. comb. The development of N. aurantiae is described both parasitising the oligochaete worm and hyperparasitising the concurrent myxosporean infection. The effect of N. aurantiae on the myxosporeans was deleterious and progressive, eventually stopping all actinospore formation. Its discovery has the potential to impact on areas examining the phase of myxosporean life cycles in the invertebrate host, from transmission studies and epidemiology to re-evaluating the basic steps of intra-oligochaete development. Recent evidence has suggested that studies using invertebrate systems should consider possible adverse effects that co-infections can have on experimental outcomes. The discovery of N. aurantiae highlights the need for careful screening of experimental animals to help circumvent erroneous results.     

An investigation of intracellular glycosylation activities in CHO cells: Effects of nucleotide sugar precursor feeding

Controlling glycosylation of recombinant proteins produced by CHO cells is highly desired as it can be directed towards maintaining or increasing product quality. To further our understanding of the different factors influencing glycosylation, a glycosylation sub‐array of 79 genes and a capillary electrophoresis method which simultaneously analyzes 12 nucleotides and 7 nucleotide sugars; were used to generate intracellular N‐glycosylation profiles. Specifically, the effects of nucleotide sugar precursor feeding on intracellular glycosylation activities were analyzed in CHO cells producing recombinant human interferon‐γ (IFN‐γ). Galactose (±uridine), glucosamine (±uridine), and N‐acetylmannosamine (ManNAc) (±cytidine) feeding resulted in 12%, 28%, and 32% increase in IFN‐γ sialylation as compared to the untreated control cultures. This could be directly attributed to increases in nucleotide sugar substrates, UDP‐Hex (～20‐fold), UDP‐HexNAc (6‐ to 15‐fold) and CMP‐sialic acid (30‐ to 120‐fold), respectively. Up‐regulation of B4gal and St3gal could also have enhanced glycan addition onto the proteins, leading to more complete glycosylation (sialylation). Combined feeding of glucosamine + uridine and ManNAc + cytidine increased UDP‐HexNAc and CMP‐sialic acid by another two‐ to fourfold as compared to feeding sugar precursors alone. However, it did not lead to a synergistic increase in IFN‐γ sialylation. Other factors such as glycosyltransferase or glycan substrate levels could have become limiting. In addition, uridine feeding increased the levels of uridine‐ and cytidine‐activated nucleotide sugars simultaneously, which could imply that uridine is one of the limiting substrates for nucleotide sugar synthesis in the study. Hence, the characterization of intracellular glycosylation activities has increased our understanding of how nucleotide sugar precursor feeding influence glycosylation of recombinant proteins produced in CHO cells. It has also led to the optimization of more effective strategies for manipulating glycan quality. Biotechnol. Bioeng. 2010;107: 321–336. © 2010 Wiley Periodicals, Inc.     

Profiling of N‐glycosylation gene expression in CHO cell fed‐batch cultures

One of the goals of recombinant glycoprotein production is to achieve consistent glycosylation. Although many studies have examined the changes in the glycosylation quality of recombinant protein with culture, very little has been done to examine the underlying changes in glycosylation gene expression as a culture progresses. In this study, the expression of 24 genes involved in N‐glycosylation were examined using quantitative RT PCR to gain a better understanding of recombinant glycoprotein glycosylation during production processes. Profiling of the N‐glycosylation genes as well as concurrent analysis of glycoprotein quality was performed across the exponential, stationary and death phases of a fed‐batch culture of a CHO cell line producing recombinant human interferon‐γ (IFN‐γ). Of the 24 N‐glycosylation genes examined, 21 showed significant up‐ or down‐regulation of gene expression as the fed‐batch culture progressed from exponential, stationary and death phase. As the fed‐batch culture progressed, there was also an increase in less sialylated IFN‐γ glycoforms, leading to a 30% decrease in the molar ratio of sialic acid to recombinant IFN‐γ. This correlated with decreased expression of genes involved with CMP sialic acid synthesis coupled with increased expression of sialidases. Compared to batch culture, a low glutamine fed‐batch strategy appears to need a 0.5 mM glutamine threshold to maintain similar N‐glycosylation genes expression levels and to achieve comparable glycoprotein quality. This study demonstrates the use of quantitative real time PCR method to identify possible “bottlenecks” or “compromised” pathways in N‐glycosylation and subsequently allow for the development of strategies to improve glycosylation quality. Biotechnol. Bioeng. 2010;107: 516–528. © 2010 Wiley Periodicals, Inc.     

Peptide gomesin triggers cell death through L-type channel calcium influx,MAPK/ERK,PKC and PI3K signaling and generation of reactive oxygen species

Gomesin is an antimicrobial peptide isolated from hemocytes of a common Brazilian tarantula spider named Acanthoscurria gomesiana. This peptide exerts antitumor activity in vitro and in vivo by an unknown mechanism. In this study, the cytotoxic mechanism of gomesin in human neuroblastoma SH-SY5Y and rat pheochromocytoma PC12 cells was investigated. Gomesin induced necrotic cell death and was cytotoxic to SH-SY5Y and PC12 cells. The peptide evoked a rapid and transient elevation of intracellular calcium levels in Fluo-4-AM loaded PC12 cells, which was inhibited by nimodipine, an L-type calcium channel blocker. Preincubation with nimodipine also inhibited cell death induced by gomesin in SH-SY5Y and PC12 cells. Gomesin-induced cell death was prevented by the pretreatment with MAPK/ERK, PKC or PI3K inhibitors, but not with PKA inhibitor. In addition, gomesin generated reactive oxygen species (ROS) in SH-SY5Y cells, which were blocked with nimodipine and MAPK/ERK, PKC or PI3K inhibitors. Taken together, these results suggest that gomesin could be a useful anticancer agent, which mechanism of cytotoxicity implicates calcium entry through L-type calcium channels, activation of MAPK/ERK, PKC and PI3K signaling as well as the generation of reactive oxygen species.