A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3

We describe a new computer program, SnpEff, for rapidly categorizing the effects of variants in genome sequences. Once a genome is sequenced, SnpEff annotates variants based on their genomic locations and predicts coding effects. Annotated genomic locations include intronic, untranslated region, upstream, downstream, splice site, or intergenic regions. Coding effects such as synonymous or non-synonymous amino acid replacement, start codon gains or losses, stop codon gains or losses, or frame shifts can be predicted. Here the use of SnpEff is illustrated by annotating ~356,660 candidate SNPs in ~117 Mb unique sequences, representing a substitution rate of ~1/305 nucleotides, between the Drosophila melanogaster w(1118); iso-2; iso-3 strain and the reference y(1); cn(1) bw(1) sp(1) strain. We show that ~15,842 SNPs are synonymous and ~4,467 SNPs are non-synonymous (N/S ~0.28). The remaining SNPs are in other categories, such as stop codon gains (38 SNPs), stop codon losses (8 SNPs), and start codon gains (297 SNPs) in the 5'UTR. We found, as expected, that the SNP frequency is proportional to the recombination frequency (i.e., highest in the middle of chromosome arms). We also found that start-gain or stop-lost SNPs in Drosophila melanogaster often result in additions of N-terminal or C-terminal amino acids that are conserved in other Drosophila species. It appears that the 5' and 3' UTRs are reservoirs for genetic variations that changes the termini of proteins during evolution of the Drosophila genus. As genome sequencing is becoming inexpensive and routine, SnpEff enables rapid analyses of whole-genome sequencing data to be performed by an individual laboratory.     

Activation of brain protein phosphatase-1(I) following cardiac arrest and resuscitation involving an interaction with 14-3-3 gamma

The intracellular signaling mechanisms that couple transient cerebral ischemia to cell death and neuroprotective mechanisms provide potential therapeutic targets for cardiac arrest. Protein phosphatase (PP)-1 is a major serine/threonine phosphatase that interacts with and dephosphorylates critical regulators of energy metabolism, ionic balance, and apoptosis. We report here that PP-1_I, a major regulated form of PP-1, is activated in brain by approximately twofold in vivo following cardiac arrest and resuscitation in a clinically relevant pig model of transient global cerebral ischemia and reperfusion. PP-1_I purified to near homogeneity from either control or ischemic pig brain consisted of the PP-1 catalytic subunit, the inhibitor-2 regulatory subunit, as well as the novel constituents 14-3-3γ, Rab GDP dissociation protein β, PFTAIRE kinase, and C-TAK1 kinase. PP-1_I purified from ischemic brain contained significantly less 14-3-3γ than PP-1_I purified from control brain, and purified 14-3-3γ directly inhibited the catalytic subunit of PP-1 and reconstituted PP-1_I. These findings suggest that activation of brain PP-1_I following global cerebral ischemia in vivo involves dissociation of 14-3-3γ, a novel inhibitory modulator of PP-1_I. This identifies modulation of PP-1_I by 14-3-3 in global cerebral ischemia as a potential signaling mechanism-based approach to neuroprotection.     

Identification of initiator B cells, a novel subset of activation-induced deaminase-dependent B-1-like cells that mediate initiation of contact sensitivity

Contact sensitivity (CS) is related to delayed-type hypersensitivity and is a well-characterized prototype of T cell-mediated inflammation. However, the inflammatory response associated with CS is additionally dependent on Ag-specific IgM produced by a subpopulation of B cells in response to sensitization. Upon re-exposure to hapten, this IgM mediates rapid vascular activation and subsequent recruitment of proinflammatory T cells to the local site. Interference with this pathway prevents the full development of the classic delayed inflammatory response and is therefore termed the "CS initiation" pathway. In this study, we show that CS initiation is defective in mice deficient in activation-induced deaminase, an enzyme central to the process of somatic hypermutation. Using adoptive transfer experiments, we demonstrate that the defect is specific to a B-1-like population of B cells and that transfer of WT cells reconstitutes CS initiation mechanisms in deficient recipients. We went on to identify a novel subpopulation of Ag-binding B cells in the spleens of sensitized mice that possess initiation activity (CD19(+)CD5(+)Thy-1(int)IgM(high)IgD(high)) that we name "initiator B cells." Analysis of BCR H chain genes isolated from these cells revealed evidence of activation-induced deaminase-mediated somatic hypermutation. The sensitivity of CS initiation to very low amounts of sensitizing hapten suggests that the responsible B cells have increased IgM receptor gene mutations enabling selection to generate Abs with sufficient affinity to mediate the response.     

Engineering of FRT-lacZ fusion constructs: induction of the Pseudomonas aeruginosa fadAB1 operon by medium and long chain-length fatty acids

Without prior knowledge of the promoters of various genes in bacteria, it can be difficult to study gene regulation using reporter-gene fusions. Regulation studies of promoters are ideal at their native locus, which do not require prior knowledge of promoter regions. Based on a previous study with FRT-lacZ-KmR constructs, we constructed two novel FRT-lacZ-GmR plasmids. This allows easy engineering of Pseudomonas aeruginosa reporter-gene fusions, post-mutant construction, with the Flp-FRT system. We demonstrate the usefulness of one of these FRT-lacZ-GmR plasmids to study the regulation of the fadAB1 operon in P. aeruginosa at its native locus. The fadAB1 operon, involved in fatty acid (FA) degradation, was significantly induced in the presence of several medium chain-length fatty acids (MCFA) and, to a lesser degree, long chain-length fatty acids (LCFA). In addition to the previous work on the FRT-lacZ-KmR tools, these new constructs increase the repertoire of tools that can be applied to P. aeruginosa or other species and strains of bacteria where kanamycin resistance may not be appropriate.     

Region [corrected] of slowed conduction acts as core for spiral wave reentry in cardiac cell monolayers

Pathophysiological heterogeneity in cardiac tissue is related to the occurrence of arrhythmias. Of importance are regions of slowed conduction, which have been implicated in the formation of conduction block and reentry. Experimentally, it has been a challenge to produce local heterogeneity in a manner that is both reversible and well controlled. Consequently, we developed a dual-zone superfusion chamber that can dynamically create a small (5 mm) central island of heterogeneity in cultured cardiac cell monolayers. Three different conditions were studied to explore the effect of regionally slowed conduction on wave propagation and reentry: depolarization by elevated extracellular potassium, sodium channel inhibition with lidocaine, and cell-cell decoupling with palmitoleic acid. Using optical mapping of transmembrane voltage, we found that the central region of slowed conduction always served as the core region around which a spiral wave formed and then revolved following a period of rapid pacing. Because of the localized slowing in the core region, we observed experimentally for the first time an S shape of the spiral wave front near its tip. These results indicate that a small region of slowed conduction can play a crucial role in the formation, anchoring, and modulation of reentrant spiral waves.     

Endogenous expression of matriptase in neural progenitor cells promotes cell migration and neuron differentiation

Recent studies show that type II transmembrane serine proteases play important roles in diverse cellular activities and pathological processes. Their expression and functions in the central nervous system, however, are largely unexplored. In this study, we show that the expression of one such member, matriptase (MTP), was cell type-restricted and primarily expressed in neural progenitor (NP) cells and neurons. Blocking MTP expression or MTP activity prevented NP cell traverse of reconstituted basement membrane, whereas overexpression of MTP promoted it. The NP cell mobilization induced by either vascular endothelial growth factor or hepatocyte growth factor was also impaired by knocking down MTP expression. MTP acts upstream of matrix metalloproteinase 2 in promoting NP cell mobility. In embryonic stem cell differentiation to neural cells, MTP knockdown had no effect on entry of embryonic stem cells into the neural lineage. High MTP expression or activity, however, shifts the population dynamics from NP cells toward neurons to favor neuronal differentiation. This is the first report to demonstrate the direct involvement of type II transmembrane serine protease in NP cell function.     

The reduction in electroporation voltages by the addition of a surfactant to planar lipid bilayers.

The effects of a nonionic surfactant, octaethyleneglycol mono n-dodecyl ether (C12E8), on the electroporation of planar bilayer lipid membranes made of the synthetic lipid 1-pamitoyl 2-oleoyl phosphatidylcholine (POPC), was studied. High-amplitude ( approximately 100-450 mV) rectangular voltage pulses were used to electroporate the bilayers, followed by a prolonged, low-amplitude ( approximately 65 mV) voltage clamp to monitor the ensuing changes in transmembrane conductance. The electroporation thresholds of the membranes were found for rectangular voltage pulses of given durations. The strength-duration relationship was determined over a range from 10 micros to 10 s. The addition of C12E8 at concentrations of 0.1, 1, and 10 microM to the bath surrounding the membranes decreased the electroporation threshold monotonically with concentration for all durations (p < 0.0001). The decrease from control values ranged from 10% to 40%, depending on surfactant concentration and pulse duration. For a 10-micros pulse, the transmembrane conductance 150 micros after electroporation (G150) increased monotonically with the surfactant concentration (p = 0.007 for 10 microM C12E8). These findings suggest that C12E8 incorporates into POPC bilayers, allowing electroporation at lower intensities and/or shorter durations, and demonstrate that surfactants can be used to manipulate the electroporation threshold of lipid bilayers.     

Glyphosate Resistance as a Novel Select-Agent-Compliant,Non-Antibiotic-Selectable Marker in Chromosomal Mutagenesis of the Essential Genes asd and dapB of Burkholderia pseudomallei

Genetic manipulation of the category B select agents Burkholderia pseudomallei and Burkholderia mallei has been stifled due to the lack of compliant selectable markers. Hence, there is a need for additional select-agent-compliant selectable markers. We engineered a selectable marker based on the gat gene (encoding glyphosate acetyltransferase), which confers resistance to the common herbicide glyphosate (GS). To show the ability of GS to inhibit bacterial growth, we determined the effective concentrations of GS against Escherichia coli and several Burkholderia species. Plasmids based on gat, flanked by unique flip recombination target (FRT) sequences, were constructed for allelic-replacement. Both allelic-replacement approaches, one using the counterselectable marker pheS and the gat-FRT cassette and one using the DNA incubation method with the gat-FRT cassette, were successfully utilized to create deletions in the asd and dapB genes of wild-type B. pseudomallei strains. The asd and dapB genes encode an aspartate-semialdehyde dehydrogenase (BPSS1704, chromosome 2) and dihydrodipicolinate reductase (BPSL2941, chromosome 1), respectively. Mutants unable to grow on media without diaminopimelate (DAP) and other amino acids of this pathway were PCR verified. These mutants displayed cellular morphologies consistent with the inability to cross-link peptidoglycan in the absence of DAP. The B. pseudomallei 1026b Δasd::gat-FRT mutant was complemented with the B. pseudomallei asd gene on a site-specific transposon, mini-Tn7-bar, by selecting for the bar gene (encoding bialaphos/PPT resistance) with PPT. We conclude that the gat gene is one of very few appropriate, effective, and beneficial compliant markers available for Burkholderia select-agent species. Together with the bar gene, the gat cassette will facilitate various genetic manipulations of Burkholderia select-agent species.Members of the genus Burkholderia, comprising more than 40 different species, are extremely diverse gram-negative, non-spore-forming bacilli. Many Burkholderia species exist as innocuous soil saprophytes or plant pathogens (47), while others cause human and animal diseases. Among these human and animal pathogens are the etiological agents of melioidosis (Burkholderia pseudomallei) and glanders (Burkholderia mallei) (9, 50, 51). Melioidosis is an emerging infectious disease generally considered endemic to Southeast Asia and Northern Australia (12). Positive diagnoses in many tropical countries around the world have expanded the global awareness of melioidosis (3, 15, 24, 25, 28, 35, 39, 42, 52). In contrast to the ubiquitous nature of B. pseudomallei, B. mallei is also a highly infectious agent causing glanders, a predominantly equine disease (34, 50). B. mallei, a clone derived from genomic downsizing of B. pseudomallei, has been used in biowarfare (17). This historical significance, along with the low infectious dose and the route of infection, has contributed to the decision by the Centers for Disease Control and Prevention (CDC) to classify these two microbes as category B select agents (43).Classification of B. pseudomallei as a select agent has stimulated interest and research into the pathogenesis of melioidosis, necessitating the development of appropriate tools for genetic manipulation. In the struggle to elucidate the molecular mechanisms of pathogenesis, selectable markers are indispensable genetic tools (45). Current CDC regulations prohibit the cloning of clinically important antibiotic resistance genes into human, animal, or plant select-agent pathogens if the transfer could compromise the ability to treat or control the disease. The only antibiotic markers currently approved for use in B. pseudomallei are based on resistance to aminoglycosides (gentamicin, kanamycin, and zeocin) (45). However, the efficacy of these markers is limited, due to high levels of aminoglycoside resistance inherent within the Burkholderia genus and high levels of spontaneous aminoglycoside resistance in B. pseudomallei (10, 19, 41). In addition, the use of aminoglycosides (e.g., gentamicin) for selection may require aminoglycoside efflux pump mutants (10, 33). Another potential drawback is that efflux pumps play a major role in bacterial physiology, and mutating them may change the pathogenic traits under investigation (7, 40). A more logical approach employs alternative, non-antibiotic-selectable markers conferring resistance to compounds that are not potentially important in clinical treatment.Very few non-antibiotic resistance markers have been utilized successfully for Burkholderia species. A non-antibiotic-selectable-marker based on tellurite resistance (Tel^r) has been successfully developed and used with Pseudomonas putida, Pseudomonas fluorescens, and Burkholderia thailandensis (2, 27, 44). The engineering of Tel^r-FRT (flip recombination target) cassettes, coupled to FRT sequences, could be used to generate unmarked mutations and allow recycling of the Tel^r selectable-marker (2). In addition, utilization of Flp-FRT resistance cassettes to generate mutants allows downstream modification and manipulation such as fusion integration (29). However, the disadvantage of the Tel^r-cassette is the number of genes required (kilA-telA-telB) and the large size (>3 kb), making it less likely to obtain PCR products for allelic replacement by natural transformation (46). Another potentially useful non-antibiotic-selectable marker is based on the bar gene, encoding resistance to bialaphos or its degradation product, phosphinothricin (PPT) (49). PPT inhibits glutamine synthetase in plants (48), starving the cell for glutamine, and the bar gene has been used successfully as a selection marker in gram-negative bacteria (21). For select-agent Burkholderia species, however, the PPT MIC was found to be greater than 1,024 μg/ml (M. Frazier, K. Choi, A. Kumar, C. Lopez, R. R. Karkhoff-Schweizer, and H. P. Schweizer, presented at the American Society for Microbiology Biodefense and Emerging Diseases Research Meeting, Washington, DC, 2007). We have found the effective concentration of PPT for B. pseudomallei and B. mallei to be ∼2.5% (25,000 μg/ml [data not shown]). The high concentration of PPT required for selection in these species may be costly, considering that purified PPT costs ∼$380 per g. Therefore, further development of non-antibiotic resistance markers, as well as a more economical source of herbicide for use with restricted select-agent species, is needed.Work by Castle et al. (5) generated a highly active glyphosate N-acetyltransferase (GAT) enzyme for plant engineering, making it possible to utilize the gat gene as an effective non-antibiotic resistance marker for bacterial selection with glyphosate (GS). The commonly used herbicide GS inhibits the 5-enolpyruvylshikimate-3-phospate synthase (EPSPS) of plants through competition with phosphoenolpyruvate for overlapping binding sites on EPSPS (14), depriving plants of three aromatic amino acids (Fig. ​(Fig.1).1). Since humans and animals obtain tryptophan and phenylalanine (giving rise to tyrosine) through dietary intake, GS is relatively nontoxic. Like plants, bacteria must make these amino acids, when they are lacking, from basic precursors. GS has been found to be inhibitory to a variety of bacteria, including Pseudomonas aeruginosa, Escherichia coli, Bacillus subtilis, and Bradyrhizobium japonicum (16, 55), while other bacterial strains are able to metabolize low concentrations of GS (26, 31). Although B. pseudomallei has been reported to have two genes (glpA and glpB) for GS degradation and metabolism (38), our searches of all available genomes of Burkholderia species in GenBank yielded no glpA or glpB genes within this genus. GS resistance by bacteria has been documented through EPSPS target mutations or GS detoxification mechanisms (36). However, these mechanisms did not confer resistance to relatively high GS concentrations. More recently, directed evolution of the gat gene, based on various bacterial gat sequences and selection in E. coli, yielded a very active GAT protein sequence with an efficiency increase of nearly 4 orders of magnitude (5), holding promise as an appropriate non-antibiotic resistance marker for select-agent species.Open in a separate windowFIG. 1.(A) A 946-ml bottle of the “superconcentrated” herbicide Roundup used in this study, available for ∼$50 from most local hardware stores and garden or farm supply centers. The active ingredient, 50% GS, is indicated on the label, and the chemical structure of GS is shown. GAT, encoded by the gat gene, catalyzes the inactivation of GS via N acetylation. (B) Pathways of aromatic amino acid biosynthesis. GS inhibits the enzyme EPSPS, which is required for the biosynthesis of aromatic amino acids, thus starving bacteria for tyrosine, phenylalanine, and tryptophan. PEP, phosphoenolpyruvate; TCA cycle, tricarboxylic acid cycle.Here we engineered and tested a novel non-antibiotic-selectable-marker (gat) for use in the select agent B. pseudomallei. GS is the active ingredient in Roundup, which was used for selection (Fig. ​(Fig.1).1). The effective compound GS is readily available, inexpensive, relatively nontoxic, very soluble, and not clinically important, and it yields tight selection. The engineered gat marker (563 bp) was optimized for Burkholderia codon usage and adapted (with a Burkholderia rpsL promoter) for use in the select agent B. pseudomallei. Effective concentrations of GS for several species of Burkholderia, including the select agents B. pseudomallei and B. mallei, were determined. Using the gat gene, we created deletion mutants of the essential B. pseudomallei asd and B. pseudomallei dapB (asd_Bp and dapB_Bp) genes (encoding aspartate-semialdehyde dehydrogenase and dihydrodipicolinate reductase, respectively) in two wild-type B. pseudomallei strains. The Δasd_Bp mutant of B. pseudomallei showed a phenotypic defect consistent with the lack of diaminopimelate (DAP) for cell wall cross-linking. Complementation of the B. pseudomallei Δasd_Bp mutant with the asd_Bp gene located on a site-specific transposon, mini-Tn7-bar, was successful by using an inexpensive source of PPT for selection.     

Monoclonal immunoglobulins in patients with carcinoma of the colon

Summary Structural studies were performed on five monoclonal immunoglobulins isolated from patients with carcinoma of the colon. Serologic analysis revealed that two of the five proteins shared idiotypic antigenic determinants; these two but none of the three others had V_HIII heavy chains. The results demonstrated a close structural similarity between the heavy chains of these two proteins both in their antigen-binding sites (the hypervariable region) and in their framework regions. Determination of the NH₂-terminal amino acid sequences indicated that the light chain variable regions of all five proteins were either V_xII or V_xIII. These data suggest that monoclonal immunoglobulins in patients with carcinoma of the colon have restricted heterogeneity and that, in some cases the production of monoclonal immunoglobulin(s) and the development of a solid tumor in a given patient may be related events.Publication no. 357 from the Department of Basic and Clinical Immunology and Microbiology, Medical University of South Carolina. Research supported in part by National Science Foundation Research Grant PCM 79-24043, USPHS Grants HD-09938 and CA-25746, and by Medical University of South Carolina Biomedical Research Appropriations A911 and A912. A. C. W. was the recipient of American Cancer Society Faculty Research Award No. 125