Crystal structures of YkuI and its complex with second messenger cyclic Di-GMP suggest catalytic mechanism of phosphodiester bond cleavage by EAL domains

Cyclic di-GMP (c-di-GMP) is a ubiquitous bacterial second messenger that is involved in the regulation of cell surface-associated traits and the persistence of infections. Omnipresent GGDEF and EAL domains, which occur in various combinations with regulatory domains, catalyze c-di-GMP synthesis and degradation, respectively. The crystal structure of full-length YkuI from Bacillus subtilis, composed of an EAL domain and a C-terminal PAS-like domain, has been determined in its native form and in complex with c-di-GMP and Ca(2+). The EAL domain exhibits a triose-phosphate isomerase-barrel fold with one antiparallel beta-strand. The complex with c-di-GMP-Ca(2+) defines the active site of the putative phosphodiesterase located at the C-terminal end of the beta-barrel. The EAL motif is part of the active site with Glu-33 of the motif being involved in cation coordination. The structure of the complex allows the proposal of a phosphodiesterase mechanism, in which the divalent cation and the general base Glu-209 activate a catalytic water molecule for nucleophilic in-line attack on the phosphorus. The C-terminal domain closely resembles the PAS-fold. Its pocket-like structure could accommodate a yet unknown ligand. YkuI forms a tight dimer via EAL-EAL and trans EAL-PAS-like domain association. The possible regulatory significance of the EAL-EAL interface and a mechanism for signal transduction between sensory and catalytic domains of c-di-GMP-specific phosphodiesterases are discussed.

Molecular determinants for interfacial binding and conformational change in a soluble diacylglycerol kinase

DgkB is a soluble diacylglycerol (DAG) kinase that is essential for membrane lipid homeostasis in many Gram-positive pathogens. Anionic phospholipids, like phosphatidylglycerol (PtdGro), were required for DgkB to recognize diacylglycerol embedded in a phospholipid bilayer. An activity-independent vesicle binding assay was used to determine the role of specific residues in DgkB-PtdGro interactions. Lys15 and Lys165 were required for DgkB to dock with PtdGro vesicles and flank the entrance to the DgkB active site. Mg2+ was required for vesicle binding. The compromised vesicle binding by mutants in the key asparate residues forming the structural Mg2+-aspartate-water network within the substrate binding domain revealed that interfacial binding of DgkB required a Mg2+-dependent conformational change. DgkB interaction with phospholipid vesicles was not influenced by the presence of ATP, but anionic vesicles decreased the Km of the enzyme for ATP. Arg100 and Lys15 are two surface residues in the ATP binding domain that were necessary for high affinity ATP binding. The key residues responsible for the structural Mg2+ binding site, the conformational changes that increase ATP affinity, and interfacial recognition of anionic phospholipids were identical in DgkB and the mammalian diacylglycerol kinase catalytic cores. This sequence conservation suggests that the mammalian enzymes also require a structural divalent cation and surface positively charged residues to bind phospholipid bilayers and trigger conformational changes that accelerate catalysis.

Lactose synthase components in milk: concentrations of alpha-lactalbumin and beta1,4-galactosyltransferase in milk of cows from several breeds at various stages of lactation

It is believed that milk production is determined by the number and activity of mammary secretory cells. Secretory activity, as assessed by milk volume, depends on secretion of the major osmole in milk, lactose, which is produced by lactose synthase. The amount of either of the two proteins in lactose synthase may regulate milk production. The objective of this study was to determine whether the concentrations in milk of the two components of lactose synthase, alpha-lactalbumin (alpha-LA) and beta1,4-galactosyltransferase (B4GALT), were related to genetic background, stage of lactation, breed or parity of dairy cows. alpha-Lactalbumin and B4GALT concentrations were measured by ELISA and by enzyme assays, respectively, from single milk samples. Two herds with a total of 279 cows were used in the analysis. One herd contained Ayrshire, Brown Swiss, Holstein and Jersey cows; the second herd contained two groups of cows; Holsteins selected for high milk production and Holsteins with 1960s genetics. The alpha-LA concentration in milk was greater in Jerseys and Ayrshires than in Holsteins and Brown Swiss. However, no difference in alpha-LA concentration was observed in milk from high and low genetic merit cows in the Minnesota herd or among different genetic backgrounds in the Illinois herd. beta1,4-Galactosyltransferase concentrations were similar for all groups that were analyzed. alpha-Lactalbumin concentrations were positively correlated with milk protein concentration, milk fat concentration and lactose concentration. beta1,4-Galactosyltransferase concentration in milk exhibited a strong positive correlation with number of days in milk. Although the concentration of B4GALT increased as lactation progressed, the values did not show any correlation with persistency of lactation or late lactation milk production. In conclusion, this survey shows that the two components of lactose synthase are each correlated to protein concentration and individually correlated to the concentration of other milk components and stage of lactation.

Porcine beta1,4-galactosyltransferase-I sequence and expression

Beta1,4-galactosyltransferase-I (B4GALT1), one of seven beta1,4-galactosyltransferases, is an enzyme commonly found in the trans-Golgi complex that adds galactose to oligosaccharides. In the three mammals studied to date, the B4GALT1 gene directs production of B4GALT1 protein using either of two transcription start sites. The product of the smaller transcript serves the traditional biosynthetic role in the Golgi. This form also complexes with alpha-lactalbumin, a mammary-specific protein, to form lactose synthase. In addition to a biosynthetic role, the protein translated from the longer transcript appears on the plasma membranes of some cells where it serves as a signalling receptor in cell-matrix interactions such as sperm-egg binding. The objective of this study was to sequence the protein-coding region of porcine B4GALT1 and examine the sequence for relationships to the bovine, human, murine and chicken B4GALT1 genes. The sequence for the 1203 base pair protein-coding region of porcine B4GALT1 was obtained. Analysis of the deduced protein sequences revealed that the transmembrane region displayed the highest identity between the four mammals. The catalytic domain was 84-88% identical between the porcine sequence and those of the bovine, human and mouse. The porcine protein had the lowest overall homology to the chicken amino acid sequence, 58% identity. Conservation of both transcription start sites in the porcine gene supports the existence of two isoforms. When compared to the other mammalian B4GALT1 genes, the porcine coding sequence contained a single threonine codon inserted into the region encoding the cytoplasmic domain. Two putative phosphorylation sites in the mouse cytoplasmic domain were conserved in the porcine sequence. Northern blots revealed a widely expressed 4.4 kb transcript that was more abundant in the mammary gland during lactation. These results are important for studies of the function of this unusual and important glycosyltransferase during glycoprotein biosynthesis, lactation and fertilization.

Analysis of the Staphylococcus aureus DgkB structure reveals a common catalytic mechanism for the soluble diacylglycerol kinases

Soluble diacylglycerol (DAG) kinases function as regulators of diacylglycerol metabolism in cell signaling and intermediary metabolism. We report the structure of a DAG kinase, DgkB from Staphylococcus aureus, both as the free enzyme and in complex with ADP. The molecule is a tight homodimer, and each monomer comprises two domains with the catalytic center located within the interdomain cleft. Two distinctive features of DkgB are a structural Mg2+ site and an associated Asp*water*Mg2+ network that extends toward the active site locale. Site-directed mutagenesis revealed that these features play important roles in the catalytic mechanism. The key active site residues and the components of the Asp*water*Mg2+ network are conserved in the catalytic cores of the mammalian signaling DAG kinases, indicating that these enzymes use the same mechanism and have similar structures as DgkB.

General statistical inference for discrete and mixed spaces by an approximate application of the maximum entropy principle

We propose a new method for learning a general statistical inference engine, operating on discrete and mixed discrete/continuous feature spaces. Such a model allows inference on any of the discrete features, given values for the remaining features. Applications are, e.g., to medical diagnosis with multiple possible diseases, fault diagnosis, information retrieval, and imputation in databases. Bayesian networks (BN's) are versatile tools that possess this inference capability. However, BN's require explicit specification of conditional independencies, which may be difficult to assess given limited data. Alternatively, Cheeseman proposed finding the maximum entropy (ME) joint probability mass function (pmf) consistent with arbitrary lower order probability constraints. This approach is in principle powerful and does not require explicit expression of conditional independence. However, until now, the huge learning complexity has severely limited the use of this approach. Here we propose an approximate ME method, which also encodes arbitrary low-order constraints but while retaining quite tractable learning. Our method uses a restriction of joint pmf support (during learning) to a subset of the feature space. Results on the University of California-Irvine repository reveal performance gains over several BN approaches and over multilayer perceptrons.

Porcine sperm zona binding ability as an indicator of fertility

The escalated use of artificial insemination in swine has increased the importance of determining fertility of a semen sample before it is used. Multiple laboratory assays have been developed to assess fertilizing potential but they have yielded inconsistent results. This experiment sought to determine the relationship between in vitro competitive zona binding ability and in vivo fertility based on heterospermic inseminations and paternity testing. The zona pellucida binding ability and fertility of sperm from 15 boars was assessed by comparing sperm from one boar with sperm from other individual boars in a pairwise fashion using four ejaculates. The relationship of zona binding ability to the mean number of piglets sired per litter for each boar as well as historic fertility data (litter size and farrowing rate) was assessed. The in vitro competition assay consisted of labeling sperm from each boar of the pair with a different fluorophore and incubating an equal number of sperm from each boar in the same droplet with porcine oocytes. The competitive assay was highly effective in ranking boars by zona binding ability (R2=0.94). Paternity testing using microsatellite markers was used to determine the mean number of piglets sired per litter for each boar during heterospermic inseminations. The pairwise heterospermic insemination assay was effective in ranking boar fertility (R2=0.59). Using historical data from these boars, average litter size and farrowing rate were correlated (r=0.81, p<0.001). However, zona binding ability was not significantly correlated with historic farrowing rate data or historic average litter size. Boar sperm zona binding ability was also not correlated significantly with the mean number of piglets sired per litter following heterospermic insemination. But the number of piglets sired by each boar was related to a combination of zona binding ability, sperm motility, normal morphology, acrosomal integrity, and the presence of distal droplets (R2=0.70). These results suggest that zona binding ability is not an accurate predictor of fertilizing ability when used alone; however, when coupled with other sperm assessments, fertility may be predicted successfully.

Light-responsive cryptochromes from a simple multicellular animal, the coral Acropora millepora

Hundreds of species of reef-building corals spawn synchronously over a few nights each year, and moonlight regulates this spawning event. However, the molecular elements underpinning the detection of moonlight remain unknown. Here we report the presence of an ancient family of blue-light-sensing photoreceptors, cryptochromes, in the reef-building coral Acropora millepora. In addition to being cryptochrome genes from one of the earliest-diverging eumetazoan phyla, cry1 and cry2 were expressed preferentially in light. Consistent with potential roles in the synchronization of fundamentally important behaviors such as mass spawning, cry2 expression increased on full moon nights versus new moon nights. Our results demonstrate phylogenetically broad roles of these ancient circadian clock-related molecules in the animal kingdom.

Structural and biochemical characterization of a novel Mn2+-dependent phosphodiesterase encoded by the yfcE gene

Escherichia coli YfcE belongs to a conserved protein family within the calcineurin-like phosphoesterase superfamily (Pfam00149) that is widely distributed in bacteria and archaea. Superfamily members are metallophosphatases that include monoesterases and diesterases involved in a variety of cellular functions. YfcE exhibited catalytic activity against bis-p-nitrophenyl phosphate, a general substrate for phosphodiesterases, and had an absolute requirement for Mn2+. However, no activity was observed with phosphodiesters and over 50 naturally occurring phosphomonoesters. The crystal structure of the YfcE phosphodiesterase has been determined to 2.25 A resolution. YfcE has a beta-sandwich architecture similar to metallophosphatases of common ancestral origin. Unlike its more complex homologs that have added structural elements for regulation and substrate recognition, the relatively small 184-amino-acid protein has retained its ancestral simplicity. The tetrameric protein carries two zinc ions per active site from the E. coli extract that reflect the conserved di-Mn2+ active site geometry. A cocrystallized sulfate inhibitor mimics the binding of phosphate moeities in known ligand/phosphatase complexes. Thus, YfcE has a similar active site and biochemical mechanism as well-characterized superfamily members, while the YfcE phosphodiester-containing substrate is unique.

Environmental effects of dredging on sediment nutrients, carbon and granulometry in a tropical estuary

This monitoring study encompassed a period prior to dredging, during dredging and post dredging between July 1999 to June 2000 in Ponggol estuary located along the northeastern coast of Singapore. Mean concentrations of sediment nutrients in mg x Kg(-1) (+/- standard error of means) prior to dredging, during dredging and post dredging were 9.75 +/- 4.24, 8.18 +/- 4.29 and 11.46 +/- 4.74 for ammonium, 0.08 +/- 0.05, 0.06 +/- 0.02 and 0.09 +/- 0.01 for nitrite, 0.04 +/- 0.04, 0.11 +/- 0.17 and 0.25 +/- 0.30 for nitrate, 4.83 +/- 3.48, 0.77 +/- 0.48 and 8.33 +/- 9.73 for phosphate respectively. Pre dredge, dredge and post dredge levels of total carbon (TC) were 18.5 +/- 3.7, 20.2 +/- 3.5 and 34.6 +/- 12.0, of total organic carbon (TOC) were 10.5 +/- 2.9, 19.5 +/- 3.6 and 34.6 +/- 12.0 and of total inorganic carbon (TIC) were 7.9 +/- 1.0, 0.7 +/- 0.4 and non detectable in the sediments, respectively. Both, sediment nutrients and carbon registered lower concentrations with onset of dredging, with the exception of nitrate and TOC. A shift in sedimentary carbon from inorganic carbon to organic carbon was also observed with the onset of the dredging activities when the organically enriched historically contaminated layer was exposed. Sediment granulometry showed that the sediments in the estuary were predominantly silt and clay prior to dredging, which changed to sand with onset of dredging. Silt load in the sediments was highest post-dredge. Sediment nutrients and sediment organic carbon were observed to associate with the finer fractions (silt and clay) of sediments. Finer fractions of sediments get resuspended during a dredging event and are dispersed spatially as the result of tides and water movements. Prior to this study, the potential for nutrient release and sediment granulometry due to dredging have been suggested, but there have been few studies of it, especially in the tropics. The baseline information gathered from this study could be used to work out effective management strategies to protect similar tropical ecosystems elsewhere, should there be no other alternative to dredging.

myo-Inositol Monophosphatase: A Challenging Target for Mood Stabilising Drugs

myo-Inositol monophosphatase has long been a target for drug discovery. Recent work has given detailed insight into its mechanism and dynamics plus new activities and some novel series of inhibitors. The goal of a bio-available inhibitor for this enzyme, however, remains a major challenge for medicinal chemistry.

The effects of short-term stimulation on fibroblast spreading in an in vitro 3D system

Although the short-term effects of mechanical and biochemical stimulation on cell protein and DNA production have recently begun to be evaluated using 3D models, the effects that such stimulation have on cell morphology and adaptation remains unclear. Using a custom-built bioreactor, we were able to create a systematic model to examine the short-term effects of stimulation on cell morphology in a 3D model, specifically by evaluating cell spreading as the short-term indicator of cell adaptation. Fibroblasts were seeded on a porous poly(L-lactic acid) scaffold and cultured in a computerized bioreactor for 24 h under various uniaxial strains (0, 0.6, 3, 6%) and frequencies (0.0125, 0.125 Hz). Also, the effects of transforming growth factor (TGF-beta1) (1, 10, 100 ng/mL) were examined on static, nonstimulated cells-scaffold constructs after 24 h. Fibroblasts that had been subjected to mechanical stretching were found to exhibit significantly more spreading than the static control group. Conversely, TGF-beta1 between 1 and 100 ng/mL did not produce any significant difference in fibroblast spreading from the control groups after 24 h. Collectively, the findings suggest that cell morphology and adaptation may be affected by short-term mechanical stimulation, as seen by increased cell spreading by the fibroblasts under these experimental conditions.

Structure of RhlG, an Essential β-Ketoacyl Reductase in the Rhamnolipid Biosynthetic Pathway of Pseudomonas aeruginosa

Rhamnolipids are extracellular biosurfactants and virulence factors secreted by the opportunistic human pathogen Pseudomonas aeruginosa that are required for swarming motility. The rhlG gene is essential for rhamnolipid formation, and the RhlG enzyme is thought to divert fatty acid synthesis intermediates into the rhamnolipid biosynthetic pathway based on its similarity to FabG, the beta-ketoacyl-acyl carrier protein (ACP) reductase of type II fatty acid synthesis. Crystallographic analysis reveals that the overall structures of the RhlG.NADP+ and FabG.NADP+ complexes are indeed similar, but there are key differences related to function. RhlG does not undergo the conformational changes upon NADP(H) binding at the active site that in FabG are the structural basis of negative allostery. Also, the acyl chain-binding pocket of RhlG is narrow and rigid compared with the larger, flexible substrate-binding subdomain in FabG. Finally, RhlG lacks a positively charged/hydrophobic surface feature adjacent to the active site that is found on enzymes like FabG that recognize the ACP of fatty acid synthesis. RhlG catalyzed the NADPH-dependent reduction of beta-ketodecanoyl-ACP to beta-d-hydroxydecanoyl-ACP. However, the enzyme was 2000-fold less active than FabG in carrying out the same reaction. These structural and biochemical studies establish RhlG as a NADPH-dependent beta-ketoacyl reductase of the SDR protein superfamily and further suggest that the ACP of fatty acid synthesis does not carry the substrates for RhlG.

Structure-activity relationships at the 5-position of thiolactomycin: an intact (5R)-isoprene unit is required for activity against the condensing enzymes from Mycobacterium tuberculosis and Escherichia coli

Thiolactomycin inhibits bacterial cell growth through inhibition of the beta-ketoacyl-ACP synthase activity of type II fatty acid synthases. The effect of modifications of the 5-position isoprenoid side chain on both IC(50) and MIC were determined. Synthesis and screening of a structurally diverse set of 5-position analogues revealed very little tolerance for substitution in purified enzyme assays, but a few analogues retained MIC, presumably through another target. Even subtle modifications such as reducing one or both double bonds of the diene were not tolerated. The only permissible structural modifications were removal of the isoprene methyl group or addition of a methyl group to the terminus. Cocrystallization of these two inhibitors with the condensing enzyme from Escherichia coli revealed that they retained the TLM binding mode at the active site with reduced affinity. These results suggest a strict requirement for a conjugated, planar side chain inserting within the condensing enzyme active site.

Robust self-assembled octadecylphosphonic acid monolayers on a mica substrate

As determined by scratch tests, self-assembled monolayers (SAMs) of octadecylphosphonic acid (OPA) on a muscovite mica substrate were found to be mechanically robust and to serve as a lubricant to protect the underlying mica substrate. For comparison purposes, three polymer films were subjected to scratch tests under the same conditions. The scratch tests were conducted using a diamond-tipped stylus, and the resultant scratches were examined using atomic force microscopy. The excellent mechanical strength of OPA SAMs is supported by analysis with time-of-flight secondary ion mass spectrometry, which suggests that the headgroup of the OPA is strongly bonded to the substrate atoms. The molecular lubrication provided by OPA SAMs suggests that the interaction between the headgroup and the substrate is sufficiently strong to endure significant shear force and that the hydrocarbon chains are able to dissipate shear energy.

Unexpected patterns of genetic structuring among locations but not colour morphs in Acropora nasuta (Cnidaria; Scleractinia)

Symbiotic relationships have contributed greatly to the evolution and maintenance of biological diversity. On the Great Barrier Reef, species of obligate coral-dwelling fishes (genus Gobiodon) coexist by selectively recruiting to colonies of Acropora nasuta that differ in branch-tip colour. In this study, we investigate genetic variability among sympatric populations of two colour morphs of A. nasuta ('blue-tip' and 'brown-tip') living in symbiosis with two fish species, Gobiodon histrio and G. quinquestrigatus, respectively, to determine whether gobies are selecting between intraspecific colour polymorphisms or cryptic coral species. We also examine genetic differentiation among coral populations containing both these colour morphs that are separated by metres between local sites, tens of kilometres across the continental shelf and hundreds of kilometres along the Great Barrier Reef. We use three nuclear DNA loci, two of which we present here for the first time for Acropora. No significant genetic differentiation was detected between sympatric colour morphs at these three loci. Hence, symbiotic gobies are selecting among colour morphs of A. nasuta, rather than cryptic species. Significant genetic geographical structuring was observed among populations, independent of colour, at regional (i.e. latitudinal separation by < 500 km) and cross-shelf (< 50 km) scales, alongside relative homogeneity between local populations on within reef scales (< 5 km). This contrasts with the reported absence of large-scale genetic structuring in A. valida, which is a member of the same species group as A. nasuta. Apparent differences in biogeographical structuring between species within the A. nasuta group emphasize the need for comparative sampling across both spatial (i.e. within reefs, between reefs and between regions) and taxonomic scales (i.e. within and between closely related species).

The relationship of porcine sperm zona-binding ability to fertility

Several laboratory assays have been designed to assess the fertility potential of a semen sample before insemination, but none have been consistent and accurate predictors of fertility. To determine whether zona-binding ability may be a useful fertility predictor, we validated and used an in vitro competitive assay to measure the ability of porcine sperm to bind to the zona pellucida. The zona-binding ability of sperm from 11 boars that exhibited a broad range in average litter size and farrowing rate was determined. Sperm from each boar were compared directly with sperm from eight other boars in a systematic, pairwise fashion. Sperm from two semen samples were labeled with fluorophores at concentrations that did not affect motility or zona-binding ability. An equal number of labeled sperm from each boar was coincubated with homologous oocytes. Least squares means from analysis of variance were used to rank boars based on zona-binding ability. The competitive assay was effective in establishing a ranking of the boars (R2 = 0.62). Furthermore, there was a correlation between zona-binding ability and fertility when estimated by average litter size (r = 0.64, P < 0.05) but not when estimated by farrowing rate (r = -0.28). The explanation for this difference was that litter size and farrowing rate were poorly correlated (r = 0.14). In conclusion, a competitive zona-binding assay distinguished boars that sired either small or large litters. Competitive zona-binding ability may be useful for identifying boars with reduced fertility that produce smaller litters following insemination.

Crystal complexes of a predicted S-adenosylmethionine-dependent methyltransferase reveal a typical AdoMet binding domain and a substrate recognition domain

S-adenosyl-L-methionine-dependent methyltransferases (MTs) are abundant, and highly conserved across phylogeny. These enzymes use the cofactor AdoMet to methylate a wide variety of molecular targets, thereby modulating important cellular and metabolic activities. Thermotoga maritima protein 0872 (TM0872) belongs to a large sequence family of predicted MTs, ranging phylogenetically from relatively simple bacteria to humans. The genes for many of the bacterial homologs are located within operons involved in cell wall synthesis and cell division. Despite preliminary biochemical studies in E. coli and B. subtilis, the substrate specificity of this group of more than 150 proteins is unknown. As part of the Midwest Center for Structural Genomics initiative (www.mcsg.anl.gov), we have determined the structure of TM0872 in complexes with AdoMet and with S-adenosyl-L-homocysteine (AdoHcy). As predicted, TM0872 has a typical MT domain, and binds endogenous AdoMet, or co-crystallized AdoHcy, in a manner consistent with other known MT structures. In addition, TM0872 has a second domain that is novel among MTs in both its location in the sequence and its structure. The second domain likely acts in substrate recognition and binding, and there is a potential substrate-binding cleft spanning the two domains. This long and narrow cleft is lined with positively charged residues which are located opposite the S(+)-CH(3) bond, suggesting that a negatively charged molecule might be targeted for catalysis. However, AdoMet and AdoHcy are both buried, and access to the methyl group would presumably require structural rearrangement. These TM0872 crystal structures offer the first structural glimpses at this phylogenetically conserved sequence family.

The highly cross-fertile coral species, Acropora hyacinthus and Acropora cytherea, constitute statistically distinguishable lineages

A major challenge for understanding the evolutionary genetics of mass-spawning corals is to explain the maintenance of discrete morphospecies in view of high rates of interspecific fertilization in vitro and nonmonophyletic patterns in molecular phylogenies. In this study, we focused on Acropora cytherea and A. hyacinthus, which have one of the highest potentials for interspecific fertilization. Using sequences of a nuclear intron, we performed phylogenetic and nested clade analyses (NCA). Both species were polyphyletic in molecular phylogenies, but the NCA indicated that they constitute statistically distinguishable lineages. Phylogenetic analysis using an intergenic region of the mitochondrial DNA (mtDNA), was inconclusive because of low levels of variability in this marker. The position of these two species differed between the nuclear DNA (nDNA) and mtDNA phylogenies and was also at odds with a cladistic analysis based on morphology. We conclude that despite the potential for high levels of hybridization and introgression, A. cytherea and A. hyacinthus constitute statistically distinguishable lineages and their taxonomic status is consistent with the cohesion species concept.

Sympatric populations of the highly cross-fertile coral species Acropora hyacinthus and Acropora cytherea are genetically distinct

High cross-fertilization rates in vitro and non-monophyletic patterns in molecular phylogenies challenge the taxonomic status of species in the coral genus Acropora. We present data from eight polymorphic allozyme loci that indicate small, but significant, differentiation between sympatric populations of Acropora cytherea and Acropora hyacinthus (F(ST) = 0.025-0.068, p < 0.05), a pair of acroporid corals with very high interspecific fertilization rates in vitro. Although no fixed allelic differences were found between these species, the absence of genetic differentiation between widely allopatric populations suggests that allele frequency differences between A. cytherea and A. hyacinthus in sympatry are biologically significant. By contrast, populations of Acropora tenuis, a species which spawns 2-3 hours earlier and shows low cross-fertilization rates with congeners in vitro, were clearly distinct from A. cytherea and A. hyacinthus (F(ST) = 0.427-0.465, p < 0.05). Moreover, allopatric populations of A. tenuis differed significantly, possibly as a consequence of its relatively short period of larval competency. Our results effectively rule out the possibility that A. hyacinthus and A. cytherea are morphotypes within a single species, and indicate that hybridization occurs relatively infrequently between these taxa in nature.

Structure-based design and characterization of novel platforms for ricin and shiga toxin inhibition

Ribosome inhibiting proteins, RIPs, are a widespread family of toxic enzymes. Ricin is a plant toxin used as a poison and biological warfare agent; shiga toxin is a homologue expressed by pathogenic strains of E. coli. There is interest in creating effective antidote inhibitors to this class of enzymes. RIPs act by binding and hydrolyzing a specific adenine base from rRNA. Previous virtual screens revealed that pterins could bind in the specificity pocket of ricin and inhibit the enzyme. In this paper we explore a range of compounds that could serve as better platforms for inhibitor design. This establishes the importance of key hydrogen bond donors and acceptors for active-site complementarity. 8-Methyl-9-oxoguanine is a soluble compound that has the best inhibitory properties of any platform tested. The X-ray structure of this complex revealed that the inhibitor binds in an unexpected way that provides insight for future design. Several inhibitors of ricin were also shown to be inhibitors of shiga toxin, suggesting this program has the potential to develop effective antidotes to an important form of food poisoning.

Flock house virus RNA replicates on outer mitochondrial membranes in Drosophila cells

The identification and characterization of host cell membranes essential for positive-strand RNA virus replication should provide insight into the mechanisms of viral replication and potentially identify novel targets for broadly effective antiviral agents. The alphanodavirus flock house virus (FHV) is a positive-strand RNA virus with one of the smallest known genomes among animal RNA viruses, and it can replicate in insect, plant, mammalian, and yeast cells. To investigate the localization of FHV RNA replication, we generated polyclonal antisera against protein A, the FHV RNA-dependent RNA polymerase, which is the sole viral protein required for FHV RNA replication. We detected protein A within 4 h after infection of Drosophila DL-1 cells and, by differential and isopycnic gradient centrifugation, found that protein A was tightly membrane associated, similar to integral membrane replicase proteins from other positive-strand RNA viruses. Confocal immunofluorescence microscopy and virus-specific, actinomycin D-resistant bromo-UTP incorporation identified mitochondria as the intracellular site of protein A localization and viral RNA synthesis. Selective membrane permeabilization and immunoelectron microscopy further localized protein A to outer mitochondrial membranes. Electron microscopy revealed 40- to 60-nm membrane-bound spherical structures in the mitochondrial intermembrane space of FHV-infected cells, similar in ultrastructural appearance to tombusvirus- and togavirus-induced membrane structures. We concluded that FHV RNA replication occurs on outer mitochondrial membranes and shares fundamental biochemical and ultrastructural features with RNA replication of positive-strand RNA viruses from other families.

Patterns of coral-dinoflagellate associations in Acropora: significance of local availability and physiology of Symbiodinium strains and host-symbiont selectivity

Like other reef-building corals, members of the genus Acropora form obligate endosymbioses with dinoflagellates (zooxanthellae) belonging to the genus Symbiodinium. Both Symbiodinium and its hosts are diverse assemblages, and the relationships between host and algal genotypes are unclear. In this study, we determined phylogenetic relationships between Symbiodinium isolates from a wide range of Acropora species and plotted the algal genotypes onto a molecular phylogeny of 28 Acropora species, using the same samples for the host and symbiont genotyping. In addition, we performed a preliminary survey of zooxanthella distribution in Acropora species from the central Great Barrier Reef. Three of the four known major zooxanthellae clades were represented in the 168 samples examined, and within the major clade C, three distinct subclades were identified. No evidence was found for coevolution, but several clear patterns of specificity were identified. Moreover, composition of the zooxanthella pool varied among locales and in one host species we found light-related patterns of zooxanthella distribution.

The search is on: finding accurate molecular markers of male fertility

Diagnosis of the fertility potential of a semen sample is essential for consistently high reproductive efficiency. The use of subfertile or infertile semen can have devastating consequences for those selling or using the semen. Therefore it is crucial to develop and use accurate diagnostic tests to determine the fertility of males and of individual semen samples. These diagnostic tests must be economically practical and provide consistent results. The goal of this review is to explore areas of fertility diagnostic research, including what we have termed functional and molecular tests, and consider the accuracy of each test. In this article, literature from several species is cited, and it is noteworthy that each diagnostic test may not be valuable in all species. Multiple functional and molecular tests will likely be needed to effectively characterize male fertility in each species.