Characterizing the flagellar filament and the role of motility in bacterial prey-penetration by Bdellovibrio bacteriovorus

The predatory bacterium Bdellovibrio bacteriovorus swims rapidly by rotation of a single, polar flagellum comprised of a helical filament of flagellin monomers, contained within a membrane sheath and powered by a basal motor complex. Bdellovibrio collides with, enters and replicates within bacterial prey, a process previously suggested to firstly require flagellar motility and then flagellar shedding upon prey entry. Here we show that flagella are not always shed upon prey entry and we study the six fliC flagellin genes of B. bacteriovorus, finding them all conserved and expressed in genome strain HD100 and the widely studied lab strain 109J. Individual inactivation of five of the fliC genes gave mutant Bdellovibrio that still made flagella, and which were motile and predatory. Inactivation of the sixth fliC gene abolished normal flagellar synthesis and motility, but a disordered flagellar sheath was still seen. We find that this non-motile mutant was still able to predate when directly applied to lawns of YFP-labelled prey bacteria, showing that flagellar motility is not essential for prey entry but important for efficient encounters with prey in liquid environments.     

Animal cognition: how archer fish learn to down rapidly moving targets

In extremely rapid maneuvers, animals including man can launch ballistic motor patterns that cannot immediately be corrected. Such patterns are difficult to direct at targets that move in three-dimensional space, and it is presently unknown how animals learn to acquire the precision required. Archer fish live in groups and are renowned for their ballistic hunting technique in which they knock down stationary aerial insect prey with a precisely aimed shot of water. Here we report that these fish can learn to release their shots so as to hit prey that moves rapidly at great height, a remarkable accomplishment in which the shooter must take both the target's three-dimensional motion as well as that of its rising shot into account. To successfully perform in the three-dimensional task, training with horizontal motion suffices. Moreover, all archer fish of a group were able to learn the complex sensomotor skill from watching a performing group member, without having to practice. This instance of social learning in a fish is most remarkable as it could imply that observers can "change their viewpoint," mapping the perceived shooting characteristics of a distant team member into angles and target distances that they later must use to hit.     

A new species of Oileus Kaup (Coleoptera, Passalidae) from Guatemala, with a key to the species of the genus

Oileus gasparilomisp. n. is described from nine specimens from the mountains of Quiché in Guatemala, from cloud forest at 1795 m elevation. This represents the second species of the genus for Guatemala, differing from the closely related Mexican species Oileus rimator (Truqui) in having a straight anterior clypeal border, the postocular sulcus divided by a keel and the pronotum almost straight (not clearly bilobed). A key to the species of Oileus is given.     

Diastolic dysfunction and intraventricular dyssynchrony are restored by low intensity exercise training in obese men

The aim of this study was to evaluate the impact of a low-intensity training program on subclinical cardiac dysfunction and on dyssynchrony in moderately obese middle aged men. Ten obese and 14 age-matched normal-weight men (BMI: 33.6 ± 1.0 and 24.2 ± 0.5 kg/m(2)) were included. Obese men participated in an 8-week low-intensity training program without concomitant diet. Cardiac function and myocardial synchrony were assessed by echocardiography with tissue Doppler imaging (TDI) and speckle tracking echocardiography (STE). At baseline, obese men showed diastolic dysfunction on standard echocardiography, lower strain values (systolic strain: 15.9 ± 0.9 vs. 18.8 ± 0.3%, diastolic strain rate: 0.81 ± 0.09 vs. 1.05 ± 0.06 s(-1)), and significant intraventricular dyssynchrony (systolic: 13.3 ± 2.1 vs. 5.4 ± 2.1 ms, diastolic: 17.4 ± 3.2 vs. 9.1 ± 2.1 ms) (P < 0.05 vs. controls for all variables). Training improved aerobic fitness, decreased systolic blood pressure and heart rate, and reduced fat mass without weight loss. Diastolic function, strain values (systolic strain: 17.4 ± 0.9%, diastolic strain rate: 0.96 ± 0.12 s(-1)) and intraventricular dyssynchrony (systolic: 3.3 ± 1.7 ms, diastolic: 5.5 ± 3.4 ms) improved significantly after training (P < 0.05 vs. baseline values for all variables), reaching levels similar to those of normal-weight men. In conclusion, in obese men, a short and easy-to-perform low intensity training program restored diastolic function and cardiac synchrony and improved body composition without weight loss.     

Motor-driven motility of fungal nuclear pores organizes chromosomes and fosters nucleocytoplasmic transport

Exchange between the nucleus and the cytoplasm is controlled by nuclear pore complexes (NPCs). In animals, NPCs are anchored by the nuclear lamina, which ensures their even distribution and proper organization of chromosomes. Fungi do not possess a lamina and how they arrange their chromosomes and NPCs is unknown. Here, we show that motor-driven motility of NPCs organizes the fungal nucleus. In Ustilago maydis, Aspergillus nidulans, and Saccharomyces cerevisiae fluorescently labeled NPCs showed ATP-dependent movements at ～1.0 μm/s. In S. cerevisiae and U. maydis, NPC motility prevented NPCs from clustering. In budding yeast, NPC motility required F-actin, whereas in U. maydis, microtubules, kinesin-1, and dynein drove pore movements. In the latter, pore clustering resulted in chromatin organization defects and led to a significant reduction in both import and export of GFP reporter proteins. This suggests that fungi constantly rearrange their NPCs and corresponding chromosomes to ensure efficient nuclear transport and thereby overcome the need for a structural lamina.     

Bacterial degradation of tert-amyl alcohol proceeds via hemiterpene 2-methyl-3-buten-2-ol by employing the tertiary alcohol desaturase function of the Rieske nonheme mononuclear iron oxygenase MdpJ

Tertiary alcohols, such as tert-butyl alcohol (TBA) and tert-amyl alcohol (TAA) and higher homologues, are only slowly degraded microbially. The conversion of TBA seems to proceed via hydroxylation to 2-methylpropan-1,2-diol, which is further oxidized to 2-hydroxyisobutyric acid. By analogy, a branched pathway is expected for the degradation of TAA, as this molecule possesses several potential hydroxylation sites. In Aquincola tertiaricarbonis L108 and Methylibium petroleiphilum PM1, a likely candidate catalyst for hydroxylations is the putative tertiary alcohol monooxygenase MdpJ. However, by comparing metabolite accumulations in wild-type strains of L108 and PM1 and in two mdpJ knockout mutants of strain L108, we could clearly show that MdpJ is not hydroxylating TAA to diols but functions as a desaturase, resulting in the formation of the hemiterpene 2-methyl-3-buten-2-ol. The latter is further processed via the hemiterpenes prenol, prenal, and 3-methylcrotonic acid. Likewise, 3-methyl-3-pentanol is degraded via 3-methyl-1-penten-3-ol. Wild-type strain L108 and mdpJ knockout mutants formed isoamylene and isoprene from TAA and 2-methyl-3-buten-2-ol, respectively. It is likely that this dehydratase activity is catalyzed by a not-yet-characterized enzyme postulated for the isomerization of 2-methyl-3-buten-2-ol and prenol. The vitamin requirements of strain L108 growing on TAA and the occurrence of 3-methylcrotonic acid as a metabolite indicate that TAA and hemiterpene degradation are linked with the catabolic route of the amino acid leucine, including an involvement of the biotin-dependent 3-methylcrotonyl coenzyme A (3-methylcrotonyl-CoA) carboxylase LiuBD. Evolutionary aspects of favored desaturase versus hydroxylation pathways for TAA conversion and the possible role of MdpJ in the degradation of higher tertiary alcohols are discussed.     

Can sugars be produced from fatty acids? A test case for pathway analysis tools

Motivation: In recent years, several methods have been proposedfor determining metabolic pathways in an automated way basedon network topology. The aim of this work is to analyse thesemethods by tackling a concrete example relevant in biochemistry.It concerns the question whether even-chain fatty acids, beingthe most important constituents of lipids, can be convertedinto sugars at steady state. It was proved five decades agothat this conversion using the Krebs cycle is impossible unlessthe enzymes of the glyoxylate shunt (or alternative bypasses)are present in the system. Using this example, we can comparethe various methods in pathway analysis. Results: Elementary modes analysis (EMA) of a set of enzymescorresponding to the Krebs cycle, glycolysis and gluconeogenesissupports the scientific evidence showing that there is no pathwaycapable of converting acetyl-CoA to glucose at steady state.This conversion is possible after the addition of isocitratelyase and malate synthase (forming the glyoxylate shunt) tothe system. Dealing with the same example, we compare EMA withtwo tools based on graph theory available online, PathFindingand Pathway Hunter Tool. These automated network generatingtools do not succeed in predicting the conversions known fromexperiment. They sometimes generate unbalanced paths and revealproblems identifying side metabolites that are not responsiblefor the carbon net flux. This shows that, for metabolic pathwayanalysis, it is important to consider the topology (includingbimolecular reactions) and stoichiometry of metabolic systems,as is done in EMA. Contact: ldpf{at}minet.uni-jena.de; schuster{at}minet.uni-jena.de Supplementary information: Supplementary data are availableat Bioinformatics online. FOOTNOTES Associate Editor: Alfonso Valencia Received on July 24, 2008; revised on September 18, 2008; accepted on September 18, 2008     

Comparison of the Complete Genome Sequences of Bifidobacterium animalis subsp. lactis DSM 10140 and Bl-04

Bifidobacteria are important members of the human gut flora, especially in infants. Comparative genomic analysis of two Bifidobacterium animalis subsp. lactis strains revealed evolution by internal deletion of consecutive spacer-repeat units within a novel clustered regularly interspaced short palindromic repeat locus, which represented the largest differential content between the two genomes. Additionally, 47 single nucleotide polymorphisms were identified, consisting primarily of nonsynonymous mutations, indicating positive selection and/or recent divergence. A particular nonsynonymous mutation in a putative glucose transporter was linked to a negative phenotypic effect on the ability of the variant to catabolize glucose, consistent with a modification in the predicted protein transmembrane topology. Comparative genome sequence analysis of three Bifidobacterium species provided a core genome set of 1,117 orthologs complemented by a pan-genome of 2,445 genes. The genome sequences of the intestinal bacterium B. animalis subsp. lactis provide insights into rapid genome evolution and the genetic basis for adaptation to the human gut environment, notably with regard to catabolism of dietary carbohydrates, resistance to bile and acid, and interaction with the intestinal epithelium. The high degree of genome conservation observed between the two strains in terms of size, organization, and sequence is indicative of a genomically monomorphic subspecies and explains the inability to differentiate the strains by standard techniques such as pulsed-field gel electrophoresis.Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes are dominant microbial phyla widely distributed in diverse ecosystems on the planet (10, 13, 20, 23, 33, 40, 51). Metagenomic analyses of the microbial landscape inhabiting various mammalian environments, notably the human gastrointestinal tract (GIT) and skin, have specifically identified Actinobacteria as an important and occasionally dominant phylum (18, 21, 33). Among the members of the large, diverse, and dynamic microbial community residing in the human GIT, Bifidobacterium is a dominant genus considered beneficial to humans and includes probiotic strains (live microorganisms which, when administered in adequate amounts, confer a health benefit on the host) (11). The population of bifidobacteria in the human intestine varies over time. Following vaginal delivery, the GIT of healthy newborns is typically colonized by bifidobacteria, especially in breast-fed infants, during the first few days of life (12). Interindividual variation, however, is remarkable in the human infant intestinal flora (41), and dominant genera are not always consistent across metagenomic analyses of the human gut flora (18, 30, 33, 41). Over time, the infant intestinal ecosystem becomes more complex as the diet becomes more diverse, with bifidobacteria typically remaining dominant until weaning (30).Bifidobacterium animalis subsp. lactis is a gram-positive lactic acid bacterium commonly found in the guts of healthy humans and has been identified in the infant gut biota, particularly in ileal, fecal, and mucosal samples (52, 56). Some strains of B. animalis subsp. lactis are able to survive in the GIT, to adhere to human epithelial cells in vitro, to modify fecal flora, to modulate the host immune response, or to prevent microbial gastroenteritis and colitis (4, 15, 20, 40, 52, 56). Additionally, B. animalis subsp. lactis has been reported to utilize nondigestible oligosaccharides, which may contribute to the organism''s ability to compete in the human gut. Carbohydrates resistant to enzymatic degradation and not absorbed in the upper intestinal tract are a primary source of energy for microbes residing in the large intestine. The benefits associated with probiotic strains of B. animalis subsp. lactis have resulted in their inclusion in the human diet via formulation into a large array of dietary supplements and foods, including dairy products such as yogurt. Deciphering the complete genome sequences of such microbes will provide additional insight into the genetic basis for survival and residence in the human gut, notably with regard to the ability to survive gastric passage and utilize available nutrients. Also, these genomes provide reference sequences for ongoing metagenomic analyses of the human environment, including the gut metagenome.Bifidobacterium animalis subsp. lactis is the most common bifidobacterium utilized as a probiotic in commercial dairy products in North America and Europe (22, 38). However, despite this commercial and probiotic significance, strain-level differentiation of B. animalis subsp. lactis strains has been hindered by the high genetic similarity of these organisms, as determined by pulsed-field gel electrophoresis and other nucleic acid-based techniques (6, 55, 56), and the lack of available genomic sequence information. The genome sequence of strain BB-12 (17) is not currently publicly available, and only a draft genome sequence in 28 contigs is available for strain HN019 (GenBank project 28807). The complete B. animalis subsp. lactis genome for strain AD011 (28) was only recently (2009) published. While this was an important first step, a single genome does not allow identification of unique targets for strain differentiation or comparative analyses within the subspecies.The objectives of this study were to determine the complete genome sequences of two B. animalis subsp. lactis strains, the type strain and a widely used commercial strain, to provide insights into the functionality of this species and into species identification and strain specialization.     

Common polymorphisms and cardiovascular factors in patients with myocardial infarction of Costa Rica

Eight common polymorphisms of known myocardial infarction (MI) risk factors (factor V Leiden (FVL), factor V HR2 (FVHR2), factor II 20210G > A (FII), factor VII IVS7 (FVII IVS7), factor VII Arg353Gln (FVII), factor XIII Va134Leu (FXIII), Methylenetetrahydrofolate reductase C677T (MTHFR), Angiotensin Converting Enzyme (ACE)) and environmental risk factors were analyzed in a MI patients of Costa Rica. This case-control study included 186 MI subjects, 95 of them < or = 45 years and 201 age and sex matched controls. With the use of PCR method the polymorphisms were detected and through interviews additional information was collected. Hypercholesterolemia and smoking were associated with a significant risk in younger patients. High fibrinogen level was an important risk factor and interaction with smoking was detected. Mainly, the genotype 34LeuLeu of FXIII showed significant protective effect, (OR 0.32, 95% CI 0.13-0.80) while the other polymorphisms showed no significant difference between the cases and the controls. Carriers of FVII (OR 2.75, 95% CI 1.07-7.02) and FXIII (OR 4.20, 95% CI 2.03-8.67) polymorphisms showed interaction with fibrinogen in the statistical analysis. It was concluded that there was an important interaction between the common risk factors and the polymorphisms (FVII; FXIII) in the development of MI. This is one of the first reports in a Latin-American population dealing with these molecular markers and MI.     

U1-like snRNAs lacking complementarity to canonical 5' splice sites

We have detected a surprising heterogeneity among human spliceosomal U1 small nuclear RNA (snRNA). Most interestingly, we have identified three U1 snRNA variants that lack complementarity to the canonical 5' splice site (5'SS) GU dinucleotide. Furthermore, we have observed heterogeneity among the identified variant U1 snRNA genes caused by single nucleotide polymorphism (SNP). The identified snRNAs were ubiquitously expressed in a variety of human tissues representing different stages of development and displayed features of functional spliceosomal snRNAs, i.e., trimethylated cap structures, association with Sm proteins and presence in nuclear RNA-protein complexes. The unanticipated heterogeneity among spliceosomal snRNAs could contribute to the complexity of vertebrates by expanding the coding capacity of their genomes.