Towards the diversification of lactococcal starter and non-starter species in mesophilic dairy culture systems

Lactococcus is one of the earliest identified fermentative bacterial genera and among its member species, the dairy-associated Lactococcus lactis and Lactococcus cremoris are undoubtedly the best studied. These two species are believed to have evolved from plant-associated lactococci and through genome decay and acquisition of plasmids, have adapted to the dairy niche. The past decade has witnessed a surge of activity in novel lactococcal species identification from insect, plant and animal sources. Currently, 22 Lactococcus species are described and in this review, we summarise the genome characteristics of and phylogenetic relationships among these species. Furthermore, we explore the role of mobile elements including plasmids and bacteriophages in the diversification of lactococcal species. The pace of identification of novel lactococcal species suggests that the number of lactococcal species is likely to continue to grow. With additional sequence data for the emerging species, it will be possible to perform pathogenicity/virulence risk evaluations and generate extensive insights into the niche adaptation strategies through which they have evolved.     

Specificity changes in the evolution of type II restriction endonucleases: a biochemical and bioinformatic analysis of restriction enzymes that recognize unrelated sequences

How restriction enzymes with their different specificities and mode of cleavage evolved has been a long standing question in evolutionary biology. We have recently shown that several Type II restriction endonucleases, namely SsoII (downward arrow CCNGG), PspGI (downward arrow CCWGG), Eco-RII (downward arrow CCWGG), NgoMIV (G downward arrow CCGGC), and Cfr10I (R downward arrow CCGGY), which recognize similar DNA sequences (as indicated, where the downward arrows denote cleavage position), share limited sequence similarity over an interrupted stretch of approximately 70 amino acid residues with MboI, a Type II restriction endonuclease from Moraxella bovis (Pingoud, V., Conzelmann, C., Kinzebach, S., Sudina, A., Metelev, V., Kubareva, E., Bujnicki, J. M., Lurz, R., Luder, G., Xu, S. Y., and Pingoud, A. (2003) J. Mol. Biol. 329, 913-929). Nevertheless, MboI has a dissimilar DNA specificity (downward arrow GATC) compared with these enzymes. In this study, we characterize MboI in detail to determine whether it utilizes a mechanism of DNA recognition similar to SsoII, PspGI, EcoRII, NgoMIV, and Cfr10I. Mutational analyses and photocross-linking experiments demonstrate that MboI exploits the stretch of approximately 70 amino acids for DNA recognition and cleavage. It is therefore likely that MboI shares a common evolutionary origin with SsoII, PspGI, EcoRII, NgoMIV, and Cfr10I. This is the first example of a relatively close evolutionary link between Type II restriction enzymes of widely different specificities.     

Restriction endonucleases R.EcoKI and R.EcoR124I are probably located in different environments within the bacterial cell

We describe the phenomenon of a transient state of R124I restriction deficiency after long-term storage of theE. coli[pCP1005] strain at 4°C, or after growth of the culture in synthetic M9 medium with the nonmutagenic solvent dimethyl sulfoxide. The unusual high reversion from the R⁺ ₁₂₄ to the R^? ₁₂₄ phenotype was observed only inE. coli strain transformed with the high-copy number plasmid pCP1005 carryingECoR124IhsdR, M and S genes cloned, but not with strains carrying the natural conjugative plasmid R124. The effect of both treatments on the expression ofEcoR124I phenotype in relation to the possible location of R.EcoR124I restriction endonuclease inE. coli is discussed.     

Restriction and modification in Bacillus subtilis: sequence specificities of restriction/modification systems BsuM, BsuE, and BsuF.

The sequence specificities of three Bacillus subtilis restriction/modification systems were established: (i) BsuM (CTCGAG), an isoschizomer to XhoI; (ii) BsuE (CGCG), an isoschizomer to FnuDII; and (iii) BsuF (CCGG), an isoschizomer to MspI, HpaII. The BsuM modification enzyme methylates the 3' cytosine of the recognition sequence. The BsuF modification enzyme methylates the 5' cytosine of the sequence, rendering such sites resistant to MspI degradation and leaving the majority of sites sensitive to HpaII degradation.     

Ecological interactions on macroevolutionary time scales: clams and brachiopods are more than ships that pass in the night

Competition among organisms has ecological and evolutionary consequences. However, whether the consequences of competition are manifested and measureable on macroevolutionary time scales is equivocal. Marine bivalves and brachiopods have overlapping niches such that competition for food and space may occur. Moreover, there is a long‐standing debate over whether bivalves outcompeted brachiopods evolutionarily, because brachiopod diversity declined through time while bivalve diversity increased. To answer this question, we estimate the origination and extinction dynamics of fossil marine bivalve and brachiopod genera from the Ordovician through to the Recent while simultaneously accounting for incomplete sampling. Then, using stochastic differential equations, we assess statistical relationships among diversification and sampling dynamics of brachiopods and bivalves and five paleoenvironmental proxies. None of these potential environmental drivers had any detectable influence on brachiopod or bivalve diversification. In contrast, elevated bivalve extinction rates causally increased brachiopod origination rates, suggesting that bivalves have suppressed brachiopod evolution.     

Sites including those of origin and termination of replication are not freely available to single-cut restriction endonucleases in the supercompact form of simian virus 40 minichromosome.

Simian virus 40 minichromosomes, isolated from both virions (MV) and infected cells (MI), have highly compact structures in buffer containing 0.15 M NaCl and sediment with S values of about 90–100 and 115–130, respectively. Under the electron microscope, also, MI appear the more compact of the two. Only 30–35% of the sites of origin and termination of replication in MV are freely available to the restriction endonucleases $\text{Bgl}$ 1 and $\text{Bam}$ H1. MV are similarly resistant to $\text{Eco}$ R1 and $\text{Hpa}$ II. In contrast, almost no sites in MI are available to any of the above single-cut endonucleases. In 0.6 M NaCl, MV and MI change to relaxed structures of 45–55 S and 50–60 S, respectively, containing 20–24 nucleosomes per genome, and become more sensitive to $\text{Bgl}$ 1, $\text{Bam}$ H1, $\text{Eco}$ R1, and $\text{Hpa}$ II.     

Energetic contributions of four arginines to phosphate-binding in thymidylate synthase are more than additive and depend on optimization of "effective charge balance"

In thymidylate synthase, four conserved arginines provide two hydrogen bonds each to the oxygens of the phosphate group of the substrate, 2'-deoxyuridine-5'-monophosphate. Of these, R23, R178, and R179 are far removed from the site of methyl transfer and contribute to catalysis solely through binding and orientation of ligands. These arginines can be substituted by other residues, while still retaining more than 1% activity of the wild-type enzyme. We compared the kinetics and determined the crystal structures of dUMP complexes of three of the most active, uncharged single mutants of these arginines, R23I, R178T, and R179T, and of double mutants (R23I, R179T) and (R178T, R179T). The dramatically higher K(m) for R178T compared to the other two single mutants arises from the effects of R178 substitution on the orientation of dUMP; 10-15-fold increases in for R23I and R178T reflect the role of these residues in stabilizing the closed conformation of TS in ternary complexes. The free energy for productive dUMP binding, DeltaG(S), increases by at least 1 kcal/mol for each mutant, even when dUMP orientation and mobility in the crystal structure is the same as in wild-type enzyme. Thus, the four arginines do not contribute excess positive charge to the PO(4)(-2) binding site; rather, they ideally complement the charge and geometry of the phosphate moiety. More-than-additive increases in DeltaG(S) seen in the double mutants are consistent with quadratic increases in DeltaG(S) predicted for deviations from ideal electrostatic interactions and may also reflect cooperative binding of the arginines to the phosphate oxygens.     

Amanita virosa peptides: viroidin and viroisin are more effective than phalloidin for the in vitro protection of actin against the effects of osmic acid

Virotoxins are a group of monocyclic peptides recently identified in the deadly mushroom Amanita virosa by Faulstich and coll. We found that two of these peptides, which have a methyl sulfonyl group, namely viroidin and viroisin are very effective to protect F-actin against oxidative degradation by osmium tetroxide in vitro. Their desoxo analogs, which have a methyl sulfoxyde group instead of methyl sulfonyl are less active, therefore there exists a relationship between the chemistry of the sulfur group and the activity of the peptides.     

Female canaries that respond and discriminate more between male songs of different quality have a larger song control nucleus (HVC) in the brain

In male songbirds the song control pathway in the forebrain is responsible for song production and learning. In most species, females do not sing and have smaller nuclei in the song control pathway. Although the function of the pathway in females is assumed to be associated with the perception of male song, there is little direct evidence to support this view. In this study on female canaries, we investigate the role of two key nuclei in the song control pathway (HVC and lMAN) in relation to playback of male song. Male canaries produce elaborate songs that function to attract and stimulate females. The songs are constructed from smaller units called syllables, and special syllables with a more complex structure (sexy syllables) are known to induce females to perform copulation solicitation displays (CSD) as an invitation to mate. By using computer-edited experimental songs, we first show that females discriminate between songs by producing significantly more CSD to those containing sexy syllables. We then sectioned the brains and used in situ hybridization to reveal song nuclei containing androgen receptors. We report positive correlations between the size of HVC and both total CSD response and the amount of discrimination between sexy and nonsexy songs. We found no such relationships between these measures and the size of lMAN. These results provide some evidence to support the view that, in female canaries HVC is involved in female perception and discrimination of male song. The results also have implications for the evolution of complex male songs by sexual selection and female choice.     

Longitudinal analysis of the vaginal microflora in pregnancy suggests that L. crispatus promotes the stability of the normal vaginal microflora and that L. gasseri and/or L. iners are more conducive to the occurrence of abnormal vaginal microflora

Background  

Despite their antimicrobial potential, vaginal lactobacilli often fail to retain dominance, resulting in overgrowth of the vagina by other bacteria, as observed with bacterial vaginosis. It remains elusive however to what extent interindividual differences in vaginal Lactobacillus community composition determine the stability of this microflora. In a prospective cohort of pregnant women we studied the stability of the normal vaginal microflora (assessed on Gram stain) as a function of the presence of the vaginal Lactobacillus index species (determined through culture and molecular analysis with tRFLP).     

TM1 and TM2: two mutant alleles that are involved in the pre-TCR/TCR signaling

It has been shown that the transgene insertional mutations TM1 and TM2 constitute a genetic trait controlling thymocyte development. Here we conducted a detailed analysis of the impact of TM1 and TM2 double mutation on thymocyte development. We found that the hemizygous TM1 and TM2 double transgenic mice possessed much smaller thymi. Flow cytometric analysis revealed a severe blockage of T-cell development at the transition from DN3 to DN4 stage and pre-T-cell receptor (pre-TCR)/TCR signaling appeared to be impaired. We could not identify any known gene that was implicated in a similar function in the chromosomal regions 7E-F1 and 11B5-C, where TM1 and TM2 mutations were mapped to respectively. Thus, TM1 and TM2 mutations represent two novel alleles that define a genetic trait controlling DN3 thymocyte development, possibly through modulating the signals downstream of the pre-TCR.     

Differential effect of the overexpression of Rad2/XPG family endonucleases on genome integrity in yeast and human cells

Eukaryotic cells possess several DNA endonucleases that are necessary to complete different steps in DNA metabolism. Rad2/XPG and Rad27/FEN1 belong to a group of evolutionary conserved proteins that constitute the Rad2 family. Given the important roles carried out by these nucleases in DNA repair and their capacity to create DNA breaks, we have investigated the effect that in vivo imbalance of these nucleases and others of the family have on genome integrity and cell proliferation. We show that overexpression of these nucleases causes genetic instability in both yeast and human cells. Interestingly, the type of recombination event and DNA damage induced suggest specific modes and timing of action of each nuclease that are beyond their known DNA repair function and are critical to preserve genome integrity. In addition to identifying new sources of genome instability, a hallmark of cancer cells, this study provides new genetic tools for studies of genome dynamics.     

Single session exercises and concurrent functional electrical stimulation are more effective on muscles’ force generation than only exercises in spinal cord injured persons: a feasibility study

Objectives:To evaluate impact of first therapy session, containing functional electrical stimulation (FES) and therapeutic exercises (TE) on erector spinae (ES) and rectus abdominis (RA) force generation in persons with spinal cord injury (SCI).Methods:Five men with SCI were divided in two groups - FES+TE received concurrent FES on ES and RA and TE, TE only TE. Participants performed exercises for improving sitting balance and posture. Muscles’ electrical activity was evaluated by electromyography; amplitude (AEMG) and median frequency (MF) were used for analysis.Results:AEMG of ES left (L) increased 292.9% (g=-0.92), right (R) 175% (g=-1.01), RA L 314.3% (g=-0,81, P<0.05), R 266.7% (g=-0.08) in FES+TE. AEMG of ES L increased 47.6% (g=-0.46), R 96.4% (g=-0.95); RA L 7.1% (g=-0.97), but R decreased 6.7% (g=0.12) in TE. MF of ES L increased 108.5% (g=-0.74), R 184% (g=-1.25); RA L 886.7% (g=3-05, P<0.05), R 817.6% (g=-2.55, P<0.05) in FES+TE. MF of ES L increased 95.2% (g=-1.02), R 161.4% (g=-1.64); RA L 3,2% (g=-0.06), R 30.8% (g=-0.46) in TE.Conclusions:In SCI persons, single session exercises and concurrent functional electrical stimulation may be more effective on muscles` force generation than only exercises. However, replication of the results is needed before clinical implementation.     

Climate and geographic distance are more influential than rivers on the beta diversity of passerine birds in Amazonia

Variation in the spatial structure of communities in terms of species composition (beta diversity) is affected by different ecological processes, such as environmental filtering and dispersal limitation. Large rivers are known as barriers for species dispersal (riverine hypothesis) in tropical regions. However, when organisms are not dispersal limited by geographic barriers, other factors, such as climatic conditions and geographic distance per se, may affect species distribution. In order to investigate the relative contribution of major rivers, climate and geographic distance on Passeriformes beta diversity, we divided Amazonia into 549 grid cells (1° of latitude and longitude) and obtained data of species occurrence, climate and geographic position for each cell. Beta diversity was measured using taxonomic, phylogenetic and functional metrics of composition. The influence of climatic variables, geographic distance and rivers on these metrics was tested using regression analyses. Passerine beta diversity is characterized mainly by the change in species taxonomic identity and in phylogenetic lineages across climatic gradients and over geographic distance. However, species with similar traits are found throughout the entire Amazonia. The size of rivers was proportional to their effect on species composition. However, climate and geographic distance are relatively more important than rivers for Amazonian taxonomic and phylogenetic species composition.