Quantifying bacterial evolution in the wild: A birthday problem for Campylobacter lineages

Measuring molecular evolution in bacteria typically requires estimation of the rate at which nucleotide changes accumulate in strains sampled at different times that share a common ancestor. This approach has been useful for dating ecological and evolutionary events that coincide with the emergence of important lineages, such as outbreak strains and obligate human pathogens. However, in multi-host (niche) transmission scenarios, where the pathogen is essentially an opportunistic environmental organism, sampling is often sporadic and rarely reflects the overall population, particularly when concentrated on clinical isolates. This means that approaches that assume recent common ancestry are not applicable. Here we present a new approach to estimate the molecular clock rate in Campylobacter that draws on the popular probability conundrum known as the ‘birthday problem’. Using large genomic datasets and comparative genomic approaches, we use isolate pairs that share recent common ancestry to estimate the rate of nucleotide change for the population. Identifying synonymous and non-synonymous nucleotide changes, both within and outside of recombined regions of the genome, we quantify clock-like diversification to estimate synonymous rates of nucleotide change for the common pathogenic bacteria Campylobacter coli (2.4 x 10⁻⁶ s/s/y) and Campylobacter jejuni (3.4 x 10⁻⁶ s/s/y). Finally, using estimated total rates of nucleotide change, we infer the number of effective lineages within the sample time frame–analogous to a shared birthday–and assess the rate of turnover of lineages in our sample set over short evolutionary timescales. This provides a generalizable approach to calibrating rates in populations of environmental bacteria and shows that multiple lineages are maintained, implying that large-scale clonal sweeps may take hundreds of years or more in these species.     

Age-associated differences in motor output variability and coordination during the simultaneous dorsiflexion of both feet

Older adults are more variable than young adults on tasks that demand the simultaneous control of more than one effector, and the difference between age groups may be related to their different capacity of coordinating the force output of the involved effectors. The goal of this study was to determine whether age-associated differences in motor output variability during tasks involving the simultaneous dorsiflexion of two feet can be partially explained by differences in coordination and possibly attenuated by physical training. Ten young and 22 old adults (10 trained and 12 untrained old adults) volunteered to participate in the study. Trained older adults had experience in a high-intensity mixed modality training (MMT) regime for a minimum of 1?year. Volunteers performed successive trials of a constant force task and a goal-directed task, with and without visual feedback. Within- and between-trial variability were calculated and coordination was quantified using the uncontrolled manifold (UCM) approach (i.e., co-variation of the force outputs of both feet were used to quantify a motor synergy index). Older adults exhibited greater variability and lower synergy (p?p?相似文献   

Fluctuations in acceleration during voluntary contractions lead to greater impairment of movement accuracy in old adults.

The purpose of the study was to assess the effect of movement velocity on the relation between fluctuations in acceleration and the ability to achieve a target velocity during voluntary contractions performed by young (29.5 +/- 4.3 yr) and old (74.9 +/- 6.2 yr) adults. Subjects performed concentric and eccentric contractions with the first dorsal interosseus muscle while lifting a submaximal load (15% of maximum) at six movement velocities (0.03-1.16 rad/s). Fluctuations in acceleration, the accuracy of matching the target velocity, and electromyographic (EMG) activity were determined from three trials for each contraction type and movement velocity. The fluctuations in acceleration increased with movement velocity for both concentric and eccentric contractions, but they were greatest during fast eccentric contractions ( approximately 135%) when there was stronger modulation of acceleration in the 5- to 10-Hz bandwidth. Nonetheless, EMG amplitude for first dorsal interosseus increased with movement velocity only for concentric and not eccentric contractions. Consistent with the minimum variance theory, movement accuracy was related to the fluctuations in acceleration for both types of contractions in all subjects. For a given level of fluctuations in acceleration, however, old subjects were three times less accurate than young subjects. Although the EMG amplitude at each speed was similar for young and old adults, only the young adults modulated the power in the EMG spectrum with speed. Thus the fluctuations in acceleration during voluntary contractions had a more pronounced effect on movement accuracy for old adults compared with young adults, probably due to factors that influenced the frequency-domain characteristics of the EMG.     

Embryoid bodies from mouse stem cells express oxytocin receptor, Oct-4 and DAZL

Oxytocin is a nine amino acid peptide involved in a wide spectrum of physiological functions; predominantly those concerning reproduction and differentiation are of interest. Oxytocin receptors are expressed at early developmental stages of mammals, suggesting that oxytocin might be involved in the determination of the germ stem cell line, at the very early stages of mammalian development. In this respect, the proximate aim of the present study was to confirm and further analyze the existence of oxytocin receptors at a very early level of cell commitment, that is, the determination of germ cells derived from embryoid bodies. To achieve our purpose we have cultured mouse embryonic stem cells under conditions inducing formation of embryoid bodies. In this work, ES cells were allowed to aggregate in a novel medium, “Stefanidis medium” from day 0 to day 14 until formed EBs. RNA was isolated from EBs and using RT-PCR we showed that EBs expressed Oct-4, OTR, OT, and DAZL. To demonstrate simultaneous expression immunocytochemistry was preformed, in which EBs showed strong immunoreactivity for both, OTR and DAZL molecular markers. We found that 35% of the cells displayed OTR, using flow cytometry. In addition, this novel medium showed to increase OTR mRNA. We propose, that at least in murine induced embryoid bodies there is simultaneous expression of oxytocin receptors and germ cell markers (DAZL) in many cells (expressing Oct-4). We thus conclude that, the oxytocin might indeed be a molecule playing a leading role in germ cell determination.     

Regulation of the xylan-degrading apparatus of Cellvibrio japonicus by a novel two-component system

The microbial degradation of lignocellulose biomass is not only an important biological process but is of increasing industrial significance in the bioenergy sector. The mechanism by which the plant cell wall, an insoluble composite structure, activates the extensive repertoire of microbial hydrolytic enzymes required to catalyze its degradation is poorly understood. Here we have used a transposon mutagenesis strategy to identify a genetic locus, consisting of two genes that modulate the expression of xylan side chain-degrading enzymes in the saprophytic bacterium Cellvibrio japonicus. Significantly, the locus encodes a two-component signaling system, designated AbfS (sensor histidine kinase) and AbfR (response regulator). The AbfR/S two-component system is required to activate the expression of the suite of enzymes that remove the numerous side chains from xylan, but not the xylanases that hydrolyze the beta1,4-linked xylose polymeric backbone of this polysaccharide. Studies on the recombinant sensor domain of AbfS (AbfS(SD)) showed that it bound to decorated xylans and arabinoxylo-oligosaccharides, but not to undecorated xylo-oligosaccharides or other plant structural polysaccharides/oligosaccharides. The crystal structure of AbfS(SD) was determined to a resolution of 2.6A(.) The overall fold of AbfS(SD) is that of a classical Per Arndt Sim domain with a central antiparallel four-stranded beta-sheet flanked by alpha-helices. Our data expand the number of molecules known to bind to the sensor domain of two-component histidine kinases to include complex carbohydrates. The biological rationale for a regulatory system that induces enzymes that remove the side chains of xylan, but not the hydrolases that cleave the backbone of the polysaccharide, is discussed.     

Molecular confirmation of Planktothrix rubescens as the cause of intense,microcystin—Synthesizing cyanobacterial bloom in Lake Ziros,Greece

Cyanobacterial blooms occur increasingly often and raise ecological concerns worldwide. In Mediterranean freshwater ecosystems algal blooms are commonly attributed to Microcystis, Anabaena, and Aphanizomenon genera while Planktothrix is the most common bloom forming cyanobacterium in deep Northern and prealpine European oligotrophic to mesotrophic lakes. In the framework of an undertaken study of cyanobacterial species in lakes of Northwestern Greece we investigated the cyanobacterial diversity in Lake Ziros throughout a 15-month period (January 2006–March 2007) by using molecular methods. Surprisingly, a severe cyanobacterial bloom occurred during the study period, which upon microscopic examination and detailed molecular characterization found to be caused by Planktothrix rubescens species. The appearance of P. rubescens from November 2006 coincided with poor cyanobacterial diversity and resulted in a thick epilimnetic bloom in March 2007 (3.1 × 10⁸ cells/l and microcystin concentration 199 μg/l). Genotype composition of the total cyanobacterial community of the lake was analyzed by using denaturing gradient gel electrophoresis (DGGE) profiling of the intergenic transcribed spacer region of the rnn operon (rRNA-ITS). A P. rubescens strain closely related to Kpr strain from Lake Klinckenberg, The Netherlands, was found to dominate. The importance of this observation is expanded by the fact that microcystin concentrations recorded in Lake Ziros were the highest measured ever in Greek aquatic ecosystems examined so far and also found amongst the highest recorded worldwide.