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.     

Calnexin co-expression and the use of weaker promoters increase the expression of correctly assembled Shaker potassium channel in insect cells

Voltage-gated potassium channels control the membrane potential of excitable cells. To understand their function, knowledge of their structure is essential. However, these channels are scarce in natural sources, and overexpression is necessary to generate material for structural studies. We have compared functional expression of the Drosophila Shaker H4 potassium channel in stable insect cell lines and in baculovirus-infected insect cells, using three different baculovirus promoters. Stable insect cell lines expressed correctly assembled channel, which was glycosylated and found predominantly at, or close to, the cell surface. In comparison, the majority of baculovirus-overexpressed Shaker was intracellular and incorrectly assembled. The proportion of functional Shaker increased, however, if the weaker basic protein promoter was used rather than the stronger p10 or polyhedrin promoters. In addition, co-expression of the molecular chaperone, calnexin, increased the quantity of correctly assembled channel protein, suggesting that calnexin can be used to increase the efficiency of channel expression in insect cells.     

Bradyrhizobia from Wild Phaseolus, Desmodium, and Macroptilium Species in Northern Mexico

rRNA genetic markers were analyzed in 97 isolates of nodule bacteria from six legume species in Chihuahua, Mexico. The most common genotypes were widely shared across host species and had 16S rRNA sequences identical to those of strains from an eastern North American legume (Amphicarpaea) that are closely related to Bradyrhizobium elkanii.     

CaGE: cardiac gene expression knowledgebase

CaGE is a Cardiac Gene Expression knowledgebase we have developed to facilitate the analysis of genes important to human cardiac function. CaGE integrates the functionality of the LocusLink database with data from several human cardiac expression libraries, phenotypic data from OMIM and data from large-scale microarray gene expression studies to create a knowledgebase of gene expression in human cardiac tissue. The knowledgebase is fully searchable via the web using several intuitive query interfaces. Results can be displayed in several concise easy to navigate formats. AVAILABILITY: CaGE is located at http://www.cage.wbmei.jhu.edu     

Hydroxyurea Use and Hospitalization Trends in a Comprehensive Pediatric Sickle Cell Program

Background

A decline in hospitalizations and pain episodes among those with sickle cell disease (SCD) who take hydroxyurea (HU) has been shown when compared to pre-HU patterns but paradoxically, when compared to those who have never been treated, HU recipients often have more frequent hospitalizations. This analysis evaluates the impact of increasing usage of HU on trends in hospitalizations and blood transfusions within a large SCD treatment program.

Methods

Eligibility was restricted to patients with Hb SS or Hb Sβ⁰-thalassemia who were 2–18 years old between 2006–2010 and received care at St. Jude Children''s Research Hospital (N = 508). Hospitalizations and blood transfusions were calculated for each of the years under study for those exposed and never exposed to HU. Differences in number of hospitalizations before and after HU initiation were compared.

Results

The proportion of patients receiving HU increased by 4% per year on average. In the HU exposed group, a modest decline in mean per-patient hospitalizations and per-patient hospital days occurred, while those never exposed to HU trended toward a slight increase over time. Rates of blood transfusions declined among those on HU but not in patients never exposed to HU. Patients on HU had a median of one fewer hospital admission in the year after initiation of HU, compared to the year prior. Two deaths occurred in the patient population, both of whom were not exposed to HU.

Conclusions

Increasing usage of HU was concurrent with decreased hospitalization rates and blood transfusions. Our results support the utility of HU on decreasing hospitalizations and transfusions for patients with SCD outside of the clinical trial setting.     

Optoporation and Genetic Manipulation of Cells Using Femtosecond Laser?Pulses

Femtosecond laser optoporation is a powerful technique to introduce membrane-impermeable molecules, such as DNA plasmids, into targeted cells in culture, yet only a narrow range of laser regimes have been explored. In addition, the dynamics of the laser-produced membrane pores and the effect of pore behavior on cell viability and transfection efficiency remain poorly elucidated. We studied optoporation in cultured cells using tightly focused femtosecond laser pulses in two irradiation regimes: millions of low-energy pulses and two higher-energy pulses. We quantified the pore radius and resealing time as a function of incident laser energy and determined cell viability and transfection efficiency for both irradiation regimes. These data showed that pore size was the governing factor in cell viability, independently of the laser irradiation regime. For viable cells, larger pores resealed more quickly than smaller pores, ruling out a passive resealing mechanism. Based on the pore size and resealing time, we predict that few DNA plasmids enter the cell via diffusion, suggesting an alternative mechanism for cell transfection. Indeed, we observed fluorescently labeled DNA plasmid adhering to the irradiated patch of the cell membrane, suggesting that plasmids may enter the cell by adhering to the membrane and then being translocated.     

Intraspecific competition and aggression for shells in the hermit crab Pagurus samuel1s

Many studies have investigated shell‐related behaviour in hermit crabs. Few studies, however, have focused specifically on the intraspecies aggression associated with shell competition. We examined intraspecies aggression in hermit crab (Pagurus samuelis) pairs as it relates to competition for a limiting resource, gastropod shells. Pairs of hermit crabs were observed in the laboratory in four different treatments that varied the presence or absence of shells for one or both of the crabs. Measurements of the latency to respond, the number of bouts, and the fight durations were recorded. There was a significant difference among treatments for all three measurements, and naked hermit crabs were much more aggressive than housed hermit crabs. There was no significant difference in aggression between males and females in any of the three treatments. The heightened aggression observed in naked P. samuelis is likely in service of acquiring a protective shell.     

Differential Resilience of Soil Microbes and Ecosystem Functions Following Cessation of Long-Term Fertilization

Ecosystems - Nitrogen (N) from anthropogenic sources has dramatically increased in terrestrial ecosystems globally. Although belowground microbial processes and events that release N into the...