Construction and performance of heterologous polyketide‐producing K‐12‐ and B‐derived Escherichia coli

Aims: Escherichia coli has emerged as a viable heterologous host for the production of complex, polyketide natural compounds. In this study, polyketide biosynthesis was compared between different E. coli strains for the purpose of better understanding and improving heterologous production. Methods and Results: Both B and K‐12 E. coli strains were genetically modified to support heterologous polyketide biosynthesis [specifically, 6‐deoxyerythronolide B (6dEB)]. Polyketide production was analysed using a helper plasmid designed to overcome rare codon usage within E. coli. Each strain was analysed for recombinant protein production, precursor consumption, by‐product production, and 6dEB biosynthesis. Of the strains tested for biosynthesis, 6dEB production was greatest for E. coli B strains. When comparing biosynthetic improvements as a function of mRNA stability vs codon bias, increased 6dEB titres were observed when additional rare codon tRNA molecules were provided. Conclusions: Escherichia coli B strains and the use of tRNA supplementation led to improved 6dEB polyketide titres. Significance and Impact of the Study: Given the medicinal potential and growing field of polyketide heterologous biosynthesis, the current study provides insight into host‐specific genetic backgrounds and gene expression parameters aiding polyketide production through E. coli.     

Association of pneumococcal carriage in infants with the risk of carriage among their contacts in Nha Trang,Vietnam: A nested cross-sectional survey

BackgroundInfants are at highest risk of pneumococcal disease. Their added protection through herd effects is a key part in the considerations on optimal pneumococcal vaccination strategies. Yet, little is currently known about the main transmission pathways to this vulnerable age group. Hence, this study investigates pneumococcal transmission routes to infants in the coastal city of Nha Trang, Vietnam.Methods and findingsIn October 2018, we conducted a nested cross-sectional contact and pneumococcal carriage survey in randomly selected 4- to 11-month-old infants across all 27 communes of Nha Trang. Bayesian logistic regression models were used to estimate age specific carriage prevalence in the population, a proxy for the probability that a contact of a given age could lead to pneumococcal exposure for the infant. We used another Bayesian logistic regression model to estimate the correlation between infant carriage and the probability that at least one of their reported contacts carried pneumococci, controlling for age and locality. In total, 1,583 infants between 4 and 13 months old participated, with 7,428 contacts reported. Few infants (5%, or 86 infants) attended day care, and carriage prevalence was 22% (353 infants). Most infants (61%, or 966 infants) had less than a 25% probability to have had close contact with a pneumococcal carrier on the surveyed day. Pneumococcal infection risk and contact behaviour were highly correlated: If adjusted for age and locality, the odds of an infant’s carriage increased by 22% (95% confidence interval (CI): 15 to 29) per 10 percentage points increase in the probability to have had close contact with at least 1 pneumococcal carrier. Moreover, 2- to 6-year-old children contributed 51% (95% CI: 39 to 63) to the total direct pneumococcal exposure risks to infants in this setting. The main limitation of this study is that exposure risk was assessed indirectly by the age-dependent propensity for carriage of a contact and not by assessing carriage of such contacts directly.ConclusionsIn this study, we observed that cross-sectional contact and infection studies could help identify pneumococcal transmission routes and that preschool-age children may be the largest reservoir for pneumococcal transmission to infants in Nha Trang, Vietnam.     

Characterization of sarcoplasmic reticulum Ca2+ ATPase nucleotide binding domain mutants using NMR spectroscopy

T-type Ca²⁺ channels have been implicated in tremorogenesis and motor coordination. The α1 subunit of the Ca_V3.1 T-type Ca²⁺ channel is highly expressed in motor pathways in the brain, but knockout of the Ca_V3.1 gene (α1G^-/-) per se causes no motor defects in mice. Thus, the role of Ca_V3.1 channels in motor control remains obscure in vivo. Here, we investigated the effect of the Ca_V3.1 knockout in the null genetic background of α1 GABA_A receptor (α1^−/−) by generating the double mutants (α1^−/−/α1G^-/-). α1^−/−/α1G^-/- mice showed severer motor abnormalities than α1^−/− mice as measured by potentiated tremor activities at 20 Hz and impaired motor learning. Propranolol, an anti-ET drug that is known to reduce the pathologic tremor in α1^−/− mice, was not effective for suppressing the potentiated tremor in α1^−/−/α1G^-/- mice. In addition, α1^−/−/α1G^-/- mice showed an age-dependent loss of cerebellar Purkinje neurons. These results suggest that α1^−/−/α1G^-/- mice are a novel mouse model for a distinct subtype of ET in human and that Ca_V3.1 T-type Ca²⁺ channels play a role in motor coordination under pathological conditions.     

ASSESSMENT OF EVOLUTIONARY AFFINITIES IN GOSSYPIUM BY PROTEIN ELECTROPHORESIS

Protein band patterns from 25 species of Gossypium were obtained by electrophoresis of crude seed extracts on polyacrylamide gel. Band homologies between species were verified by electrophoresis of a mixture of their extracts. The patterns were found to be largely consistent with the conventional classification of the diploids into 6 genomic groups, A–F. However, G. triphyllum and G. bickii showed unique patterns differing respectively from those of the B and C groups, and G. australe showed closer affinity with the Arabian E- than with the Australian C-genome species. Affinities among the D-genome species were different from those implied by their former grouping into taxonomic sections but remarkably similar to those indicated in the most recent taxonomic revision of the genus. They were classifiable into two subgroups, β and ɛ. The clustering pattern of the diploids based on correlation coefficients calculated from densitometer curves of the electrophoretic spectra suggested that the genomic groups were derived from an African progenitor type, and that the American β and ɛ subgroups, most closely related to the African B- and the Arabian E-genome groups respectively, evolved under comparative mutual isolation, possibly separated by the Tertiary Amazonas basin.     

Chemical exchange effects during refocusing pulses in constant-time CPMG relaxation dispersion experiments

In the analysis of the constant-time Carr-Purcell-Meiboom-Gill (CT-CPMG) relaxation dispersion experiment, chemical exchange parameters, such as rate of exchange and population of the exchanging species, are typically optimized using equations that predict experimental relaxation rates recorded as a function of effective field strength. In this process, the effect of chemical exchange during the CPMG pulses is typically assumed to be the same as during the free-precession. This approximation may introduce systematic errors into the analysis of data because the number of CPMG pulses is incremented during the constant-time relaxation period, and the total pulse duration therefore varies as a function of the effective field strength. In order to estimate the size of such errors, we simulate the time-dependence of magnetization during the entire constant time period, explicitly taking into account the effect of the CPMG pulses on the spin relaxation rate. We show that in general the difference in the relaxation dispersion profile calculated using a practical pulse width from that calculated using an extremely short pulse width is small, but under certain circumstances can exceed 1 s^?1. The difference increases significantly when CPMG pulses are miscalibrated.     

Spatial and temporal deforestation dynamics in protected and unprotected dry forests: a case study from Myanmar (Burma)

Tropical dry forests are more threatened, less protected and especially susceptible to deforestation. However, most deforestation research focuses on tropical rain forests. We analyzed spatial and temporal changes in land cover from 1972 through 2005 at Chatthin Wildlife Sanctuary (CWS), a tropical dry forest in Myanmar (Burma). CWS is one of the largest protected patches of tropical dry forest in Southeast Asia and supports over half the remaining wild population of the endangered Eld’s deer. Between 1973 and 2005, 62% of forest was lost at an annual rate of 1.86% in the area, while forest loss inside CWS was only 16% (0.45% annually). Based on trends found during our study period, dry forests outside CWS would not persist beyond 2019, while forests inside CWS would persist for at least another 100 years. Analysis of temporal deforestation patterns indicates the highest rate of loss occurred between 1992 and 2001. Conversion to agriculture, shifting agriculture, and flooding from a hydro-electric development were the main deforestation drivers. Fragmentation was also severe, halving the area of suitable Eld’s deer habitat between 1973 and 2001, and increasing its isolation. CWS protection efforts were effective in reducing deforestation rates, although deforestation effects extended up to 2 km into the sanctuary. Establishing new protected areas for dry forests and finding ways to mitigate human impacts on existing forests are both needed to protect remaining dry forests and the species they support.     

Estimating abundance with sparse data: tigers in northern Myanmar

As part of a national strategy for recovering tiger populations, the Myanmar Government recently proposed its first and the world’s largest tiger reserve in the Hukaung Valley, Kachin State. During November 2002–June 2004, camera-traps were used to record tigers, identify individuals, and, using capture–recapture approaches, estimate density in the reserve. Despite extensive (203 trap locations, 275–558 km² sample plots) and intensive (>4,500 trap nights, 9 months of sampling) survey efforts, only 12 independent detections of six individual tigers were made across three study sites. Due to the sparse data, estimates of tiger abundance generated by Program CAPTURE could not be made for all survey sites. Other approaches to estimating density, based on numbers of tigers caught, or derived from borrowed estimates of detection probability, offer an alternative to capture–recapture analysis. Tiger densities fall in the range of 0.2–2.2 tigers/100 km², with 7–71 tigers inside a 3,250 km² area of prime tiger habitat, where efforts to protect tigers are currently focused. Tiger numbers might be stabilized if strict measures are taken to protect tigers and their prey from seasonal hunting and to suppress illegal trade in wildlife. Efforts to monitor abundance trends in the tiger population will be expensive given the difficulty with which tiger data can be obtained and the lack of available surrogate indices of tiger density. Monitoring occupancy patterns, the subject of a separate ongoing study, may be more efficient.