A population‐based temporal logic gate for timing and recording chemical events

Engineered bacterial sensors have potential applications in human health monitoring, environmental chemical detection, and materials biosynthesis. While such bacterial devices have long been engineered to differentiate between combinations of inputs, their potential to process signal timing and duration has been overlooked. In this work, we present a two‐input temporal logic gate that can sense and record the order of the inputs, the timing between inputs, and the duration of input pulses. Our temporal logic gate design relies on unidirectional DNA recombination mediated by bacteriophage integrases to detect and encode sequences of input events. For an E. coli strain engineered to contain our temporal logic gate, we compare predictions of Markov model simulations with laboratory measurements of final population distributions for both step and pulse inputs. Although single cells were engineered to have digital outputs, stochastic noise created heterogeneous single‐cell responses that translated into analog population responses. Furthermore, when single‐cell genetic states were aggregated into population‐level distributions, these distributions contained unique information not encoded in individual cells. Thus, final differentiated sub‐populations could be used to deduce order, timing, and duration of transient chemical events.     

An innovative approach for testing bioinformatics programs using metamorphic testing

Background  

Recent advances in experimental and computational technologies have fueled the development of many sophisticated bioinformatics programs. The correctness of such programs is crucial as incorrectly computed results may lead to wrong biological conclusion or misguide downstream experimentation. Common software testing procedures involve executing the target program with a set of test inputs and then verifying the correctness of the test outputs. However, due to the complexity of many bioinformatics programs, it is often difficult to verify the correctness of the test outputs. Therefore our ability to perform systematic software testing is greatly hindered.     

Intraspecific phylogeography of the gopher tortoise, Gopherus polyphemus: RFLP analysis of amplified mtDNA segments

The slow rate of mtDNA evolution in turtles poses a limitation on the levels of intraspecific variation detectable by conventional restriction fragment surveys. We examined mtDNA variation in the gopher tortoise (Gopherus polyphemus) using an alternative restriction assay, one in which PCR-amplified segments of the mitochondrial genome were digested with tetranucleotide-site endonucleases. Restriction fragment polymorphisms representing four amplified regions were analysed to evaluate population genetic structure among 112 tortoises throughout the species' range. Thirty-six haplotypes were identified, and three major geographical assemblages (Eastern, Western, and Mid-Florida) were resolved by UPGMA and parsimony analyses. Eastern and Western assemblages abut near the Apalachicola drainage, whereas the Mid-Florida assemblage appears restricted to the Brooksville Ridge. The Eastern/Western assemblage boundary is remarkably congruent with phylogeographic profiles for eight additional species from the southeastern U.S., representing both freshwater and terrestrial realms.     

Genetically and geographically isolated lineages of a tropical bat (Chiroptera: Molossidae) show demographic stability over the late Pleistocene

The newly described molossid bat, Chaerephon atsinanana Goodman et al., 2010, endemic to eastern Madagascar, shows notably high levels of phylogeographic and genetic structure compared with allopatric Chaerephon leucogaster Grandidier, 1869 from western Madagascar. Such highly significant structuring of haplotypes among altitudinally and latitudinally stratified population groups is contrary to the expected panmixia in strong flying bats. The null model of concordance in historical demographic patterns across these two Chaerephon species was not supported. Mismatch and Bayesian skyline analyses indicated ancient stable C. atsinanana populations of constant size during the last two major Pleistocene glacial periods, making retreat into and expansion from glacial refugia an unlikely explanation for such high levels of structure, in accordance with expectations for tropical bats. Analyses were consistent with post‐refugial population expansion in the less diverse and structured C. leucogaster during the end of the last Pleistocene glacial period. We hypothesise that the pronounced genetic structuring in C. atsinanana may result from female philopatry. Furthermore, differing demographic histories of the two species may have been shaped by differing climate or habitat preferences, consistent with evidence from MaxEnt ecological niche modelling, which shows differences in variables influencing the current predicted distributions. Fossil Quaternary pollen deposits further indicate greater stability in past climatic patterns in eastern versus western Madagascar. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 106 , 18–40.     

Trace elements in the Upper Fly River, Papua New Guinea

SUMMARY. Measurements were made of calcium, magnesium and eight trace elements (Cu, Zn, Fe, Mn, Ni, Pb, Cd, Co) in waters, sediment and biota at eight sites in the Upper Fly River, Papua New Guinea. Determinations from streams draining an area rich in copper ore showed relatively low values for soluble copper and this was attributed to the small amount of ore exposed to weathering, heavy rainfall and high pH of water associated with the limestone bedrock. More iron was transported in a soluble form down a headwater tributary (Alice River) than in the Fly River but higher iron concentrations were associated with particulate matter in the Fly than in the Alice. The geochemistry of the catchment and the distance from the headwaters were important influences on the amount of particulate iron and its distribution between soluble and particulate forms.
Levels of metals in the biota generally reflected the background concentrations of metals encountered at each site. Concentrations of Cu, Cd, and Zn were lower in starved invertebrates compared with unstarved individuals but no consistent changes were observed in Fe or Mn content.     

Fine Needle Aspiration Cytology of Breast In Invasive Carcinoma of Tubular Type and In Radial Scar/Complex Sclerosing Lesions

Fine needle aspirates (FNA) from 31 invasive carcinomas of tubular type and 22 radial scar/complex sclerosing lesions (RS/CSL), diagnosed in Edinburgh between 1986 and 1991, were reviewed. the lesions in this study varied in size and palpability at presentation, but are of increasing interest in the differential diagnosis of non-palpable areas of increased mammographic density. In agreement with previously published information^1'5'8, it was found that the tubular cancers were usually selected for biopsy following aspiration, but less often definitively diagnosed as malignant. Nearly 50% of the RS/CSL group were correctly reported benign on cytology, but in 40%, biopsy was recommended to exclude malignancy. In addition, cytological features helpful in suggesting malignancy in aspirates from tubular cancers, also raised suspicion in aspirates from the RS/CSL group, with a risk of overdiagnosis of cancer.