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61.
Eike Steinig Sebastin Duchêne Izzard Aglua Andrew Greenhill Rebecca Ford Mition Yoannes Jan Jaworski Jimmy Drekore Bohu Urakoko Harry Poka Clive Wurr Eri Ebos David Nangen Laurens Manning Moses Laman Cadhla Firth Simon Smith William Pomat Steven Y C Tong Lachlan Coin Emma McBryde Paul Horwood 《Molecular biology and evolution》2022,39(3)
Nanopore sequencing and phylodynamic modeling have been used to reconstruct the transmission dynamics of viral epidemics, but their application to bacterial pathogens has remained challenging. Cost-effective bacterial genome sequencing and variant calling on nanopore platforms would greatly enhance surveillance and outbreak response in communities without access to sequencing infrastructure. Here, we adapt random forest models for single nucleotide polymorphism (SNP) polishing developed by Sanderson and colleagues (2020. High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic nanopore sequencing. Genome Res. 30(9):1354–1363) to estimate divergence and effective reproduction numbers (Re) of two methicillin-resistant Staphylococcus aureus (MRSA) outbreaks from remote communities in Far North Queensland and Papua New Guinea (PNG; n = 159). Successive barcoded panels of S. aureus isolates (2 × 12 per MinION) sequenced at low coverage (>5× to 10×) provided sufficient data to accurately infer genotypes with high recall when compared with Illumina references. Random forest models achieved high resolution on ST93 outbreak sequence types (>90% accuracy and precision) and enabled phylodynamic inference of epidemiological parameters using birth–death skyline models. Our method reproduced phylogenetic topology, origin of the outbreaks, and indications of epidemic growth (Re > 1). Nextflow pipelines implement SNP polisher training, evaluation, and outbreak alignments, enabling reconstruction of within-lineage transmission dynamics for infection control of bacterial disease outbreaks on portable nanopore platforms. Our study shows that nanopore technology can be used for bacterial outbreak reconstruction at competitive costs, providing opportunities for infection control in hospitals and communities without access to sequencing infrastructure, such as in remote northern Australia and PNG. 相似文献
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在合适的结晶条件下 ,从含Cr无氨培养基中生长的固氮菌 (AzotobactervinelandiiLipmann)突变种UW3 中纯化出的CrFe蛋白可从溶液中析出深棕色斜四棱柱晶体 ,晶体最大的两条对角线长度分别可达 0 .2 5mm和 0 .12mm。PEG 80 0 0、MgCl2 、NaCl、Tris和Hepes缓冲液的浓度及结晶方法等对该蛋白的出晶率、晶核数目、晶体大小和质量都有明显影响。CrFe蛋白结晶所需的上述化合物的最适浓度与在Mn中生长的固氮菌突变种UW3 的MnFe蛋白和缺失nifZ固氮菌突变种的ΔnifZMoFe蛋白结晶所需的最适浓度有所不同。结果表明 ,该蛋白晶体可能为CrFe蛋白的晶体 相似文献
63.
Extracellular signals responsible for spatially regulated proliferation in the differentiating Drosophila eye 总被引:3,自引:0,他引:3
Spatially and temporally choreographed cell cycles accompany the differentiation of the Drosophila retina. The extracellular signals that control these patterns have been identified through mosaic analysis of mutations in signal transduction pathways. All cells arrest in G1 prior to the start of neurogenesis. Arrest depends on Dpp and Hh, acting redundantly. Most cells then go through a synchronous round of cell division before fate specification and terminal cell cycle exit. Cell cycle entry is induced by Notch signaling and opposed in subsets of cells by EGF receptor activity. Unusually, Cyclin E levels are not limiting for retinal cell cycles. Rbf/E2F and the Cyclin E antagonist Dacapo are important, however. All retinal cells, including the postmitotic photoreceptor neurons, continue dividing when rbf and dacapo are mutated simultaneously. These studies identify the specific extracellular signals that pattern the retinal cell cycles and show how differentiation can be uncoupled from cell cycle exit. 相似文献
64.
Dr. S. F. Contractor B. M. Eaton J. A. Firth K. F. Baumain 《Cell and tissue research》1984,237(3):609-617
Summary Isolated lobules of normal term human placentas were perfused using two different procedures. In the first more conventional system, open-circuit perfusion of both the maternal and the fetal circulations with Earle's solution containing dextran was established and maintained for either 30 min or 1 h. In the second series of experiments both circulations were perfused in separate closed circuits with a mixture of fresh autologous fetal blood and Earle's solution for 0, 1, 2 or 3 h. In both series the lobule was then fixed by perfusion through the fetal circulation.Light and electron-microscopic examination of a set of tissue samples from each perfused lobule showed substantial differences between the effects of these two types of perfusion procedure. Tissue from lobules perfused by the open-circuit blood-free procedure showed patchy but severe cell swelling and vacuolation of the trophoblast after only one hour's perfusion. Particularly striking was swelling and disruption of a large proportion of the mitochondria in all placental cell types. By contrast, placental tissue from the closed-circuit perfusion with blood-containing medium showed little change over a period of two hours, while after three hours it showed oedema and microvillous damage, but no sign of cell swelling and little mitochondrial damage.It is concluded that the viability of the perfused human placental lobule depends on the type of perfusate used, and that the use of a fetal blood-enriched perfusate is of considerable value in maintenance of the preparation as assessed by structural criteria. 相似文献
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applications of electroporation of adherent cellsIn Situ,on a partly conductive slide 总被引:5,自引:0,他引:5
Raptis Leda H. Brownell Heather L. Liu Stanley K. W. Firth Kevin L. MacKenzie Leslie W. Stiles Charles D. Alberta John A. 《Molecular biotechnology》1995,3(2):129-134
One of the most important factors affecting the quality of PCR is the choice of primers. In general, the longer the PCR product
the more difficult it is to select efficient primers and set appropriate designing primers, and in general, the more DNA sequence
information is available, the better the ch0ance of finding an optimal primer pair. Efficient primers can be designed by avoiding
the following flaws: primer-dimer formation, self-complementarity, too lowT
m
of the primers, and/or their incorrect internal stability profile. Tips on subcloning PCR products, calculating duplex stability
(predicting dimer formation strength), and designing degenerate primers are given. 相似文献
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Fakiola M Mishra A Rai M Singh SP O'Leary RA Ball S Francis RW Firth MJ Radford BT Miller EN Sundar S Blackwell JM 《PloS one》2010,5(12):e15807