Bacterial microevolution and the Pangenome

The comparison of multiple genome sequences sampled from a bacterial population reveals considerable diversity in both the core and the accessory parts of the pangenome. This diversity can be analysed in terms of microevolutionary events that took place since the genomes shared a common ancestor, especially deletion, duplication, and recombination. We review the basic modelling ingredients used implicitly or explicitly when performing such a pangenome analysis. In particular, we describe a basic neutral phylogenetic framework of bacterial pangenome microevolution, which is not incompatible with evaluating the role of natural selection. We survey the different ways in which pangenome data is summarised in order to be included in microevolutionary models, as well as the main methodological approaches that have been proposed to reconstruct pangenome microevolutionary history

G76-292 Home Fruit Spray Schedules (Revised May 1986)

Insects and diseases of home fruit plantings must be controlled to produce quality fruit. Home orchards must be sprayed several times during the growing season. Spraying only a few times will not produce acceptable results for most fruits. This NebGuide discusses the types of sprays, sprayers, insecticides, insecticides and fungicides used to control insects

CarpeDeam: A De Novo Metagenome Assembler for Heavily Damaged Ancient Datasets

De novo assembly of ancient metagenomic datasets is a challenging task. Ultra-short fragment size and characteristic postmortem damage patterns of sequenced ancient DNA molecules leave current tools ill-equipped for ideal assembly. We present CarpeDeam, a novel damage-aware de novo assembler designed specifically for ancient metagenomic samples. Utilizing maximum-likelihood frameworks that integrate sample-specific damage patterns, CarpeDeam recovers longer continuous sequences and more protein sequences from both simulated and empirical datasets compared to existing assemblers. As a pioneering ancient metagenome assembler, CarpeDeam opens the door for new opportunities in functional and taxonomic analyses of ancient microbial communities

AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms

Deep-learning (DL) methods like DeepMind's AlphaFold2 (AF2) have led to substantial improvements in protein structure prediction. We analyse confident AF2 models from 21 model organisms using a new classification protocol (CATH-Assign) which exploits novel DL methods for structural comparison and classification. Of ~370,000 confident models, 92% can be assigned to 3253 superfamilies in our CATH domain superfamily classification. The remaining cluster into 2367 putative novel superfamilies. Detailed manual analysis on 618 of these, having at least one human relative, reveal extremely remote homologies and further unusual features. Only 25 novel superfamilies could be confirmed. Although most models map to existing superfamilies, AF2 domains expand CATH by 67% and increases the number of unique 'global' folds by 36% and will provide valuable insights on structure function relationships. CATH-Assign will harness the huge expansion in structural data provided by DeepMind to rationalise evolutionary changes driving functional divergence

Towards the Discovery of New Elements: Production of Livermorium (Z=116) with 50Ti

The $^{244}$Pu($^{50}$Ti,$xn$)$^{294-x}$Lv reaction was investigated at Lawrence Berkeley National Laboratory\u27s 88-Inch Cyclotron facility. The experiment was aimed at the production of a superheavy element with $Z\ge 114$ by irradiating an actinide target with a beam heavier than $^{48}$Ca. Produced Lv ions were separated from the unwanted beam and nuclear reaction products using the Berkeley Gas-filled Separator and implanted into a newly commissioned focal plane detector system. Two decay chains were observed and assigned to the decay of $^{290}$Lv. The production cross section was measured to be $σ_{\rm prod}=0.44(^{+58}_{-28})$~pb at a center-of-target center-of-mass energy of 220(3)~MeV. This represents the first published measurement of the production of a superheavy element near the `Island-of-Stability\u27, with a beam of $^{50}$Ti and is an essential precursor in the pursuit of searching for new elements beyond $Z=118$.Submitted to Physical Review Letter

Toward the Discovery of New Elements: Production of Livermorium ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mi>Z</mml:mi><mml:mo>=</mml:mo><mml:mn>116</mml:mn></mml:mrow></mml:math> ) with <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mmultiscripts><mml:mrow><mml:mi>Ti</mml:mi></mml:mrow><mml:mprescripts/><mml:none/><mml:mrow><mml:mn>50</mml:mn></mml:mrow></mml:mmultiscripts></mml:mrow></mml:math>

The Pu244(Ti50,xn)Lv294-x reaction was investigated at Lawrence Berkeley National Laboratory's 88-Inch Cyclotron. The experiment was aimed at the production of a superheavy element with Z≥114 by irradiating an actinide target with a beam heavier than Ca48. Produced Lv ions were separated from the unwanted beam and nuclear reaction products using the Berkeley Gas-filled Separator and implanted into a newly commissioned focal-plane detector system. Two decay chains were observed and assigned to the decay of Lv290. The production cross section was measured to be σprod=0.44(-0.28+0.58) pb at a center-of-target center-of-mass energy of 220(3) MeV. This represents the first published measurement of the production of a superheavy element near the "island of stability,"with a beam of Ti50 and is an essential precursor in the pursuit of searching for new elements beyond Z=118

Fusion reaction 48Ca+249Bk leading to formation of the element Ts (Z=117)

The heaviest currently known nuclei, which have up to 118 protons, have been produced in 48Ca induced reactions with actinide targets. Among them, the element tennessine (Ts), which has 117 protons, has been synthesized by fusing 48Ca with the radioactive target 249Bk, which has a half-life of 327 d. The experiment was performed at the gas-filled recoil separator TASCA. Two long and two short α decay chains were observed. The long chains were attributed to the decay of 294Ts. The possible origin of the short-decay chains is discussed in comparison with the known experimental data. They are found to fit with the decay chain patterns attributed to 293Ts. The present experimental results confirm the previous findings at the Dubna Gas-Filled Recoil Separator on the decay chains originating from the nuclei assigned to Ts

Performance of the neutron time-of-flight facility n_TOF at CERN

copyright The Author(s) 2013. This article is published with open access at Springerlink.comThe neutron time-of-flight facility n_TOF features a white neutron source produced by spallation through 20 GeV/c protons impinging on a lead target. The facility, aiming primarily at the measurement of neutron-induced reaction cross sections, was operating at CERN between 2001 and 2004, and then underwent a major upgrade in 2008. This paper presents in detail all the characteristics of the new neutron beam in the currently available configurations, which correspond to two different collimation systems and two choices of neutron moderator. The characteristics discussed include the intensity and energy dependence of the neutron flux, the spatial profile of the beam, the in-beam background components and the energy resolution/broadening. The discussion of these features is based on dedicated measurements and Monte Carlo simulations, and includes estimations of the systematic uncertainties of the mentioned quantities.Peer reviewedFinal Published versio