Abstract
Summary
Genome-level evolutionary inference (i.e. phylogenomics) is becoming an increasingly essential step in many biologists’ work. Accordingly, there are several tools available for the ...major steps in a phylogenomics workflow. But for the biologist whose main focus is not bioinformatics, much of the computational work required—such as accessing genomic data on large scales, integrating genomes from different file formats, performing required filtering, stitching different tools together etc.—can be prohibitive. Here I introduce GToTree, a command-line tool that can take any combination of fasta files, GenBank files and/or NCBI assembly accessions as input and outputs an alignment file, estimates of genome completeness and redundancy, and a phylogenomic tree based on a specified single-copy gene (SCG) set. Although GToTree can work with any custom hidden Markov Models (HMMs), also included are 13 newly generated SCG-set HMMs for different lineages and levels of resolution, built based on searches of ∼12 000 bacterial and archaeal high-quality genomes. GToTree aims to give more researchers the capability to make phylogenomic trees.
Availability and implementation
GToTree is open-source and freely available for download from: github.com/AstrobioMike/GToTree. It is implemented primarily in bash with helper scripts written in python.
Supplementary information
Supplementary data are available at Bioinformatics online.
To study and report the clinical outcomes and patterns of failure after intensity-modulated radiotherapy (IMRT) for nasopharyngeal carcinoma (NPC).
The treatment outcomes of NPC patients treated with ...IMRT at Pamela Youde Nethersole Eastern Hospital between 2005 and 2007 were reviewed. The location and extent of locoregional failures were transferred to the pretreatment planning computed tomography for dosimetry analysis. Statistical analyses were performed on dose coverage and locoregional failures.
A total of 193 NPC patients were analyzed; 93% had Stage III/IV disease. Median follow-up was 30 months. Overall disease failure (at any site) developed in 35 patients. Among these, there were 23 distant metastases, 16 local failures, and 9 regional failures. Four of the locoregional failures were marginal. Dose conformity with IMRT was excellent. Patients with at least 66.5 Gy to their target volumes had significantly less locoregional failure. The 2-year local progression-free, regional progression-free, distant metastasis-free, and overall survival rates were 95%, 96%, 90%, and 92%, respectively.
Intensity-modulated radiotherapy provides excellent locoregional control for NPC. Distant metastasis remains the most difficult challenge, and more effective systemic agents should be explored for patients presenting with advanced locoregional diseases.
Purpose
The nutritional quality of final products is attracting an increased level of attention within life cycle assessment (LCA) literature of agri-food systems. The majority of these studies, ...however, are based on comparisons at the dietary level and, therefore, are unable to offer immediate implications for farmers as to how best to produce food. This article evaluates recent literature examining the nutrition-environment nexus at the commodity level, with the aim to identify potential pathways towards sustainability analysis that can inform both consumers and producers.
Methods
A systematic search of literature was carried out to produce a shortlist of studies, and strict exclusion criteria were applied to them afterwards to eliminate irrelevant material. The studies thus selected were classified into one of three tiers based on the level of complexity with regard to their functional units: (1) based on single nutrients, (2) based on composite indicators derived from multiple nutrients and (3) based on commodity-level analysis in a dietary context.
Results and discussion
Sixteen papers were identified for inclusion in the review. All of them accounted for climate change either directly or indirectly, whilst only five addressed different impact categories at the same time. Nine studies estimated environmental impacts under functional units associated with nutrient density scores, and the others utilised alternative approaches to account for nutritional value such as linear programming and end-point modelling combined with epidemiological data. A recently developed method to calculate the marginal contribution of a commodity to the overall nutritional value of a specific diet was considered to be a successful first step in bridging the aforementioned knowledge gap.
Conclusions
The LCA community should continue the ongoing effort to link farm management decisions to diet-level environmental impacts through an enhanced focus on human nutrition across the entire value chain. Future research comparing environmental performances of multiple food groups or multiple production systems should acknowledge differences in nutritional composition and bioavailability between the final products and, ideally, the effects of these nutrients on overall dietary quality.
Evolutionary trees underpin virtually all of biology, and the wealth of new genomic data has enabled us to reconstruct them with increasing detail and confidence. While phenotypic (typically ...morphological) traits are becoming less important in reconstructing evolutionary trees, they still serve vital and unique roles in phylogenetics, even for living taxa for which vast amounts of genetic information are available. Morphology remains a powerful independent source of evidence for testing molecular clades, and — through fossil phenotypes — the primary means for time-scaling phylogenies. Morphological phylogenetics is therefore vital for transforming undated molecular topologies into dated evolutionary trees. However, if morphology is to be employed to its full potential, biologists need to start scrutinising phenotypes in a more objective fashion, models of phenotypic evolution need to be improved, and approaches for analysing phenotypic traits and fossils together with genomic data need to be refined.
Lee and Palci review how phenotypic traits and fossils remain essential for constructing the dated phylogenetic trees that underpin much of modern biology.
Trilobites are often considered exemplary for understanding the Cambrian explosion of animal life, due to their unsurpassed diversity and abundance. These biomineralized arthropods appear abruptly in ...the fossil record with an established diversity, phylogenetic disparity, and provincialism at the beginning of Cambrian Series 2 (∼521 Ma), suggesting a protracted but cryptic earlier history that possibly extends into the Precambrian. However, recent analyses indicate elevated rates of phenotypic and genomic evolution for arthropods during the early Cambrian, thereby shortening the phylogenetic fuse. Furthermore, comparatively little research has been devoted to understanding the duration of the Cambrian explosion, after which normal Phanerozoic evolutionary rates were established. We test these hypotheses by applying Bayesian tip-dating methods to a comprehensive dataset of Cambrian trilobites. We show that trilobites have a Cambrian origin, as supported by the trace fossil record and molecular clocks. Surprisingly, they exhibit constant evolutionary rates across the entire Cambrian, for all aspects of the preserved phenotype: discrete, meristic, and continuous morphological traits. Our data therefore provide robust, quantitative evidence that by the time the typical Cambrian fossil record begins (∼521 Ma), the Cambrian explosion had already largely concluded. This suggests that a modern-style marine biosphere had rapidly emerged during the latest Ediacaran and earliest Cambrian (∼20 million years), followed by broad-scale evolutionary stasis throughout the remainder of the Cambrian.
Crosstalk and complexity within signaling pathways and their perturbation by oncogenes limit component-by-component approaches to understanding human disease. Network analysis of how normal and ...oncogenic signaling can be rewired by drugs may provide opportunities to target tumors with high specificity and efficacy. Using targeted inhibition of oncogenic signaling pathways, combined with DNA-damaging chemotherapy, we report that time-staggered EGFR inhibition, but not simultaneous coadministration, dramatically sensitizes a subset of triple-negative breast cancer cells to genotoxic drugs. Systems-level analysis—using high-density time-dependent measurements of signaling networks, gene expression profiles, and cell phenotypic responses in combination with mathematical modeling—revealed an approach for altering the intrinsic state of the cell through dynamic rewiring of oncogenic signaling pathways. This process converts these cells to a less tumorigenic state that is more susceptible to DNA damage-induced cell death by reactivation of an extrinsic apoptotic pathway whose function is suppressed in the oncogene-addicted state.
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► The efficacy of combination treatments for cancer depends on drug order and timing ► Dynamic rewiring of signaling networks by drugs can provide therapeutic benefit ► Sustained EGFR inhibition sensitizes triple-negative breast cancer cells to DNA damage ► EGFR activity, but not EGFR expression, is a biomarker of response to this treatment
The effectiveness of combination therapy for triple-negative breast cancer may be increased by delivering the drugs sequentially. Inhibiting EGFR dynamically rewires tumor cell signaling networks to enhance subsequent susceptibility to DNA-damaging agents, an effect not seen when the drugs are applied simultaneously.
•The elaboration likelihood model of persuasion models the persuasion process.•Superstar social media influencers rely on traditionally peripheral elements.•Linguistic style and emotional contagion ...are the central route to performance.•Content and production expertise are the peripheral route to performance.
In an aggressively growing market, influencers exploit social media platforms to make videos on their chosen interests in an attempt to attract viewers worldwide. Consequently, the platforms provide monetary rewards to these influencers that are commensurate with the number of views and subscribers. We use the language expectancy theory and the emotional contagion theory in an elaboration likelihood model of persuasion to understand why the financial success of influencers varies so widely. We conduct the analysis with speech-to-text data, survey data, archival data, and structural equation modelling. Contrary to the pre-internet persuasion research, the able, motivated, and focused viewers of superstar social media influencers identify the traditionally peripheral elements of linguistic style and emotional contagion as central to increasing the number of views and subscribers. However, these viewers identify content and production expertise, traditionally central elements, as peripheral to viewing and subscriber performance.
Recent discoveries have highlighted the dramatic evolutionary transformation of massive, ground-dwelling theropod dinosaurs into light, volant birds. Here, we apply Bayesian approaches (originally ...developed for inferring geographic spread and rates of molecular evolution in viruses) in a different context: to infer size changes and rates of anatomical innovation (across up to 1549 skeletal characters) in fossils. These approaches identify two drivers underlying the dinosaur-bird transition. The theropod lineage directly ancestral to birds undergoes sustained miniaturization across 50 million years and at least 12 consecutive branches (internodes) and evolves skeletal adaptations four times faster than other dinosaurs. The distinct, prolonged phase of miniaturization along the bird stem would have facilitated the evolution of many novelties associated with small body size, such as reorientation of body mass, increased aerial ability, and paedomorphic skulls with reduced snouts but enlarged eyes and brains.
The use of lithium metal anodes in solid-state batteries has emerged as one of the most promising technologies for replacing conventional lithium-ion batteries
. Solid-state electrolytes are a key ...enabling technology for the safe operation of lithium metal batteries as they suppress the uncontrolled growth of lithium dendrites. However, the mechanical properties and electrochemical performance of current solid-state electrolytes do not meet the requirements for practical applications of lithium metal batteries. Here we report a class of elastomeric solid-state electrolytes with a three-dimensional interconnected plastic crystal phase. The elastomeric electrolytes show a combination of mechanical robustness, high ionic conductivity, low interfacial resistance and high lithium-ion transference number. The in situ-formed elastomer electrolyte on copper foils accommodates volume changes for prolonged lithium plating and stripping processes with a Coulombic efficiency of 100.0 per cent. Moreover, the elastomer electrolytes enable stable operation of the full cells under constrained conditions of a limited lithium source, a thin electrolyte and a high-loading LiNi
Mn
Co
O
cathode at a high voltage of 4.5 volts at ambient temperature, delivering a high specific energy exceeding 410 watt-hours per kilogram of electrode plus electrolyte. The elastomeric electrolyte system presents a powerful strategy for enabling stable operation of high-energy, solid-state lithium batteries.
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