Most genomes contain thousands of genes, but for most functional responses, only a subset of those genes are relevant. To facilitate many single-cell RNASeq (scRNASeq) analyses the set of genes is ...often reduced through feature selection, i.e. by removing genes only subject to technical noise.
We present M3Drop, an R package that implements popular existing feature selection methods and two novel methods which take advantage of the prevalence of zeros (dropouts) in scRNASeq data to identify features. We show these new methods outperform existing methods on simulated and real datasets.
M3Drop is freely available on github as an R package and is compatible with other popular scRNASeq tools: https://github.com/tallulandrews/M3Drop.
Supplementary data are available at Bioinformatics online.
Single-cell RNA sequencing (scRNA-seq) is a popular and powerful technology that allows you to profile the whole transcriptome of a large number of individual cells. However, the analysis of the ...large volumes of data generated from these experiments requires specialized statistical and computational methods. Here we present an overview of the computational workflow involved in processing scRNA-seq data. We discuss some of the most common tasks and the tools available for addressing central biological questions. In this article and our companion website ( https://scrnaseq-course.cog.sanger.ac.uk/website/index.html ), we provide guidelines regarding best practices for performing computational analyses. This tutorial provides a hands-on guide for experimentalists interested in analyzing their data as well as an overview for bioinformaticians seeking to develop new computational methods.
Each year, the American Cancer Society publishes a summary of its guidelines for early cancer detection, data and trends in cancer screening rates, and select issues related to cancer screening. In ...this issue of the journal, the current American Cancer Society cancer screening guidelines are summarized, and the most current data from the National Health Interview Survey are provided on the utilization of cancer screening for men and women and on the adherence of men and women to multiple recommended screening tests.
Calcium is an extraordinarily versatile signaling ion, encoding cellular responses to a wide variety of external stimuli. In neurons, mitochondria can accumulate enormous amounts of calcium, with the ...consequence that mitochondrial calcium uptake, sequestration and release play pivotal roles in orchestrating calcium-dependent responses as diverse as gene transcription and cell death. In this review, we consider the basic chemistry of calcium as a 'sticky' cation, which leads to extremely high bound/free ratios, and discuss areas of current interest or controversy. Topics addressed include methodologies for measuring local intracellular calcium, mitochondrial calcium buffering and loading capacity, mitochondrially directed spatial calcium gradients, and the role of calcium overload-dependent mitochondrial dysfunction in glutamate-evoked excitotoxic injury and neurodegeneration. Finally, we consider the relationship between delayed calcium de-regulation, the mitochondrial permeability transition and the generation of reactive oxygen species, and propose a unified view of the 'source specificity' and 'calcium overload' models of N-methyl- d-aspartate (NMDA) receptor-dependent excitotoxicity. Non-NMDA receptor mechanisms of excitotoxicity are discussed briefly.
Knowledge of the midplane temperature of protoplanetary disks is one of the key ingredients in theories of dust growth and planet formation. However, direct measurement of this quantity is ...complicated, and often depends on the fitting of complex models to data. In this paper we demonstrate a method to directly measure the midplane gas temperature from an optically thick molecular line if the disk is moderately inclined. The only model assumption that enters is that the line is very optically thick, specifically in the midplane region where we wish to measure the temperature. Freeze-out of the molecule onto dust grains could thwart this. However, in regions that are expected to be warm enough to avoid freeze-out, this method should work. We apply the method to the CO 2–1 line channel maps of the disk around HD 163296. We find that the midplane temperature between 100 and 400 au drops only mildly from 25 K down to 18 K. While we see no direct evidence of the midplane being optically thin due to strong CO depletion by freeze-out, we cannot rule it out either. The fact that the inferred temperatures are close to the expected CO freeze-out temperature could be an indication of this. Incidently, for the disk around HD 163296 we also find dynamic evidence for a rather abrupt outer edge of the disk, suggestive of outside-in photoevaporation or truncation by an unseen companion.
Lipid A is a highly conserved component of lipopolysaccharide (LPS), itself a major component of the outer membrane of Gram-negative bacteria. Lipid A is essential to cells and elicits a strong ...immune response from humans and other animals. We developed a quantitative model of the nine enzyme-catalyzed steps of Escherichia coli lipid A biosynthesis, drawing parameters from the experimental literature. This model accounts for biosynthesis regulation, which occurs through regulated degradation of the LpxC and WaaA (also called KdtA) enzymes. The LpxC degradation signal appears to arise from the lipid A disaccharide concentration, which we deduced from prior results, model results, and new LpxK overexpression results. The model agrees reasonably well with many experimental findings, including the lipid A production rate, the behaviors of mutants with defective LpxA enzymes, correlations between LpxC half-lives and cell generation times, and the effects of LpxK overexpression on LpxC concentrations. Its predictions also differ from some experimental results, which suggest modifications to the current understanding of the lipid A pathway, such as the possibility that LpxD can replace LpxA and that there may be metabolic channeling between LpxH and LpxB. The model shows that WaaA regulation may serve to regulate the lipid A production rate when the 3-deoxy-D-manno-oct-2-ulosonic acid (KDO) concentration is low and/or to control the number of KDO residues that get attached to lipid A. Computation of flux control coefficients showed that LpxC is the rate-limiting enzyme if pathway regulation is ignored, but that LpxK is the rate-limiting enzyme if pathway regulation is present, as it is in real cells. Control also shifts to other enzymes if the pathway substrate concentrations are not in excess. Based on these results, we suggest that LpxK may be a much better drug target than LpxC, which has been pursued most often.
Akt is a pro‐survival kinase frequently activated in human cancers and is associated with more aggressive tumors that resist therapy. Here, we connect Akt pathway activation to reduced sensitivity to ...chemotherapy via Akt phosphorylation of Bax at residue S184, one of the pro‐apoptotic Bcl‐2 family proteins required for cells to undergo apoptosis. We show that phosphorylation by Akt converts the pro‐apoptotic protein Bax into an anti‐apoptotic protein. Mechanistically, we show that phosphorylation (i) enables Bax binding to pro‐apoptotic BH3 proteins in solution, and (ii) prevents Bax inserting into mitochondria. Together, these alterations promote resistance to apoptotic stimuli by sequestering pro‐apoptotic activator BH3 proteins. Bax phosphorylation correlates with cellular resistance to BH3 mimetics in primary ovarian cancer cells. Further, analysis of the TCGA database reveals that 98% of cancer patients with increased BAX levels also have an upregulated Akt pathway, compared to 47% of patients with unchanged or decreased BAX levels. These results suggest that in patients, increased phosphorylated anti‐apoptotic Bax promotes resistance of cancer cells to inherent and drug‐induced apoptosis.
Synopsis
Phosphorylation of Bax at S184 by Akt converts it from pro‐ to anti‐apoptotic and confers resistance to drugs and pro‐apoptotic signalling. In patients, Akt is increased in tumours with high Bax and phosphorylation correlates with drug resistance.
Phosphorylation of Bax at residue S184 by Akt inhibits apoptosis in cancer cell lines.
Phosphorylation converts pro‐apoptotic Bax into an anti‐apoptotic protein.
Phosphomimetic Bax sequesters and thereby inactivates pro‐apoptotic BH3‐proteins.
In patients, levels of Akt and Bax are correlated and Bax phosphorylation correlates with resistance to BH3‐mimetics.
Phosphorylation of Bax at S184 by Akt converts it from pro‐ to anti‐apoptotic and confers resistance to drugs and pro‐apoptotic signalling. In patients, Akt is increased in tumours with high Bax and phosphorylation correlates with drug resistance.
The American Cancer Society (ACS) recommends that individuals with a cervix initiate cervical cancer screening at age 25 years and undergo primary human papillomavirus (HPV) testing every 5 years ...through age 65 years (preferred); if primary HPV testing is not available, then individuals aged 25 to 65 years should be screened with cotesting (HPV testing in combination with cytology) every 5 years or cytology alone every 3 years (acceptable) (strong recommendation). The ACS recommends that individuals aged >65 years who have no history of cervical intraepithelial neoplasia grade 2 or more severe disease within the past 25 years, and who have documented adequate negative prior screening in the prior 10 years, discontinue all cervical cancer screening (qualified recommendation). These new screening recommendations differ in 4 important respects compared with the 2012 recommendations: 1) The preferred screening strategy is primary HPV testing every 5 years, with cotesting and cytology alone acceptable where access to US Food and Drug Administration‐approved primary HPV testing is not yet available; 2) the recommended age to start screening is 25 years rather than 21 years; 3) primary HPV testing, as well as cotesting or cytology alone when primary testing is not available, is recommended starting at age 25 years rather than age 30 years; and 4) the guideline is transitional, ie, options for screening with cotesting or cytology alone are provided but should be phased out once full access to primary HPV testing for cervical cancer screening is available without barriers. Evidence related to other relevant issues was reviewed, and no changes were made to recommendations for screening intervals, age or criteria for screening cessation, screening based on vaccination status, or screening after hysterectomy. Follow‐up for individuals who screen positive for HPV and/or cytology should be in accordance with the 2019 American Society for Colposcopy and Cervical Pathology risk‐based management consensus guidelines for abnormal cervical cancer screening tests and cancer precursors.
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