Alternative mechanisms of structuring biomembranes: Self-assembly vs. self-organization

We study two mechanisms for the formation of protein patterns near membranes of living cells by mathematical modelling. Self-assembly of protein domains by electrostatic lipid-protein interactions is contrasted with self-organization due to a nonequilibrium biochemical reaction cycle of proteins near the membrane. While both processes lead eventually to quite similar patterns, their evolution occurs on very different length and time scales. Self-assembly produces periodic protein patterns on a spatial scale below 0.1 micron in a few seconds followed by extremely slow coarsening, whereas self-organization results in a pattern wavelength comparable to the typical cell size of 100 micron within a few minutes suggesting different biological functions for the two processes.Comment: 4 pages, 5 figure

SmartTrack: Efficient Predictive Race Detection

Widely used data race detectors, including the state-of-the-art FastTrack algorithm, incur performance costs that are acceptable for regular in-house testing, but miss races detectable from the analyzed execution. Predictive analyses detect more data races in an analyzed execution than FastTrack detects, but at significantly higher performance cost. This paper presents SmartTrack, an algorithm that optimizes predictive race detection analyses, including two analyses from prior work and a new analysis introduced in this paper. SmartTrack's algorithm incorporates two main optimizations: (1) epoch and ownership optimizations from prior work, applied to predictive analysis for the first time; and (2) novel conflicting critical section optimizations introduced by this paper. Our evaluation shows that SmartTrack achieves performance competitive with FastTrack-a qualitative improvement in the state of the art for data race detection.Comment: Extended arXiv version of PLDI 2020 paper (adds Appendices A-E) #228 SmartTrack: Efficient Predictive Race Detectio

RacerD: compositional static race detection

Automatic static detection of data races is one of the most basic problems in reasoning about concurrency. We present RacerD—a static program analysis for detecting data races in Java programs which is fast, can scale to large code, and has proven effective in an industrial software engineering scenario. To our knowledge, RacerD is the first inter-procedural, compositional data race detector which has been empirically shown to have non-trivial precision and impact. Due to its compositionality, it can analyze code changes quickly, and this allows it to perform continuous reasoning about a large, rapidly changing codebase as part of deployment within a continuous integration ecosystem. In contrast to previous static race detectors, its design favors reporting high-confidence bugs over ensuring their absence. RacerD has been in deployment for over a year at Facebook, where it has flagged over 2500 issues that have been fixed by developers before reaching production. It has been important in enabling the development of new code as well as fixing old code: it helped support the conversion of part of the main Facebook Android app from a single-threaded to a multi-threaded architecture. In this paper we describe RacerD’s design, implementation, deployment and impact

ZFP36L1 negatively regulates plasmacytoid differentiation of BCL1 cells by targeting BLIMP1 mRNA

The ZFP36/Tis11 family of zinc-finger proteins regulate cellular processes by binding to adenine uridine rich elements in the 3′ untranslated regions of various mRNAs and promoting their degradation. We show here that ZFP36L1 expression is largely extinguished during the transition from B cells to plasma cells, in a reciprocal pattern to that of ZFP36 and the plasma cell transcription factor, BLIMP1. Enforced expression of ZFP36L1 in the mouse BCL1 cell line blocked cytokine-induced differentiation while shRNA-mediated knock-down enhanced differentiation. Reconstruction of regulatory networks from microarray gene expression data using the ARACNe algorithm identified candidate mRNA targets for ZFP36L1 including BLIMP1. Genes that displayed down-regulation in plasma cells were significantly over-represented (P = <0.0001) in a set of previously validated ZFP36 targets suggesting that ZFP36L1 and ZFP36 target distinct sets of mRNAs during plasmacytoid differentiation. ShRNA-mediated knock-down of ZFP36L1 in BCL1 cells led to an increase in levels of BLIMP1 mRNA and protein, but not for mRNAs of other transcription factors that regulate plasmacytoid differentiation (xbp1, irf4, bcl6). Finally, ZFP36L1 significantly reduced the activity of a BLIMP1 3′ untranslated region-driven luciferase reporter. Taken together, these findings suggest that ZFP36L1 negatively regulates plasmacytoid differentiation, at least in part, by targeting the expression of BLIMP1

Heart failure patients demonstrate impaired changes in brachial artery blood flow and shear rate pattern during moderate-intensity cycle exercise

New Findings What is the central question of this study? We explored whether heart failure (HF) patients demonstrate different exercise-induced brachial artery shear rate patterns compared with control subjects. What is the main finding and its importance? Moderate-intensity cycle exercise in HF patients is associated with an attenuated increase in brachial artery anterograde and mean shear rate and skin temperature. Differences between HF patients and control subjects cannot be explained fully by differences in workload. HF patients demonstrate a less favourable shear rate pattern during cycle exercise compared with control subjects. Repeated elevations in shear rate (SR) in conduit arteries, which occur during exercise, represent a key stimulus to improve vascular function. We explored whether heart failure (HF) patients demonstrate distinct changes in SR in response to moderate-intensity cycle exercise compared with healthy control subjects. We examined brachial artery SR during 40 min of cycle exercise at a work rate equivalent to 65% peak oxygen uptake in 14 HF patients (65 ± 7 years old, 13 men and one woman) and 14 control subjects (61 ± 5 years old, 12 men and two women). Brachial artery diameter, SR and oscillatory shear index (OSI) were assessed using ultrasound at baseline and during exercise. The HF patients demonstrated an attenuated increase in mean and anterograde brachial artery SR during exercise compared with control subjects (time × group interaction, P = 0.003 and P 0.05). In conclusion, HF patients demonstrate a less favourable SR pattern during cycle exercise than control subjects, characterized by an attenuated mean and anterograde SR and by increased OSI

Post-Transcriptional Regulation of BCL2 mRNA by the RNA-Binding Protein ZFP36L1 in Malignant B Cells

The human ZFP36 zinc finger protein family consists of ZFP36, ZFP36L1, and ZFP36L2. These proteins regulate various cellular processes, including cell apoptosis, by binding to adenine uridine rich elements in the 3′ untranslated regions of sets of target mRNAs to promote their degradation. The pro-apoptotic and other functions of ZFP36 family members have been implicated in the pathogenesis of lymphoid malignancies. To identify candidate mRNAs that are targeted in the pro-apoptotic response by ZFP36L1, we reverse-engineered a gene regulatory network for all three ZFP36 family members using the ‘maximum information coefficient’ (MIC) for target gene inference on a large microarray gene expression dataset representing cells of diverse histological origin. Of the three inferred ZFP36L1 mRNA targets that were identified, we focussed on experimental validation of mRNA for the pro-survival protein, BCL2, as a target for ZFP36L1. RNA electrophoretic mobility shift assay experiments revealed that ZFP36L1 interacted with the BCL2 adenine uridine rich element. In murine BCL1 leukemia cells stably transduced with a ZFP36L1 ShRNA lentiviral construct, BCL2 mRNA degradation was significantly delayed compared to control lentiviral expressing cells and ZFP36L1 knockdown in different cell types (BCL1, ACHN, Ramos), resulted in increased levels of BCL2 mRNA levels compared to control cells. 3′ untranslated region luciferase reporter assays in HEK293T cells showed that wild type but not zinc finger mutant ZFP36L1 protein was able to downregulate a BCL2 construct containing the BCL2 adenine uridine rich element and removal of the adenine uridine rich core from the BCL2 3′ untranslated region in the reporter construct significantly reduced the ability of ZFP36L1 to mediate this effect. Taken together, our data are consistent with ZFP36L1 interacting with and mediating degradation of BCL2 mRNA as an important target through which ZFP36L1 mediates its pro-apoptotic effects in malignant B-cells

Third Report on Chicken Genes and Chromosomes 2015

Following on from the First Report on Chicken Genes and Chromosomes [Schmid et al., 2000] and the Second Report in 2005 [Schmid et al., 2005], we are pleased to publish this long-awaited Third Report on the latest developments in chicken genomics. The First Report highlighted the availability of genetic and physical maps, while the Second Report was published as the chicken genome sequence was released. This report comes at a time of huge technological advances (particularly in sequencing methodologies) which have allowed us to examine the chicken genome in detail not possible until now. This has also heralded an explosion in avian genomics, with the current availability of more than 48 bird genomes [Zhang G et al., 2014b; Eöry et al., 2015], with many more planned