Introducing the FAIR Principles for research software.

Research software is a fundamental and vital part of research, yet significant challenges to discoverability, productivity, quality, reproducibility, and sustainability exist. Improving the practice of scholarship is a common goal of the open science, open source, and FAIR (Findable, Accessible, Interoperable and Reusable) communities and research software is now being understood as a type of digital object to which FAIR should be applied. This emergence reflects a maturation of the research community to better understand the crucial role of FAIR research software in maximising research value.

Erratum: Taking a fresh look at FAIR for research software.

[This corrects the article DOI: 10.1016/j.patter.

Taking a fresh look at FAIR for research software.

Software is increasingly essential in most research, and much of this software is developed specifically for and during research. To make this research software findable, accessible, interoperable, and reusable (FAIR), we need to define exactly what FAIR means for research software and acknowledge that software is a living and complex object for which it is impossible to propose one solution that fits all software.

Effects of phytoestrogens on sarcoplasmic/endoplasmic reticulum calcium ATPase 2a and Ca2+ uptake into cardiac sarcoplasmic reticulum.

Phytoestrogens are naturally occurring estrogenic compounds found in plants and plant products. These compounds are also known to exert cellular effects independent of their interactions with estrogen receptors. We studied the effects of the phytoestrogens phloretin, phloridzin, genistein, and biochanin A on Ca(2+) uptake into the cardiac muscle sarcoplasmic reticulum (SR).

Intracellular events in the initiation of calcium oxalate stones.

This review summarizes our current understanding of intracellular events in the initiation of kidney stone formation, focusing on results from studies using renal epithelial cells in vitro. Such studies have shown that oxalate - either in crystalline or in soluble form - triggers a spectrum of responses in renal cells that favor stone formation, including alterations in membrane surface properties that promote crystal attachment and alterations in cell viability that provide debris for crystal nucleation. Activation of cytosolic PLA2 appears to play an important role in oxalate actions, triggering a signaling cascade that generates several lipid mediators (arachidonic acid, AA; lysophosphatidylcholine, Lyso-PC; ceramide) that act on key intracellular targets (mitochondria, nucleus).

Mitochondrial dysfunction is a primary event in renal cell oxalate toxicity.

Background: In cultured renal epithelial cells, exposure to oxalate, a constituent of many kidney stones, elicits a cascade of responses that often leads to cell death. Oxalate toxicity is mediated via generation of reactive oxygen species (ROS) in a process that depends at least in part upon lipid signaling molecules that are generated through membrane events that culminate in phospholipase A2 (PLA2) activation. The present studies asked whether mitochondria, a major site of ROS production, were targets of oxalate toxicity, and if so, whether mitochondrial responses to oxalate were mediated by PLA2 activation.

How elevated oxalate can promote kidney stone disease: changes at the surface and in the cytosol of renal cells that promote crystal adherence and growth.

The present review assesses the mechanisms by which oxalate-induced alterations in renal cell function may promote stone disease focusing on 1) changes in membrane surface properties that promote the attachment of nascent crystals and 2) changes in the expression/secretion of urinary macromolecules that alter the kinetics of crystal nucleation, agglomeration and growth. The general role of renal cellular injury in promoting these responses and the specific role of urinary oxalate in producing injury is emphasized, and the signaling pathways that lead to the observed changes in cell surface properties and in the viability and growth of renal cells are discussed. Particular attention is paid to evidence linking oxalate-induced activation of cytosolic phospholipase A2 to changes in gene expression and to the activation of a second signaling pathway involving ceramide.

Mechanisms mediating oxalate-induced alterations in renal cell functions.

Oxalate is a major component of the most common form of kidney stones--calcium oxalate stones. High concentrations of oxalate promote stone formation in two ways: (1) by providing urinary conditions favorable to the formation of calcium oxalate crystals, and (2) by inducing renal injury that generates cellular debris and promotes crystal nucleation and attachment. Oxalate toxicity is mediated in part by activation of lipid signaling pathways that produce arachidonic acid, lysophospholipids, and ceramide.

Oxalate-induced redistribution of phosphatidylserine in renal epithelial cells: implications for kidney stone disease.

Aims: The present studies assessed the possibility that exposure to oxalate leads to alterations in membrane structure that promote crystal binding to renal epithelial cells. Specifically, we determined whether oxalate exposure produces a redistribution of membrane phosphatidylserine (PS) and an increase in the binding of (14)C-oxalate crystals to renal epithelial cells.

Methods: PS distribution was monitored in MDCK cells and in phospholipid-containing vesicles using NBD-PS, a fluorescent derivative of PS.

Oxalate-induced changes in renal epithelial cell function: role in stone disease.

Many studies on the etiology of stone disease have focused on the properties of urine that affect crystal nucleation and growth. More recent studies have focused on the properties of the renal epithelium and the role of injury in crystal retention. The latter studies have shown that oxalate exposure per se can damage renal epithelial cells and enhance crystal binding.

Binding of 1alpha,25-dihydroxyvitamin D(3) to annexin II: effect of vitamin D metabolites and calcium.

We have recently reported that annexin II serves as a membrane receptor for 1alpha,25-(OH)(2)D(3) and mediates the rapid effect of the hormone on intracellular calcium. The purpose of these studies was to characterize the binding of the hormone to annexin II, determine the specificity of binding, and assess the effect of calcium on binding. The binding of [(14)C]-1alpha,25-(OH)(2)D(3) bromoacetate to purified annexin II was inhibited by 1alpha, 25-(OH)(2)D(3) in a concentration-dependent manner.

Phospholipase A2 mediates immediate early genes in cultured renal epithelial cells: possible role of lysophospholipid.

Background: Exposure to high levels of oxalate induces oxidant stress in renal epithelial cells and produces diverse changes in cell function, ranging from cell death to cellular adaptation, as evidenced by increased DNA synthesis, cellular proliferation, and induction of genes associated with remodeling and repair. These studies focused on cellular adaptation to this oxidant stress, examining the manner by which oxalate exposure leads to increased expression of immediate early genes (IEGs). Specifically, our studies assessed the possibility that oxalate-induced changes in IEG expression are mediated by phospholipase A2 (PLA2), a common pathway in cellular stress responses.

TGF-beta signaling in A549 lung carcinoma cells: lipid second messengers.

Transforming growth factor-beta (TGF-beta) is a potent inducer of numerous extracellular matrix components, largely through a transcriptional mechanism. To define the postreceptor signaling pathways used by TGF-beta in the induction of extracellular matrix gene expression, we have utilized the human lung carcinoma cell line, A549, in transfection experiments with the TGF-beta inducible reporter construct, p3TP-Lux. Previous work from this laboratory using pharmacologic agents suggested that a phosphatidylcholine-specific phospholipase C and protein kinase C may be involved in early aspects of TGF-beta signaling.

Oxalate-induced ceramide accumulation in Madin-Darby canine kidney and LLC-PK1 cells.

Background: Oxalate exposure produces oxidant stress in renal epithelial cells leading to death of some cells and adaptation of others. The pathways involved in these diverse actions remain unclear, but appear to involve activation of phospholipase A2 (PLA2) and redistribution of membrane phospholipids. The present studies examined the possibility that oxalate actions may also involve increased accumulation of ceramide, a lipid-signaling molecule implicated in a variety of pathways, including those leading to apoptotic cell death.

Annexin II is the membrane receptor that mediates the rapid actions of 1alpha,25-dihydroxyvitamin D(3).

1alpha,25-Dihydroxyvitamin D(3) has been shown to exert its effects by both genomic (minutes to hours) and rapid (seconds to minutes) mechanisms. The genomic effects are mediated by interaction with the nuclear vitamin D receptor. We show that the vitamin D analog, [(14)C]-1alpha,25-dihydroxyvitamin D(3) bromoacetate, is specifically bound to a protein (molecular weight 36 kDa) in the plasma membrane of rat osteoblastlike cells (ROS 24/1).

Oxalate toxicity in renal epithelial cells: characteristics of apoptosis and necrosis.

Studies in various tissues, including the kidney, have demonstrated that toxins elicit apoptosis under certain conditions and necrosis under others. The nature of the response has important consequences for the injured tissue in that necrotic cells elicit inflammatory responses, whereas apoptotic cells do not. Thus, there has been considerable interest in defining the mode of cell death elicited by known cytotoxins.

Oxalate-induced changes in the viability and growth of human renal epithelial cells.

Previous studies on the porcine renal epithelial LLC-PK1 cell line demonstrated that oxalate exposure produces concentration-dependent effects on renal cell growth and viability via process(es) involving free radicals. The present studies were conducted to determine whether these findings could be extended to a renal proximal tubular epithelial cell line derived from the human kidney. These studies examined oxalate-induced changes in membrane integrity after short-term exposure (4 h) and changes in cell survival after longer-term exposure (24 to 72 h).

Role of phospholipase A2 in the cytotoxic effects of oxalate in cultured renal epithelial cells.

Background: Oxalate, a common constituent of kidney stones, is cytotoxic for renal epithelial cells. Although the exact mechanism of oxalate-induced cell death remains unclear, studies in various cell types, including renal epithelial cells, have implicated phospholipase A2 (PLA2) as a prominent mediator of cellular injury. Thus, these studies examined the role of PLA2 in the cytotoxic effects of oxalate.

Adenosine A2a-receptor activation enhances cardiomyocyte shortening via Ca2+-independent and -dependent mechanisms.

Adenosine A2a receptor (A2aR) stimulation enhances the shortening of ventricular myocytes. Whether the A2aR-mediated increase in myocyte contractility is associated with alterations in the amplitude of intracellular Ca2+ transients was investigated in isolated, contracting rat ventricular myocytes using the Ca2+-sensitive fluorescent dye fura 2-AM. In the presence of intact inhibitory G protein pathways, 10(-4) M 2-p-(2-carboxyethyl)phenethyl-amino-5'-N-ethylcarboxamidoadenosine (CGS-21680), an A2aR agonist, insignificantly increased Ca2+ transients by 8 +/- 5%, whereas myocyte shortening increased by 54 +/- 1%.

Adenosine A1 receptor-mediated antiadrenergic effects are modulated by A2a receptor activation in rat heart.

Presently, the physiological significance of myocardial adenosine A2a receptor stimulation is unclear. In this study, the influence of adenosine A2a receptor activation on A1 receptor-mediated antiadrenergic actions was studied using constant-flow perfused rat hearts and isolated rat ventricular myocytes. In isolated perfused hearts, the selective A2a receptor antagonists 8-(3-chlorostyryl)caffeine (CSC) and 4-(2-[7-amino-2-(2-furyl)[1,2, 4]triazolo[2,3-a][1,3,5]triazin-5-ylamino]ethyl)phenol (ZM-241385) potentiated adenosine-mediated decreases in isoproterenol (Iso; 10(-8) M)-elicited contractile responses (+dP/dtmax) in a dose-dependent manner.

Effect of bovine bone constituents on broadband ultrasound attenuation measurements.

Broadband ultrasound attenuation (BUA) has been found to correlate positively with bone mineral density (BMD) measured by dual-energy X-ray absorptiometry. However, because there is a significant amount of unexplained variation in this correlation, it has been suggested that BUA might also provide information about bone structure. The purpose of this study was to determine the contribution of bone mineral and organic matrix to BUA and BMD measurements.

Transfection and overexpression of the calcium binding protein calbindin-D28k results in a stimulatory effect on insulin synthesis in a rat beta cell line (RIN 1046-38).

Calbindin-D28k, a calcium binding protein that is thought to act as a facilitator of calcium diffusion in intestine and kidney, is known to be regulated by vitamin D in these tissues. Calbindin-D28k is also present in pancreatic beta cells, but its function in these cells is not known. To determine a role for calbindin-D28k in the beta cell, rat calbindin-D28k was overexpressed in the pancreatic beta cell line RIN 1046-38 by transfection of calbindin in expression vector, and changes in insulin mRNA were examined.

Activation of c-myc gene mediates the mitogenic effects of oxalate in LLC-PK1 cells, a line of renal epithelial cells.

Recent studies on LLC-PK1 cells demonstrated that oxalate, a simple dicarboxylic acid, acts as a mitogen for these renal epithelial cells. Exposure to oxalate initiates DNA synthesis, induces the expression of one of the early growth response genes c-myc and stimulates proliferation of quiescent cultures of LLC-PK1 cells. The present studies examined the possibility that expression of the c-myc protooncogene is obligatory for this mitogenic response.

Inhibitory effect of Ca2+ on renin secretion elicited by chemiosmotic stimuli through actomyosin mediation.

We had previously shown that several experimental manipulations, which are likely to produce osmotic swelling of renin secretory granules, stimulate secretion of renin (C.S. Park, T.

Oxalate toxicity in LLC-PK1 cells, a line of renal epithelial cells.

Purpose: The present studies assessed the possibility that high concentrations of oxalate may be toxic to renal epithelial cells.

Materials And Methods: Subconfluent cultures of LLC-PK1 cells were exposed to oxalate, and the effects on cell morphology, membrane permeability to vital dyes, DNA integrity and cell density were assessed.

Results: Oxalate exposure produced time- and concentration-dependent changes in the light microscopic appearance of LLC-PK1 cells with higher concentrations ( > 140 microM.