Search

Morbidity and mortality from ischaemic heart disease (IHD) and heart failure (HF) remain significant in Europe and are increasing worldwide. Patients with IHD or HF might benefit from novel therapeutic strategies, such as cell-based therapies. We recently discussed the therapeutic potential of cell-based therapies and provided recommendations on how to improve the therapeutic translation of these novel strategies for effective cardiac regeneration and repair. Despite major advances in optimizing these strategies with respect to cell source and delivery method, the clinical outcome of cell-based therapy remains unsatisfactory. Major obstacles are the low engraftment and survival rate of transplanted cells in the harmful microenvironment of the host tissue, and the paucity or even lack of endogenous cells with repair capacity. Therefore, new ways of delivering cells and their derivatives are required in order to empower cell-based cardiac repair and regeneration in patients with IHD or HF. Strategies using tissue engineering (TE) combine cells with matrix materials to enhance cell retention or cell delivery in the transplanted area, and have recently received much attention for this purpose. Here, we summarize knowledge on novel approaches emerging from the TE scenario. In particular, we will discuss how combinations of cell/bio-materials (e.g. hydrogels, cell sheets, prefabricated matrices, microspheres, and injectable matrices) combinations might enhance cell retention or cell delivery in the transplantation areas, thereby increase the success rate of cell therapies for IHD and HF. We will not focus on the use of classical engineering approaches, employing fully synthetic materials, because of their unsatisfactory material properties which render them not clinically applicable. The overall aim of this Position Paper from the ESC Working Group Cellular Biology of the Heart is to provide recommendations on how to proceed in research with these novel TE strategies combined with cell-based therapies to boost cardiac repair in the clinical settings of IHD and HF. [ABSTRACT FROM AUTHOR]

The aim of this study was to develop a PCR-based rapid method to detect Bacillus cereus group cells from paper and cardboard. Primers targeting the 16S rDNA and real-time PCR with SYBR green I detection were used in order to be able to also quantify the target. Both autoclaved cardboard samples spiked with B. cereus vegetative cells or spores and naturally contaminated paper and cardboard samples were studied. Results were compared with culturing verified by commercial (API) tests. Several different methods were tested for DNA isolation from the paper and cardboard samples. Two commercial kits intended for soils, the UltraClean soil DNA kit and the FastDNA spin kit for soil, gave the most reproducible results. In spiked samples, the average yield was 50% of added vegetative cells, but spore yield was only about 10%. PCR results from adding vegetative cells correlated with added colony-forming unit (cfu) values (r=0.93, P <0.001) in the range 100–10,000 cfu g-1. Three out of nine studied paper and cardboard samples contained B. cereus group bacteria, based both on culturing and real-time PCR. The numbers were 102–103 bacteria g-1; and PCR gave somewhat higher results than culturing. Thus, real-time PCR can be used as a rapid semi-quantitative method to screen paper and cardboard samples for contamination with B. cereus group bacteria. [ABSTRACT FROM AUTHOR]

The proposal that yeast, and cells in general, contains redundant genes that enable cells to survive mutational change has been supported by experiments and a strong metaphor. The redundant gene proposal is analyzed, and it is noted that there are many problems with the redundant gene model. An alternative metaphor is suggested to explain the genetic composition of a yeast culture. [ABSTRACT FROM AUTHOR]

Motivation: Quantitative models are increasingly used in systems biology. Usually, these quantitative models involve many molecular species and their associated reactions. When simulating a tissue with thousands of cells, using these large models becomes computationally and time limiting. Results: In this paper, we propose to construct abstractions using information theory notions. Entropy is used to discretize the state space and mutual information is used to select a subset of all original variables and their mutual dependencies. We apply our method to an hybrid model of TRAIL-induced apoptosis in HeLa cell. Our abstraction, represented as a Dynamic Bayesian Network (DBN), reduces the number of variables from 92 to 10, and accelerates numerical simulation by an order of magnitude, yet preserving essential features of cell death time distributions. [ABSTRACT FROM AUTHOR]

The arihritogenic properties of adjuvant oil upon percutaneous administration in DA rats was investigated. Groups of rats were administered single or repeated percutaneous applications of Freund's incomplete adjuvant (FIA) or olive oil on shaved skin with or without prior abrasion of the skin. Control rats were shaved and abrased only. A transient arthritis developed in 8/16 animals after repeated applications of FIA on abrased skin. The incidence of arthritis increased to 7/8 animals when FIA was repeatedly administered via filter paper on abrased skin and covered with a bandage. Histological examination of the arthritic joints showed proliferation of the synovial lining layer, infiltration of mononuclear cells and polymorphonuclear cells in the subsynovial tissue. Some bone and cartilage destruction was also seen. Repeated treatment with olive oil on abrased skin induced joint swelling in 3/15 animals, which did not, however, correspond to any microscopically observable signs of inflammation. Also, a single application of FIA on abrased skin or repeated applications of FIA without abrasion induced arthritis, although with low penetration, whereas control animals had no clinical signs of joint involvement. These findings demonstrate that percutaneous administration of adjuvant oil can cause arthritis in genetically susceptible animals. [ABSTRACT FROM AUTHOR]

Ferrous ion biooxidation is a process with many promising industrial applications: mainly regeneration of ferric ion as an oxidizing reagent in bioleaching processes and depuration of acid mine drainage. The flooded packed-bed bioreactor (FPB) is the design that leads to the highest biooxidation rate. In this bioreactor, biomass is immobilized in a biofilm that consists of an inorganic matrix, formed by precipitated ferric compounds, in the pores of which cells are attached. This biofilm covers the surface of particles (siliceous stone) that form the bed. The chemical stability of this inorganic matrix defines the widest possible pH range in FPBs. At pH below 1, ferric matrix is dissolved and cells are washed out. At pH higher than 2, ferric ion precipitates massively, greatly hindering mass transfer to cells. Thus, among other parameters, pH is recognised as a key factor for operational control in FPBs. This paper aims to explain the effect of pH on FPB operation, with an emphasis on microbial population behaviour. FPBs seeded with mixed inocula were assayed in the pH range from 2.3 to 0.8 and the microbial population was characterised. The microbial consortium in the bioreactor is modified by pH; at pH above 1.3 Acidithiobacillus ferrooxidans is the dominant microorganism, whereas at pH below 1.3 Leptospirillum ferrooxidans dominates. Inoculum can be adapted to acidity during continuous operation by progressively decreasing the pH of the inlet solution. Thus, in the pH range from 2.3 to 1, the biotic factor does not compromise the bioreactor performance. [ABSTRACT FROM AUTHOR]

Yeast flocculation has been found to be important in many biotechnological processes. It has been suggested that flocculation is promoted by decreasing electrostatic repulsion between cells. In this study, we used an unconventional rapid technique-permittivity test-for determination of the flocculation properties and surface charge values of three industrial yeast strains with well-known flocculation characteristics: Saccharomyces cerevisiae NCYC 1017 (brewery, ale), S. pastorianus NCYC 680 (brewery, lager), and Debaryomyces occidentalis LOCK 0251 (unconventional amylolytic yeast). The measurements of permittivity were compared with the results from two classical methods for determination of surface charge: Alcian blue retention and Sephadex DEAE attachment. The permittivity values for particular strains correlated directly with the results of Alcian blue retention ( r = 0.9). The results also confirmed a strong negative relationship between the capacitance of yeast suspensions and their flocculation abilities. The highest permittivity was noted for the ale strain NCYC 1017, with weak flocculation abilities, and the lowest for the flocculating lager yeast NCYC 680. This paper is the first to describe the possibility of using a rapid permittivity test to evaluate the surface charge of yeast cells and their flocculation abilities. This method is of practical value in various biotechnological industries where flocculation is applied as a major method of cell separation. [ABSTRACT FROM AUTHOR]

In this paper, we analyze the pattern of distribution of three populations of picoplanktonic autotrophs measured using flow cytometry. Prochlorococcus sp., Synechococcus sp. and eukaryotic picoplankton were investigated at 58 stations to the south of the Iberian Peninsula including the northeastern Gulf of Cádiz, Strait of Gibraltar and northwestern Alborán Sea, during July 1995. There were important differences in the oceanographic conditions in these regions, with warmer, low-nutrient and low-chlorophyll waters in the Atlantic sector and colder, high-nutrient and high-chlorophyll waters in the Alborán sector in which upwelling occurred. The biomass concentration of picoplanktonic cells was two times higher in the Atlantic area than in the richer Alborán Sea waters. The average integrated abundance of picophytoplankton was negatively correlated with chlorophyll a concentration as well as with inorganic nitrogen availability. Prochlorococcus and Synechococcus were the most abundant groups, and they showed a complementarity in their spatial distribution, with a shallower and more coastal distribution of Synechococcus and the presence of Prochlorococcus mainly at offshore stations and at deeper depths. The ratio of autotrophic picoplankton/total autotrophic biomass showed significant differences on both sides of the Strait, with much higher values in the Gulf of Cádiz sector. [ABSTRACT FROM PUBLISHER]

The comet assay is a technique used to quantify DNA damage and repair at a cellular level. In the assay, cells are embedded in agarose and the cellular content is stripped away leaving only the DNA trapped in an agarose cavity which can then be electrophoresed. The damaged DNA can enter the agarose and migrate while the undamaged DNA cannot and is retained. DNA damage is measured as the proportion of the migratory ‘tail’ DNA compared to the total DNA in the cell. The fundamental basis of these arbitrary values is obtained in the comet acquisition phase using fluorescence microscopy with a stoichiometric stain in tandem with image analysis software. Current methods deployed in such an acquisition are expected to be both objectively and randomly obtained. In this paper we examine the ‘randomness’ of the acquisition phase and suggest an alternative method that offers both objective and unbiased comet selection. In order to achieve this, we have adopted a survey sampling approach widely used in stereology, which offers a method of systematic random sampling (SRS). This is desirable as it offers an impartial and reproducible method of comet analysis that can be used both manually or automated. By making use of an unbiased sampling frame and using microscope verniers, we are able to increase the precision of estimates of DNA damage. Results obtained from a multiple-user pooled variation experiment showed that the SRS technique attained a lower variability than that of the traditional approach. The analysis of a single user with repetition experiment showed greater individual variances while not being detrimental to overall averages. This would suggest that the SRS method offers a better reflection of DNA damage for a given slide and also offers better user reproducibility. [ABSTRACT FROM PUBLISHER]

We develop a general dynamical model as a framework for causal interpretation. We first state a criterion of local independence in terms of measurability of processes that are involved in the Doob–Meyer decomposition of stochastic processes; then we define direct and indirect influence. We propose a definition of causal influence using the concepts of a ‘physical system’. This framework makes it possible to link descriptive and explicative statistical models, and encompasses quantitative processes and events. One of the features of the paper is the clear distinction between the model for the system and the model for the observation. We give a dynamical representation of a conventional joint model for human immunodeficiency virus load and CD4 cell counts. We show its inadequacy to capture causal influences whereas in contrast known mechanisms of infection by the human immunodeficiency virus can be expressed directly through a system of differential equations. [ABSTRACT FROM AUTHOR]

The Saccharomyces cerevisiae BDF1 gene encodes a bromodomain-containing transcription factor. We previously reported that deletion of Bdf1p in yeast cells resulted in increased sensitivity to NaCl stress. In this paper, we show that the function of Bdf1p in salt tolerance is not directly linked with the Ena1p-mediated Na+ extrusion system, and a number of other well-characterized stress-response pathways. Interestingly, however, our data demonstrate that, under the NaCl stress, the absence of Bdf1p leads to mitochondrial dysfunction, including decreasing of mitochondrial membrane potential (ΔΨ) and accumulation of reactive oxygen species, and chromatin fragmentation and condensation. These results indicate that the bromodomain-containing protein, Bdf1p, is involved in the regulation of apoptosis in yeast cells. [ABSTRACT FROM AUTHOR]

Recent technical and conceptual advances in the biological sciences opened the possibility of the construction of newly designed cells. In this paper we review the state of the art of cell engineering in the context of genome research, paying particular attention to what we can learn on naturally reduced genomes from either symbiotic or free living bacteria. Different minimal hypothetically viable cells can be defined on the basis of several computational and experimental approaches. Projects aiming at simplifying living cells converge with efforts to make synthetic genomes for minimal cells. The panorama of this particular view of synthetic biology lead us to consider the use of defined minimal cells to be applied in biomedical, bioremediation, or bioenergy application by taking advantage of existing naturally minimized cells. [ABSTRACT FROM AUTHOR]

Recent studies indicate that during tumorigenic transformations, cells may generate mutations by themselves as a result of error-prone cell division with participation of error-prone polymerases and aberrant mitosis. These mechanisms may be activated in cells by continuing proliferative and survival signaling in a sustained stress environment (SSE). The paper hypothesizes that long-term exposure to this signaling epigenetically reprograms the genome of some cells and, in addition, leads to their senescence. The epigenetic reprogramming results in: (i) hypermethylation of tumor-suppressor genes involved in the onset of cell-cycle arrest, apoptosis and DNA repair; (ii) hypomethylation of proto-oncogenes associated with persistent proliferative activity; and (iii) the global demethylation of the genome and activation of DNA repeats. These epigenetic changes in the proliferating cells associate with their replicative senescence and allow the reprogrammed senescent cells to overcome the cell-cycle arrest and to activate error-prone replications. It is hypothesized that the generation of mutations in the error-prone replications of the epigenetically reprogrammed cells is not random. The mutations match epigenetic alterations in the cellular genome, namely gain of function mutations in the case of hypomethylation and loss of functions in the case of hypermethylation. In addition, continuing proliferation of the cells imposed by signaling in SSE speeds up the natural selection of the mutant cells favoring the survival of the cells with mutations that are beneficial in the environment. In this way, a stress-induced replication of the cells epigenetically reprograms their genome for quick adaptation to stressful environments providing an increased rate of mutations, epigenetic tags to beneficial mutations and quick selection process. In combination, these processes drive the origin of the transformed mammalian cells, cancer development and progression. Support from genomic, biochemical and medical studies for the proposed hypothesis, and its implementations are discussed. [ABSTRACT FROM AUTHOR]

Different studies dealing with the start of progesterone supplementation in assisted reproduction treatment cycles have shown that the problem apparently is the correct timing. We therefore would like to discuss the data on: (i) the start of progesterone replacement in oocyte donation programmes; (ii) the start of progesterone replacement in frozenthawed hormone-supplemented cycles; (ii) the problem of too early a rise of progesterone in fresh IVF cycles as a model of too early an administration of progesterone; and (iv) the benefit of high progesterone levels on the day of embryo transfer in fresh IVF cycles. From the data reviewed in this paper it seems to be appropriate to start progesterone administration before transfer in oocyte donation programmes as well as transfer of cryopreserved/thawed cells as soon as the endometrium is developed sufficiently (=8?mm, trilaminar pattern), and to perform the embryo transfer not before day 34 of progesterone treatment, i.e. embryo development on day 23. Studies dealing with the influence of too early a rise of progesterone in fresh IVF cycles have shown different results. In fact high progesterone levels seem to reflect a high response but not a lower probability of conception. Furthermore, high progesterone levels on the day of embryo transfer in fresh IVF cycles could lower myometrial contractility and therefore increase implantation rates. Since the experience from oocyte donation programes shows the benefit of a longer preparation time using progesterone, and high progesterone levels seem to have a benefit during embryo transfer, this would suggest extending progesterone administration before transfer. However, we have to find the optimal individual transfer protocol after mock cycles, for example with pinopode detection or other methods applicable in routine IVF programmes. We need more studies to be sure whether reproductive outcome after transfer of cryopreservedthawed cells in estrogen/progesterone supplement cycles is influenced by the duration of progesterone pretreatment. If this is so, we must look for practicable methods to modify the protocols according to the individual patient, the embryonic developmental stage during transfer and other variables. [ABSTRACT FROM AUTHOR]

All living cells accumulate high concentrations of K+ in order to keep themselves alive. To this end they have developed a great diversity of transporters. The internal level of K+ is the result of the net balance between the activities of the K+ influx and the K+ efflux transporters. Potassium fluxes have been extensively studied and characterized in Saccharomyces cerevisiae. However, this is not the case in the fission yeast and, in addition, the information available indicates that both yeasts present substantial and interesting differences. In this paper we have reviewed and summarized the information on K+ fluxes in Schizosaccharomyces pombe. We have included some unpublished results recently obtained in our laboratory and, in particular, we have highlighted the significant differences found between the well-known yeast S. cerevisiae and the fission yeast Sch. pombe. [Copyright &y& Elsevier]

The in vivo alkaline single cell gel electrophoresis assay, hereafter the Comet assay, can be used to investigate the genotoxicity of industrial chemicals, biocides, agrochemicals and pharmaceuticals. The major advantages of this assay include the relative ease of application to any tissue of interest, the detection of multiple classes of DNA damage and the generation of data at the level of the single cell. These features give the Comet assay potential advantages over other in vivo test methods, which are limited largely to proliferating cells and/or a single tissue. The Comet assay has demonstrated its reliability in many testing circumstances and is, in general, considered to be acceptable for regulatory purposes. However, despite the considerable data published on the in vivo Comet assay and the general agreement within the international scientific community over many protocol-related issues, it was felt that a document giving detailed practical guidance on the protocol required for regulatory acceptance of the assay was required. In a recent meeting held in conjunction with the 4th International Comet Assay Workshop (Ulm, Germany, 22–25 July 2001) an expert panel reviewed existing data and recent developments of the Comet assay with a view to developing such a document. This paper is intended to act as an update to the more general guidelines which were published as a result of the International Workshop on Genotoxicity Test Procedures. The recommendations are also seen as a major step towards gaining more formal regulatory acceptance of the Comet assay. [ABSTRACT FROM PUBLISHER]

Occupational exposure to ionizing radiation causes chromosomal damage. Some of the damaged cells show a large number of aberrations such as dicentrics, polycentrics, rings and numerous acentric fragments. This paper describes an analysis of the frequency of dicentric chromosomes and acentric fragments in 1260 subjects occupationally exposed to X-rays and 241 controls. Special attention was paid to the incidence of multi-aberrant cells. The 3 year cumulative dose was a significant predictor for all analyzed aberrations. The duration of exposure was a highly significant predictor of the frequency of rogue cells, but not of acentrics and dicentrics. Age and sex were not found to be significant predictors of the analyzed aberrations. [ABSTRACT FROM PUBLISHER]

This paper describes how biological function can be represented in terms of molecular activities and processes. It presents several key features of a data model that is based on a conceptual description of the network of interactions between molecular entities within the cell and between cells. This model is implemented in the aMAZE database that presently deals with information on metabolic pathways, gene regulation, sub- or supracellular locations, and transport. It is shown that this model constitutes a useful generalisation of data representations currently implemented in metabolic pathway databases, and that it can furthermore include multiple schemes for categorising and classifying molecular entities, activities, processes and localisations. In particular, we highlight the flexibility offered by our system in representing multiple molecular activities and their control, in viewing biological function at different levels of resolution and in updating this view as our knowledge evolves. [ABSTRACT FROM AUTHOR]

In this paper we report a study of the effects of splenectomy on the immunosuppressive action of essential fatty acids (EFA) which is thought to be mediated through prostaglandins (PG) produced in the spleen. Experimental allergic encephalomyelitis (EAE) was induced in normal, splenectomized and sham splenectomized Lewis rats. EFA were administered orally, the animals in the control groups being treated with liquid paraffin. Treatment with EFA significantly suppressed clinical disease in those animals in which EAE was induced by the inoculation of central nervous system material of guinea-pigs or by passive transfer by Con A-stimulated spleen cells. Splenectomy abrogated the suppressive effect of EFA. This observation, together with previous results showing the abrogation of EFA immunosuppression by an inhibitor of the biosynthesis of PG from EFA, led us to postulate a close relationship between EFA, PG and a splenic factor suppressing immunopathological mechanisms in EAE. [ABSTRACT FROM AUTHOR]

This paper describes further confirmation of the successful application of the macrophage electrophoretic mobility (MEM) test to the detection of malignant disease. Results from fifty-one patients and eighteen controls are presented. The apparatus and technique used for the measurement of macrophage elctrophoretic mobility differed from those previously used in other investigations. Further information is presented on the nature and behaviour of macrophage slowing factor(s), and experiments concerning the possible use of cells other than guinea-pig macrophages as indicators of slowing factor production are also described. [ABSTRACT FROM AUTHOR]

This paper demonstrates that CD40 is expressed on rheumatoid synovial pannus and primary fibroblast cell lines established from rheumatoid and osteoarthritic synovium as well as normal skin. Among various tested cytokines, interferon-gamma (IFN-γ) and lo a lower extent, tumour necrosis factor-alpha (TNE-α) were found to upregulate CD40 expression on fibroblasts. Synovial and skin fibroblasts cultured over CD40 Ligand transfected L cells (L-CD40L) demonstrate a CD40 specific increase of DNA synthesis as measured by tritiated thymidine incorporation. Cell-cycle analysis and enumeration of viable cells further show that CD40 induced fibroblast proliferation. Costimulation with L-CD40 L and IFN-γ, resulted in maximal proliferation. Engagement of fibroblasts CD40 increased the IL-l-induced production of granulocyte macrophage-colony stimulating factor and macrophage inflammatory protein-Iα MIP-lα, CD40L activated fibroblasts showed decreased levels of CD40, but only marginal alterations of other cell-surface antigens. Taken together, the present results indicate that fibroblasts express functional CD40 and suggest a possible role of CD40L expressing cells, such as activated T cells and mast cells, in the development of synovium hyperplasia. [ABSTRACT FROM AUTHOR]

Patients affected by AIDS-related complex (ARC) show several immunological abnormalities which may lead to a disregulation of immunosurveillance against viral latent infections. In this paper evidence for Epstein-Barr virus (EBV) reactivation in seven out of eight affected by persistent generalized lymphadenopathy is given. These patients showed either elevated levels of circulating EBNA-positive transformed cells or depressed EBV-specific T cell cytotoxicity, as assessed by the regression assay, or both. A direct involvement of EBV in the pathogenesis of ARC is thus suggested. Natural killer cell activity was found decreased, correlating to the evidence of circulating EBV-infected cells and of impaired EBV-specific immune control. These data provide evidence that, when specific immune mechanisms lose control on ubiquitous latent viruses, the risk for reactivation becomes higher. In the case of EBV, direct evidence of this event is provided by the emergence in the peripheral blood of clones of infected cells with unlimited growth potential. [ABSTRACT FROM AUTHOR]

The presence of J chain in human immunocytes containing various immunoglobulin classes has already been reported and in this paper we investigated the presence of J chain in human myeloma cells using light and electron microscopy. Myeloma cells were positive for cytoplasmic J chain in thirteen cases six of fifteen IgG myeloma, two of seven IgA myeloma, two of nine B J myeloma and three of three primary macroglobulinaemia. None of the four with benign monoclonal gammopathy was positive for J chain. The ultrastructural localization of J chain in IgG myeloma cells was similar to that γ chain, i.e. around the nuclear membrane, in the endoplasmic reticulum (ER) and it the Golgi apparatus. The latter finding is compatible with the presence of J chain in the urine of the same patient. We examined the urine from nine patients with J chain-positive cells and secretion of J chain was confirmed in three patients two with IgG myeloma and one with B J myeloma. In none of twelve in whom the immunocytochemical findings were negative for J chain was there evidence of urinary J chain. [ABSTRACT FROM AUTHOR]

Females show a disproportionate burden of Alzheimer's disease pathology and higher Alzheimer's disease dementia prevalences compared to males, yet the mechanisms driving these vulnerabilities are unknown. There is sexual dimorphism in immunological functioning, and neuroimmune processes are implicated in Alzheimer's disease genesis. Using neuropathology indicators from human brain tissue, we examined the mediational role of microglial activation on the relationship between amyloid and tau and how it differs by sex. 187 decedents (64% female; 89 mean age at death; 62% non-demented) from the Rush Memory and Aging Project completed neuropathological evaluations with brain tissue quantified for microglial activation, amyloid-β and tau. Proportion of morphologically activated microglia was determined via immunohistochemistry (HLA-DP-DQ-DR) and morphological staging (stage I, II or III). Amyloid-β and tau burden were quantified via immunohistochemistry (M00872 or AT8, respectively). Using causal counterfactual modelling, we estimated the mediational effect of microglial activation on the amyloid-β to tau relationship in the whole sample and stratified by sex (amyloid-β → microglial activation → tau). Alternative models tested the role of microglia activation as the precipitating event (microglial activation → amyloid-β → tau). Microglial activation significantly mediated 33% [95% confidence interval (CI) 10-67] of the relationship between amyloid-β and tau in the whole sample; stratified analyses suggested this effect was stronger and only statistically significant in females. 57% (95% CI 22-100) of the effect of amyloid-β on tau was mediated through microglial activation in females, compared to 19% (95% CI 0-64) in males. Regional analyses suggested that mediational effects were driven by greater cortical versus subcortical microglial activation. Relationships were independent of cerebrovascular disease indices. Alternative models suggested that in females, microglial activation was a significant exposure both preceding the amyloid-β to tau relationship (mediational effect: 50%, 95% CI 23-90) and directly related to tau burden (microglia direct effect: 50%, 95% CI 10-77). By contrast, in males, only the direct effect of microglial activation to tau reached significance (74%, 95% CI 32-100) (mediational effect: 26%, 95% CI 0-68). Our models suggest a reciprocal, bidirectional relationship between amyloid-β and microglial activation that significantly accounts for tau burden in females. By contrast, in males, direct independent (non-mediational) relationships between microglial activation or amyloid-β with tau were observed. Microglial activation may be disproportionately important for Alzheimer's disease pathogenesis in females. Determining sex-specific vulnerabilities to Alzheimer's disease development both inform fundamental pathophysiology and support precision health approaches for this heterogeneous disease. [ABSTRACT FROM AUTHOR]

Study Question: Does age affect endometrial gene expression?Summary Answer: Using unsupervised artificial intelligence methods, we report for the first time that endometrial gene expression changes from 35 years of age in women.What Is Known Already: Female fertility declines with age, largely attributed to declining oocyte quality and ovarian reserve. Combined with other evidence, a longstanding paradigm holds that age does not affect the endometrial function and age has not been controlled for properly in endometrial studies.Study Design, Size, Duration: A retrospective in silico analysis was performed of endometrial transcriptomic data from the Gene Expression Omnibus (GEO) sample repository for 27 women of different ages. Results were validated in an independent gene expression dataset of 20 endometrial samples from women aged 23-43 years.Participants/materials, Setting, Methods: A systematic search was performed in GEO from October 2016 to January 2019 to identify transcriptomic studies involving women of different ages. Included samples were from norm-ovulatory, women of reproductive age (23-49 years) with regular menstrual cycles who were free of endometriosis and used as controls in a previous endometrial study. We used raw gene expression data and metadata from these samples to investigate the effect of age on endometrial gene expression. Files were downloaded, pre-processed and explored for potential confounding variables and outliers. Artificial intelligence methods were applied to define age groups, and differential expression and functional analyses were applied to demonstrate and understand the effect of age on gene expression at the molecular level. Functional results were validated in an independent gene expression dataset of 20 endometrial samples from women aged 23-43 years.Main Results and the Role Of Chance: Analysis of the initially retrieved endometrial datasets revealed the age of participants was not available (33.33%) or traceable (43.33%) in most studies. However, one study was suitable for age analysis (GSE4888, n = 27, 23-49 years). Samples showed different transcriptomic profiles according to age, beginning at 35 years. A total of 5778 differentially expressed genes and 27 significantly altered endometrial functions (false discovery rate (FDR) < 0.05) were associated with endometrial gene expression changes related to age. Interestingly, 81.48% of affected functions were related to up-regulation of ciliary processes, with 91 genes involved in cilia motility and ciliogenesis. Other functions included dysregulation of the vascular endothelial growth factor signalling pathway and inhibition of epithelial proliferation triggered by 37 genes involved in cell cycle arrest, angiogenesis, insulin signalling and telomere protection. These findings were validated in an independent dataset using a non-targeted approach; 20 up-regulated ciliary processes (FDR < 0.02) and 6 down-regulated functions related to cell cycle arrest were identified as affected by age, among other hallmarks of ageing such as DNA repair inhibition or sugar metabolism (FDR < 0.05).Large Scale Data: Data underlying this article are available in GEO, IDs: GSE4888 (main dataset) and GSE102131 (validation dataset).Limitations, Reasons For Caution: This study is limited in size, as are most studies of endometrial transcriptomics where whole-transcriptome analysis considers nearly 22 000 variables in a relatively small population. Yet, our study includes a main sample set and subsequent validation set that enhances reproducibility of our results and provides reasonable evidence for concluding that age affects endometrial gene expression. A larger study prospectively controlling for patient characteristics is needed to accurately describe changes related to age, with a higher sample size and across a wide age range. Additional studies also are necessary to determine the endometrial ageing contribution to infertility for ultimate translation to a clinical setting.Wider Implications Of the Findings: Our findings support an influence of age on the endometrium in a genome-wide functional approach, breaking the endometrial ageing paradigm in human reproduction. To our knowledge, this work is the first to identify, using a genome-wide functional non-targeted approach, ciliary processes as the primary dysregulated function associated with maternal age. These results should guide the research community to control for age as a potential confounding variable in endometrial gene expression studies and to consider endometrial ageing in further studies as a potential cause of infertility in the clinical setting. The reported functional dysregulations could contribute to diminished embryo implantation with age and further studies will demonstrate if such dysregulation underlies some cases of implantation failure. Additionally, the discovery of these functional alterations could enable mechanistic studies, particularly around the age-related increase in uterine pathologies.Study Funding/competing Interest(s): This research was funded by the Instituto de Salud Carlos III through Miguel Servet programme (CP20/00118) granted to Patricia Diaz-Gimeno (Spanish Government) co-funded by FEDER; and by IVI Foundation (1706-FIVI-041-PD). A.D.-P. (FPU/15/01398) and A.P.-L. (FPU18/01777) are granted by the pre-doctoral programme fellowship from the Ministry of Science, Innovation and Universities (Spanish Government). The authors do not have any competing interests to declare.Trial Registration Number: N/A. [ABSTRACT FROM AUTHOR]

Plant programmed cell death (PCD) is a genetically controlled process that plays an important role in development and stress responses. Reactive oxygen species (ROS) are key inducers of PCD. The addition of 50 mM H2O2 to tobacco Bright Yellow-2 (TBY-2) cell cultures induces PCD. A comparative proteomic analysis of TBY-2 cells treated with 50 mM H2O2 for 30 min and 3 h was performed. The results showed early down-regulation of several elements in the cellular redox hub and inhibition of the protein repair–degradation system. The expression patterns of proteins involved in the homeostatic response, in particular those associated with metabolism, were consistently altered. The changes in abundance of several cytoskeleton proteins confirmed the active role of the cytoskeleton in PCD signalling. Cells undergoing H2O2-induced PCD fail to cope with oxidative stress. The antioxidant defence system and the anti-PCD signalling cascades are inhibited. This promotes a genetically programmed cell suicide pathway. Fifteen differentially expressed proteins showed an expression pattern similar to that previously observed in TBY-2 cells undergoing heat shock-induced PCD. The possibility that these proteins are part of a core complex required for PCD induction is discussed. [ABSTRACT FROM PUBLISHER]

An abscisic acid (ABA)-insensitive Vicia faba mutant, fia (fava bean impaired in ABA-induced stomatal closure) had previously been isolated. In this study, it was investigated how FIA functions in ABA signalling in guard cells of Vicia faba. Unlike ABA, methyl jasmonate (MeJA), H2O2, and nitric oxide (NO) induced stomatal closure in the fia mutant. ABA did not induce production of either reactive oxygen species or NO in the mutant. Moreover, ABA did not suppress inward-rectifying K+ (Kin) currents or activate ABA-activated protein kinase (AAPK) in mutant guard cells. These results suggest that FIA functions as an early signal component upstream of AAPK activation in ABA signalling but does not function in MeJA signalling in guard cells of Vicia faba. [ABSTRACT FROM PUBLISHER]

The chain-forming diatom Chaetoceros vixvisibilis is one of the most abundant and frequent diatoms in the northeastern Adriatic Sea. This species had not been previously studied by electron microscopy. Its general morphology is similar to those species allocated in the subgenus Hyalochaete: cells and chains (straight, of variable length, usually 4–8 cells per chain, but can be longer) of delicate appearance, valves thinly silicified, with slightly eccentric annulus and costae radiating from it, a single rimoportula present only at terminal valves, long, thin and delicate setae perforated by tiny poroids with no spines, and one plate-like chloroplast per cell. Setae with no spines are not common among members of Hyalochaete (and the whole genus Chaetoceros), except C. socialis. The most characteristic feature is, however, the resting spores commonly found, which also show morphological variability, from solitary to paired, both valves convex to domed and surface smooth or with small granules, and one to four strong spines often branching dichotomically. Abundances of C. vixvisibilis are positively correlated to the Po River inflow. Maximum abundances (>106 cells L−1) were found in the period April–July, in the temperature range between 12 and 16°C, salinity between 33 and 38, when total phosphorus concentration is higher than 0.4 µmol L−1, but occasionally also in nitrogen limited conditions. [ABSTRACT FROM PUBLISHER]

Iron ranks fourth in the sequence of abundance of the elements in the Earth's crust, but its low bio-availability often limits plant growth. When present in suboptimal amounts, the acquisition of iron by plants is aided by a suite of responses, comprising molecular and developmental changes that facilitate the uptake of iron from sparingly soluble pools. The expression of genes involved in the mobilization of iron (CsHA1), the reduction of ferric chelates (CsFRO1), and in the uptake of ferrous iron (CsIRT1) was investigated in epidermal cells of Fe-sufficient and Fe-deficient cucumber (Cucumis sativum L.) roots using the Laser Microdissection and Pressure Catapulting (LMPC) method. Growing plants hydroponically in media deprived of iron induced the differentiation of almost all epidermal cells into root hairs. No root hairs were formed under iron-replete conditions. The formation of root hairs in response to Fe starvation was associated with a dramatic increase in message levels of CsFRO1, CsIRT1, and the iron-inducible H+-ATPase isoform CsHA1, when compared to epidermal cells of Fe-sufficient plants. On the contrary, transcripts of a housekeeping ATPase isoform, CsHA2, were not detected in root hairs, suggesting that Fe-deficiency-induced acidification is predominantly mediated by CsHA1. These data show that the formation of root hairs in response to iron deficiency is associated with cell-specific accumulation of transcripts that are involved in iron acquisition. The results also show that this includes the differential regulation of ATPase isoforms with similar function, but supposedly different characteristics, to counteract the imbalance in nutrient supply efficiently. [ABSTRACT FROM PUBLISHER]

In an important class of problems involving mixture distributions, interest focuses on the mixture proportions, considering other possible parameters as nuisance parameters. We formulate a new variation on such problems that arose in a study on the link between the number of cells in a charge-coupled detector image sensor that turned defective because of cosmic radiation and the storage conditions of such sensors. In this variation, the component densities are bivariate, there are two classes and only a subset of the mixture proportions is of relevance. We propose a nonparametric method to estimate the relevant subset of the proportions and apply our method to the data in our study. [ABSTRACT FROM AUTHOR]

Presents a test conducted at the cell level that compared numbers of part types in free-living eukaryotic cells, cells of metazoans and land plants. Categorization and counts of part types in a metazoan and a protist; Alternative evolutionary interpretations; Alternative views of the complexity drain.

Mechanical properties such as substrate stiffness are a ubiquitous feature of a cell's environment. Many types of animal cells exhibit canonical phenotypic plasticity when grown on substrates of differing stiffness, in vitro and in vivo. Whether such plasticity is a multivariate optimum due to hundreds of millions of years of animal evolution, or instead is a compromise between conflicting selective demands, is unknown. We addressed these questions by means of experimental evolution of populations of mouse fibroblasts propagated for approximately 90 cell generations on soft or stiff substrates. The ancestral cells grow twice as fast on stiff substrate as on soft substrate and exhibit the canonical phenotypic plasticity. Soft-selected lines derived from a genetically diverse ancestral population increased growth rate on soft substrate to the ancestral level on stiff substrate and evolved the same multivariate phenotype. The pattern of plasticity in the soft-selected lines was opposite of the ancestral pattern, suggesting that reverse plasticity underlies the observed rapid evolution. Conversely, growth rate and phenotypes did not change in selected lines derived from clonal cells. Overall, our results suggest that the changes were the result of genetic evolution and not phenotypic plasticity per se. Whole-transcriptome analysis revealed consistent differentiation between ancestral and soft-selected populations, and that both emergent phenotypes and gene expression tended to revert in the soft-selected lines. However, the selected populations appear to have achieved the same phenotypic outcome by means of at least two distinct transcriptional architectures related to mechanotransduction and proliferation. [ABSTRACT FROM AUTHOR]

Increasing evidence suggests that microglial activation is strongly linked to the initiation and progression of Parkinson's disease. Cell-to-cell propagation of α-synuclein pathology is a highlighted feature of Parkinson's disease, and the focus of such research has been primarily on neurons. However, recent studies as well as the data contained herein suggest that microglia, the primary phagocytes in the brain, play a direct role in the spread of α-synuclein pathology. Recent data revealed that plasma exosomes derived from Parkinson's disease patients (PD-EXO) carry pathological α-synuclein and target microglia preferentially. Hence, PD-EXO are likely a key tool for investigating the role of microglia in α-synuclein transmission. We showed that intrastriatal injection of PD-EXO resulted in the propagation of exosomal α-synuclein from microglia to neurons following microglia activation. Toll-like receptor 2 (TLR2) in microglia was activated by exosomal α-synuclein and acted as a crucial mediator of PD-EXO-induced microglial activation. Additionally, partial microglia depletion resulted in a significant decrease of exogenous α-synuclein in the substantia nigra. Furthermore, exosomal α-synuclein internalization was initiated by binding to TLR2 of microglia. Excessive α-synuclein phagocytosis may induce the inflammatory responses of microglia and provide the seed for microglia-to-neuron transmission. Consistently, TLR2 silencing in microglia mitigated α-synuclein pathology in vivo. Overall, the present data support the idea that the interaction of exosomal α-synuclein and microglial TLR2 contribute to excessive α-synuclein phagocytosis and microglial activation, which lead to the further propagation and spread of α-synuclein pathology, thereby highlighting the pivotal roles of reactive microglia in α-synuclein transmission. [ABSTRACT FROM AUTHOR]

Bilaterian animals display a wide variety of cell types, organized into defined anatomical structures and organ systems, which are mostly absent in prebilaterian animals. Xenacoelomorpha are an early-branching bilaterian phylum displaying an apparently relatively simple anatomical organization that have greatly diverged from other bilaterian clades. In this study, we use whole-body single-cell transcriptomics on the acoel Isodiametra pulchra to identify and characterize different cell types. Our analysis identifies the existence of ten major cell type categories in acoels all contributing to main biological functions of the organism: metabolism, locomotion and movements, behavior, defense, and development. Interestingly, although most cell clusters express core fate markers shared with other animal clades, we also describe a surprisingly large number of clade-specific marker genes, suggesting the emergence of clade-specific common molecular machineries functioning in distinct cell types. Together, these results provide novel insight into the evolution of bilaterian cell types and open the door to a better understanding of the origins of the bilaterian body plan and their constitutive cell types. [ABSTRACT FROM AUTHOR]

The article presents various research papers related to inhibitory proteins and non-lethal effects, published in an earlier issue of the journal "Clinical & Experimental Immunology". One of the abstracts talk about role of inhibitory membrane proteins in the complement dependent killing of trophoblast cells. Trophoblast cells are known to be highly resistant to killing by decidual NK cells. HRF20 is deficient in a patient suffering from paroxysmal nocturnal hemoglobinuria. This deficiency in HRF20 is not only on blood cells but also other tissues including endothelial cells and peripheral nerves.

The article focuses on the physiological prerequisites required for the transition of autotrophic plants from water to terrestrial life. It is stated that the presence of cells with central vacuoles seems to be a prerequisite for invasion of land by plants. An inner aqueous medium is provided by their cell sap which determines the status of protoplasmic hydration. There is an reemphasis of the fact that the protoplasm is the site of all vital processes. Therefore, it is important to study the hydration of protoplasm.

Traumatic brain injury (TBI) is a leading cause of death and disability worldwide and is a risk factor for dementia later in life. Research into the pathophysiology of TBI has focused on the impact of injury on the neuron. However, recent advances have shown that TBI has a major impact on synapse structure and function through a combination of the immediate mechanical insult and the ensuing secondary injury processes, leading to synapse loss. In this review, we highlight the role of the synapse in TBI pathophysiology with a focus on the confluence of multiple secondary injury processes including excitotoxicity, inflammation and oxidative stress. The primary insult triggers a cascade of events in each of these secondary processes and we discuss the complex interplay that occurs at the synapse. We also examine how the synapse is impacted by traumatic axonal injury and the role it may play in the spread of tau after TBI. We propose that astrocytes play a crucial role by mediating both synapse loss and recovery. Finally, we highlight recent developments in the field including synapse molecular imaging, fluid biomarkers and therapeutics. In particular, we discuss advances in our understanding of synapse diversity and suggest that the new technology of synaptome mapping may prove useful in identifying synapses that are vulnerable or resistant to TBI. [ABSTRACT FROM AUTHOR]

Study Question: How does exposure to a testosterone rich environment affect the function and gene expression of human fallopian tube epithelium (hFTE)?Summary Answer: Elevated testosterone level alters several gene transcripts that regulate cilia expression and negatively impacts the rate of cilia beating.What Is Known Already: The presence of estrogen in the follicular phase of the menstrual cycle increases the human fallopian tube ciliary beating frequency. The luteal phase, triggered by ovulation and increasing progesterone, is marked by a decrease in ciliary beating. Women with polycystic ovarian syndrome (PCOS) may have twice the serum level of testosterone than ovulatory women. To date, the effect of elevated androgens on the function of the human fallopian tube is not well-understood. We chose to examine the impact of elevated testosterone on hFTE.Study Design, Size, Duration: A prospective basic science study of human fallopian tube specimens from reproductive-aged women undergoing benign gynecologic surgery was performed. Fallopian tube removal at a large US academic center was collected and provided to us to continue with epithelium isolation and culturing. A total of 12 patients were analyzed in the study.Participants/materials, Setting, Methods: Fallopian tube epithelium was isolated and exposed to two different conditions: normal with low testosterone concentration of 0.8 nM and PCOS-like, with high testosterone concentration of 2 nM. The study was conducted in both static and dynamic conditions in microfluidic devices for a total of 14 days, after which the tissue was collected for processing including RNA extraction, quantitative PCR and immunohistochemistry. After the first 7 days of each experiment, a sample of tissue from each condition was imaged to quantify cilia beating frequency.Main Results and the Role Of Chance: hFTE exposed to the 2 nM testosterone displayed slower cilia beating, inhibited estrogen signaling and decreased expression of the ciliary marker FOXJ1 when compared to stimulation with 0.8 nM testosterone.Large Scale Data: N/A.Limitations, Reasons For Caution: The in vivo response to elevated testosterone may differ from in vitro studies. RNA amount was limited from tissue cultured in the microfluidic devices as compared to static culture.Wider Implications Of the Findings: Understanding elevated testosterone in tubal function may explain an additional contribution to subfertility in women with PCOS and other hyper-androgen disorders, aside from oligo-ovulation. Furthermore, this adds to the body of literature of fallopian tube function using a microfluidic device.Study Funding/competing Interest(s): NIH grants: UH3 ES029073 and R01 CA240301. There are no competing interests. [ABSTRACT FROM AUTHOR]

Precursor T-cell lymphoblastic neoplasms are aggressive malignancies in need for more effective and specific therapeutic treatments. A significant fraction of these neoplasms harbor deletions on the locus 9p21, targeting the tumor suppressor CDKN2A but also deleting the aconitase 1 (ACO1) gene, a neighboring housekeeping gene involved in cytoplasm and mitochondrial metabolism. Here we show that reducing the aconitase activity with fluorocitrate decreases the viability of T-cell lymphoblastic neoplasia cells in correlation to the differential aconitase expression. The consequences of the treatment were evidenced in vitro using T-cell lymphoblastic neoplasia cell lines exhibiting 9p21 deletions and variable levels of ACO1 expression or activity. Similar results were observed in melanoma cell lines, suggesting a true potential for fluorocitrate in different cancer types. Notably, ectopic expression of ACO1 alleviated the susceptibility of cell lines to fluorocitrate and, conversely, knockdown experiments increased susceptibility of resistant cell lines. These findings were confirmed in vivo on athymic nude mice by using tumor xenografts derived from two T-cell lines with different levels of ACO1. Taken together, our results indicate that the non-targeted ACO1 deficiency induced by common deletions exerts a collateral cellular lethality that can be used as a novel therapeutic strategy in the treatment of several types of cancer. [ABSTRACT FROM AUTHOR]

Single-cell RNA sequencing (scRNA-seq) has generated numerous data and renewed our understanding of biological phenomena at the cellular scale. Identification of cell types has been one of the most prevalent means for interpreting scRNA-seq data, based upon which connections are made between the transcriptome and phenotype. Herein, we attempt to review the methods and tools that dedicate to the task regarding their feature and usage and look at the possibilities for scRNA-seq development in the near future. [ABSTRACT FROM AUTHOR]

Motivation Cells in an organism share a common evolutionary history, called cell lineage tree. Cell lineage tree can be inferred from single cell genotypes at genomic variation sites. Cell lineage tree inference from noisy single cell data is a challenging computational problem. Most existing methods for cell lineage tree inference assume uniform uncertainty in genotypes. A key missing aspect is that real single cell data usually has non-uniform uncertainty in individual genotypes. Moreover, existing methods are often sampling based and can be very slow for large data. Results In this article, we propose a new method called ScisTree, which infers cell lineage tree and calls genotypes from noisy single cell genotype data. Different from most existing approaches, ScisTree works with genotype probabilities of individual genotypes (which can be computed by existing single cell genotype callers). ScisTree assumes the infinite sites model. Given uncertain genotypes with individualized probabilities, ScisTree implements a fast heuristic for inferring cell lineage tree and calling the genotypes that allow the so-called perfect phylogeny and maximize the likelihood of the genotypes. Through simulation, we show that ScisTree performs well on the accuracy of inferred trees, and is much more efficient than existing methods. The efficiency of ScisTree enables new applications including imputation of the so-called doublets. Availability and implementation The program ScisTree is available for download at: https://github.com/yufengwudcs/ScisTree. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Plant cell walls are sophisticated carbohydrate-rich structures representing the immediate contact surface with the extracellular environment, often serving as the first barrier against biotic and abiotic stresses. Notably, a variety of perturbations in plant cell walls result in upregulated jasmonate (JA) production, a phytohormone with essential roles in defense and growth responses. Hence, cell wall-derived signals can initiate intracellular JA-mediated responses and the elucidation of the underlying signaling pathways could provide novel insights into cell wall maintenance and remodeling, as well as advance our understanding on how is JA biosynthesis initiated. This Mini Review will describe current knowledge about cell wall-derived damage signals and their effects on JA biosynthesis, as well as provide future perspectives. [ABSTRACT FROM AUTHOR]

Glycomics is a developing field that provides structural information on complex populations of glycans isolated from tissues, cells and organs. Strategies employing matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) are central to glycomic analysis. Current MALDI-based glycomic strategies are capable of efficiently analyzing glycoprotein and glycosphingolipid glycomes but little attention has been paid to devising glycomic methodologies suited to the analysis of glycosaminoglycan (GAG) polysaccharides which pose special problems for MALDI analysis because of their high level of sulfation and large size. In this paper, we describe MALDI strategies that have been optimized for the analysis of highly sulfated GAG-derived oligosaccharides. A crystalline matrix norharmane, as well as an ionic liquid 1-methylimidazolium α-cyano-4-hydroxycinnamate (ImCHCA), have been used for the analysis of heparin di-, tetra-, hexa- and decasaccharides carrying from 2 to 13 sulfate groups. Information about the maximum number of sulfate groups is obtained using the ionic liquid whereas MALDI-TOF/TOF MS/MS experiments using norharmane allowed the determination of the nature of the glycosidic backbone, and more precise information about the presence and the position in the sequence of N-acetylated residues. [ABSTRACT FROM AUTHOR]

Up to prescribed limits, the maximum test compound concentrations used in mammalian cell genotoxicity assays in vitro are determined by cytotoxicity, unless limited by solubility in solvents or culture medium. However, ‘cytotoxicity’ is different in the various test systems, both in the methods used to estimate it and the levels of toxicity that must be achieved. For example, in cytogenetic assays, the acceptable level of toxicity is defined as a ‘significant reduction (>50%)’ in cell number, culture confluency or mitotic index (MI) (OECD 473, ICH S2A), whereas mutation tests require relative total growth or cloning efficiency (CE) to be reduced by 80–90% (OECD 476, ICH S2A). In this study using mouse lymphoma cells, it was shown that, for a variety of agents with differing modes of action, cytotoxicity varies considerably depending on the method used to estimate it. Specifically, trypan blue exclusion, MI and binucleate incidence all grossly underestimate cytotoxicity in comparison with cell growth or CE. If the performance of different test systems is to be compared, or if data from different assays are to be used for the meaningful assessment of a novel chemical entity, it is essential that similar methods to determine cytotoxicity are used for them all. The purpose of this paper is not to recommend a specific method to determine cytotoxicity, although it can be argued that any such method must quantify the proportion of cells capable of division following treatment, but rather to draw attention to the fact that apparent toxicity depends upon the method used to estimate it. [ABSTRACT FROM AUTHOR]

Motivation The development of single-cell RNA-sequencing (scRNA-seq) provides a new perspective to study biological problems at the single-cell level. One of the key issues in scRNA-seq analysis is to resolve the heterogeneity and diversity of cells, which is to cluster the cells into several groups. However, many existing clustering methods are designed to analyze bulk RNA-seq data, it is urgent to develop the new scRNA-seq clustering methods. Moreover, the high noise in scRNA-seq data also brings a lot of challenges to computational methods. Results In this study, we propose a novel scRNA-seq cell type detection method based on similarity learning, called SinNLRR. The method is motivated by the self-expression of the cells with the same group. Specifically, we impose the non-negative and low rank structure on the similarity matrix. We apply alternating direction method of multipliers to solve the optimization problem and propose an adaptive penalty selection method to avoid the sensitivity to the parameters. The learned similarity matrix could be incorporated with spectral clustering, t-distributed stochastic neighbor embedding for visualization and Laplace score for prioritizing gene markers. In contrast to other scRNA-seq clustering methods, our method achieves more robust and accurate results on different datasets. Availability and implementation Our MATLAB implementation of SinNLRR is available at, https://github.com/zrq0123/SinNLRR. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

Paclitaxel is a main impressive chemotherapeutic agent with unique mode of action and broad-spectrum activity against cancers. Hazel (Corylus avellana) is a paclitaxel-producing species through bioprospection. Endophytic fungi have significant roles in plant paclitaxel production. This study evaluated the effect of co-culture of C. avellana cells and paclitaxel-producing endophytic fungus, Epicoccum nigrum strain YEF2 and also the effect of elicitors derived from this fungal strain on paclitaxel production. The results clearly revealed that co-culture of C. avellana cells and E. nigrum was more effective than elicitation of C. avellana cells by only cell extract or culture filtrate of this fungal strain. Co-culture of C. avellana cells and E. nigrum surpassed monocultures in terms of paclitaxel production designating their synergistic interaction potential. Fungal inoculum amount, co-culture establishment time and co-culture period were important factors for achieving the maximum production of paclitaxel in this co-culture system. The highest total yield of paclitaxel (404.5 µg L−1) was produced in co-culture established on 13th day using 3.2% (v/v) of E. nigrum mycelium suspension, which was about 5.5 and 136.6 times that in control cultures of C. avellana cells and E. nigrum, respectively. This is the first report on positive effect of co-culture of paclitaxel-producing endophytic fungus and non-host plant cells for enhancing paclitaxel production. [ABSTRACT FROM AUTHOR]