Search

Among multimessenger observations of the next Galactic core-collapse supernova, Super-Kamiokande (SK) plays a critical role in detecting the emitted supernova neutrinos, determining the direction to the supernova (SN), and notifying the astronomical community of these observations in advance of the optical signal. In 2022, SK has increased the gadolinium dissolved in its water target (SK-Gd) and has achieved a Gd concentration of 0.033%, resulting in enhanced neutron detection capability, which in turn enables more accurate determination of the supernova direction. Accordingly, SK-Gd’s real-time supernova monitoring system has been upgraded. SK_SN Notice, a warning system that works together with this monitoring system, was released on 2021 December 13, and is available through GCN Notices. When the monitoring system detects an SN-like burst of events, SK_SN Notice will automatically distribute an alarm with the reconstructed direction to the supernova candidate within a few minutes. In this paper, we present a systematic study of SK-Gd’s response to a simulated Galactic SN. Assuming a supernova situated at 10 kpc, neutrino fluxes from six supernova models are used to characterize SK-Gd’s pointing accuracy using the same tools as the online monitoring system. The pointing accuracy is found to vary from 3° to 7° depending on the models. However, if the supernova is closer than 10 kpc, SK_SN Notice can issue an alarm with three-degree accuracy, which will benefit follow-up observations by optical telescopes with large fields of view.

We report the first search result for the flux of astrophysical electron antineutrinos for energies ${ \mathcal O }(10)\,\mathrm{MeV}$ in the gadolinium-loaded Super-Kamiokande (SK) detector. In 2020 June, gadolinium was introduced to the ultrapure water of the SK detector in order to detect neutrons more efficiently. In this new experimental phase, SK-Gd, we can search for electron antineutrinos via inverse beta decay with efficient background rejection thanks to the high efficiency of the neutron tagging technique. In this paper, we report the result for the initial stage of SK-Gd, during 2020 August 26, and 2022 June 1 with a 22.5 × 552 kton · day exposure at 0.01% Gd mass concentration. No significant excess over the expected background in the observed events is found for the neutrino energies below 31.3 MeV. Thus, the flux upper limits are placed at the 90% confidence level. The limits and sensitivities are already comparable with the previous SK result with pure water (22.5 × 2970 kton · day) owing to the enhanced neutron tagging. Operation with Gd increased to 0.03% started in 2022 June.

The formation of silica particles by the ammonia-catalyzed hydrolysis of tetraethyl orthosilicate (TEOS) in the polyoxyethylene (5) nonylphenyl ether (NP-5)/cyclohexane/water microemulsion system was investigated by time-resolved small-angle X-ray scattering (SAXS). The SAXS data could be modeled as a combination of two species where one describes the silica-particle containing microemulsion droplets and the other the reverse droplets. The analysis allowed the determination of the evolution of the system of particles of silica and reverse droplets. A model of nucleation and growth of the silica particles is confirmed and the volume fraction versus time data for the silica particles is in agreement with first order kinetics with respect to TEOS concentration. Moreover to describe the long time evolution of the system, a correlation among the silica particles has been taken into account by introducing a structure factor with a local silica volume fraction η = 0.1. This high local density is 2 orders of magnitude larger than the global silica fraction and can be explained in terms of depleting interaction. [ABSTRACT FROM AUTHOR]

We report a search for time variations of the solar ^{8}B neutrino flux using 5804 live days of Super-Kamiokande data collected between May 31, 1996, and May 30, 2018. Super-Kamiokande measured the precise time of each solar neutrino interaction over 22 calendar years to search for solar neutrino flux modulations with unprecedented precision. Periodic modulations are searched for in a dataset comprising five-day interval solar neutrino flux measurements with a maximum likelihood method. We also applied the Lomb-Scargle method to this dataset to compare it with previous reports. The only significant modulation found is due to the elliptic orbit of the Earth around the Sun. The observed modulation is consistent with astronomical data: we measured an eccentricity of (1.53±0.35)%, and a perihelion shift of (-1.5±13.5) days.

Fluorescence microscopy data describe protein localization patterns at single-cell resolution and have the potential to reveal whole-proteome functional information with remarkable precision. Yet, extracting biologically meaningful representations from cell micrographs remains a major challenge. Existing approaches often fail to learn robust and noise-invariant features or rely on supervised labels for accurate annotations. We developed PIFiA (Protein Image-based Functional Annotation), a self-supervised approach for protein functional annotation from single-cell imaging data. We imaged the global yeast ORF-GFP collection and applied PIFiA to generate protein feature profiles from single-cell images of fluorescently tagged proteins. We show that PIFiA outperforms existing approaches for molecular representation learning and describe a range of downstream analysis tasks to explore the information content of the feature profiles. Specifically, we cluster extracted features into a hierarchy of functional organization, study cell population heterogeneity, and develop techniques to distinguish multi-localizing proteins and identify functional modules. Finally, we confirm new PIFiA predictions using a colocalization assay, suggesting previously unappreciated biological roles for several proteins. Paired with a fully interactive website ( https://thecellvision.org/pifia/ ), PIFiA is a resource for the quantitative analysis of protein organization within the cell., (© 2024. The Author(s).)

Bioimage analysis plays a critical role in extracting information from biological images, enabling deeper insights into cellular structures and processes. The integration of machine learning and deep learning techniques has revolutionized the field, enabling the automated, reproducible, and accurate analysis of biological images. Here, we provide an overview of the history and principles of machine learning and deep learning in the context of bioimage analysis. We discuss the essential steps of the bioimage analysis workflow, emphasizing how machine learning and deep learning have improved preprocessing, segmentation, feature extraction, object tracking, and classification. We provide examples that showcase the application of machine learning and deep learning in bioimage analysis. We examine user-friendly software and tools that enable biologists to leverage these techniques without extensive computational expertise. This review is a resource for researchers seeking to incorporate machine learning and deep learning in their bioimage analysis workflows and enhance their research in this rapidly evolving field., (© 2023 The Authors. BioEssays published by Wiley Periodicals LLC.)

We report a search for cosmic-ray boosted dark matter with protons using the 0.37  megaton×years data collected at Super-Kamiokande experiment during the 1996-2018 period (SKI-IV phase). We searched for an excess of proton recoils above the atmospheric neutrino background from the vicinity of the Galactic Center. No such excess is observed, and limits are calculated for two reference models of dark matter with either a constant interaction cross section or through a scalar mediator. This is the first experimental search for boosted dark matter with hadrons using directional information. The results present the most stringent limits on cosmic-ray boosted dark matter and exclude the dark matter-nucleon elastic scattering cross section between 10^{-33}cm^{2} and 10^{-27}cm^{2} for dark matter mass from 1  MeV/c^{2} to 300  MeV/c^{2}.

Single-cell image analysis provides a powerful approach for studying cell-to-cell heterogeneity, which is an important attribute of isogenic cell populations, from microbial cultures to individual cells in multicellular organisms. This phenotypic variability must be explained at a mechanistic level if biologists are to fully understand cellular function and address the genotype-to-phenotype relationship. Variability in single-cell phenotypes is obscured by bulk readouts or averaging of phenotypes from individual cells in a sample; thus, single-cell image analysis enables a higher resolution view of cellular function. Here, we consider examples of both small- and large-scale studies carried out with isogenic cell populations assessed by fluorescence microscopy, and we illustrate the advantages, challenges, and the promise of quantitative single-cell image analysis., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021. Published by Elsevier Inc.)

We describe a protocol for live-cell high-throughput (HTP) screening of yeast mutant strains carrying fluorescent protein markers for subcellular compartments of choice using automated confocal microscopy. This procedure, which combines HTP genetics and microscopy, results in the acquisition of thousands of images that can be analyzed in a systematic and quantitative way to identify morphology defects in the tagged subcellular compartments. This HTP protocol is readily adapted for screening any combination of markers and can be expanded to different growth conditions or higher order mutant genetic backgrounds.

We describe a protocol for high-content screening in budding yeast that can be used to study genetic interactions from a cell biological perspective. This approach can be used to map genetic interactions by monitoring one or more subcellular fluorescent markers of interest. In this case, changes in the morphology or abundance of a subcellular compartment, pathway or bioprocess are monitored in the background of a systematic array of yeast double mutants. Alternatively, the protocol can be used to monitor proteome-wide abundance and localization changes in a double mutant of interest by screening the yeast ORF-GFP collection. The protocol can be readily adapted for high-content screening of triple mutants, other large-scale yeast collections or expanded to screening of multiple growth conditions., (© 2021. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Our ability to understand the genotype-to-phenotype relationship is hindered by the lack of detailed understanding of phenotypes at a single-cell level. To systematically assess cell-to-cell phenotypic variability, we combined automated yeast genetics, high-content screening and neural network-based image analysis of single cells, focussing on genes that influence the architecture of four subcellular compartments of the endocytic pathway as a model system. Our unbiased assessment of the morphology of these compartments-endocytic patch, actin patch, late endosome and vacuole-identified 17 distinct mutant phenotypes associated with ~1,600 genes (~30% of all yeast genes). Approximately half of these mutants exhibited multiple phenotypes, highlighting the extent of morphological pleiotropy. Quantitative analysis also revealed that incomplete penetrance was prevalent, with the majority of mutants exhibiting substantial variability in phenotype at the single-cell level. Our single-cell analysis enabled exploration of factors that contribute to incomplete penetrance and cellular heterogeneity, including replicative age, organelle inheritance and response to stress., (© 2020 The Authors. Published under the terms of the CC BY 4.0 license.)

To systematically explore complex genetic interactions, we constructed ~200,000 yeast triple mutants and scored negative trigenic interactions. We selected double-mutant query genes across a broad spectrum of biological processes, spanning a range of quantitative features of the global digenic interaction network and tested for a genetic interaction with a third mutation. Trigenic interactions often occurred among functionally related genes, and essential genes were hubs on the trigenic network. Despite their functional enrichment, trigenic interactions tended to link genes in distant bioprocesses and displayed a weaker magnitude than digenic interactions. We estimate that the global trigenic interaction network is ~100 times as large as the global digenic network, highlighting the potential for complex genetic interactions to affect the biology of inheritance, including the genotype-to-phenotype relationship., (Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Fluorescent reporter genes have long been used to quantify various cell features such as transcript and protein abundance. Here, we describe a method, reporter synthetic genetic array (R-SGA) analysis, which allows for the simultaneous quantification of any fluorescent protein readout in thousands of yeast strains using an automated pipeline. R-SGA combines a fluorescent reporter system with standard SGA analysis and can be used to examine any array-based strain collection available to the yeast community. This protocol describes the R-SGA methodology for screening different arrays of yeast mutants including the deletion collection, a collection of temperature-sensitive strains for the assessment of essential yeast genes and a collection of inducible overexpression strains. We also present an alternative pipeline for the analysis of R-SGA output strains using flow cytometry of cells in liquid culture. Data normalization for both pipelines is discussed.

Background: Measuring service quality aids health care providers to recognize specific and unmet needs of patients. Nevertheless, perceived quality of health care services (PQC) is often investigated with inadequate techniques which may lead to biased results., Objective: The aim of the present study is to develop a proof-of-concept for estimating the PQC using the scale-up estimator, with reference to a concrete assessment in patients of a major Oncology Hospital in Veneto (IOV). Results have then been compared with those collected by the Customer Relations Office (CRO) after the annual survey conducted with traditional questionnaire based techniques., Material and Methods: Seven hundred and eighty-three sets consisting of two questionnaires were handed out to IOV patients between 26 and 28 November 2012. The first questionnaire was the CRO annual one composed by 15 direct questions about the perception of quality satisfaction rate using a Likert scale. The second questionnaire was the scale-up (NSUM) one, composed by 20 indirect questions, 5 of which were reproducing the main target of CRO for estimating PQC., Results: The comparisons made over 299 sets of questionnaires showed differences between the two techniques. Network Scale-Up Method (NSUM) questionnaire seems to be able to produce lower estimates of PQC with respect to the CRO annual questionnaire. In some cases, the NSUM showed dissatisfaction rates which are 20-fold higher respect to CRO., Conclusion: NSUM could be a promising method for assessing the perceived quality of care.

Background: Acute Ischemic Stroke (AIS) represents an economic challenge for health systems all over the globe. Changes of neuroactive steroids have been found in different neurological diseases. We have previously demonstrated that old patients with AIS show changes of plasma cortisol and estradiol concentrations, in that increased steroid levels are associated with a deterioration of neurological status and a worse cognitive decline., Objective: The present study assessed in patients with AIS if changes of behavior, Brain-Derived Neurotrophic Factor (BDNF) and Nitrites (NO-2) bear a relationship with the degree of hypercortisolism., Methods: We recruited patients hospitalized within the first 24 hours of AIS. Subjects were divided into two groups, each one composed of 40 control subjects and 40 AIS patients, including men and women. The neurological condition was assessed using the National Institute of Health Stroke Scale (NIHSS) and the cognitive status with the Montreal Cognitive Assessment (MoCA). The emotional status was evaluated using the Montgomery-Asberg Depression Rating Scale (MADRS), whereas the Modified Rankin Scale (MRS) was used to determine the functional condition. BDNF and NO-2 plasma levels were measured by ELISA and the Griess reaction method, respectively., Results: We found that in AIS patients, increased plasma cortisol was negatively correlated with plasma BDNF and NO-2 levels, neurological condition, cognition, functional responses and emotional status, suggesting a relationship between the declines of clinical, behavioral and blood parameters with stress-induced cortisol elevation., Conclusion: Nitrites and BDNF may represent potential biomarkers for cortisol negative effects on the area of cerebral ischemia and penumbra, potentiating ischemic cell damage., (Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.)

Despite several scientific and technological advances, there is no single neuroprotective treatment that can reverse the brain damage after acute ischemic stroke (AIS). Neuroactive steroids are cholesterol-derived hormones that have the ability to modulate the normal and pathologic nervous system employing genomic and nongenomic mechanisms. In this work, we first investigated if AIS affects the plasma concentration of 5 neuroactive steroids (cortisol, estradiol, progesterone, testosterone, and 3α-androstenediol glucuronide). Second, we studied if levels of circulating steroids associate with neurological, cognitive, and functional outcome in a cohort of 60- to 90 year-old male and female patients with AIS. For this purpose, we recruited patients who were hospitalized at the Emergency Room of the Central Military Hospital within the first 24 h after stroke onset. We designed 2 experimental groups, each one composed of 30 control subjects and 30 AIS patients, both males and females. The assessment of neurological deficit was performed with the NIHSS and the tests used for the functional and cognitive status were: (1) modified Rankin Scale; (2) Photo test, and (3) abbreviated Pfeiffer's mental status questionnaire. We observed a significant difference in plasma concentration of cortisol and estradiol between both experimental groups. In the AIS group, higher levels of these neuroactive steroids were associated with more pronounced neurological, cognitive and functional deficits in women compared to men. We propose that in elderly patients, high levels of circulating neuroactive steroids like cortisol and estradiol could potentiate AIS-mediated neuropathology in the ischemic and penumbra areas., (© Georg Thieme Verlag KG Stuttgart · New York.)

High-content screening (HCS), which combines automated fluorescence microscopy with quantitative image analysis, allows the acquisition of unbiased multiparametric data at the single cell level. This approach has been used to address diverse biological questions and identify a plethora of quantitative phenotypes of varying complexity in numerous different model systems. Here, we describe some recent applications of HCS, ranging from the identification of genes required for specific biological processes to the characterization of genetic interactions. We review the steps involved in the design of useful biological assays and automated image analysis, and describe major challenges associated with each. Additionally, we highlight emerging technologies and future challenges, and discuss how the field of HCS might be enhanced in the future., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

The functional link between zinc homeostasis and membrane-related processes, including lipid metabolism regulation, extends from yeast to humans, and has a likely role in the pathogenesis of diabetes. The yeast Izh2 protein has been previously implicated in zinc ion homeostasis and in the regulation of lipid and phosphate metabolism, but its precise molecular function is not known. We performed a chemogenomics experiment to determine the genes conferring resistance or sensitivity to different environmental zinc concentrations. We then determined at normal, depleted and excess zinc concentrations, the genetic interactions of IZH2 at the genome-wide level and measured changes in the transcriptome caused by deletion of IZH2. We found evidence for an important cellular function of the Rim101 pathway in zinc homeostasis in neutral or acidic environments, and observed that phosphatidylinositol is a source of inositol when zinc availability is limited. Comparison of our experimental profiles with published gene expression and genetic interaction profiles revealed pleiotropic functions for Izh2. We propose that Izh2 acts as an integrator of intra- and extracellular signals in providing adequate cellular responses to maintain homeostasis under different external conditions, including - but not limited to - alterations in zinc concentrations.

Pex11 is a peroxin that regulates the number of peroxisomes in eukaryotic cells. Recently, it was found that a mutation in one of the three mammalian paralogs, PEX11β, results in a neurological disorder. The molecular function of Pex11, however, is not known. Saccharomyces cerevisiae Pex11 has been shown to recruit to peroxisomes the mitochondrial fission machinery, thus enabling proliferation of peroxisomes. This process is essential for efficient fatty acid β-oxidation. In this study, we used high-content microscopy on a genome-wide scale to determine the subcellular localization pattern of yeast Pex11 in all non-essential gene deletion mutants, as well as in temperature-sensitive essential gene mutants. Pex11 localization and morphology of peroxisomes was profoundly affected by mutations in 104 different genes that were functionally classified. A group of genes encompassing MDM10, MDM12 and MDM34 that encode the mitochondrial and cytosolic components of the ERMES complex was analyzed in greater detail. Deletion of these genes caused a specifically altered Pex11 localization pattern, whereas deletion of MMM1, the gene encoding the fourth, endoplasmic-reticulum-associated component of the complex, did not result in an altered Pex11 localization or peroxisome morphology phenotype. Moreover, we found that Pex11 and Mdm34 physically interact and that Pex11 plays a role in establishing the contact sites between peroxisomes and mitochondria through the ERMES complex. Based on these results, we propose that the mitochondrial/cytosolic components of the ERMES complex establish a direct interaction between mitochondria and peroxisomes through Pex11., (Copyright © 2015. Published by Elsevier Ltd.)

Neonicotinoid insecticides are an important contribution to plant protection products. At the same time, their environmental impact on non-target organisms is often problematic. It has been shown that the toxicity of formulations of neonicotinoid insecticides can originate from non-neonicotinoid additives. In the present study we used chemogenomics to analyse side effects of purified neonicotinoids, additives and formulations on the genome-wide scale. We show that the additives in formulations have more pronounced effects than the active components, and that these effects could explain previously observed negative effects of neonicotinoid insecticides on spermatogenesis in animals. We also demonstrate that cell wall organization and biogenesis in yeast is negatively affected by neonicotinoid substances., (Copyright © 2013 Elsevier Ltd. All rights reserved.)

Cell signaling, one of key processes in both normal cellular function and disease, is coordinated by numerous interactions between membrane proteins that change in response to stimuli. We present a split ubiquitin-based method for detection of integral membrane protein-protein interactions (PPIs) in human cells, termed mammalian-membrane two-hybrid assay (MaMTH). We show that this technology detects stimulus (hormone or agonist)-dependent and phosphorylation-dependent PPIs. MaMTH can detect changes in PPIs conferred by mutations such as those in oncogenic ErbB receptor variants or by treatment with drugs such as the tyrosine kinase inhibitor erlotinib. Using MaMTH as a screening assay, we identified CRKII as an interactor of oncogenic EGFR(L858R) and showed that CRKII promotes persistent activation of aberrant signaling in non-small cell lung cancer cells. MaMTH is a powerful tool for investigating the dynamic interactomes of human integral membrane proteins.

The budding yeast Saccharomyces cerevisiae has been used extensively for the study of cell polarity, owing to both its experimental tractability and the high conservation of cell polarity and other basic biological processes among eukaryotes. The budding yeast has also served as a pioneer model organism for virtually all genome-scale approaches, including functional genomics, which aims to define gene function and biological pathways systematically through the analysis of high-throughput experimental data. Here, we outline the contributions of functional genomics and high-throughput methodologies to the study of cell polarity in the budding yeast. We integrate data from published genetic screens that use a variety of functional genomics approaches to query different aspects of polarity. Our integrated dataset is enriched for polarity processes, as well as some processes that are not intrinsically linked to cell polarity, and may provide new areas for future study.

The molecular mechanism of action of presynaptically neurotoxic secreted phospholipases A2 (sPLA2s) has not been fully elucidated. We have recently proposed a model to explain one of the hallmarks of their action - the reduction in endocytosis leading to synaptic vesicle depletion in nerve terminals. Our results speak strongly in favor of a mechanism in which both specific protein-protein interactions and enzymatic activity of the neurotoxic sPLA2 ammodytoxin A (AtxA) are necessary for impairment of clathrin-dependent endocytosis in yeast cells. The reduction of endocytosis was strictly dependent on the enzymatic activity of sPLA2s expressed ectopically in our yeast model cells and was not observed with the catalytically inactive, non-neurotoxic AtxA-homolog, ammodytin L (AtnL). Here we confirm the validity of the model in mammalian cells also, by demonstrating that the enzymatically active mutant of AtnL, shown to inhibit endocytosis in yeast, acts as a presynaptically neurotoxic sPLA2 at the mammalian neuromuscular junction.

Yeast Saccharomyces cerevisiae has proven to be a relevant and convenient model organism for the study of diverse biological phenomena, due to its straightforward genetics, cost-effectiveness and rapid growth, combined with the typical characteristics of a eukaryotic cell. More than 40% of yeast proteins share at least part of their primary amino acid sequence with the corresponding human protein, making yeast a valuable model in biomedical research. In the last decade, high-throughput and genome-wide experimental approaches developed in yeast have paved the way to functional genomics that aims at a global understanding of the relationship between genotype and phenotype. In this review we first present the yeast strain and plasmid collections for genome-wide experimental approaches to study complex interactions between genes, proteins and endo- or exogenous small molecules. We describe methods for protein-protein, protein-DNA, genetic and chemo-genetic interactions, as well as localization studies, focussing on their application in research on small pharmacologically active molecules. Next we review the use of yeast as a model organism in neurobiology, emphasizing work done towards elucidating the pathogenesis of neurodegenerative diseases and the mechanism of action of neurotoxic phospholipases A(2)., (Copyright © 2012 Elsevier Ltd. All rights reserved.)

Background: Presynaptically neurotoxic phospholipases A(2) inhibit synaptic vesicle recycling through endocytosis., Principal Findings: Here we provide insight into the action of a presynaptically neurotoxic phospholipase A(2) ammodytoxin A (AtxA) on clathrin-dependent endocytosis in budding yeast. AtxA caused changes in the dynamics of vesicle formation and scission from the plasma membrane in a phospholipase activity dependent manner. Our data, based on synthetic dosage lethality screen and the analysis of the dynamics of sites of endocytosis, indicate that AtxA impairs the activity of amphiphysin., Conclusions: We identified amphiphysin and endocytosis as the target of AtxA intracellular activity. We propose that AtxA reduces endocytosis following a mechanism of action which includes both a specific protein-protein interaction and enzymatic activity, and which is applicable to yeast and mammalian cells. Knowing how neurotoxic phospholipases A(2) work can open new ways to regulate endocytosis.

Inference of new and useful hypotheses from heterogeneous sources of genome-scale experimental data requires new computational methods that can integrate different types of data. Gene expression and genetic interaction data are two most informative data types, each allowing the identification of genes at different levels of cellular regulatory network hierarchy. We present an integrative data analysis approach, which, rather than correlating the findings from the two data sets, uses each type of data independently to identify the components of molecular pathways and combines them into a single directed network. Our computational genomics approach is based on a set of inference rules traditionally used for reasoning on genetic experiments, which we have formalized and implemented in a software tool. The approach uses chemogenetic interaction and expression data to infer the type of relation between the chemical substance (perturber) and a transcription factor by using previous knowledge on the set of genes whose expression the transcription factor in question regulates. We have used the proposed approach to successfully infer the models for the action of the drug rapamycin and of a DNA damaging agent on their molecular targets and pathways in yeast cells. The developed method is available as a web-based tool at http://www.ailab.si/perturbagen.

Modulating composition and shape of biological membranes is an emerging mode of regulation of cellular processes. We investigated the global effects that such perturbations have on a model eukaryotic cell. Phospholipases A(2) (PLA(2)s), enzymes that cleave one fatty acid molecule from membrane phospholipids, exert their biological activities through affecting both membrane composition and shape. We have conducted a genome-wide analysis of cellular effects of a PLA(2) in the yeast Saccharomyces cerevisiae as a model system. We demonstrate functional genetic and biochemical interactions between PLA(2) activity and the Rim101 signaling pathway in S. cerevisiae. Our results suggest that the composition and/or the shape of the endosomal membrane affect the Rim101 pathway. We describe a genetically and functionally related network, consisting of components of the Rim101 pathway and the prefoldin, retromer and SWR1 complexes, and predict its functional relation to PLA(2) activity in a model eukaryotic cell. This study provides a list of the players involved in the global response to changes in membrane composition and shape in a model eukaryotic cell, and further studies are needed to understand the precise molecular mechanisms connecting them.

We describe an imaging-based method in intact cells to systematically screen yeast mutant libraries for abnormal morphology and distribution of fluorescently labeled subcellular structures. In this study, chromosomally expressed green fluorescent protein (GFP) fused to the peroxisomal targeting sequence 1, consisting of serine-lysine-leucine, was introduced into 4740 viable yeast deletion mutants using a modified synthetic genetic array (SGA) technology. A benchtop robot was used to create ordered high-density arrays of GFP-expressing yeast mutants on solid media plates. Immobilized live yeast colonies were subjected to high-resolution, multidimensional confocal imaging. A software tool was designed for automated processing and quantitative analysis of acquired multichannel three-dimensional image data. The study resulted in the identification of two novel proteins, as well as of all previously known proteins required for import of proteins bearing peroxisomal targeting signal PTS1, into yeast peroxisomes. The modular method enables reliable microscopic analysis of live yeast mutant libraries in a universally applicable format on standard microscope slides, and provides a step toward fully automated high-resolution imaging of intact yeast cells.

The formation of silica particles by the ammonia-catalyzed hydrolysis of tetraethyl orthosilicate (TEOS) in the polyoxyethylene (5) nonylphenyl ether (NP-5)/cyclohexane/water microemulsion system was investigated by time-resolved small-angle X-ray scattering (SAXS). The SAXS data could be modeled as a combination of two species where one describes the silica-particle containing microemulsion droplets and the other the reverse droplets. The analysis allowed the determination of the evolution of the system of particles of silica and reverse droplets. A model of nucleation and growth of the silica particles is confirmed and the volume fraction versus time data for the silica particles is in agreement with first order kinetics with respect to TEOS concentration. Moreover to describe the long time evolution of the system, a correlation among the silica particles has been taken into account by introducing a structure factor with a local silica volume fraction eta = 0.1. This high local density is 2 orders of magnitude larger than the global silica fraction and can be explained in terms of depleting interaction.

Two point mutations (T>G and T>C) at the same 8993 nucleotide of mitochondrial DNA (at comparable mutant load), affecting the ATPase 6 subunit of the F1F0-ATPase, result in neurological phenotypes of variable severity in humans. We have investigated mitochondrial function in lymphocytes from individuals carrying the 8993T>C mutation: the results were compared with data from five 8993T>G NARP (Neuropathy, Ataxia and Retinitis Pigmentosa) patients. Both 8993T>G and 8993T>C mutations led to energy deprivation and ROS overproduction. However, the relative contribution of the two pathogenic components is different depending on the mutation considered. The 8993T>G change mainly induces an energy deficiency, whereas the 8993T>C favours an increased ROS production. These results possibly highlight the different pathogenic mechanism generated by the two mutations at position 8993 and provide useful information to better characterize the biochemical role of the highly conserved Leu-156 in ATPase 6 subunit of the mitochondrial ATP synthase complex.

Ocular involvement is a prevalent feature in mitochondrial diseases. Leber's hereditary optic neuropathy (LHON) and dominant optic atrophy (DOA) are both non-syndromic optic neuropathies with a mitochondrial etiology. LHON is associated with point mutations in the mitochondrial DNA (mtDNA), which affect subunit genes of complex I. The majority of DOA patients harbor mutations in the nuclear-encoded protein OPA1, which is targeted to mitochondria and participates to cristae organization and mitochondrial network dynamics. In both disorders the retinal ganglion cells (RGCs) are specific cellular targets of the degenerative process. We here review the clinical features and the genetic bases, and delineate the possible common pathomechanism for both these disorders.

Background: There is pre-clinical evidence of synergism between cisplatin (P) and temozolomide (T) due to higher inhibition by T of O6-alkyl-guanine-alkyltransferase (AGAT), an enzyme involved in the mismatch repair system. T and P are active against malignant gliomas while thalidomide (TH) is emerging as an inhibitor of angiogenesis., Patients and Methods: Triplets of patients with malignant brain tumors received escalating doses of P, T and TH up to the dose-limiting-toxicity (DLT) and the maximal tolerated dose (MTD)., Results: Seventeen patients were enrolled and a total of 74 cycles were delivered. The MTD was P 75 mg/m2 day 1 and T 150 mg/m2 days 1 to 5 every 21 days with a concomitant 200 mg total daily dose of TH. DLT events were G4 thrombocytopenia and febrile neutropenia., Conclusion: Concomitant administration of P 75 mg/m2 day 1, T 150 mg/m2 days 1 to 5 every 21 days and concomitant TH at a total daily dose of 150 mg is feasible and safe. Early efficacy data are encouraging and a phase II study is ongoing.

Background: Advanced biliary tract cancers have a poor prognosis. Gemcitabine (G) as a single agent or in combination represents an active treatment option. Systemic chemotherapy in hepatocellular carcinoma represents a palliative treatment. Gemcitabine in combination with Liposomal Doxorubicin (LD) may represent an active treatment option., Patients and Methods: Clinical trials for biliary and hepatic carcinoma have been reviewed., Results: We obtained RC (1 pt), RP (4 pts), SD (8 pts) and seven pts had PD (RR 25% and SD 40%). Our chemotherapy regimen was Gemcitabine 1000 mg/m(2) d 1 and 8, Liposomal Doxorubicin 30 mg d 1, q 28. Patients were 21 (17 M), aged 44 to 78 (median 63 yrs). Only in 8 pts we observed G 3-4 haematological toxicity, thrombocytopenia and neutropenia (7 G3, 1 G4).

The mitochondrial DNA (mtDNA) of 87 index cases with Leber hereditary optic neuropathy (LHON) sequentially diagnosed in Italy, including an extremely large Brazilian family of Italian maternal ancestry, was evaluated in detail. Only seven pairs and three triplets of identical haplotypes were observed, attesting that the large majority of the LHON mutations were due to independent mutational events. Assignment of the mutational events into haplogroups confirmed that J1 and J2 play a role in LHON expression but narrowed the association to the subclades J1c and J2b, thus suggesting that two specific combinations of amino acid changes in the cytochrome b are the cause of the mtDNA background effect and that this may occur at the level of the supercomplex formed by respiratory-chain complexes I and III. The families with identical haplotypes were genealogically reinvestigated, which led to the reconnection into extended pedigrees of three pairs of families, including the Brazilian family with its Italian counterpart. The sequencing of entire mtDNA samples from the reconnected families confirmed the genealogical reconstruction but showed that the Brazilian family was heteroplasmic at two control-region positions. The survey of the two sites in 12 of the Brazilian subjects revealed triplasmy in most cases, but there was no evidence of the tetraplasmy that would be expected in the case of mtDNA recombination.

Mitochondrial respiratory chain dysfunction, impaired intracellular Ca2+ homeostasis and activation of the mitochondrial apoptotic pathway are pathological hallmarks in animal and cellular models of familial amyotrophic lateral sclerosis associated with Cu/Zn-superoxide dismutase mutations. Although intracellular Ca2+ homeostasis is thought to be intimately associated with mitochondrial functions, the temporal and causal correlation between mitochondrial Ca2+ uptake dysfunction and motor neuron death in familial amyotrophic lateral sclerosis remains to be established. We investigated mitochondrial Ca2+ handling in isolated brain, spinal cord and liver of mutant Cu/Zn-superoxide dismutase transgenic mice at different disease stages. In G93A mutant transgenic mice, we found a significant decrease in mitochondrial Ca2+ loading capacity in brain and spinal cord, as compared with age-matched controls, very early on in the course of the disease, long before the onset of motor weakness and massive neuronal death. Ca2+ loading capacity was not significantly changed in liver G93A mitochondria. We also confirmed Ca2+ capacity impairment in spinal cord mitochondria from a different line of mice expressing G85R mutant Cu/Zn-superoxide dismutase. In excitable cells, such as motor neurons, mitochondria play an important role in handling rapid cytosolic Ca2+ transients. Thus, mitochondrial dysfunction and Ca2+-mediated excitotoxicity are likely to be interconnected mechanisms that contribute to neuronal degeneration in familial amyotrophic lateral sclerosis.