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2.
Early Child Educ J ; 51(4): 675-684, 2023.
Article in English | MEDLINE | ID: mdl-35287284

ABSTRACT

The COVID-19 pandemic has profound implications for education of young children worldwide and especially for children in developing economies like India. This article presents a qualitative study that explored the challenges that private school teachers in low budget, mid-ranged, and high fee charging private schools faced in two cities in India. All the private schools in this study also followed the government mandate to reserve 25% of seats for children from low-income families. During the school closure, remote instruction was employed in schools where participating teachers taught. Teachers faced challenges related to parental involvement and children's participation in remote instruction. Parental involvement challenges included parental lack of access to technological devices and no or minimal access to internet for their children to participate in remote instruction activities. Parental lack of support due to their low technological literacy and literacy in general, lack of fluency in the English Language, as well as lack of time also contributed to their children's low participation in remote instruction. Teachers faced challenges in implementing remote instruction with children from different socio-economic backgrounds; however, the challenges were greater with families from low-income backgrounds. The study's findings suggest that governments around the world need to ensure children's access to digital tools and internet services which are essential elements in children's participation in remote instruction. For children in families where parents are unable to support their children's education at home, other support services may be instituted to take the pressure off of parents. Future studies may explore the 'learning loss' that may have resulted from the long school closure during the pandemic.

3.
Front Neurosci ; 16: 936897, 2022.
Article in English | MEDLINE | ID: mdl-36161178

ABSTRACT

Progressive development of pathology is one of the major characteristic features of neurodegenerative diseases. Alzheimer's disease (AD) is the most prevalent among them. Extracellular amyloid-ß (Aß) plaques and intracellular tau neurofibrillary tangles are the pathological phenotypes of AD. However, cellular and animal studies implicate tau as a secondary pathology in developing AD while Aß aggregates is considered as a trigger point. Interaction of Aß peptides with plasma membrane (PM) seems to be a promising site of involvement in the events that lead to AD. Aß binding to the lipid membranes initiates formation of oligomers of Aß species, and these oligomers are known as primary toxic agents for neuronal toxicities. Once initiated, neuropathological toxicities spread in a "prion-like" fashion probably through the mechanism of intercellular transfer of pathogenic aggregates. In the last two decades, several studies have demonstrated neuron-to-neuron transfer of neurodegenerative proteins including Aß and tau via exosomes and tunneling nanotubes (TNTs), the two modes of long-range intercellular transfer. Emerging pieces of evidence indicate that molecular pathways related to the biogenesis of exosomes and TNTs interface with endo-lysosomal pathways and cellular signaling in connection to vesicle recycling-imposed PM and actin remodulation. In this review, we discuss interactions of Aß aggregates at the membrane level and its implications in intercellular spread of pathogenic aggregates. Furthermore, we hypothesize how spread of pathogenic aggregates contributes to complex molecular events that could regulate pathological and synaptic changes related to AD.

4.
J Vis Exp ; (186)2022 08 31.
Article in English | MEDLINE | ID: mdl-36121261

ABSTRACT

Recent discoveries have revealed that cells perform direct, long-range, intercellular transfer via nano-scale, actin-membrane conduits, namely "tunneling nanotubes" (TNTs). TNTs are defined as open-ended, lipid bilayer-encircled membrane extensions that mediate continuity between neighboring cells of diameters ranging between 50 nm and 1 µm. TNTs were demonstrated initially in neuronal cells, but successive studies have revealed the existence of TNTs in several cell types and diseases, such as neurodegenerative diseases, viral infections, and cancer. Several studies have referred to close-ended, electrically coupled membrane nanostructures between neighboring cells as TNTs or TNT-like structures. The elucidation of ultrastructure in terms of membrane continuity at the endpoint is technically challenging. In addition, studies on cell-cell communication are challenging in terms of the characterization of TNTs using conventional methods due to the lack of specific markers. TNTs are primarily defined as F-actin-based, open-ended membrane protrusions. However, one major limitation is that F-actin is present in all types of protrusions, making it challenging to differentiate TNTs from other protrusions. One of the notable characteristics of F-actin-based TNTs is that these structures hover between two cells without touching the substratum. Therefore, distinct F-actin-stained TNTs can conveniently be distinguished from other protrusions such as filopodia and neurites based on their hovering between cells. We have recently shown that the internalization of oligomeric amyloid-ß1-42 (oAß) via actin-dependent endocytosis stimulates activated p21-activated kinase-1 (PAK1), which mediates the formation of F-actin-containing TNTs coexpressed with phospho-PAK1 between SH-SY5Y neuronal cells. This protocol outlines a 3D volume analysis method to identify and characterize TNTs from the captured z-stack images of F-actin- and phospho-PAK1-immunostained membrane protrusions in oAß-treated neuronal cells. Further, TNTs are distinguished from developing neurites and neuronal outgrowths based on F-actin- and ß-III tubulin-immunostained membrane conduits.


Subject(s)
Nanotubes , Neuroblastoma , Actins/metabolism , Humans , Lipid Bilayers , Nanotubes/chemistry , Tubulin , p21-Activated Kinases
5.
Cell Mol Life Sci ; 79(1): 36, 2021 Dec 18.
Article in English | MEDLINE | ID: mdl-34921322

ABSTRACT

Tunnelling nanotubes (TNTs) are an emerging route of long-range intercellular communication that mediate cell-to-cell exchange of cargo and organelles and contribute to maintaining cellular homeostasis by balancing diverse cellular stresses. Besides their role in intercellular communication, TNTs are implicated in several ways in health and disease. Transfer of pathogenic molecules or structures via TNTs can promote the progression of neurodegenerative diseases, cancer malignancy, and the spread of viral infection. Additionally, TNTs contribute to acquiring resistance to cancer therapy, probably via their ability to rescue cells by ameliorating various pathological stresses, such as oxidative stress, reactive oxygen species (ROS), mitochondrial dysfunction, and apoptotic stress. Moreover, mesenchymal stem cells play a crucial role in the rejuvenation of targeted cells with mitochondrial heteroplasmy and oxidative stress by transferring healthy mitochondria through TNTs. Recent research has focussed on uncovering the key regulatory molecules involved in the biogenesis of TNTs. However further work will be required to provide detailed understanding of TNT regulation. In this review, we discuss possible associations with Rho GTPases linked to oxidative stress and apoptotic signals in biogenesis pathways of TNTs and summarize how intercellular trafficking of cargo and organelles, including mitochondria, via TNTs plays a crucial role in disease progression and also in rejuvenation/therapy.


Subject(s)
Cell Communication , Oxidative Stress , rho GTP-Binding Proteins/physiology , Humans , Mitochondria/metabolism , Neoplasms/metabolism , Neoplasms/pathology , Neurodegenerative Diseases/metabolism , Neurodegenerative Diseases/pathology , Organelles/metabolism , Reactive Oxygen Species/metabolism , Virus Diseases/metabolism , Virus Diseases/pathology
6.
Biochim Biophys Acta Mol Basis Dis ; 1867(12): 166246, 2021 12 01.
Article in English | MEDLINE | ID: mdl-34403739

ABSTRACT

Alzheimer's disease (AD) pathology progresses gradually via anatomically connected brain regions. Direct transfer of amyloid-ß1-42 oligomers (oAß) between connected neurons has been shown, however, the mechanism is not fully revealed. We observed formation of oAß induced tunneling nanotubes (TNTs)-like nanoscaled f-actin containing membrane conduits, in differentially differentiated SH-SY5Y neuronal models. Time-lapse images showed that oAß propagate from one cell to another via TNT-like structures. Preceding the formation of TNT-like conduits, we detected oAß-induced plasma membrane (PM) damage and calcium-dependent repair through lysosomal-exocytosis, followed by massive endocytosis to re-establish the PM. Massive endocytosis was monitored by an influx of the membrane-staining dye TMA-DPH and PM damage was quantified by propidium iodide influx in the absence of Ca2+. The massive endocytosis eventually caused accumulation of internalized oAß in Lamp1 positive multivesicular bodies/lysosomes via the actin cytoskeleton remodulating p21-activated kinase1 (PAK1) dependent endocytic pathway. Three-dimensional quantitative confocal imaging, structured illumination superresolution microscopy, and flowcytometry quantifications revealed that oAß induces activation of phospho-PAK1, which modulates the formation of long stretched f-actin extensions between cells. Moreover, the formation of TNT-like conduits was inhibited by preventing PAK1-dependent internalization of oAß using the small-molecule inhibitor IPA-3, a highly selective cell-permeable auto-regulatory inhibitor of PAK1. The present study reveals that the TNT-like conduits are probably instigated as a consequence of oAß induced PM damage and repair process, followed by PAK1 dependent endocytosis and actin remodeling, probably to maintain cell surface expansion and/or membrane tension in equilibrium.


Subject(s)
Alzheimer Disease/genetics , Amyloid beta-Peptides/genetics , Disulfides/pharmacology , Naphthols/pharmacology , p21-Activated Kinases/genetics , Alzheimer Disease/drug therapy , Alzheimer Disease/pathology , Brain/drug effects , Brain/pathology , Cell Membrane/drug effects , Cell Membrane/pathology , Endocytosis/drug effects , Exocytosis/drug effects , Humans , Lysosomes/drug effects , Nanotubes/chemistry , p21-Activated Kinases/antagonists & inhibitors
7.
Cell Rep ; 34(13): 108884, 2021 03 30.
Article in English | MEDLINE | ID: mdl-33789103

ABSTRACT

Plants respond to bacterial infection acutely with actin remodeling during plant immune responses. The mechanisms by which bacterial virulence factors (VFs) modulate plant actin polymerization remain enigmatic. Here, we show that plant-type-I formin serves as the molecular sensor for actin remodeling in response to two bacterial VFs: Xanthomonas campestris pv. campestris (Xcc) diffusible signal factor (DSF), and pathogen-associated molecular pattern (PAMP) flagellin in pattern-triggered immunity (PTI). Both VFs regulate actin assembly by tuning the clustering and nucleation activity of formin on the plasma membrane (PM) at the nano-sized scale. By being integrated within the cell-wall-PM-actin cytoskeleton (CW-PM-AC) continuum, the dynamic behavior and function of formins are highly dependent on each scaffold layer's composition within the CW-PM-AC continuum during both DSF and PTI signaling. Our results reveal a central mechanism for rapid actin remodeling during plant-bacteria interactions, in which bacterial signaling molecules fine tune plant formin nanoclustering in a host mechanical-structure-dependent manner.


Subject(s)
Actins/metabolism , Bacterial Proteins/metabolism , Flagellin/metabolism , Formins/metabolism , Nanoparticles/chemistry , Signal Transduction , Arabidopsis/microbiology , Cell Wall/metabolism , Cellulose/metabolism , Host-Pathogen Interactions , Models, Biological , Pathogen-Associated Molecular Pattern Molecules/metabolism , Protein Binding , Xanthomonas campestris/metabolism
8.
Methods Mol Biol ; 2205: 3-18, 2020.
Article in English | MEDLINE | ID: mdl-32809190

ABSTRACT

Biological computer-aided design and manufacturing (bioCAD/CAM) tools facilitate the design and build processes of engineering biological systems using iterative design-build-test-learn (DBTL) cycles. In this book chapter, we highlight some of the bioCAD/CAM tools developed and used at the US Department of Energy (DOE) Joint Genome Institute (JGI), Joint BioEnergy Institute (JBEI), and Agile BioFoundry (ABF). We demonstrate the use of these bioCAD/CAM tools on a common workflow for designing and building a multigene pathway in a hierarchical fashion. Each tool presented in this book chapter is specifically tailored to support one or more specific steps in a workflow, can be integrated with the others into design and build workflows, and can be deployed at academic, government, or commercial entities.


Subject(s)
Synthetic Biology/methods , Computer-Aided Design , Software , Workflow
9.
Life Sci Alliance ; 3(10)2020 10.
Article in English | MEDLINE | ID: mdl-32788227

ABSTRACT

Quorum sensing (QS) is a recognized phenomenon that is crucial for regulating population-related behaviors in bacteria. However, the direct specific effect of QS molecules on host biology is largely understudied. In this work, we show that the QS molecule DSF (cis-11-methyl-dodecenoic acid) produced by Xanthomonas campestris pv. campestris can suppress pathogen-associated molecular pattern-triggered immunity (PTI) in Arabidopsis thaliana, mediated by flagellin-induced activation of flagellin receptor FLS2. The DSF-mediated attenuation of innate immunity results from the alteration of FLS2 nanoclusters and endocytic internalization of plasma membrane FLS2. DSF altered the lipid profile of Arabidopsis, with a particular increase in the phytosterol species, which impairs the general endocytosis pathway mediated by clathrin and FLS2 nano-clustering on the plasma membrane. The DSF effect on receptor dynamics and host immune responses could be entirely reversed by sterol removal. Together, our results highlighted the importance of sterol homeostasis to plasma membrane organization and demonstrate a novel mechanism by which pathogenic bacteria use their communicating molecule to manipulate pathogen-associated molecular pattern-triggered host immunity.


Subject(s)
Plant Immunity/physiology , Quorum Sensing/physiology , Sterols/biosynthesis , Arabidopsis/immunology , Arabidopsis/metabolism , Arabidopsis Proteins/immunology , Arabidopsis Proteins/metabolism , Arabidopsis Proteins/physiology , Cell Membrane/physiology , Clathrin/metabolism , Flagellin/metabolism , Immunity, Innate/immunology , Immunity, Innate/physiology , Plant Diseases/immunology , Plant Immunity/immunology , Protein Kinases/metabolism , Protein Kinases/physiology , Signal Transduction , Sterols/metabolism , Xanthomonas campestris/metabolism
10.
Mol Biol Cell ; 31(7): 561-579, 2020 03 19.
Article in English | MEDLINE | ID: mdl-31577524

ABSTRACT

Transmembrane adhesion receptors at the cell surface, such as CD44, are often equipped with modules to interact with the extracellular matrix (ECM) and the intracellular cytoskeletal machinery. CD44 has been recently shown to compartmentalize the membrane into domains by acting as membrane pickets, facilitating the function of signaling receptors. While spatial organization and diffusion studies of membrane proteins are usually conducted separately, here we combine observations of organization and diffusion by using high spatio-temporal resolution imaging on living cells to reveal a hierarchical organization of CD44. CD44 is present in a meso-scale meshwork pattern where it exhibits enhanced confinement and is enriched in nanoclusters of CD44 along its boundaries. This nanoclustering is orchestrated by the underlying cortical actin dynamics. Interaction with actin is mediated by specific segments of the intracellular domain. This influences the organization of the protein at the nano-scale, generating a selective requirement for formin over Arp2/3-based actin-nucleation machinery. The extracellular domain and its interaction with elements of ECM do not influence the meso-scale organization, but may serve to reposition the meshwork with respect to the ECM. Taken together, our results capture the hierarchical nature of CD44 organization at the cell surface, with active cytoskeleton-templated nanoclusters localized to a meso-scale meshwork pattern.


Subject(s)
Actins/metabolism , Cell Membrane/metabolism , Hyaluronan Receptors/metabolism , Nanoparticles/chemistry , Actomyosin/metabolism , Animals , Cell Line , Cytoplasm/metabolism , Diffusion , Formins/metabolism , Humans , Hyaluronan Receptors/chemistry , Models, Biological , Protein Domains , Single Molecule Imaging
11.
Reprod Biol ; 18(1): 94-98, 2018 Mar.
Article in English | MEDLINE | ID: mdl-29396284

ABSTRACT

Green tea is a commonly used beverage and green tea extract is a common dietary herbal supplement manufactured into different over-the-counter products. The aim of this in vitro study was to examine the steroid hormone secretion (progesterone and 17-ß estradiol), proliferation and apoptosis of porcine ovarian granulosa cells after addition of green tea extract. Granulosa cells were incubated with green tea extract at five doses (0.1, 1, 10, 100 and 200 µg/ml) and the release of hormones by granulosa cells was assessed by EIA after 24 h exposure. The presence of proliferation and apoptotic markers was assessed by immunocytochemistry. Secretion of steroid hormones was not affected by green tea extract at all the doses in comparison to control. Also, markers of proliferation (PCNA and cyclin B1) were not affected by green tea extract. However, the highest dose (200 µg/ml) of green tea extract used in this study increased the accumulation of apoptotic markers caspase-3 and p53 in granulosa cells. In conclusion, our results indicate the impact of green tea extract at the highest dose used in this study on ovarian apoptosis through pathway that includes activation of caspase-3 and p53. Potential stimulation of these intracellular regulators could induce the process of apoptosis in ovarian cells.


Subject(s)
Apoptosis , Camellia sinensis/chemistry , Granulosa Cells/metabolism , Ovary/metabolism , Plant Extracts/metabolism , Plant Leaves/chemistry , Abattoirs , Animals , Animals, Inbred Strains , Biomarkers/metabolism , Cell Proliferation , Cells, Cultured/classification , Dietary Supplements , Estradiol/metabolism , Female , Food Handling , Granulosa Cells/cytology , Ovary/cytology , Oxidation-Reduction , Progesterone/metabolism , Slovakia , Sus scrofa
12.
Article in English | MEDLINE | ID: mdl-28093975

ABSTRACT

BACKGROUND: Hormone based birth control often causes various side effects. A recent study revealed that temporary infertility without changing hormone levels can be attained by inhibiting Katanin p60 ATPase-containing subunit A-like 1 protein (KATNAL1) which is critical for sperm maturation in the testes. OBJECTIVE: This study aimed at attaining the most energetically stable three dimensional (3D) structure of KATNAL1 protein using comparative modeling followed by screening of a ligand library of known natural spermicidal compounds for their binding affinity with KATNAL1. This in turn may inhibit the development of mature sperm in the seminiferous epithelium. METHOD: A series of computational techniques were used for building the 3D structure of KATNAL1 which was further optimized by molecular dynamics (MD) simulation. For revealing the ATP binding mode of KATNAL1, docking study was carried out using the optimized model obtained from the MD simulation. The docking study was also employed to test the binding efficiency of the ligand library. RESULTS: Molecular docking study confirmed the ATP binding of KATNAL1 with various hydrophobic and hydrogen bond interactions. Binding efficiency of the ligand library suggested that calotropin, a cardenolide of Calotropis procera showed the highest binding efficiency against the target protein without toxicity. MD simulation of the docked complex validated the results of the docking study. CONCLUSION: This study revealed the ATP binding mode of KATNAL1 and identified calotropin as a potential lead molecule against it showing high binding efficiency with good bioavailability and no mutagenicity. Further in vitro and in vivo bioassay of calotropin could facilitate the development of novel non-hormonal male-specific contraceptive in near future.


Subject(s)
Adenosine Triphosphatases/antagonists & inhibitors , Adenosine Triphosphatases/metabolism , Contraceptive Agents, Male/pharmacology , Drug Discovery , Sperm Maturation/drug effects , Adenosine Triphosphatases/chemistry , Adenosine Triphosphate/metabolism , Binding Sites , Cardenolides/pharmacology , Humans , Katanin , Ligands , Male , Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Binding , Quantitative Structure-Activity Relationship , Small Molecule Libraries/pharmacology
13.
Eur J Cell Biol ; 96(2): 99-109, 2017 Mar.
Article in English | MEDLINE | ID: mdl-28109635

ABSTRACT

Parkinson's disease is characterized by accumulation of intraneuronal cytoplasmic inclusions, Lewy bodies, which mainly consist of aggregated α-synuclein. Controversies exist as to whether high blood cholesterol is a risk factor for the development of the disease and whether statin treatment could have a protective effect. Using a model system of BE(2)-M17 neuroblastoma cells treated with the neurotoxin 1-methyl-4-phenylpyridinium (MPP+), we found that MPP+-induced cell death was accompanied by cholesterol accumulation in a lysosomal-like pattern in pre-apoptotic cells. To study the effects of lysosomal cholesterol accumulation, we increased lysosomal cholesterol through pre-treatment with U18666A and found delayed leakage of lysosomal contents into the cytosol, which reduced cell death. This suggests that increased lysosomal cholesterol is a stress response mechanism to protect lysosomal membrane integrity in response to early apoptotic stress. However, high cholesterol also stimulated the accumulation of α-synuclein. Treatment with the cholesterol-lowering drug lovastatin reduced MPP+-induced cell death by inhibiting the production of reactive oxygen species, but did not prevent lysosomal cholesterol increase nor affect α-synuclein accumulation. Our study indicates a dual role of high cholesterol in Parkinson's disease, in which it acts both as a protector against lysosomal membrane permeabilization and as a stimulator of α-synuclein accumulation.


Subject(s)
Cholesterol/metabolism , Lysosomes/metabolism , Parkinson Disease/metabolism , alpha-Synuclein/metabolism , Anticholesteremic Agents/pharmacology , Cell Line, Tumor , Cell Survival/physiology , Humans , Lovastatin/pharmacology , Parkinson Disease/pathology , Reactive Oxygen Species/metabolism
14.
J Clin Diagn Res ; 10(10): UC06-UC09, 2016 Oct.
Article in English | MEDLINE | ID: mdl-27891425

ABSTRACT

INTRODUCTION: In a patient, the skin to Subarachnoid Space Depth (SSD) varies considerably at different levels of the spinal cord. It also varies from patient to patient at the same vertebral level as per age, sex and Body Mass Index (BMI). Estimation of the skin to SSD reduces complications related to spinal anaesthesia. AIM: To measure the skin to SSD in the Indian population and to find a formula for predicting this depth. MATERIALS AND METHODS: Three hundred adult patients belonging to American Society of Anaesthesiologist class I and II, undergoing surgery using spinal anaesthesia in various surgical specialities of Gauhati Medical College were selected by systemic sampling for this prospective, observational study. Patients were divided into three groups: Group M containing male patients, Group F containing non-pregnant female patients, and Group PF containing pregnant female's patients. SSD was measured after performing lumbar puncture. The relationship between SSD and patient characteristics were studied, correlated and statistical analysis was used to find a formula for predicting the skin to SSD. Statistical analysis was done using Statistical Package for Social Sciences (SPSS 21.0, Chicago, IL, USA). One-way ANOVA with post-hoc(Bonferroni correction factor) analysis was applied to compare the three groups. Multivariate analysis was done for the covariates followed by a multivariate regression analysis to evaluate the covariates influencing SSD for each group separately. RESULTS: Mean SSD was 4.37±0.31cm in the overall population. SSD in adult males was 4.49±0.19cm which was significantly longer than that observed in female's 4.18±0.39cm which was comparable with SSD in parturient 4.43±0.19 cm. The formula for predicting the skin to SSD in the male population was 1.718+0.077×BMI+0.632×Height, in nonpregnant female population was 1.828+0.077×BMI+0.018×Height+0.007×Age and 0.748+0.209×BMI+4.703×Height-0.054×weight in parturient females, respectively. CONCLUSION: Skin to SSD correlated with the BMI in all the patients in our study.

15.
FEBS J ; 283(19): 3508-3522, 2016 10.
Article in English | MEDLINE | ID: mdl-27562772

ABSTRACT

Genetic polymorphisms of immune genes that associate with higher risk to develop Alzheimer's disease (AD) have led to an increased research interest on the involvement of the immune system in AD pathogenesis. A link between amyloid pathology and immune gene expression was suggested in a genome-wide gene expression study of transgenic amyloid mouse models. In this study, the gene expression of lysozyme, a major player in the innate immune system, was found to be increased in a comparable pattern as the amyloid pathology developed in transgenic mouse models of AD. A similar pattern was seen at protein levels of lysozyme in human AD brain and CSF, but this lysozyme pattern was not seen in a tau transgenic mouse model. Lysozyme was demonstrated to be beneficial for different Drosophila melanogaster models of AD. In flies that expressed Aß1-42 or AßPP together with BACE1 in the eyes, the rough eye phenotype indicative of toxicity was completely rescued by coexpression of lysozyme. In Drosophila flies bearing the Aß1-42 variant with the Arctic gene mutation, lysozyme increased the fly survival and decreased locomotor dysfunction dose dependently. An interaction between lysozyme and Aß1-42 in the Drosophila eye was discovered. We propose that the increased levels of lysozyme, seen in mouse models of AD and in human AD cases, were triggered by Aß1-42 and caused a beneficial effect by binding of lysozyme to toxic species of Aß1-42 , which prevented these from exerting their toxic effects. These results emphasize the possibility of lysozyme as biomarker and therapeutic target for AD.


Subject(s)
Alzheimer Disease/enzymology , Muramidase/metabolism , Alzheimer Disease/genetics , Alzheimer Disease/pathology , Amyloid beta-Peptides/genetics , Amyloid beta-Peptides/metabolism , Animals , Brain/enzymology , Brain/pathology , Disease Models, Animal , Drosophila melanogaster/genetics , Drosophila melanogaster/metabolism , Drosophila melanogaster/ultrastructure , Eye/metabolism , Eye/ultrastructure , Female , Humans , Male , Mice, Inbred C57BL , Mice, Transgenic , Muramidase/genetics , Mutation , Peptide Fragments/metabolism , RNA, Messenger/metabolism
16.
Nature ; 536(7615): 179-83, 2016 08 11.
Article in English | MEDLINE | ID: mdl-27487207

ABSTRACT

Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N2 gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here, genomic analysis of single cells from the world's largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductases (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted ~40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. These results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth's most abundant organismal group.


Subject(s)
Alphaproteobacteria/classification , Alphaproteobacteria/metabolism , Aquatic Organisms/metabolism , Nitrogen/analysis , Oceans and Seas , Oxygen/analysis , Seawater/chemistry , Adaptation, Physiological/genetics , Alphaproteobacteria/genetics , Alphaproteobacteria/isolation & purification , Anaerobiosis/genetics , Aquatic Organisms/enzymology , Aquatic Organisms/genetics , Aquatic Organisms/isolation & purification , Denitrification , Gene Expression Profiling , Genes, Bacterial , Genome, Bacterial/genetics , Nitrate Reductases/genetics , Nitrate Reductases/metabolism , Nitrates/metabolism , Nitrites/metabolism , Nitrogen/metabolism , Oxidation-Reduction , Oxygen/metabolism , Phylogeny , Single-Cell Analysis , Transcription, Genetic
17.
Neurobiol Dis ; 83: 122-33, 2015 Nov.
Article in English | MEDLINE | ID: mdl-26334479

ABSTRACT

The hallmarks of Alzheimer disease are amyloid-ß plaques and neurofibrillary tangles accompanied by signs of neuroinflammation. Lysozyme is a major player in the innate immune system and has recently been shown to prevent the aggregation of amyloid-ß1-40 in vitro. In this study we found that patients with Alzheimer disease have increased lysozyme levels in the cerebrospinal fluid and lysozyme co-localized with amyloid-ß in plaques. In Drosophila neuronal co-expression of lysozyme and amyloid-ß1-42 reduced the formation of soluble and insoluble amyloid-ß species, prolonged survival and improved the activity of amyloid-ß1-42 transgenic flies. This suggests that lysozyme levels rise in Alzheimer disease as a compensatory response to amyloid-ß increases and aggregation. In support of this, in vitro aggregation assays revealed that lysozyme associates with amyloid-ß1-42 and alters its aggregation pathway to counteract the formation of toxic amyloid-ß species. Overall, these studies establish a protective role for lysozyme against amyloid-ß associated toxicities and identify increased lysozyme in patients with Alzheimer disease. Therefore, lysozyme has potential as a new biomarker as well as a therapeutic target for Alzheimer disease.


Subject(s)
Alzheimer Disease/enzymology , Alzheimer Disease/pathology , Amyloid beta-Peptides/metabolism , Brain/metabolism , Muramidase/metabolism , Peptide Fragments/metabolism , Adult , Aged , Aged, 80 and over , Alzheimer Disease/cerebrospinal fluid , Alzheimer Disease/metabolism , Amyloid beta-Peptides/ultrastructure , Animals , Brain/pathology , Cell Death , Drosophila melanogaster , Female , Humans , Insect Proteins/metabolism , Locomotion , Male , Middle Aged , Muramidase/blood , Muramidase/cerebrospinal fluid , Muramidase/pharmacology , Peptide Fragments/ultrastructure , Plaque, Amyloid/metabolism , Plaque, Amyloid/ultrastructure , Tumor Cells, Cultured , tau Proteins/metabolism
18.
ACS Chem Biol ; 9(9): 2082-91, 2014 Sep 19.
Article in English | MEDLINE | ID: mdl-24984213

ABSTRACT

Harnessing the biotechnological potential of the large number of proteins available in sequence databases requires scalable methods for functional characterization. Here we propose a workflow to address this challenge by combining phylogenomic guided DNA synthesis with high-throughput mass spectrometry and apply it to the systematic characterization of GH1 ß-glucosidases, a family of enzymes necessary for biomass hydrolysis, an important step in the conversion of lignocellulosic feedstocks to fuels and chemicals. We synthesized and expressed 175 GH1s, selected from over 2000 candidate sequences to cover maximum sequence diversity. These enzymes were functionally characterized over a range of temperatures and pHs using nanostructure-initiator mass spectrometry (NIMS), generating over 10,000 data points. When combined with HPLC-based sugar profiling, we observed GH1 enzymes active over a broad temperature range and toward many different ß-linked disaccharides. For some GH1s we also observed activity toward laminarin, a more complex oligosaccharide present as a major component of macroalgae. An area of particular interest was the identification of GH1 enzymes compatible with the ionic liquid 1-ethyl-3-methylimidazolium acetate ([C2mim][OAc]), a next-generation biomass pretreatment technology. We thus searched for GH1 enzymes active at 70 °C and 20% (v/v) [C2mim][OAc] over the course of a 24-h saccharification reaction. Using our unbiased approach, we identified multiple enzymes of different phylogentic origin with such activities. Our approach of characterizing sequence diversity through targeted gene synthesis coupled to high-throughput screening technologies is a broadly applicable paradigm for a wide range of biological problems.


Subject(s)
Biotechnology/methods , Cellulases/analysis , Cellulases/genetics , Cellulases/metabolism , DNA/biosynthesis , Mass Spectrometry/methods , Phylogeny , Biomass , Chromatography, High Pressure Liquid/methods , Glucans/metabolism , High-Throughput Screening Assays/methods , Hydrogen-Ion Concentration , Hydrolysis , Imidazoles/chemistry , Ionic Liquids/chemistry , Nanostructures , Substrate Specificity , Temperature , Workflow
19.
Nat Cell Biol ; 16(5): 415-24, 2014 May.
Article in English | MEDLINE | ID: mdl-24747438

ABSTRACT

The components supporting autophagosome growth on the cup-like isolation membrane are likely to be different from those found on closed and maturing autophagosomes. The highly curved rim of the cup may serve as a functionally required surface for transiently associated components of the early acting autophagic machinery. Here we demonstrate that the E2-like enzyme, Atg3, facilitates LC3/GABARAP lipidation only on membranes exhibiting local lipid-packing defects. This activity requires an amino-terminal amphipathic helix similar to motifs found on proteins targeting highly curved intracellular membranes. By tuning the hydrophobicity of this motif, we can promote or inhibit lipidation in vitro and in rescue experiments in Atg3-knockout cells, implying a physiologic role for this stress detection. The need for extensive lipid-packing defects suggests that Atg3 is designed to work at highly curved membranes, perhaps including the limiting edge of the growing phagophore.


Subject(s)
Adaptor Proteins, Signal Transducing/metabolism , Cell Membrane/enzymology , Cytoskeletal Proteins/metabolism , Membrane Proteins/metabolism , Microfilament Proteins/metabolism , Microtubule-Associated Proteins/metabolism , Signal Transduction , Ubiquitin-Conjugating Enzymes/metabolism , Adaptor Proteins, Signal Transducing/genetics , Amino Acid Motifs , Animals , Apoptosis Regulatory Proteins , Autophagy-Related Protein 7 , Autophagy-Related Protein 8 Family , Autophagy-Related Proteins , Cytoskeletal Proteins/genetics , HeLa Cells , Humans , Hydrophobic and Hydrophilic Interactions , Liposomes , Membrane Proteins/genetics , Mice , Mice, Knockout , Microfilament Proteins/genetics , Microtubule-Associated Proteins/genetics , Mutation , Phosphatidylethanolamines/metabolism , Rats , Stress, Physiological , Transfection , Ubiquitin-Activating Enzymes/genetics , Ubiquitin-Activating Enzymes/metabolism , Ubiquitin-Conjugating Enzymes/deficiency , Ubiquitin-Conjugating Enzymes/genetics
20.
Neurobiol Dis ; 65: 82-92, 2014 May.
Article in English | MEDLINE | ID: mdl-24412310

ABSTRACT

The spreading of pathology through neuronal pathways is likely to be the cause of the progressive cognitive loss observed in Alzheimer's disease (AD) and other neurodegenerative diseases. We have recently shown the propagation of AD pathology via cell-to-cell transfer of oligomeric amyloid beta (Aß) residues 1-42 (oAß1-42) using our donor-acceptor 3-D co-culture model. We now show that different Aß-isoforms (fluorescently labeled 1-42, 3(pE)-40, 1-40 and 11-42 oligomers) can transfer from one cell to another. Thus, transfer is not restricted to a specific Aß-isoform. Although different Aß isoforms can transfer, differences in the capacity to clear and/or degrade these aggregated isoforms result in vast differences in the net amounts ending up in the receiving cells and the net remaining Aß can cause seeding and pathology in the receiving cells. This insufficient clearance and/or degradation by cells creates sizable intracellular accumulations of the aggregation-prone Aß1-42 isoform, which further promotes cell-to-cell transfer; thus, oAß1-42 is a potentially toxic isoform. Furthermore, cell-to-cell transfer is shown to be an early event that is seemingly independent of later appearances of cellular toxicity. This phenomenon could explain how seeds for the AD pathology could pass on to new brain areas and gradually induce AD pathology, even before the first cell starts to deteriorate, and how cell-to-cell transfer can act together with the factors that influence cellular clearance and/or degradation in the development of AD.


Subject(s)
Amyloid beta-Peptides/metabolism , Cell Communication/physiology , Neurites/metabolism , Peptide Fragments/metabolism , Amyloid beta-Peptides/ultrastructure , Brain-Derived Neurotrophic Factor/pharmacology , Cell Differentiation/drug effects , Cell Line, Transformed , Coculture Techniques , Extracellular Matrix/physiology , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Humans , Lysosomes/metabolism , Lysosomes/ultrastructure , Membrane Potential, Mitochondrial/drug effects , Nerve Growth Factor/pharmacology , Neuregulin-1/pharmacology , Neurites/ultrastructure , Neuroblastoma/pathology , Peptide Fragments/ultrastructure , Protein Isoforms , Time Factors , Tretinoin/pharmacology
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