Assessing the Impact of the Nutrient Microenvironment on the Metabolism of Effector CD8+ T Cells.
J, Fendt SM Abstract Immune cell function is tightly regulated by cellular metabolism, which in turn is strongly linked to the nutrient availability in the microenvironment surrounding the cells. This link is critical for effector CD8+ T cells which, after activation, must migrate from nutrient-rich environments into nutrient-scarce regions such as the tumor microenvironment. Assessing how nutrient availability modulates the metabolism of effector CD8+ T cells is thus key for understanding how harsh environments may impair their proliferation and effector function. Here, we describe an approach to systematically s...
Source: Mol Biol Cell - October 14, 2018 Category: Molecular Biology Authors: Fernández-García J, Fendt SM Tags: Methods Mol Biol Source Type: research

Development of Patient-Derived Tumor Xenograft Models.
Abstract In spite of the latest advancements in understanding cancer development and progression, drugs successful in preclinical testing often fail upon reaching phase III clinical trials. A reason for this is the use of inappropriate preclinical models that do not preserve tumor heterogeneity. Although used for decades, cell cultures derived from patients substantially deviate from their original biopsy upon culturing; moreover, they cannot predict the response of an organism as a whole.Patient-derived xenograft (PDX) models are emerging as powerful tools since they have a predictive therapeutic value and preser...
Source: Mol Biol Cell - October 14, 2018 Category: Molecular Biology Authors: Annibali D, Leucci E, Hermans E, Amant F Tags: Methods Mol Biol Source Type: research

Imaging Glioma Progression by Intravital Microscopy.
We describe here a method for generating mouse orthotopic gliomas in order to follow their progression over time by multi-photon laser scanning microscopy. After craniotomy of the parietal bone, glioma cells are implanted in the brain cortex and a glass window is cemented atop, allowing chronical imaging of the tumor. The expression of different fluorescent proteins in tumor cells and in specific cell types of a number of currently available transgenic mouse strains allows obtaining multicolor 3D images of the tumor over time. This technique is suitable both to evaluate the effect of pharmacological treatments and to unrav...
Source: Mol Biol Cell - October 14, 2018 Category: Molecular Biology Authors: Stanchi F, Matsumoto K, Gerhardt H Tags: Methods Mol Biol Source Type: research

Determining the Intracellular Organization of Organelles.
uer K Abstract Many studies have found alterations in the positioning and morphology of intracellular organelles under different experimental conditions. Although the precise quantification of these changes is challenging, it is strongly facilitated in single cells that are seeded on micropatterned substrates. Indeed, the controlled microenvironment of the cell leads to a reproducible distribution of organelles, simplifying image analysis and minimizing the number of cells required for robust phenotypes. Here, we outline how alterations in the intracellular organization of lysosomes and mitochondria, as a result o...
Source: Mol Biol Cell - October 14, 2018 Category: Molecular Biology Authors: Latgé B, Schauer K Tags: Methods Mol Biol Source Type: research

High-Throughput Reconstruction of Ancestral Protein Sequence, Structure, and Molecular Function.
Abstract Ancestral protein sequence reconstruction is a powerful technique for explicitly testing hypotheses about the evolution of molecular function, allowing researchers to meticulously dissect how historical changes in protein sequence impacted functional repertoire by altering the protein's 3D structure. These techniques have provided concrete, experimentally validated insights into ancient evolutionary processes and help illuminate the complex relationship between protein sequence, structure, and function. Inferring the protein family phylogenies on which ancestral sequence reconstruction depends and reconst...
Source: Mol Biol Cell - October 11, 2018 Category: Molecular Biology Authors: Aadland K, Pugh C, Kolaczkowski B Tags: Methods Mol Biol Source Type: research

Proteomic Detection of Carbohydrate-Active Enzymes (CAZymes) in Microbial Secretomes.
lash; Abstract Secretomes from microorganisms growing on biomass contain carbohydrate-active enzymes (CAZymes) of potential biotechnological interest. By analyzing such secretomes, we may discover key enzymes involved in degradation processes and potentially infer the mode-of-action of biomass conversion. Some of these enzymes may have predicted functions in carbohydrate degradation, while others may not, while yet exhibiting a similar expression pattern; these latter enzymes constitute potential novel enzymes involved in the degradation process and provide a basis for further biochemical exploration. Hence, secre...
Source: Mol Biol Cell - October 4, 2018 Category: Molecular Biology Authors: Tuveng TR, Eijsink VGH, Arntzen MØ Tags: Methods Mol Biol Source Type: research

Functional Proteomic Analysis to Characterize Signaling Crosstalk.
Abstract The biological activities of a cell are determined by its response to external stimuli. The signals are transduced from either intracellular or extracellular milieu through networks of multi-protein complexes and post-translational modifications of proteins (PTMs). Most PTMs including phosphorylation, acetylation, ubiquitination, and SUMOylation, among others, modulate activities of proteins and regulate biological processes such as proliferation, differentiation, as well as host pathogen interaction. Conventionally, reverse genetics analysis and single molecule-based studies were employed to identify and...
Source: Mol Biol Cell - October 4, 2018 Category: Molecular Biology Authors: Pinto SM, Subbannayya Y, Prasad TSK Tags: Methods Mol Biol Source Type: research

Label-Free LC-MS/MS Strategy for Comprehensive Proteomic Profiling of Human Islets Collected Using Laser Capture Microdissection from Frozen Pancreata.
Abstract Diabetes mellitus is caused by either loss of pancreatic islets β-cells (Type 1 Diabetes, T1D), insufficient insulin release in the islet β-cells coupled with insulin resistance in target tissues (Type 2 Diabetes, T2D), or impaired insulin release (genetic forms of diabetes and, possibly, T1D subtypes). The investigation of the islet proteome could elucidate facets of the pathogenesis of diabetes. Enzymatically isolated and cultured (EIC) islets are frequently used to investigate biochemical signaling pathways that could trigger β-cell changes and death in diabetes. However, they cannot ful...
Source: Mol Biol Cell - October 4, 2018 Category: Molecular Biology Authors: Zhang L, Lanzoni G, Battarra M, Inverardi L, Zhang Q Tags: Methods Mol Biol Source Type: research

Proteases: Pivot Points in Functional Proteomics.
Abstract Proteases drive the life cycle of all proteins, ensuring the transportation and activation of newly minted, would-be proteins into their functional form while recycling spent or unneeded proteins. Far from their image as engines of protein digestion, proteases play fundamental roles in basic physiology and regulation at multiple levels of systems biology. Proteases are intimately associated with disease and modulation of proteolytic activity is the presumed target for successful therapeutics. "Proteases: Pivot Points in Functional Proteomics" examines the crucial roles of proteolysis across a wi...
Source: Mol Biol Cell - October 4, 2018 Category: Molecular Biology Authors: Verhamme IM, Leonard SE, Perkins RC Tags: Methods Mol Biol Source Type: research

Efficient Extraction and Digestion of Gluten Proteins.
Abstract Coeliac disease (CD) is a T-cell mediated autoimmune disorder triggered by ingestion of cereal gluten found in wheat (gliadins and glutenins), barley (hordeins), and rye (secalins). As the only treatment for CD is a lifelong gluten-free diet, the measurement of gluten in raw ingredients and processed food products is critical to protecting people with CD or gluten intolerance. The most commonly employed method is the enzyme-linked immunosorbent assay (ELISA), but more recently mass spectrometry has been employed wherein the extracted gluten proteins are digested to peptides that are then directly measured...
Source: Mol Biol Cell - October 4, 2018 Category: Molecular Biology Authors: Li H, Byrne K, Howitt CA, Colgrave ML Tags: Methods Mol Biol Source Type: research

Glycosylation Profiling of Tumor Marker in Plasma Using Bead-Based Immunoassay.
Abstract As one of the most important posttranslational modifications, glycosylation plays critical roles in protein folding, trafficking, cell differentiation, immune recognition, etc. The alteration of glycosylation is closely associated with the pathological processes during and after caner development, and thus holds great value in cancer detection. In this chapter, we describe a protocol on the glycosylation profiling of tumor marker in plasma using bead-based immunoassay with CA125 as a model, including bead coupling, coupling control, glycosylation assay, as well as the plasma screening for breast cancer pa...
Source: Mol Biol Cell - October 4, 2018 Category: Molecular Biology Authors: Wang H, Cao Z, Duan H, Yu X Tags: Methods Mol Biol Source Type: research

Two-Dimensional Biochemical Purification for Global Proteomic Analysis of Macromolecular Protein Complexes.
Abstract A high-resolution two-dimensional (2-D) proteomic fractionation technique for the systematic purification and subsequent mass spectrometry-based identification of endogenous protein macromolecular complexes is described. The method hyphenates preparative isoelectric focusing (IEF) with mixed-bed ion exchange chromatography (IEX) to efficiently separate cell- or tissue- derived soluble protein mixtures, allowing for more effective and less biased physiochemical characterization of stable multiprotein assemblies. After comprehensive 2D fractionation of cell-free lysates, each fraction is subjected to quanti...
Source: Mol Biol Cell - October 4, 2018 Category: Molecular Biology Authors: Pourhaghighi R, Emili A Tags: Methods Mol Biol Source Type: research

Oxidoreductases and Reactive Oxygen Species in Conversion of Lignocellulosic Biomass.
g;K, Eijsink VGH Abstract SUMMARYBiomass constitutes an appealing alternative to fossil resources for the production of materials and energy. The abundance and attractiveness of vegetal biomass come along with challenges pertaining to the intricacy of its structure, evolved during billions of years to face and resist abiotic and biotic attacks. To achieve the daunting goal of plant cell wall decomposition, microorganisms have developed many (enzymatic) strategies, from which we seek inspiration to develop biotechnological processes. A major breakthrough in the field has been the discovery of enzymes today known as...
Source: Mol Biol Cell - September 29, 2018 Category: Molecular Biology Authors: Bissaro B, Várnai A, Røhr ÅK, Eijsink VGH Tags: Microbiol Mol Biol Rev Source Type: research

Cytosolic Recognition of Microbes and Pathogens: Inflammasomes in Action.
Abstract SUMMARYInfection is a dynamic biological process underpinned by a complex interplay between the pathogen and the host. Microbes from all domains of life, including bacteria, viruses, fungi, and protozoan parasites, have the capacity to cause infection. Infection is sensed by the host, which often leads to activation of the inflammasome, a cytosolic macromolecular signaling platform that mediates the release of the proinflammatory cytokines interleukin-1β (IL-1β) and IL-18 and cleavage of the pore-forming protein gasdermin D, leading to pyroptosis. Host-mediated sensing of the infection occurs wh...
Source: Mol Biol Cell - September 14, 2018 Category: Molecular Biology Authors: Hayward JA, Mathur A, Ngo C, Man SM Tags: Microbiol Mol Biol Rev Source Type: research

DDX17 Specifically, and Independently of DDX5, Controls Use of the HIV A4/5 Splice Acceptor Cluster and Is Essential for Efficient Replication of HIV.
Abstract HIV splicing involves five splice donor and eight splice acceptor sequences which, together with cryptic splice sites, generate over 100 mRNA species. Ninety percent of both partially spliced and fully spliced transcripts utilize the intrinsically weak A4/A5 3' splice site cluster. We show that DDX17, but not its close paralog DDX5, specifically controls the usage of this splice acceptor group. In its absence, production of the viral envelope protein and other regulatory and accessory proteins is grossly reduced, while Vif, which uses the A1 splice acceptor, is unaffected. This is associated with a profou...
Source: Mol Biol Cell - August 24, 2018 Category: Molecular Biology Authors: Sithole N, Williams CA, Vaughan AM, Kenyon JC, Lever AML Tags: J Mol Biol Source Type: research

Correction for Agudo-Ib áñez et al., "H-Ras Distribution and Signaling in Plasma Membrane Microdomains Are Regulated by Acylation and Deacylation Events".
Correction for Agudo-Ibáñez et al., "H-Ras Distribution and Signaling in Plasma Membrane Microdomains Are Regulated by Acylation and Deacylation Events". Mol Cell Biol. 2018 Sep 01;38(17): Authors: Agudo-Ibáñez L, Herrero A, Barbacid M, Crespo P PMID: 30111615 [PubMed - in process] (Source: Mol Biol Cell)
Source: Mol Biol Cell - August 18, 2018 Category: Molecular Biology Authors: Agudo-Ibáñez L, Herrero A, Barbacid M, Crespo P Tags: Mol Cell Biol Source Type: research

The Validated Embryonic Stem Cell Test with Murine Embryonic Stem Cells.
Abstract Birth defects are the leading cause of infant mortality in the USA, yet the causes of most of these conditions are unknown. While a combination of genetic and environmental factors are suspected in most cases, little information exists about the health risks that prenatal exposure to many common chemicals poses for the fetus. Thus, development and refinement of procedures that can accurately predict embryotoxicity of compounds is important for curtailing the number of infants born with birth defects. The embryonic stem cell test (EST) is a procedure that utilizes comparison of cytotoxicity in embryonic an...
Source: Mol Biol Cell - June 15, 2018 Category: Molecular Biology Authors: Walker LM, McClelland-Descalzo DLV, Zur Nieden NI Tags: Methods Mol Biol Source Type: research

Human Pluripotent Stem Cells to Assess Developmental Toxicity in the Osteogenic Lineage.
Abstract Musculoskeletal birth defects are frequent, yet their causes remain insufficiently investigated. Aside from genetic factors, exposure to environmental toxicants is suspected to contribute to the etiology of skeletal malformations. However, most chemicals in the environment are insufficiently characterized for their potential to cause harm to the differentiation of osteoblasts, the bone-forming cells and thereby the development of the skeleton.This lack of information primarily stems from animal testing being prohibitively expensive and time-consuming, which has prompted the development of predictive in vi...
Source: Mol Biol Cell - June 15, 2018 Category: Molecular Biology Authors: Madrid JV, Sera SR, Sparks NRL, Zur Nieden NI Tags: Methods Mol Biol Source Type: research

Chick Embryonic Cardiomyocyte Micromass System for Assessing Developmental Cardiotoxicity of Drugs.
Abstract Heart is the first mesodermal organ to develop and is sensitive to life-threatening toxic effects of drugs during development. A number of methods have been devised to study developmental cardiotoxic effects of drugs including micromass system. The micromass system involves the culture of primary embryonic cells and reestablishment of tissue system in vitro. In chick embryonic cardiomyocyte micromass system the chick heart cells are cultured in a small volume at a very high cell density. These cells form synchronized contracting foci. Addition of drugs to this system allows us to study the developmental c...
Source: Mol Biol Cell - June 15, 2018 Category: Molecular Biology Authors: Qureshi WMS, Pratten MK Tags: Methods Mol Biol Source Type: research

Flow Cytometry to Evaluate Potential Developmental Toxicants in the Embryonic Stem Cell.
io CE Abstract Embryonic stem cells (ESC) are widely used due to their unlimited capacity of differentiation into different cell lineages, which makes ESC a viable choice as a toxicology test model. Toxicological analysis using embryonic stem cells (ESC) has become an important tool in toxicology procedures. Regarding toxicological analysis methods, flow cytometry (FC) is one technique designed to detect and evaluate cells in suspension, for example, ESC suspension, thus making possible to study different biological, physical, and/or chemical characteristics of cells. Thus, FC can be very useful for cell toxicolog...
Source: Mol Biol Cell - June 15, 2018 Category: Molecular Biology Authors: Lara VM, Santos Roballo KC, Gotardo AT, Ambrósio CE Tags: Methods Mol Biol Source Type: research

Western Blot Methodologies for Analysis of In Vitro Protein Expression Induced by Teratogenic Agents.
Abstract Western blotting permits immunodetection, characterization, and quantification of proteins in cell (or tissue) homogenates. It also enables detection of protein modification (e.g., phosphorylation) or degradation (e.g., hydrolysis), even at low abundance. Sodium dodecyl sulfate (SDS)-polyacrylamide gel is used to separate proteins from homogenate which are then transferred electrophoretically to polyvinylidene difluoride (PVDF) membranes. After membrane "blocking," to reduce nonspecific binding, proteins of interest are detected using specific antibodies (antigen detection), which are then bound...
Source: Mol Biol Cell - June 15, 2018 Category: Molecular Biology Authors: Martins-Gomes C, Silva AM Tags: Methods Mol Biol Source Type: research

Effect of Teratogens on Development of Drosophila melanogaster.
Abstract Prenatal exposure to various environmental teratogens such as drugs, toxins, and infectious etiologies results in a wide range of developmental abnormalities, including growth deficiency, developmental delay, structural defects, functional CNS abnormalities, and fetal death. Here, we describe the use of Drosophila melanogaster as a model organism for investigating teratogenic effects on embryonic development. PMID: 29896696 [PubMed - in process] (Source: Mol Biol Cell)
Source: Mol Biol Cell - June 15, 2018 Category: Molecular Biology Authors: Li D, Bi X Tags: Methods Mol Biol Source Type: research

Immunohistochemical Assessment as a Tool for Investigating Developmental Toxicity in Zebrafish (Danio rerio).
Abstract Immunohistochemistry has been proven to be one of the most important ancillary techniques in understanding early development processes as it allows both a focus on specific, individual cell behaviors as well as an expanded view of tissue architecture, critical to the morphogenesis of complex and integrated organ systems. The zebrafish (Danio rerio) is a well-established model in the area of developmental toxicology and immunohistochemistry methods have been extensively applied to embryos and larvae to ascertain abnormal development resulting from toxic exposure. This chapter outlines the immunohistochemis...
Source: Mol Biol Cell - June 15, 2018 Category: Molecular Biology Authors: Santos C, Pinto ML Tags: Methods Mol Biol Source Type: research

Western Blot Analysis and Immunostaining for Prediction of Embryotoxicity in Mus musculus.
Abstract A broad range of research must be answered in order to gain a complete understanding of the histological and histochemical profile of teratological exposure in Mus musculus. Continued research is needed to track patterns of teratogen effects on the DNA expression of the embryonic brain and its variation impact. An important technique used in cell and molecular biology is Western blotting. By using a Western blot analysis and immunostaining, researchers are able to predict embryotoxicity in Mus musculus. The method uses three elements to accomplish this task: (1) Nonspecific antibody binding to a nitrocell...
Source: Mol Biol Cell - June 15, 2018 Category: Molecular Biology Authors: Irnidayanti Y, Darmanto W, Sutiono DR Tags: Methods Mol Biol Source Type: research

In Vivo Analysis of Apoptosis in Embryonic Hippocampus.
We describe here a of techniques that are currently for the detection of apoptotic cells in the central nervous system (CNS) directly on tissue sections in postnatal mice. PMID: 29896714 [PubMed - in process] (Source: Mol Biol Cell)
Source: Mol Biol Cell - June 15, 2018 Category: Molecular Biology Authors: Salimi A, Pourahmad J Tags: Methods Mol Biol Source Type: research

Measurement of Mitochondrial Toxicity Parameters in Embryonic Hippocampus.
Abstract Recent discoveries have focused on mitochondria functions in the neuroscience research for approaches to study mitochondria dysfunction in neurodegenerative diseases. Mitochondrion is one of the organelles that is possibly worst affected in cognitive impairments. These are known as "powerhouse" of the cell as they are the main source of generation of ATP through aerobic respiration. They have role in oxidative phosphorylation and metabolism, they play central role in cell differentiation, apoptosis, oxygen sensing and detoxification of reactive oxygen species, innate immunity, mitochondrial matr...
Source: Mol Biol Cell - June 15, 2018 Category: Molecular Biology Authors: Salimi A, Pourahmad J Tags: Methods Mol Biol Source Type: research

Replication Fork Breakage and Restart in Escherichia coli.
Abstract In all organisms, replication impairments are an important source of genome rearrangements, mainly because of the formation of double-stranded DNA (dsDNA) ends at inactivated replication forks. Three reactions for the formation of dsDNA ends at replication forks were originally described for Escherichia coli and became seminal models for all organisms: the encounter of replication forks with preexisting single-stranded DNA (ssDNA) interruptions, replication fork reversal, and head-to-tail collisions of successive replication rounds. Here, we first review the experimental evidence that now allows us to kno...
Source: Mol Biol Cell - June 15, 2018 Category: Molecular Biology Authors: Michel B, Sinha AK, Leach DRF Tags: Microbiol Mol Biol Rev Source Type: research

In memoriam: George Oster, UC Berkeley, 1940-2018.
PMID: 29902126 [PubMed - in process] (Source: Mol Biol Cell)
Source: Mol Biol Cell - June 15, 2018 Category: Molecular Biology Authors: Mogilner A Tags: Mol Biol Cell Source Type: research

Designing an In Vivo Efficacy Study of Nanomedicines for Preclinical Tumor Growth Inhibition.
Abstract Novel nanoformulated chemotherapeutics and diagnostics require demonstration of efficacy and safety in appropriate animal models prior to conducting early-phase clinical trials. In vivo efficacy experiments are tailored to the tumor model type and route of administration as well as several parameters related to the nanoformulation, like drug loading to determine dosing volume. When designing in vivo efficacy studies for nanomedicines, understanding the relationship between tumor biology and the nanoformulation characteristics is critical to achieving meaningful results, along with applying appropriate dru...
Source: Mol Biol Cell - June 1, 2018 Category: Molecular Biology Authors: Adiseshaiah PP, Stern ST Tags: Methods Mol Biol Source Type: research

Correction for Ballarino et al., "Novel Long Noncoding RNAs (lncRNAs) in Myogenesis: a miR-31 Overlapping lncRNA Transcript Controls Myoblast Differentiation".
Correction for Ballarino et al., "Novel Long Noncoding RNAs (lncRNAs) in Myogenesis: a miR-31 Overlapping lncRNA Transcript Controls Myoblast Differentiation". Mol Cell Biol. 2018 Jun 15;38(12): Authors: Ballarino M, Cazzella V, D'Andrea D, Grassi L, Bisceglie L, Cipriano A, Santini T, Pinnarò C, Morlando M, Tramontano A, Bozzoni I PMID: 29844107 [PubMed - in process] (Source: Mol Biol Cell)
Source: Mol Biol Cell - June 1, 2018 Category: Molecular Biology Authors: Ballarino M, Cazzella V, D'Andrea D, Grassi L, Bisceglie L, Cipriano A, Santini T, Pinnarò C, Morlando M, Tramontano A, Bozzoni I Tags: Mol Cell Biol Source Type: research

Correction for Deng et al., "HMGN1 Modulates Nucleosome Occupancy and DNase I Hypersensitivity at the CpG Island Promoters of Embryonic Stem Cells".
Correction for Deng et al., "HMGN1 Modulates Nucleosome Occupancy and DNase I Hypersensitivity at the CpG Island Promoters of Embryonic Stem Cells". Mol Cell Biol. 2018 Jun 15;38(12): Authors: Deng T, Zhu ZI, Zhang S, Leng F, Cherukuri S, Hansen L, Mariño-Ramírez L, Meshorer E, Landsman D, Bustin M PMID: 29844108 [PubMed - in process] (Source: Mol Biol Cell)
Source: Mol Biol Cell - June 1, 2018 Category: Molecular Biology Authors: Deng T, Zhu ZI, Zhang S, Leng F, Cherukuri S, Hansen L, Mariño-Ramírez L, Meshorer E, Landsman D, Bustin M Tags: Mol Cell Biol Source Type: research

A High-Throughput Chemical Screening Method for Inhibitors and Potentiators of Hypersensitive Cell Death Using Suspension Cell Culture of Arabidopsis thaliana.
Abstract Chemical biology provides an alternative way to identify genes involved in a particular biological process. It has the potential to overcome issues such as redundancy or lethality often found in genetic approaches, since the chemical compounds can simultaneously target all homologous proteins that function at the same step, and chemicals can be applied conditionally. Even with a variety of genetic approaches, the molecular mechanisms of plant hypersensitive cell death that occurs during disease resistance responses remain unclear. Therefore, application of chemical biology should provide new insights into...
Source: Mol Biol Cell - June 1, 2018 Category: Molecular Biology Authors: Noutoshi Y, Shirasu K Tags: Methods Mol Biol Source Type: research

Phenotype-Based Screening of Small Molecules to Modify Plant Cell Walls Using BY-2 Cells.
Abstract The plant cell wall is an important and abundant biomass with great potential for use as a modern recyclable resource. For effective utilization of this cellulosic biomass, its ability to degrade efficiently is key point. With the aim of modifying the cell wall to allow easy decomposition, we used chemical biological technology to alter its structure. As a first step toward evaluating the chemicals in the cell wall we employed a phenotype-based approach using high-throughput screening. As the plant cell wall is essential in determining cell morphology, phenotype-based screening is particularly effective i...
Source: Mol Biol Cell - June 1, 2018 Category: Molecular Biology Authors: Okubo-Kurihara E, Matsui M Tags: Methods Mol Biol Source Type: research

Chemical Screening for Strigolactone Receptor Antagonists Using Arabidopsis thaliana.
Abstract Strigolactones are a class of terpenoid-based plant hormones that are best known for their role in the suppression of axillary branching. However, strigolactones also play a role as stimulants for the germination of parasitic plants of the genera Striga and Orobanche. This dual role for strigolactones as endogenous hormones and interspecies signaling molecules has led to significant research directed toward understanding mechanisms of strigolactone perception from both the perspective of host plants and of their parasites. Antagonists for strigolactone receptors serve as potentially important tools in bot...
Source: Mol Biol Cell - June 1, 2018 Category: Molecular Biology Authors: Holbrook-Smith D, McCourt P Tags: Methods Mol Biol Source Type: research

Chemical Control of ABA Receptors to Enable Plant Protection Against Water Stress.
Abstract This chapter describes procedures to find small molecules that bind to abscisic acid (ABA) receptors and improve plant tolerance to water stress. Abscisic acid promotes the interaction between ABA receptors and protein phosphatase 2Cs (PP2Cs), which are negative regulators of ABA signaling. This receptor-mediated ABA-dependent inhibition of PP2C activity is required for ABA action in vivo. ABA agonists can be identified by high-throughput screening for molecules that promote agonist-induced ABA receptor-PP2C interactions using yeast two-hybrid assays. In addition to in vitro assays, an in vivo test to eva...
Source: Mol Biol Cell - June 1, 2018 Category: Molecular Biology Authors: Okamoto M, Cutler SR Tags: Methods Mol Biol Source Type: research

Chemical Screening for Flagella-Associated Phenotypes in Chlamydomonas reinhardtii.
Abstract Flagella of the unicellular green alga Chlamydomonas reinhardtii are nearly identical to cilia of vertebrate cells and provide an excellent model to study ciliogenesis. Cilia and flagella are important organelles used for motility and sensing the extracellular environment. Abnormalities in cilia structure or ciliary dysfunction can have devastating consequences ranging from diabetes and obesity to polycystic kidney disease and mental retardation. Small-molecule inhibitor libraries can be used to screen for flagellum-associated phenotypes in assembly, length, motility, deflagellation, and cellular toxicity...
Source: Mol Biol Cell - June 1, 2018 Category: Molecular Biology Authors: Jack B, Avasthi P Tags: Methods Mol Biol Source Type: research

Shifts in Selective Pressures on Snake Phototransduction Genes Associated with Photoreceptor Transmutation and Dim-Light Ancestry.
Abstract The visual systems of snakes are heavily modified relative to other squamates, a condition often thought to reflect their fossorial origins. Further modifications are seen in caenophidian snakes, where evolutionary transitions between rod and cone photoreceptors, termed photoreceptor transmutations, have occurred in many lineages. Little previous work, however, has focused on the molecular evolutionary underpinnings of these morphological changes. To address this, we sequenced seven snake eye transcriptomes and utilized new whole-genome and targeted capture sequencing data. We used these data to analyze g...
Source: Mol Biol Cell - May 30, 2018 Category: Molecular Biology Authors: Schott RK, Van Nynatten A, Card DC, Castoe TA, S W Chang B Tags: Mol Biol Evol Source Type: research

Retraction for Zehorai and Seger, "Beta-Like Importins Mediate the Nuclear Translocation of Mitogen-Activated Protein Kinases".
Retraction for Zehorai and Seger, "Beta-Like Importins Mediate the Nuclear Translocation of Mitogen-Activated Protein Kinases". Mol Cell Biol. 2018 Jun 01;38(11): Authors: Zehorai E, Seger R PMID: 29764995 [PubMed - in process] (Source: Mol Biol Cell)
Source: Mol Biol Cell - May 18, 2018 Category: Molecular Biology Authors: Zehorai E, Seger R Tags: Mol Cell Biol Source Type: research

Retraction for Plotnikov et al., "Nuclear Extracellular Signal-Regulated Kinase 1 and 2 Translocation Is Mediated by Casein Kinase 2 and Accelerated by Autophosphorylation".
Retraction for Plotnikov et al., "Nuclear Extracellular Signal-Regulated Kinase 1 and 2 Translocation Is Mediated by Casein Kinase 2 and Accelerated by Autophosphorylation". Mol Cell Biol. 2018 Jun 01;38(11): Authors: Plotnikov A, Chuderland D, Karamansha Y, Livnah O, Seger R PMID: 29764996 [PubMed - in process] (Source: Mol Biol Cell)
Source: Mol Biol Cell - May 18, 2018 Category: Molecular Biology Authors: Plotnikov A, Chuderland D, Karamansha Y, Livnah O, Seger R Tags: Mol Cell Biol Source Type: research

Isoprenoids and protein prenylation: implications in the pathogenesis and therapeutic intervention of Alzheimer's disease.
Abstract The mevalonate-isoprenoid-cholesterol biosynthesis pathway plays a key role in human health and disease. The importance of this pathway is underscored by the discovery that two major isoprenoids, farnesyl and geranylgeranyl pyrophosphate, are required to modify an array of proteins through a process known as protein prenylation, catalyzed by prenyltransferases. The lipophilic prenyl group facilitates the anchoring of proteins in cell membranes, mediating protein-protein interactions and signal transduction. Numerous essential intracellular proteins undergo prenylation, including most members of the small ...
Source: Mol Biol Cell - May 3, 2018 Category: Molecular Biology Authors: Jeong A, Suazo KF, Wood WG, Distefano MD, Li L Tags: Crit Rev Biochem Mol Biol Source Type: research

Fungal Morphogenesis, from the Polarized Growth of Hyphae to Complex Reproduction and Infection Structures.
ez RR, Takeshita N, Fischer R Abstract Filamentous fungi constitute a large group of eukaryotic microorganisms that grow by forming simple tube-like hyphae that are capable of differentiating into more-complex morphological structures and distinct cell types. Hyphae form filamentous networks by extending at their tips while branching in subapical regions. Rapid tip elongation requires massive membrane insertion and extension of the rigid chitin-containing cell wall. This process is sustained by a continuous flow of secretory vesicles that depends on the coordinated action of the microtubule and actin cytoskeletons...
Source: Mol Biol Cell - April 13, 2018 Category: Molecular Biology Authors: Riquelme M, Aguirre J, Bartnicki-García S, Braus GH, Feldbrügge M, Fleig U, Hansberg W, Herrera-Estrella A, Kämper J, Kück U, Mouriño-Pérez RR, Takeshita N, Fischer R Tags: Microbiol Mol Biol Rev Source Type: research

Kinetic Modeling of Virus Growth in Cells.
Abstract When a virus infects a host cell, it hijacks the biosynthetic capacity of the cell to produce virus progeny, a process that may take less than an hour or more than a week. The overall time required for a virus to reproduce depends collectively on the rates of multiple steps in the infection process, including initial binding of the virus particle to the surface of the cell, virus internalization and release of the viral genome within the cell, decoding of the genome to make viral proteins, replication of the genome, assembly of progeny virus particles, and release of these particles into the extracellular...
Source: Mol Biol Cell - March 30, 2018 Category: Molecular Biology Authors: Yin J, Redovich J Tags: Microbiol Mol Biol Rev Source Type: research

The Ontogeny of a Neutrophil: Mechanisms of Granulopoiesis and Homeostasis.
Abstract Comprising the majority of leukocytes in humans, neutrophils are the first immune cells to respond to inflammatory or infectious etiologies and are crucial participants in the proper functioning of both innate and adaptive immune responses. From their initial appearance in the liver, thymus, and spleen at around the eighth week of human gestation to their generation in large numbers in the bone marrow at the end of term gestation, the differentiation of the pluripotent hematopoietic stem cell into a mature, segmented neutrophil is a highly controlled process where the transcriptional regulators C/EBP-&alp...
Source: Mol Biol Cell - February 15, 2018 Category: Molecular Biology Authors: Lawrence SM, Corriden R, Nizet V Tags: Microbiol Mol Biol Rev Source Type: research

Transmission, Evolution, and Endogenization: Lessons Learned from Recent Retroviral Invasions.
Abstract Viruses of the subfamily Orthoretrovirinae are defined by the ability to reverse transcribe an RNA genome into DNA that integrates into the host cell genome during the intracellular virus life cycle. Exogenous retroviruses (XRVs) are horizontally transmitted between host individuals, with disease outcome depending on interactions between the retrovirus and the host organism. When retroviruses infect germ line cells of the host, they may become endogenous retroviruses (ERVs), which are permanent elements in the host germ line that are subject to vertical transmission. These ERVs sometimes remain infectious...
Source: Mol Biol Cell - December 16, 2017 Category: Molecular Biology Authors: Greenwood AD, Ishida Y, O'Brien SP, Roca AL, Eiden MV Tags: Microbiol Mol Biol Rev Source Type: research

Erratum to: Introduction to Cancer Stem Cells: Past, Present, and Future.
PMID: 29185235 [PubMed - in process] (Source: Mol Biol Cell)
Source: Mol Biol Cell - December 2, 2017 Category: Molecular Biology Authors: Bakhshinyan D, Adile AA, Qazi MA, Singh M, Kameda-Smith MM, Yelle N, Chokshi C, Venugopal C, Singh SK Tags: Methods Mol Biol Source Type: research

Amyloid-Like β-Aggregates as Force-Sensitive Switches in Fungal Biofilms and Infections.
Amyloid-Like β-Aggregates as Force-Sensitive Switches in Fungal Biofilms and Infections. Microbiol Mol Biol Rev. 2018 Mar;82(1): Authors: Lipke PN, Klotz SA, Dufrene YF, Jackson DN, Garcia-Sherman MC Abstract Cellular aggregation is an essential step in the formation of biofilms, which promote fungal survival and persistence in hosts. In many of the known yeast cell adhesion proteins, there are amino acid sequences predicted to form amyloid-like β-aggregates. These sequences mediate amyloid formation in vitro. In vivo, these sequences mediate a phase transition from a disordered state to a p...
Source: Mol Biol Cell - December 2, 2017 Category: Molecular Biology Authors: Lipke PN, Klotz SA, Dufrene YF, Jackson DN, Garcia-Sherman MC Tags: Microbiol Mol Biol Rev Source Type: research

Small Scale Production of Recombinant Adeno-Associated Viral Vectors for Gene Delivery to the Nervous System.
Abstract Adeno-associated viral vectors have numerous applications in neuroscience, including the study of gene function in health and disease, targeting of light-sensitive proteins to anatomically distinct sets of neurons to manipulate neuronal activity (optogenetics), and the delivery of fluorescent protein to study anatomical connectivity in the brain. Moreover several phase I/II clinical trials for gene therapy of eye and brain diseases with adeno-associated viral vectors have shown that these vectors are well tolerated by human patients. In this chapter we describe a detailed protocol for the small scale prod...
Source: Mol Biol Cell - December 2, 2017 Category: Molecular Biology Authors: Verhaagen J, Hobo B, Ehlert EME, Eggers R, Korecka JA, Hoyng SA, Attwell CL, Harvey AR, Mason MRJ Tags: Methods Mol Biol Source Type: research

Development of Multigenic Lentiviral Vectors for Cell-Specific Expression of Antiangiogenic miRNAs and Protein Factors.
Abstract Generation of lentivirus (LV)-based vectors holding multiple gene cassettes for coexpression of several therapeutic factors provides potent tools in both gene delivery studies as well as in gene therapy. Here we describe the development of such multigenic LV gene delivery vectors enabling cell-specific coexpression of antiangiogenic microRNA (miRNA) and protein factors and, if preferred, a fluorescent reporter, from RNApol(II)-driven expression cassettes orientated in a back-to-back fashion. This configuration may contribute to the development of new combination therapies for amelioration of diseases invo...
Source: Mol Biol Cell - December 2, 2017 Category: Molecular Biology Authors: Askou AL, Corydon TJ Tags: Methods Mol Biol Source Type: research

Retinal Gene Therapy for Choroideremia: In Vitro Testing for Gene Augmentation Using an Adeno-Associated Viral (AAV) Vector.
en RE Abstract As gene therapy of choroideremia is becoming a clinical reality, there is a need for reliable and sensitive assays to determine the expression of exogenously delivered Rab Escort Protein-1 (REP1), in particular to test new gene therapy vectors and as a quality control screen for clinical vector stocks. Here we describe an in vitro protocol to test transgene expression following AAV2/2-REP1 transduction of a human cell line. Gene augmentation can be confirmed by western blot and quantification of the fold-increase of human REP1 levels over untransduced controls. PMID: 29188508 [PubMed - in proce...
Source: Mol Biol Cell - December 2, 2017 Category: Molecular Biology Authors: Patrício MI, MacLaren RE Tags: Methods Mol Biol Source Type: research

In Vivo Electroporation of Developing Mouse Retina.
Abstract In vivo electroporation enables the transformation of retinal tissue with engineered DNA plasmids, facilitating the selective expression of desired gene products. This method achieves plasmid transfer via the application of an external electrical field, which both generates a transient increase in the permeability of cell plasma membranes, and promotes the incorporation of DNA plasmids by electrophoretic transfer through the permeabilized membranes. Here we describe a method for the preparation, injection, and electroporation of DNA plasmids into neonatal mouse retinal tissue. This method can be utilized ...
Source: Mol Biol Cell - December 2, 2017 Category: Molecular Biology Authors: de Melo J, Blackshaw S Tags: Methods Mol Biol Source Type: research