Gene Dosage and the Expression of Electrophoretic Patterns in Heteroploid Mouse Cell Lines

Spontaneously transformed mouse cell lines heterozygous for electrophoretic markers have been studied to determine the relationship between gene dosage and phenotype. It is shown that a clone with an electrophoretic pattern for glucosephosphate isomerase of three bands in a ratio of 4A:4AB:1B contains three copies of chromosome 7, which carries the gene for this enzyme. A clone from a different line with a pattern of three bands in a ratio of 1A:6AB:9B for NADP-isocitrate dehydrogenase has four copies of the chromosome carrying this gene or three copies plus a rearrangement which apparently involves this chromosome. These results show that all of the alleles for each enzyme are expressed to an equal extent in these cells.     

Robust and Sensitive Analysis of Mouse Knockout Phenotypes

A significant challenge of in-vivo studies is the identification of phenotypes with a method that is robust and reliable. The challenge arises from practical issues that lead to experimental designs which are not ideal. Breeding issues, particularly in the presence of fertility or fecundity problems, frequently lead to data being collected in multiple batches. This problem is acute in high throughput phenotyping programs. In addition, in a high throughput environment operational issues lead to controls not being measured on the same day as knockouts. We highlight how application of traditional methods, such as a Student’s t-Test or a 2-way ANOVA, in these situations give flawed results and should not be used. We explore the use of mixed models using worked examples from Sanger Mouse Genome Project focusing on Dual-Energy X-Ray Absorptiometry data for the analysis of mouse knockout data and compare to a reference range approach. We show that mixed model analysis is more sensitive and less prone to artefacts allowing the discovery of subtle quantitative phenotypes essential for correlating a gene’s function to human disease. We demonstrate how a mixed model approach has the additional advantage of being able to include covariates, such as body weight, to separate effect of genotype from these covariates. This is a particular issue in knockout studies, where body weight is a common phenotype and will enhance the precision of assigning phenotypes and the subsequent selection of lines for secondary phenotyping. The use of mixed models with in-vivo studies has value not only in improving the quality and sensitivity of the data analysis but also ethically as a method suitable for small batches which reduces the breeding burden of a colony. This will reduce the use of animals, increase throughput, and decrease cost whilst improving the quality and depth of knowledge gained.     

Evaluation of Planar-Cell-Polarity Phenotypes in Ciliopathy Mouse Mutant Cochlea

In recent years, primary cilia have emerged as key regulators in development and disease by influencing numerous signaling pathways. One of the earliest signaling pathways shown to be associated with ciliary function was the non-canonical Wnt signaling pathway, also referred to as planar cell polarity (PCP) signaling. One of the best places in which to study the effects of planar cell polarity (PCP) signaling during vertebrate development is the mammalian cochlea. PCP signaling disruption in the mouse cochlea disrupts cochlear outgrowth, cellular patterning and hair cell orientation, all of which are affected by cilia dysfunction. The goal of this protocol is to describe the analysis of PCP signaling in the developing mammalian cochlea via phenotypic analysis, immunohistochemistry and scanning electron microscopy. Defects in convergence and extension are manifested as a shortening of the cochlear duct and/or changes in cellular patterning, which can be quantified following dissection from developing mouse mutants. Changes in stereociliary bundle orientation and kinocilia length or positioning can be observed and quantitated using either immunofluorescence or scanning electron microscopy (SEM). A deeper insight into the role of ciliary proteins in cellular signaling pathways and other biological phenomena is crucial for our understanding of cellular and developmental biology, as well as for the development of targeted treatment strategies.     

Weak Epistasis Generally Stabilizes Phenotypes in a Mouse Intercross

The extent and strength of epistasis is commonly unresolved in genetic studies, and observed epistasis is often difficult to interpret in terms of biological consequences or overall genetic architecture. We investigated the prevalence and consequences of epistasis by analyzing four body composition phenotypes—body weight, body fat percentage, femoral density, and femoral circumference—in a large F2 intercross of B6-lit/lit and C3.B6-lit/lit mice. We used Combined Analysis of Pleiotropy and Epistasis (CAPE) to examine interactions for the four phenotypes simultaneously, which revealed an extensive directed network of genetic loci interacting with each other, circulating IGF1, and sex to influence these phenotypes. The majority of epistatic interactions had small effects relative to additive effects of individual loci, and tended to stabilize phenotypes towards the mean of the population rather than extremes. Interactive effects of two alleles inherited from one parental strain commonly resulted in phenotypes closer to the population mean than the additive effects from the two loci, and often much closer to the mean than either single-locus model. Alternatively, combinations of alleles inherited from different parent strains contribute to more extreme phenotypes not observed in either parental strain. This class of phenotype-stabilizing interactions has effects that are close to additive and are thus difficult to detect except in very large intercrosses. Nevertheless, we found these interactions to be useful in generating hypotheses for functional relationships between genetic loci. Our findings suggest that while epistasis is often weak and unlikely to account for a large proportion of heritable variance, even small-effect genetic interactions can facilitate hypotheses of underlying biology in well-powered studies.     

Phenotypes and Karyotypes of Human Malignant Mesothelioma Cell Lines

Background

Malignant mesothelioma is an aggressive tumour of serosal surfaces most commonly pleura. Characterised cell lines represent a valuable tool to study the biology of mesothelioma. The aim of this study was to develop and biologically characterise six malignant mesothelioma cell lines to evaluate their potential as models of human malignant mesothelioma.

Methods

Five lines were initiated from pleural biopsies, and one from pleural effusion of patients with histologically proven malignant mesothelioma. Mesothelial origin was assessed by standard morphology, Transmission Electron Microscopy (TEM) and immunocytochemistry. Growth characteristics were assayed using population doubling times. Spectral karyotyping was performed to assess chromosomal abnormalities. Authentication of donor specific derivation was undertaken by DNA fingerprinting using a panel of SNPs.

Results

Most of cell lines exhibited spindle cell shape, with some retaining stellate shapes. At passage 2 to 6 all lines stained positively for calretinin and cytokeratin 19, and demonstrated capacity for anchorage-independent growth. At passage 4 to 16, doubling times ranged from 30–72 hours, and on spectral karyotyping all lines exhibited numerical chromosomal abnormalities ranging from 41 to 113. Monosomy of chromosomes 8, 14, 22 or 17 was observed in three lines. One line displayed four different karyotypes at passage 8, but only one karyotype at passage 42, and another displayed polyploidy at passage 40 which was not present at early passages. At passages 5–17, TEM showed characteristic features of mesothelioma ultrastructure in all lines including microvilli and tight intercellular junctions.

Conclusion

These six cell lines exhibit varying cell morphology, a range of doubling times, and show diverse passage-dependent structural chromosomal changes observed in malignant tumours. However they retain characteristic immunocytochemical protein expression profiles of mesothelioma during maintenance in artificial culture systems. These characteristics support their potential as in vitro model systems for studying cellular, molecular and genetic aspects of mesothelioma.     

Specific Tandem 3'UTR Patterns and Gene Expression Profiles in Mouse Thy1+ Germline Stem Cells

A recently developed strategy of sequencing alternative polyadenylation (APA) sites (SAPAS) with second-generation sequencing technology can be used to explore complete genome-wide patterns of tandem APA sites and global gene expression profiles. spermatogonial stem cells (SSCs) maintain long-term reproductive abilities in male mammals. The detailed mechanisms by which SSCs self-renew and generate mature spermatozoa are not clear. To understand the specific alternative polyadenylation pattern and global gene expression profile of male germline stem cells (GSCs, mainly referred to SSCs here), we isolated and purified mouse Thy1⁺ cells from testis by magnetic-activated cell sorting (MACS) and then used the SAPAS method for analysis, using pluripotent embryonic stem cells (ESCs) and differentiated mouse embryonic fibroblast cells (MEFs) as controls. As a result, we obtained 99,944 poly(A) sites, approximately 40% of which were newly detected in our experiments. These poly(A) sites originated from three mouse cell types and covered 17,499 genes, including 831 long non-coding RNA (lncRNA) genes. We observed that GSCs tend to have shorter 3''UTR lengths while MEFs tend towards longer 3''UTR lengths. We also identified 1337 genes that were highly expressed in GSCs, and these genes were highly consistent with the functional characteristics of GSCs. Our detailed bioinformatics analysis identified APA site-switching events at 3''UTRs and many new specifically expressed genes in GSCs, which we experimentally confirmed. Furthermore, qRT-PCR was performed to validate several events of the 334 genes with distal-to-proximal poly(A) switch in GSCs. Consistently APA reporter assay confirmed the total 3''UTR shortening in GSCs compared to MEFs. We also analyzed the cis elements around the proximal poly(A) site preferentially used in GSCs and found C-rich elements may contribute to this regulation. Overall, our results identified the expression level and polyadenylation site profiles and these data provide new insights into the processes potentially involved in the GSC life cycle and spermatogenesis.     

Manipulating Each MreB of Bdellovibrio bacteriovorus Gives Diverse Morphological and Predatory Phenotypes

We studied the two mreB genes, encoding actinlike cytoskeletal elements, in the predatory bacterium Bdellovibrio bacteriovorus. This bacterium enters and replicates within other Gram-negative bacteria by attack-phase Bdellovibrio squeezing through prey outer membrane, residing and growing filamentously in the prey periplasm forming an infective “bdelloplast,” and septating after 4 h, once the prey contents are consumed. This lifestyle brings challenges to the Bdellovibrio cytoskeleton. Both mreB genes were essential for viable predatory growth, but C-terminal green fluorescent protein tagging each separately with monomeric teal-fluorescent protein (mTFP) gave two strains with phenotypic changes at different stages in predatory growth and development. MreB1-mTFP cells arrested growth early in bdelloplast formation, despite successful degradation of prey nucleoid. A large population of stalled bdelloplasts formed in predatory cultures and predation proceeded very slowly. A small proportion of bdelloplasts lysed after several days, liberating MreB1-mTFP attack-phase cells of wild-type morphology; this process was aided by subinhibitory concentrations of an MreB-specific inhibitor, A22. MreB2-mTFP, in contrast, was predatory at an almost wild-type rate but yielded attack-phase cells with diverse morphologies, including spherical, elongated, and branched, the first time such phenotypes have been described. Wild-type predatory rates were seen for all but spherical morphotypes, and septation of elongated morphotypes was achieved by the addition of A22.The predatory bacterium Bdellovibrio bacteriovorus shows novel filamentous growth within the periplasm of the Gram-negative prey bacterium on which it feeds. This study focuses on the cytoskeletal protein MreB and the role that two homologues of it play in B. bacteriovorus predatory or host-dependent (HD) growth. The HD B. bacteriovorus life cycle can be split into two phases: an attack phase and a growth phase (Fig. ​(Fig.1).1). The attack-phase B. bacteriovorus is a small free-swimming, highly motile cell within which replication has been arrested and which does not take up organic nutrients from the environment or grow extensively (24, 26). Once an attack-phase cell has collided with a suitable prey bacterium, B. bacteriovorus opens and squeezes through a small hole, formed in the outer membrane, using type IV pili to pull itself inside (7, 10). The B. bacteriovorus reseals the hole upon entering the periplasm. Once inside, the prey is killed rapidly within 15 min, and the prey cell wall is partially digested (35), forming a rounded structure called the bdelloplast (see Fig. ​Fig.11 and 4Ac and d). The HD B. bacteriovorus cell then enters the second, growth phase, part of the life cycle, (Fig. ​(Fig.1),1), whereby it grows filamentously while simultaneously coordinating the digestion and transportation of monomers from the prey cytoplasm. The mature growth-phase cell is multiploid and elongates typically 3 to 10 times the length of an attack-phase cell, its length being a reflection of the nutritional resources available in the prey (20). Once resources within the bdelloplast are depleted, the mature filament septates sequentially from one pole to form multiple progeny. These lyse the exhausted bdelloplast, mature into attack-phase cells, and repress growth once again (Fig. ​(Fig.1).1). B. bacteriovorus can be cultured slowly, without prey, as host-independent (HI) cells growing upon peptone-rich medium (30). In these conditions they grow pleiomorphically as mainly long filamentous or serpentine cells, from which some small attack-phase cells septate (30).Open in a separate windowFIG. 1.Schematic host-dependent (HD) predatory cycle for B. bacteriovorus on E. coli prey, showing the different phases of growth and inferred demands on the B. bacteriovorus cell cytoskeleton. References where the roles of the cytoskeleton in cell development have been proven for other bacteria are provided in parentheses. The status of the prey genome is both drawn from an earlier study (26) and confirmed by our work in the present study (see Fig. ​Fig.44).The predatory lifestyle of B. bacteriovorus presents a number of novel developmental challenges to the B. bacteriovorus cell and its cytoskeleton. It is not known how the attack-phase cells deform, allowing the B. bacteriovorus to squeeze through a pore it makes in the prey outer membrane that is narrower than the width of an attack-phase cell, as was imaged by Burnham et al. in the 1960s and more recently by Evans et al. (7, 10). It is also not known how the growth-phase filamentous cell within the bdelloplast is generated and remains resistant to division until terminal sequential septation begins, despite having multiple potential sites for septation along its length while elongating.The processes of cell elongation in rod-shaped bacteria are coordinated by an internal MreB cell cytoskeleton (9). MreB is a eukaryotic actin homologue and has been well studied in Escherichia coli, Bacillus subtilis, and Caulobacter crescentus (38). MreB monomers polymerize on ATP binding, forming helical structures in vivo that appear to associate with the cytoplasmic side of the bacterial cytoplasmic membrane (11, 18, 31). Bacterial two-hybrid experiments in Escherichia coli suggest that MreB forms a transmembrane complex with the two proteins MreC and MreD, each of which have been shown to form helical structures in vivo (21). A complex of MreBCD, together with the RodA protein, influences the shape of the peptidoglycan cell wall and thus the shape of the cell by positioning the peptidoglycan biosynthetic machinery so that its action is directionally specific (9, 19, 37). The MreB filament has also been shown to have roles in chromosome segregation, septation, and cell polarity (13, 14, 22, 37).Depletion of the MreB protein levels in E. coli and B. subtilis led to cells taking on a spherical morphology and eventual loss of viability since new peptidoglycan is not synthesized evenly along the cell wall (9, 36). Uneven incorporation of new peptidoglycan is potentially driven by the tubulin homologue FtsZ (4, 36). A similar phenotype is achieved by addition of the MreB inhibitor A22 that causes the reversible loss of MreB filament localization in vivo (14, 17). A22 was discovered in a chemical library being screened for the ability to generate anucleate minicells from E. coli (16, 17). It has been used extensively by others to examine MreB function in bacteria of many different genera. The addition of A22 to E. coli cells at 3.13 μg/ml leads to the breakdown of MreB filaments, spheroplasting and the generation of minicells (16). In B. subtilis, A22 at concentrations in excess of 100 μg/ml is required to generate spheroplasts; in C. crescentus 6-h incubations of A22 at 10 μg/ml are needed before any change to the cell shape can be observed—in this case cells take on a characteristic “lemon shape” (14, 16). Isolation and sequencing of A22-resistant mutants of C. crescentus, as well as biochemical evidence from purified MreB from Thermotoga maritima, revealed that A22 binds in the nucleotide binding pocket of MreB (3, 14). In vitro light scattering assays of MreB filamentation showed that A22 acted as a competitive inhibitor of ATP binding and was able in inhibit the formation of MreB filaments, presumably by sequestering and inactivating MreB monomers preventing their recycling (3). This study also demonstrated that in vitro A22 can have a role in stabilizing ADP-bound MreB (3).In the present study we investigated the functions of the two MreB homologues found in B. bacteriovorus, testing the role each has in predation and cell morphology by a combination of genetic approaches and A22 treatment. A reduction in function in both MreB proteins, achieved by C-terminal teal fluorescent protein (TFP) tagging, suggests that the MreB1 (Bd0211) protein was required in the growth-phase cell in bdelloplasts, whereas the MreB2 (Bd1737) protein is required later in the predatory process, for maintaining and allowing successful resolution of the growth-phase filament into short attack-phase vibroid cells.     

Alanine Aminotransferase Variants Conferring Diverse NUE Phenotypes in Arabidopsis thaliana

Alanine aminotransferase (AlaAT, E.C. 2.6.1.2), is a pyridoxal-5’-phosphate-dependent (PLP) enzyme that catalyzes the reversible transfer of an amino group from alanine to 2-oxoglutarate to produce glutamate and pyruvate, or vice versa. It has been well documented in both greenhouse and field studies that tissue-specific over-expression of AlaAT from barley (Hordeum vulgare, HvAlaAT) results in a significant increase in plant NUE in both canola and rice. While the physical phenotypes associated with over-expression of HvAlaAT have been well characterized, the role this enzyme plays in vivo to create a more N efficient plant remains unknown. Furthermore, the importance of HvAlaAT, in contrast to other AlaAT enzyme homologues in creating this phenotype has not yet been explored. To address the role of AlaAT in NUE, AlaAT variants from diverse sources and different subcellular locations, were expressed in the wild-type Arabidopsis thaliana Col-0 background and alaat1;2 (alaat1-1;alaat2-1) knockout background in various N environments. The analysis and comparison of both the physical and physiological properties of AlaAT over-expressing transgenic plants demonstrated significant differences between plants expressing the different AlaAT enzymes under different external conditions. This analysis indicates that the over-expression of AlaAT variants other than HvAlaAT in crop plants could further increase the NUE phenotype(s) previously observed.     

Chromatin-Based Classification of Genetically Heterogeneous AMLs into Two Distinct Subtypes with Diverse Stemness Phenotypes

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A GRAS-Type Transcription Factor with a Specific Function in Mycorrhizal Signaling

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Diverse Routes toward Early Somites in the Mouse Embryo

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Mapping Pathological Phenotypes in a Mouse Model of CDKL5 Disorder

Mutations in cyclin-dependent kinase-like 5 (CDKL5) cause early-onset epileptic encephalopathy, a neurodevelopmental disorder with similarities to Rett Syndrome. Here we describe the physiological, molecular, and behavioral phenotyping of a Cdkl5 conditional knockout mouse model of CDKL5 disorder. Behavioral analysis of constitutive Cdkl5 knockout mice revealed key features of the human disorder, including limb clasping, hypoactivity, and abnormal eye tracking. Anatomical, physiological, and molecular analysis of the knockout uncovered potential pathological substrates of the disorder, including reduced dendritic arborization of cortical neurons, abnormal electroencephalograph (EEG) responses to convulsant treatment, decreased visual evoked responses (VEPs), and alterations in the Akt/rpS6 signaling pathway. Selective knockout of Cdkl5 in excitatory and inhibitory forebrain neurons allowed us to map the behavioral features of the disorder to separable cell-types. These findings identify physiological and molecular deficits in specific forebrain neuron populations as possible pathological substrates in CDKL5 disorder.     

Variation in Type 2 Diabetes-Related Phenotypes among Apolipoprotein E-Deficient Mouse Strains

We recently have found that apolipoprotein E-deficient (Apoe^-/-) mice with the C57BL/6 background develop type 2 diabetes when fed a Western diet for 12 weeks. In the present study we constructed multiple Apoe^-/- mouse strains to find diabetes-related phenotyptic variations that might be linked to atherosclerosis development. Evaluation of both early and advanced lesion formation in aortic root revealed that C57BL/6, SWR/J, and SM/J Apoe^-/- mice were susceptible to atherosclerosis and that C3H/HeJ and BALB/cJ Apoe^-/- mice were relatively resistant. On a chow diet, fasting plasma glucose varied among strains with C3H/HeJ having the highest (171.1 ± 9.7 mg/dl) and BALB/cJ the lowest level (104.0 ± 6.6 mg/dl). On a Western diet, fasting plasma glucose rose significantly in all strains, with C57BL/6, C3H/HeJ and SWR/J exceeding 250 mg/dl. BALB/cJ and C3H/HeJ were more tolerant to glucose loading than the other 3 strains. C57BL/6 was sensitive to insulin while other strains were not. Non-fasting blood glucose was significantly lower in C3H/HeJ and BALB/cJ than C57BL/6, SM/J, and SWR/J. Glucose loading induced the 1st and the 2nd phase of insulin secretion in BALB/cJ, but the 2nd phase was not observed in other strains. Morphological analysis showed that BALB/cJ had the largest islet area (1,421,493 ± 61,244 μm²) and C57BL/6 had the smallest one (747,635 ± 41,798 μm²). This study has demonstrated strain-specific variations in the metabolic and atherosclerotic phenotypes, thus laying the basis for future genetic characterization.     

Generation of Mouse Small Intestinal Epithelial Cell Lines That Allow the Analysis of Specific Innate Immune Functions

Cell lines derived from the small intestine that reflect authentic properties of the originating intestinal epithelium are of high value for studies on mucosal immunology and host microbial homeostasis. A novel immortalization procedure was applied to generate continuously proliferating cell lines from murine E19 embryonic small intestinal tissue. The obtained cell lines form a tight and polarized epithelial cell layer, display characteristic tight junction, microvilli and surface protein expression and generate increasing transepithelial electrical resistance during in vitro culture. Significant up-regulation of Cxcl2 and Cxcl5 chemokine expression upon exposure to defined microbial innate immune stimuli and endogenous cytokines is observed. Cell lines were also generated from a transgenic interferon reporter (Mx2-Luciferase) mouse, allowing reporter technology-based quantification of the cellular response to type I and III interferon. Thus, the newly created cell lines mimic properties of the natural epithelium and can be used for diverse studies including testing of the absorption of drug candidates. The reproducibility of the method to create such cell lines from wild type and transgenic mice provides a new tool to study molecular and cellular processes of the epithelial barrier.