CGCDB: a web-based resource for the investigation of gene coexpression in CHO cell culture

Coexpression analysis is a powerful, widely used methodology for the investigation of underlying patterns in gene expression data. This "guilt-by-association" approach aims to find groups of genes with closely correlated expression profiles. Observation of consistent correlations across phenotypically diverse samples indicates that these genes have a shared function. We have recently described the application of weighted gene coexpression network analysis (WGCNA) to a 295 sample production CHO cell line microarray dataset and elucidated groups of genes related to growth rate and cell-specific productivity (Qp). In this study, we present the CHO gene coexpression database (CGCDB), a web-based system, designed specifically for researchers in the CHO community to provide user-friendly access to these gene-gene coexpression patterns. In addition to correlation between genes, the direct correlations between probesets and either growth rate or Qp are provided. Results are presented to the user via an interactive network diagram and in a downloadable tabular format. It is hoped that this resource will allow researchers to prioritize cell line engineering and/or biomarker candidates to enhance CHO-based cell culture for the production of biotherapeutics. Availability: www.cgcdb.org.     

Chronic administration of the angiotensin-converting enzyme inhibitor, ramipril, prevents fractionated whole-brain irradiation-induced perirhinal cortex-dependent cognitive impairment

We hypothesized that chronic administration of the angiotensin-converting enzyme inhibitor, ramipril, to young adult male rats would prevent/ameliorate fractionated whole-brain irradiation-induced perirhinal cortex-dependent cognitive impairment. Eighty 12-14-week-old young adult male Fischer 344 rats received either: (1) sham irradiation, (2) 40 Gy of fractionated whole-brain irradiation delivered as two 5 Gy fractions/week for 4 weeks, (3) sham irradiation plus continuous administration of 15 mg/L of ramipril in the drinking water starting 3 days before irradiation, or (4) fractionated whole-brain irradiation plus ramipril. Cognitive function was assessed using a perirhinal cortex-dependent version of the novel object recognition task 26 weeks after irradiation. Microglial activation was determined in the perirhinal cortex and the dentate gyrus of the hippocampus 28 weeks after irradiation using the ED1 antibody. Neurogenesis was assessed in the granular cell layer and subgranular zones of the dentate gyrus using a doublecortin antibody. Fractionated whole-brain irradiation led to: (1) a significant impairment in perirhinal cortex-dependent cognitive function, (2) a significant increase in activated microglia in the dentate gyrus but not in the perirhinal cortex, and (3) a significant decrease in neurogenesis. Continuous administration of ramipril before, during, and after irradiation prevented the fractionated whole-brain irradiation-induced changes in perirhinal cortex-dependent cognitive function, as well as in microglial activation in the dentate gyrus. Thus, as hypothesized, continuous administration of the angiotensin-converting enzyme inhibitor, ramipril, can prevent the fractionated whole-brain irradiation-induced impairment in perirhinal cortex-dependent cognitive function.     

The effect of hydration on the UV absorption coefficient of intact melanosomes

The physical properties of melanosomes have been shown to depend on water content. Herein, the ultraviolet absorption coefficient at λ = 244 nm for intact bovine choroidal melanosomes is determined from photoemission electron microscopy images recorded as a function of vacuum exposure. The dehydration of the melanosome under ultra-high vacuum manifests itself by a decrease in the absorption coefficient to about 60% of its initial value, and a concomitant increase in its image brightness. This change in the absorption of the melanosome is consistent with the influence of solvent polarity on the UV absorption coefficient of model systems for the pigment eumelanin, the predominant UV absorber contained in the choroid melanosomes.     

HSP60 is transported through the secretory pathway of 3-MCA-induced fibrosarcoma tumour cells and undergoes N-glycosylation

There is increasing evidence localizes the mitochondrial chaperone heat shock protein (HSP)60, outside the cell, where it mediates interactions between immune cells and other body tissues. However, the mechanisms by which HSP60 is secreted into the extracellular environment are not fully understood. Recent studies have shown that HSP60 is actively released by a nonconventional secretion mechanism, the lipid raft-exosome pathway. In the present study, we show for the first time that HSP60, produced by 3-methylcholantrene-induced fibrosarcoma tumour cells, is secreted through the conventional endoplasmic reticulum-Golgi secretory pathway. Confocal microscopy using anti-TGN38 and anti-HSP60 antibodies together with monensin, a Golgi transport inhibitor, demonstrated the relocation of HSP60 to the Golgi of malignant cells but not primary fibroblast cells subjected to heat shock or fibroblast cell lines. Transmission electron microscopy, flow cytometry and cell fractionation of cell treated with brefeldin A, an inhibitor of endoplasmic reticulum to Golgi protein transport, further indicated that HSP60 is present both in the endoplasmic reticulum and the Golgi complex of malignant cells. We found a single mRNA with a mitochondrial targeting sequence encoding for HSP60 in the malignant cells but two HSP60 translation products, namely the native unmodified protein and a protein post-translationally modified by N-glycosylation. The N-glycans observed were composed of high-mannose structures and bi-, tri- and tetra-antennary complex type structures occupying sites of the three potential glycosylation sites present on HSP60. Accordingly, we propose that HSP60 in malignant cells is transported through the endoplasmic reticulum-Golgi secretion pathway, where it acquires N-glycans, and thus can affect the immunological properties of the proteins in the tumour microenvironment.     

Spatial distribution of microbial communities in the cystic fibrosis lung

Cystic fibrosis (CF) is a common fatal genetic disorder with mortality most often resulting from microbial infections of the lungs. Culture-independent studies of CF-associated microbial communities have indicated that microbial diversity in the CF airways is much higher than suggested by culturing alone. However, these studies have relied on indirect methods to sample the CF lung such as expectorated sputum and bronchoalveolar lavage (BAL). Here, we characterize the diversity of microbial communities in tissue sections from anatomically distinct regions of the CF lung using barcoded 16S amplicon pyrosequencing. Microbial communities differed significantly between different areas of the lungs, and few taxa were common to microbial communities in all anatomical regions surveyed. Our results indicate that CF lung infections are not only polymicrobial, but also spatially heterogeneous suggesting that treatment regimes tailored to dominant populations in sputum or BAL samples may be ineffective against infections in some areas of the lung.     

Daily variation of serum acylcarnitines and amino acids

To characterize daily variation of amino acids (AAs) and acylcarnitines (ACs) in response to feeding and activity, we measured serum metabolites at various times and after various activities during the day. Subjects were admitted overnight for serial serum sampling, collected in the evening (6?C8 p.m., n?=?40), before rising from bed or eating (8 a.m., n?=?40), 1?h after rising but before eating (9 a.m., n?=?20), 1?C2?h after rising and breakfast (9?C10 a.m., n?=?40), and at noon (12 p.m., n?=?20). Measurements of 15 AAs and 45 ACs were performed by quantitative tandem mass spectrometry using stable-isotope dilution. Coefficients of variation within and between patients were calculated for individual metabolite values and factors derived from principal components analysis. The change of state between timepoints was evaluated by nearest neighbor non-parametric analysis of values at one timepoint compared to the next subsequent value. Relative to baseline a.m. recumbent concentrations, AA concentrations rose after activity and feeding while AC concentrations rose after activity and decreased with feeding. Furthermore, for all AAs, ACs, and their factors, biological variation was quantifiably evident and distinct from daily variation. This study confirms the daily variation of AAs and provides the first report of daily variation for a large panel of ACs. Although standardization of sample collection is highly desirable to control for daily variation (within a subject due to activity or feeding), this study demonstrated measurable biological variability (across subjects) suggesting that non-standardized sample collections could potentially provide insights into specific AA and AC metabolic pathways and disease mechanisms.     

CC2D2A is mutated in Joubert syndrome and interacts with the ciliopathy-associated basal body protein CEP290

Joubert syndrome and related disorders (JSRD) are primarily autosomal-recessive conditions characterized by hypotonia, ataxia, abnormal eye movements, and intellectual disability with a distinctive mid-hindbrain malformation. Variable features include retinal dystrophy, cystic kidney disease, and liver fibrosis. JSRD are included in the rapidly expanding group of disorders called ciliopathies, because all six gene products implicated in JSRD (NPHP1, AHI1, CEP290, RPGRIP1L, TMEM67, and ARL13B) function in the primary cilium/basal body organelle. By using homozygosity mapping in consanguineous families, we identify loss-of-function mutations in CC2D2A in JSRD patients with and without retinal, kidney, and liver disease. CC2D2A is expressed in all fetal and adult tissues tested. In ciliated cells, we observe localization of recombinant CC2D2A at the basal body and colocalization with CEP290, whose cognate gene is mutated in multiple hereditary ciliopathies. In addition, the proteins can physically interact in vitro, as shown by yeast two-hybrid and GST pull-down experiments. A nonsense mutation in the zebrafish CC2D2A ortholog (sentinel) results in pronephric cysts, a hallmark of ciliary dysfunction analogous to human cystic kidney disease. Knockdown of cep290 function in sentinel fish results in a synergistic pronephric cyst phenotype, revealing a genetic interaction between CC2D2A and CEP290 and implicating CC2D2A in cilium/basal body function. These observations extend the genetic spectrum of JSRD and provide a model system for studying extragenic modifiers in JSRD and other ciliopathies.     

Revival of saprotrophic and mycorrhizal basidiomycete cultures after 20 years in cold storage in sterile water

Vegetatively colonized agar cores of 69 basidiomycete fungus isolates (48 species in 30 genera and 17 families) were stored at 5 degrees C in tubes of sterile distilled water without manipulation for 20 years. These were represented by 34 isolates of saprotrophic fungi (29 species in 19 genera) and 35 isolates of mycorrhizal fungi (19 species in 11 genera). Viability was evaluated based on revived growth on agar media at room temperature. Fifty-seven of the 69 isolates (82.6%) grew vigorously when revived after storage for 20 years; of the 34 saprotrophic fungus isolates, 30 revived (88.2%); of the 35 mycorrhizal fungus isolates, 27 revived (77.1%). Thirteen isolates of Laccaria were all viable after 20 years, indicating cold storage in sterile water to be a good method for maintaining this important genus of mycorrhizal fungi. In general, however, mycorrhizal fungus species demonstrated lower viability than saprotrophic fungi.