Microarray and comparative genomics-based identification of genes and gene regulatory regions of the mouse immune system

Background  

In this study we have built and mined a gene expression database composed of 65 diverse mouse tissues for genes preferentially expressed in immune tissues and cell types. Using expression pattern criteria, we identified 360 genes with preferential expression in thymus, spleen, peripheral blood mononuclear cells, lymph nodes (unstimulated or stimulated), orin vitroactivated T-cells.     

Increased Larval Growth and Preference for Virus-Infected Leaves by the Mexican Bean Beetle, Epilachna varivestis Mulsant, a Plant Virus Vector

Phaseolus vulgaris L. cv. 'Black Valentine' is a systemic host for the plant viruses Southern bean mosaic virus (SBMV) and bean pod mottle virus (BPMV). The Mexican bean beetle, Epilachna varivestis Mulsant, is a vector of SBMV and BPMV. Our objective was to determine if the interaction of SBMV and BPMV with 'Black Valentine' bean plants would affect beetle behavior and growth. In adult feeding preference test assays, beetles preferred and ingested more of the virus-infected bean leaf tissue than the noninfected leaf tissue. Beetle larvae that fed on SBMV- or BPMV-infected plants weighed more than those that fed on healthy plants. Our experiments suggest that there might be a mutually beneficial relationship between the beetle and the viruses that it vectors. The virus benefits from being transmitted and the beetle benefits from better larval growth when feeding on virus-infected leaf tissue. This study further demonstrates the complexity of relationships between multiple organisms.     

Role of Listeria monocytogenes σB in Survival of Lethal Acidic Conditions and in the Acquired Acid Tolerance Response

The food-borne pathogen Listeria monocytogenes can acquire enhanced resistance to lethal acid conditions through multiple mechanisms. We investigated contributions of the stress-responsive alternative sigma factor, σ^B, which is encoded by sigB, to growth phase-dependent acid resistance (AR) and to the adaptive acid tolerance response in L. monocytogenes. At various points throughout growth, we compared the relative survival of L. monocytogenes wild-type and ΔsigB strains that had been exposed to either brain heart infusion (pH 2.5) or synthetic gastric fluid (pH 2.5) with and without prior acid adaptation. Under these conditions, survival of the ΔsigB strain was consistently lower than that of the wild-type strain throughout all phases of growth, ranging from 4 orders of magnitude less in mid-log phase to 2 orders of magnitude less in stationary phase. Survival of both ΔsigB and wild-type L. monocytogenes strains increased by 6 orders of magnitude upon entry into stationary phase, demonstrating that the L. monocytogenes growth phase-dependent AR mechanism is σ^B independent. σ^B-mediated contributions to acquired acid tolerance appear to be greatest in early logarithmic growth. Loss of a functional σ^B reduced the survival of L. monocytogenes at pH 2.5 to a greater extent in the presence of organic acid (100 mM acetic acid) than in the presence of inorganic acid alone (HCl), suggesting that L. monocytogenes protection against organic and inorganic acid may be mediated through different mechanisms. σ^B does not appear to contribute to pH_i homeostasis through regulation of net proton movement across the cell membrane or by regulation of pH_i buffering by the GAD system under the conditions examined in this study. In summary, a functional σ^B protein is necessary for full resistance of L. monocytogenes to lethal acid treatments.     

Diapause in copepods (Crustacea) from ephemeral habitats with different hydroperiods in Everglades National Park (Florida,U.S.A.)

Water management practices in the Everglades have severely stressed the natural system, particularly by reducing the hydroperiods of much of the region. During the dry season of 1999, we investigated the influence of hydroperiod on the species composition and dormancy patterns of freshwater copepod communities in seasonal wetlands of Everglades National Park, Florida, U.S.A. The habitats were characterized by an annual dry season, from December through June. We sampled at two locations: the Long Pine Key area of the Rocky Glades region (short hydroperiod, ca. 4–5 months), and western Taylor Slough (intermediate hydroperiod, ca. 8–10 months). Both areas have experienced a reduction in natural hydroperiods and an increase in the frequency of dry-down. We collected weekly plankton samples from Rocky Glades solution holes to assess the potential species pool of copepods. To document the taxa capable of surviving dry-down by resting, we performed three immersion trials in which we rehydrated, in laboratory aquaria, sediment patches from solution holes and surface soils from all stations. Only a subset of the planktonic species collected emerged from the dried sediments. The cyclopoids Microcyclops rubellus and Paracyclops poppei were dominant. This is the first record of diapause for P. poppei. Species distributions from the different hydroperiod soil patches indicated that more diapausing species occurred at the sites that dried for shorter periods. Emerging individuals of M. rubellus and P. poppei were mainly ovigerous females, demonstrating a resting strategy seldom before recorded. The cyclopoid Diacyclops nearcticushad not been previously reported to diapause, but they emerged from the dried sediments in our trials. Our collections included six new records for Florida: Diacyclops nearcticus, Megacyclops latipes, Orthocyclops modestus, Elaphoidella marjoryae, Bryocamptus sp. and Bryocamptuscf. newyorkensis. Paracyclops poppei, Macrocyclops fuscus and Arctodiaptomus floridanus are new records for Everglades National Park. Clearly, diapause is an important strategy for the persistence of copepods in short-hydroperiod wetlands. The duration of the dry period appears to be inversely related to the number of species that emerge from diapause.     

Optimization of culture media for large‐scale lutein production by heterotrophic Chlorella vulgaris

Lutein is a carotenoid with a purported role in protecting eyes from oxidative stress, particularly the high‐energy photons of blue light. Statistical optimization was performed to growth media that supports a higher production of lutein by heterotrophically cultivated Chlorella vulgaris. The effect of media composition of C. vulgaris on lutein was examined using fractional factorial design (FFD) and central composite design (CCD). The results indicated that the presence of magnesium sulfate, EDTA‐2Na, and trace metal solution significantly affected lutein production. The optimum concentrations for lutein production were found to be 0.34 g/L, 0.06 g/L, and 0.4 mL/L for MgSO₄·7H₂O, EDTA‐2Na, and trace metal solution, respectively. These values were validated using a 5‐L jar fermenter. Lutein concentration was increased by almost 80% (139.64 ± 12.88 mg/L to 252.75 ± 12.92 mg/L) after 4 days. Moreover, the lutein concentration was not reduced as the cultivation was scaled up to 25,000 L (260.55 ± 3.23 mg/L) and 240,000 L (263.13 ± 2.72 mg/L). These observations suggest C. vulgaris as a potential lutein source. © 2014 American Institute of Chemical Engineers Biotechnol. Prog., 30:736–743, 2014     

Critical role of constitutive type I interferon response in bronchial epithelial cell to influenza infection

Innate antiviral responses in bronchial epithelial cells (BECs) provide the first line of defense against respiratory viral infection and the effectiveness of this response is critically dependent on the type I interferons (IFNs). However the importance of the antiviral responses in BECs during influenza infection is not well understood. We profiled the innate immune response to infection with H3N2 and H5N1 virus using Calu-3 cells and primary BECs to model proximal airway cells. The susceptibility of BECs to influenza infection was not solely dependent on the sialic acid-bearing glycoprotein, and antiviral responses that occurred after viral endocytosis was more important in limiting viral replication. The early antiviral response and apoptosis correlated with the ability to limit viral replication. Both viruses reduced RIG-I associated antiviral responses and subsequent induction of IFN-β. However it was found that there was constitutive release of IFN-β by BECs and this was critical in inducing late antiviral signaling via type I IFN receptors, and was crucial in limiting viral infection. This study characterizes anti-influenza virus responses in airway epithelial cells and shows that constitutive IFN-β release plays a more important role in initiating protective late IFN-stimulated responses during human influenza infection in bronchial epithelial cells.     

Human cellular sequences detectable with adenovirus probes

Previous studies suggesting homology between human cellular DNA and the DNAs from adenovirus types 2 and 5 are extended in the present paper. A clone (ChAd^h), isolated from a human genomic DNA library using an adenovirus probe, hybridized to discrete regions of adenovirus 2 DNA, including part of the transforming genes E1a and E1b, as well as to repeated sequences within human DNA. The E1a and E1b genes both hybridize to the same 300 base pair Sau3AI fragment within ChAd^h although there is no obvious homology between E1a and E1b. The Ad 2 E1a gene was also used as a probe to screen other cellular DNAs to determine whether repeated sequences detectable with Ad 2 DNA probes were conserved over long evolutionary periods. Hybridization was detected to the genomes of man, rat, mouse and fruit fly, but not to those of yeast and bacteria. In addition to a smear hybridization, discrete fragments were detected in both rodent and fruit fly DNAs. The experiments reported suggest the existence of two different types of cellular sequences detected by Ad 2 DNA: (1) repeated sequences conserved in a variety of eukaryote genomes and (2) a possible unique sequence detected with an E1a probe different from that responsible for hybridization to repeated sequences. This unique sequence was detected as an EcoRI fragment in mouse DNA and had a molecular size of about 8.8 kb.