DNA2 drives processing and restart of reversed replication forks in human cells

Accurate processing of stalled or damaged DNA replication forks is paramount to genomic integrity and recent work points to replication fork reversal and restart as a central mechanism to ensuring high-fidelity DNA replication. Here, we identify a novel DNA2- and WRN-dependent mechanism of reversed replication fork processing and restart after prolonged genotoxic stress. The human DNA2 nuclease and WRN ATPase activities functionally interact to degrade reversed replication forks with a 5′-to-3′ polarity and promote replication restart, thus preventing aberrant processing of unresolved replication intermediates. Unexpectedly, EXO1, MRE11, and CtIP are not involved in the same mechanism of reversed fork processing, whereas human RECQ1 limits DNA2 activity by preventing extensive nascent strand degradation. RAD51 depletion antagonizes this mechanism, presumably by preventing reversed fork formation. These studies define a new mechanism for maintaining genome integrity tightly controlled by specific nucleolytic activities and central homologous recombination factors.     

Steady state growth space study of <Emphasis Type="Italic">Lactococcus lactis</Emphasis> in D-stat cultures

Growth space of Lactococcus lactis subsp. lactis IL1403 was studied at constant growth rate using D-stat cultivation technique. Starting from steady state conditions in a chemostat culture (μ = 0.2 h⁻¹), the pH and/or temperature were continuously changed in the range of 5.4–6.4 and 26–34°C, respectively, followed by the return to the initial environmental conditions. Based on substrate consumption and product formation yields and expression changes of 1,920 genes, it was shown that changes of physiological state were not dependent on the direction of movement (from pH 6.3 to 5.4 or from 5.4 to 6.3), showing that quasi steady state values in D-stat corresponded to the steady state values in chemostats. Relative standard deviation of growth characteristics in triplicate D-stat experiments was below 10%. Continuing the experiment and reestablishing initial growth conditions revealed in average 7% difference (hysteresis) in growth characteristics when comparing chemostat steady state cultures prior and after the change of environmental conditions. Similarly, shifts were also seen at gene expression levels. The large amount of quantitatively reliable data obtained in this study provided a new insight into dynamic properties of bacterial physiology, and can be used for describing the growth space of microorganisms by modeling cell metabolism.     

<Emphasis Type="Italic">Virgibacillus xinjiangensis</Emphasis> sp. nov., isolated from a Salt Lake of Xin-jiang Province in China

A strictly aerobic Gram-positive, moderately halophilic spore forming bacterium, designated strain SL6-1^T, was isolated from a salt lake in Xin-jiang province, China. Growth of strain SL6-1^T was observed at NaCl concentrations of 0∼20% (w/v) (the optimum being 5∼7%, w/v). The peptidoglycan type of strain SL6-1^T was Alγ-meso-diaminopimelic acid and its major cellular fatty acids were iso-C_14:0 and iso-C_16:0 and ante-iso-C_15:0. The major respiratory isoprenoid quinone was MK-7 and the G+C content of the genomic DNA was 44.5 mol%. The major cellular phospholipids were phosphatidylglycerol and diphosphatidylglycerol. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain SL6-1^T formed a phylogenetic lineage within the genus Virgibacillus. Based on 16S rRNA gene sequence similarity, the strain was most closely related to Virgibacillus olivae E₃₀8^T, Virgibacillus kekensis YIM kkny16^T, Virgibacillus marismortui DSM 12325^T with 97.1%, 97.1%, and 97.0% gene sequence similarities, respectively and the sequence similarities to other related taxa were less than 96.7%. The DNA relatedness values between strain SL6-1^T and V. olivae E₃₀8^T, V. kekensis YIM kkny16^T, V. marismortui DSM 12325^T were 16.7%, 51.0%, and 22.8%, respectively. On the basis of physiological, biochemical and phylogenetic properties, strain SL6-1^T represents a novel species, for which the name Virgibacillus xinjiangensis sp. nov. is proposed. The type strain is SL6-1^T (=KCTC 13128^T =DSM 19031^T).     

Comparison of the metabolic activities of four wild-type <Emphasis Type="Italic">Clostridium perfringens</Emphasis> strains with their gatifloxacin-selected resistant mutants

The production of short-chain fatty acids, reductive enzymes, and hydrolytic enzymes by four gatifloxacin-selected, fluoroquinolone-resistant, mutant strains of C. perfringens, with stable mutations either in DNA gyrase or in both DNA gyrase and topoisomerase IV, was compared with that produced by the wild-type parent strains to investigate the effect of mutations associated with the selection of gatifloxacin resistance on bacterial metabolic activities. The mutants differed from their respective wild-type parent strains in the enzymatic activities of azoreductase, nitroreductase, and β-glucosidase and in the ratio of butyric acid to acetic acid production. Microarray analysis of one wild type and the corresponding mutant revealed different levels of mRNA expression for the enzymes involved in short-chain fatty acid (SCFA) synthesis and for β-glucosidase and oxidoreductases. In addition to mutations in the target genes, selection of resistance to gatifloxacin resulted in strain-specific physiological changes in the resistant mutants of C. perfringens that affected their metabolic activities.     

A genetic variant of immunoglobulin γ2 is strongly associated with immunity to mucin 1 in patients with breast cancer

High levels of antibodies to mucin 1 (MUC1), a membrane-bound glycoprotein that is overexpressed in adenocarcinomas, are associated with good prognosis in patients with breast cancer. The aim of the present investigation was to determine whether GM and KM allotypes—genetic markers of IgG heavy chains and κ-type light chains, respectively—contribute to the magnitude of natural antibody responsiveness to MUC1 in patients with breast cancer. A total of 153 Caucasian subjects with breast cancer were allotyped for several GM and KM markers. These subjects were also characterized for IgG and IgM antibodies to MUC1. Anti-MUC1 IgG antibody levels in subjects who were carriers of the immunoglobulin γ2 allele GM 23 were significantly higher than in those who were noncarriers (P = 0.003). These results could potentially divide the population into high or low responders to MUC1, which has important implications for MUC1-based immunotherapeutic interventions in breast cancer.     

Effect of fungal pellet morphology on enzyme activities involved in phthalate degradation

Pellet size of white rot fungus, Pleurotus ostreatus may affect the secretion of its degradative enzymes and accompanying biodegrading capability, but could be controlled by several physical culture conditions in liquid culture. The pellet size of P. ostreatus was affected by the volume of inoculum, flask, and medium, but the agitation speed was the most important control factor. At the lower agitation speed of 100 rpm, the large pellets were formed and the laccase activity was higher than that of small pelleted culture at 150 rpm, which might be due to loose intrapellet structure. However, the biodegradation rates of benzylbutylphthalate and dimethylphthalate were higher in the small pelleted culture, which indicated the involvement of other degradative enzyme rather than laccase. The activity of esterase which catalyzes the nonphenolic compounds before the reaction of ligninolytic enzymes was higher in the small pelleted culture, and coincided with the degradation pattern of phthalates. This study suggests the optimization of pellet morphology and subsequent secretion of degradative enzymes is necessary for the efficient removal of recalcitrants by white rot fungi.     

No neural evidence for dynamic auditory tuning of the A1 receptor in the ear of the noctuid moth, <Emphasis Type="Italic">Noctua pronuba</Emphasis>

By examining the mechanical properties of the tympanum of the noctuid moth, Noctua pronuba, Windmill et al. (2006) suggested that this insect increases (up-tunes) the frequencies of its best hearing when exposed to high intensity sounds (HIS) resembling the echolocation calls of attacking bats. We tested whether this biophysical phenomenon was encoded in the neural responses of this moth’s most sensitive auditory receptor (A1 cell) before and after exposure to HIS. We measured: (1) the number of A1 action potentials (spikes) per stimulus pulse; (2) the proportion of A1 spike periods below that determined to elicit evasive flight maneuvers and, (3) the change in A1 cell firing (spike number, interspike interval, stimulus/spike latency) over a duration of time similar to that in which up-tuning lasts. We observed no significant spiking response changes in the predicted direction to any of the frequencies tested following exposure to HIS and we observed only two of the 24 predicted time-dependent changes to A1 firing. These results indicate that tympanal up-tuning does not result in a change to this moth’s auditory frequency sensitivity and we suggest either sensillar resonances or increases in thoracic muscle tension following exposure to HIS as alternative explanations.     

The Presence and Localization of Melatonin Receptors in the Rat Aorta

Melatonin is involved in blood pressure modulation in rats and humans. Some of the effects of melatonin are presumably mediated via two G-protein-coupled receptors (MT₁ and MT₂), but the distribution of MT₁ and MT₂ in the cardiovascular system remains to be explored comprehensively. We investigated the expression of both the receptors in the rat aorta on mRNA level by RT-PCR and real time RT-PCR as well as on protein level via western blotting and immunofluorescence microscopy. We verified MT₁ mRNA expression in the rat aorta and demonstrated the absence of MT₂ mRNA in this vessel type. MT₁ receptors were confirmed also at the protein level, and surprisingly they were preferentially localized to the tunica adventitia. Since no daily changes in MT₁ mRNA expression were detected, we suppose that the circadian changes in circulating melatonin concentrations are sufficient to mediate circadian effects of melatonin in the aorta. The localization of MT₁ in the tunica adventitia suggests an influence of melatonin on vasa vasorum function and signal transduction in the aorta wall.     

Monitoring of Na<Superscript>+</Superscript>/K<Superscript>+</Superscript>-ATPase mRNA expression in the cinnamon clownfish, <Emphasis Type="Italic">Amphiprion melanopus</Emphasis>, exposed to an osmotic stress environment: profiles on the effects of exogenous hormone

We examined changes in the expression of Na⁺/K⁺-ATPase mRNA in the gills of the cinnamon clownfish using quantitative real-time PCR in an osmotically changing environment [seawater (35 psu; practical salinity unit, 1 psu ≈ 1‰) → brackish water (17.5 psu) and brackish water with prolactin]. The expression of Na⁺/K⁺-ATPase mRNA in gills was increased after the transfer to brackish water, and the expression was repressed by prolactin treatment. Also, activities of gill Na⁺/K⁺-ATPase and plasma cortisol levels increased after the transfer to brackish water and were repressed in brackish water with prolactin treatment. Na⁺/K⁺-ATPase-immunoreactive cells were almost consistently observed in the gill filaments, but absent from the lamella epithelia. The plasma osmolality level decreased in brackish water, but the level of this parameter increased in brackish water with prolactin treatment during salinity change. These results suggest that the Na⁺/K⁺-ATPase gene plays an important role in osmoregulation in gills, and prolactin improves the hyperosmoregulatory ability of cinnamon clownfish in a brackish water (hypoosmotic) environment.     

A cell permeable peptide analog as a potential-specific PET imaging probe for prostate cancer detection

Non-invasive detection of prostate cancer or metastases still remains a challenge in the field of molecular imaging. In our recent work of screening arginine- or lysine-rich peptides for intracellular delivery of a therapeutic agent into prostate cancer cells, an arginine-rich cell permeable peptide (NH₂GR₁₁) was found with an unexpectedly preferential uptake in prostate cancer cell lines. The goal of this work was to develop this peptide as a positron emission tomography (PET) imaging probe for specific detection of distant prostate cancer metastases. The optimal length of arginine-rich peptides was evaluated by the cell uptake efficiency of three fluorescein isothiocyanate (FITC)-tagged oligoarginines (NHGR₉, NHGR₁₁, and NHGR₁₃) in four human prostate cell lines (LNCaP, PZ-HPV-7, DU145, and PC3). Of the three oligoarginines, NH₂GR₁₁ showed the highest cell uptake and internalization efficiency with its subcellular localization in cytosol. The biodistribution of FITC-NHGR₉, FITC-NHGR₁₁, and FITC-NHGR₁₃ performed in control nude mice displayed the unique preferential accumulation of FITC-NHGR₁₁ in the prostate tissue. Further in vivo evaluation of FITC-NHGR₁₁ in PC3 tumor-bearing nude mice revealed elevated uptake of this peptide in tumors as compared to other organs. In vivo pharmacokinetics evaluated with ⁶⁴Cu-labeled NH₂GR₁₁ showed that the peptide was rapidly cleared from the blood (t _1/2 = 10.7 min) and its elimination half-life was 17.2 h. The PET imaging specificity of ⁶⁴Cu-labled NH₂GR₁₁ was demonstrated for the detection of prostate cancer in a comparative imaging experiment using two different human cancer xenograft models.