Adaptive Evolution of Mus Apobec3 Includes Retroviral Insertion and Positive Selection at Two Clusters of Residues Flanking the Substrate Groove

Mouse APOBEC3 (mA3) is a cytidine deaminase with antiviral activity. mA3 is linked to the Rfv3 virus resistance factor, a gene responsible for recovery from infection by Friend murine leukemia virus, and mA3 allelic variants differ in their ability to restrict mouse mammary tumor virus. We sequenced mA3 genes from 38 inbred strains and wild mouse species, and compared the mouse sequence and predicted structure with human APOBEC3G (hA3G). An inserted sequence was identified in the virus restrictive C57BL strain allele that disrupts a splice donor site. This insertion represents the long terminal repeat of the xenotropic mouse gammaretrovirus, and was acquired in Eurasian mice that harbor xenotropic retrovirus. This viral regulatory sequence does not alter splicing but is associated with elevated mA3 expression levels in spleens of laboratory and wild-derived mice. Analysis of Mus mA3 coding sequences produced evidence of positive selection and identified 10 codons with very high posterior probabilities of having evolved under positive selection. Six of these codons lie in two clusters in the N-terminal catalytically active cytidine deaminase domain (CDA), and 5 of those 6 codons are polymorphic in Rfv3 virus restrictive and nonrestrictive mice and align with hA3G CDA codons that are critical for deaminase activity. Homology models of mA3 indicate that the two selected codon clusters specify residues that are opposite each other along the predicted CDA active site groove, and that one cluster corresponds to an hAPOBEC substrate recognition loop. Substitutions at these clustered mA3 codons alter antiviral activity. This analysis suggests that mA3 has been under positive selection throughout Mus evolution, and identified an inserted retroviral regulatory sequence associated with enhanced expression in virus resistant mice and specific residues that modulate antiviral activity.     

Analysis of circular genome rearrangement by fusions, fissions and block-interchanges

Background  

Analysis of genomes evolving via block-interchange events leads to a combinatorial problem of sorting by block-interchanges, which has been studied recently to evaluate the evolutionary relationship in distance between two biological species since block-interchange can be considered as a generalization of transposition. However, for genomes consisting of multiple chromosomes, their evolutionary history should also include events of chromosome fusions and fissions, where fusion merges two chromosomes into one and fission splits a chromosome into two.     

Higher urine desmosine levels are associated with mortality in patients with acute lung injury

Desmosine is a stable breakdown product of elastin that can be reliably measured in urine samples. We tested the hypothesis that higher baseline urine desmosine would be associated with higher mortality in 579 of 861 patients included in the recent Acute Respiratory Distress Syndrome Network trial of lower tidal volume ventilation (1). We also correlated urine desmosine levels with indexes of disease severity. Finally, we assessed whether urine desmosine was lower in patients who received lower tidal volumes. Desmosine was measured by radioimmunoassay in urine samples from days 0, 1, and 3 of the study. The data were expressed as a ratio of urine desmosine to urine creatinine to control for renal dilution. The results show that higher baseline (day 0) urine desmosine-to-creatinine concentration was associated with a higher risk of death on adjusted analysis (odds ratio 1.36, 95% confidence interval 1.02-1.82, P=0.03). Urine desmosine increased in both ventilator groups from day 0 to day 3, but the average rise was higher in the 12-ml/kg predicted body weight group compared with the 6-ml/kg predicted body weight group (P=0.053, repeated-measures model). In conclusion, patients with acute lung injury ventilated with lower tidal volumes have lower urine desmosine levels, a finding that may reflect reduced extracellular matrix breakdown. These results illustrate the value of evaluating urinary biological markers that may have prognostic and pathogenetic significance in acute lung injury.     

Role of mitogen‐activated protein kinase in Zn‐BC‐AM PDT‐induced apoptosis in nasopharyngeal carcinoma cells

Photodynamic therapy (PDT) with a recently developed photosensitizer Zn‐BC‐AM was found to effectively induce apoptosis in a well‐differentiated nasopharyngeal carcinoma (NPC) HK‐1 cell line. Sustained activation of p38 mitogen‐activated protein kinase (MAPK) and c‐jun N‐terminal kinase (JNK) as well as a transient increase in activation of extracellular signal‐regulated kinase (ERK) were observed immediately after Zn‐BC‐AM PDT. A commonly used p38 MAPK/JNK pharmacological inhibitor PD169316 was found to reduce PDT‐induced apoptosis of HK‐1 cells. PD169316 also prevented the loss of Bcl‐2 and Bcl‐xL in PDT‐treated HK‐1 cells. However, inhibition of JNK with SP600125 had no effect on Zn‐BC‐AM PDT‐induced apoptosis while inhibition of ERK with PD98059 or p38 MAPK with SB203580 significantly increased Zn‐BC‐AM PDT‐induced apoptosis. Further study showed that knockdown of the p38β isoform with siRNA also increased Zn‐BC‐AM PDT‐induced apoptosis, indicating that the anti‐apoptotic effect of PD169316 in PDT‐treated HK‐1 cells was probably independent of p38 MAPK or JNK activation. Taken together, the results suggest that inhibition of p38β and ERK may enhance the therapeutic efficacy of Zn‐BC‐AM PDT on NPC cells. It should be noted that data only based on the use of PD169316 should be interpreted in caution. Copyright © 2010 John Wiley & Sons, Ltd.     

Ex vivo gene therapy in autologous critical-size craniofacial bone regeneration

In therapeutic bone repairs, autologous bone grafts, conventional or vascularized allografts, and biocompatible artificial bone substitutes all have their shortcomings. The bone formed from peptides [recombinant human bone morphogenetic proteins (BMPs)], demineralized bone powder, or a combination of both is small in size. Tissue engineering may be an alternative for cranial bone repair. In this study, the authors developed an animal model to test the hypothesis that replication-defective, adenovirus-mediated human BMP-2 gene transfer to bone marrow stromal cells enhances the autologous bone formation for repairing a critical-size craniofacial defect. The mesenchymal stromal cells of miniature swine were separated from the iliac crest aspirate and expanded in monolayer culture 1 month before implantation. The cultured mesenchymal stromal cells were infected with recombinant, replication-defective human adenovirus BMP-2, 7 days before implantation. Bilateral 2 x 5-cm2 cranial defects were created, leaving no osteogenic periosteum and dura behind. Mesenchymal stromal cells at 5 x 10(7)/ml were mixed with collagen type I to form mesenchymal stromal cell/polymer constructs. Mesenchymal stromal cells used for the control site were infected with adenovirus beta-Gal under the same conditions. After 6 weeks and 3 months, 10 miniature swine were euthanized and the cranium repair was examined. Near-complete repair of the critical-size cranial defect by tissue-engineered mesenchymal stromal cell/collagen type I construct was observed. The new bone formation area (in square centimeters) measured by three-dimensional computed tomography demonstrated that the improvement from 6 weeks to 3 months was significantly greater on the experimental side than on the control side (2.15 cm2 versus 0.54 cm2, p < 0.001) and significantly greater at 3 months than at 6 weeks (2.13 cm2 versus 0.52 cm2, p < 0.001). The difference between the experimental and control groups was significant at 3 months (mean difference, 2.13 cm2; p < 0.001). The maximal compressive strength of the new bone was similar to that of the normal cranial bone when evaluated by biomechanical testing (cranium bone versus tissue-engineered bone, 88.646 +/- 5.121 MPa versus 80.536 +/- 19.302 MPa; p = 0.227). Adenovirus was absent from all constructs by immunochemical staining at 6 weeks and 3 months after implantation. The successful repair of cranial defects in this experiment demonstrates the efficacy of the integration of the autologous stem cell concept, gene medicine, and polymers in producing tissue-engineered bone.     

Monitoring bone loss using ELISA and surface plasmon resonance (SPR) technology

Osteoporosis influences the health of the females who are in menopause phase. The techniques to detect the markers of bone turnover is very important for preventing osteoporosis. ELISA was developed for detection of urinary N-telopeptide (NTx) as an osteoporosis marker. Our aim is to develop a sensitive method to detect NTx excretion using surface plasmon resonance (SPR). Samples collected were assayed and results suggest that our SPR-based method is promising for monitoring bone loss.     

The introduction of a phytase gene from Bacillus subtilis improved the growth performance of transgenic tobacco

Phytate, the main form of phosphorus storage in plant seeds, is well known to be an anti-nutrient and a major source of phosphorus pollution in animal manure. To improve phosphorus bio-availability, we introduced a recently characterized phytase from Bacillus subtilis into the cytoplasm of tobacco cells. Although the introduction of acid fungal phytase from Aspergillus niger in previous studies did not result in any phenotypic changes in tobacco, here we show that a tobacco line transformed with a neutral phytase exhibited phenotypic changes in flowering, seed development, and response to phosphate deficiency. The transgenic line showed an increase in flower and fruit numbers, small seed syndrome, lower seed IP6/IP5 ratio, and enhanced growth under phosphate-starvation conditions compared with the wildtype. The results suggest that the over-expression of Bacillus phytase in the cytoplasm of tobacco cells shifts the equilibrium of the inositol phosphate biosynthesis pathway, thereby making more phosphate available for primary metabolism. The approach presented here can be applied as a strategy for boosting productivity in agriculture and horticulture.     

Assessing fragmentation and disturbance of west Kenyan rainforests by means of remotely sensed time series data and landscape metrics

Biodiversity in tropical rainforests is heavily influenced by land use/cover change (LUCC), but so far there have been few LUCC studies conducted in Africa. We present several methods that make use of remotely sensed data and landscape metrics and allow for assessment of the development of land cover and thus forest fragmentation and disturbance over a substantial period of time. The study covers Kakamega Forest and its associated forest areas in western Kenya, over the last 30 years. The accuracy of a supervised multispectral classification of Landsat time series data encompassing seven time steps between 1972 and 2001 is numerically assessed using ground truth reference data considering the 2001 time step. Here, buffering the forest areas by 1 km, highest user's accuracies for the forest classes ‘near natural + old secondary forest’ (87.50%), ‘secondary forest’ (80.00%) and ‘bushland/shrubs’ (81.08%) are revealed. Images of a spatially distributed fragmentation index derived from the land cover time series by applying a three by 3 pixel‐sized moving window to determine forest pixels’ adjacency, highlight trends in forest fragmentation, e.g. the splitting into two separate forests along the Yala/Ikuywa corridor. Calculations of mean fragmentation indices for the Biodiversity Monitoring Transect Analysis in Eastern Africa (BIOTA‐East Africa) focus research areas are used to evaluate the fragmentation index and to demonstrate its potential to extrapolate (e.g. biological) field findings in space and time. Here we argue for a correlation of the fragmentation indices results not only with forest management regimes, but with population distribution and accessibility (e.g. by roads). A cluster analysis applying the isodata‐algorithm on the classification results of all seven times steps allows for a rapid visual assessment of the distinct pattern of typical land cover development trends since 1972. This reveals that parts of Kakamega Forest have experienced severe forest loss while others, especially in the north‐east, show signs of succession.