Elucidation of molecular mechanisms underlying the protective effects of thymoquinone against rheumatoid arthritis

Thymoquinone (TQ) is the major active compound derived from the medicinal Nigella sativa. A few studies have shown that TQ exhibits anti‐inflammatory activities in experimental models of rheumatoid arthritis (RA) through mechanisms that are not fully understood. The aim of this work was to evaluate the in vitro and in vivo effects of TQ and to investigate its influence on the major signalling pathways involved in pathophysiological RA changes. We used isolated human RA fibroblast‐like synoviocytes (FLS) and a rat adjuvant‐induced arthritis model of RA. In isolated RA FLS, TQ (0–10 µM) was not cytotoxic and inhibited slightly lipopolysaccharide (LPS)‐induced FLS proliferation and strongly H₂O₂‐induced 4‐hydroxynonenal (HNE) generation. By studying different inflammatory and catabolic factors, we determined that TQ significantly abolished LPS‐induced interleukin‐1beta (IL‐1β), tumour necrosis factor‐alpha (TNFα), metalloproteinase‐13, cyclooxygenase‐2, and prostaglandin E₂. Furthermore, LPS‐induced the phosphorylation of p38 mitogen‐activated protein kinase, extracellular‐regulated kinases ½, and nuclear factor‐kappaB‐p65 were also blocked by TQ in time‐dependent manner. In our experimental RA model, the oral administration of TQ 5 mg/kg/day significantly reduced the serum levels of HNE, IL‐1β and TNFα as well as bone turnover markers, such as alkaline phosphatase and tartrate‐resistant acid phosphatase. The protective effects of TQ against RA were also evident from the decrease in arthritis scoring and bone resorption. In conclusion, the fact that TQ abolishes a number of factors known to be involved in RA pathogenesis renders it a clinically valuable agent in the prevention of articular diseases, including RA. J. Cell. Biochem. 112: 107–117, 2011. © 2010 Wiley‐Liss, Inc.     

Inhibition of CXCR4 by LY2624587, a Fully Humanized Anti-CXCR4 Antibody Induces Apoptosis of Hematologic Malignancies

SDF-1 and CXCR4 are a chemokine and chemokine receptor pair playing critical roles in tumorigenesis. Overexpression of CXCR4 is a hallmark of many hematological malignancies including acute myeloid leukemia, chronic lymphocytic leukemia and non-Hodgkin’s lymphoma, and generally correlates with a poor prognosis. In this study, we developed a humanized anti-CXCR4 monoclonal antibody, LY2624587 as a potent CXCR4 antagonist that was advanced into clinical study for cancer. LY2624587 blocked SDF-1 binding to CXCR4 with an IC₅₀ of 0.26 nM, and inhibited SDF-1-induced GTP binding with a K_b of 0.66 nM. In human lymphoma U937 and leukemia CCRF-CEM cells expressing endogenous CXCR4, LY2624587 inhibited SDF-1-induced cell migration with IC₅₀ values of 3.7 and 0.26 nM, respectively. This antibody also inhibited CXCR4 and SDF-1 mediated cell signaling including activation of MAPK and AKT in tumor cells expressing CXCR4. Bifocal microscopic and flow cytometry analyses revealed that LY2624587 mediated receptor internalization and caused CXCR4 down-regulation on the cell surface. In human hematologic cancer cells, LY2624587 caused dose dependent apoptosis in vitro and in vivo. In mouse xenograft models developed with human leukemia and lymphoma cells expressing high levels of CXCR4, LY2624587 exhibited dose-dependent tumor growth inhibition and provided significant survival benefit in a disseminated lymphoma model. Collectively, we have demonstrated that CXCR4 inhibition by LY2624587 has the potential for the treatment of human hematological malignancies.     

Allozyme variation and conservation of the Tasmanian endemics, Eucalyptus risdonii, E. tenuiramis and E. coccifera

The rare Tasmanian endemic Eucalyptus risdonii is thought tohave arisen as a result of small, heterochronic changes to the genome ofits more widespread sister species, E. tenuiramis. Previousmorphological studies have shown that genetic differentiation betweenpopulations of E. risdonii and southern E. tenuiramisis continuous and much smaller than the separation between the southernand northern morphotypes of E. tenuiramis. However,morphological traits may be influenced by selection, possibly leading toconvergence, requiring an independent measure of genetic variation. Westudied allozyme frequency variation in E. risdonii, southernE. tenuiramis (parapatric with E. risdonii), northernE. tenuiramis (disjunct from southern populations), and E.coccifera (as an outgroup). Each morphotype had a level of geneticdiversity close to the average reported in ten other eucalypt specieswith similar distributions but the coefficients of populationdifferentiation within morphotypes were lower than in most othereucalypt species. The overall difference between morphotypes wasextremely small, possibly as a result of recent and rapiddifferentiation, but may also be the result of gene flow from otherpeppermint taxa, including E. amygdalina and E.pulchella. Southern E. tenuiramis has greater geneticaffinity with E. risdonii than with northern E.tenuiramis which supports recent evolutionary divergence of E.risdonii. In this study we have shown that taxonomic units are notnecessarily aligned with an equitable partition of the gene pool andthat conservation units should be much broader than single taxa in orderto preserve evolutionary processes.     

The Ins and Outs of Ring-Cleaving Dioxygenases

ABSTRACT

Ring-cleaving dioxygenases catalyze the oxygenolytic fission of catecholic compounds, a critical step in the aerobic degradation of aromatic compounds by bacteria. Two classes of these enzymes have been identified, based on the mode of ring cleavage: intradiol dioxygenases utilize non-heme Fe(III) to cleave the aromatic nucleus ortho to the hydroxyl substituents; and extradiol dioxygenases utilize non-heme Fe(II) or other divalent metal ions to cleave the aromatic nucleus meta to the hydroxyl substituents. Recent genomic, structural, spectroscopic, and kinetic studies have increased our understanding of the distribution, evolution, and mechanisms of these enzymes. Overall, extradiol dioxygenases appear to be more versatile than their intradiol counterparts. Thus, the former cleave a wider variety of substrates, have evolved on a larger number of structural scaffolds, and occur in a wider variety of pathways, including biosynthetic pathways and pathways that degrade non-aromatic compounds. The catalytic mechanisms of the two enzymes proceed via similar iron-alkylperoxo intermediates. The ability of extradiol enzymes to act on a variety of non-catecholic compounds is consistent with proposed differences in the breakdown of this iron-alkylperoxo intermediate in the two enzymes, involving alkenyl migration in extradiol enzymes and acyl migration in intradiol enzymes. Nevertheless, despite recent advances in our understanding of these fascinating enzymes, the major determinant of the mode of ring cleavage remains unknown.     

Genome‐wide scans detect adaptation to aridity in a widespread forest tree species

Patterns of adaptive variation within plant species are best studied through common garden experiments, but these are costly and time‐consuming, especially for trees that have long generation times. We explored whether genome‐wide scanning technology combined with outlier marker detection could be used to detect adaptation to climate and provide an alternative to common garden experiments. As a case study, we sampled nine provenances of the widespread forest tree species, Eucalyptus tricarpa, across an aridity gradient in southeastern Australia. Using a Bayesian analysis, we identified a suite of 94 putatively adaptive (outlying) sequence‐tagged markers across the genome. Population‐level allele frequencies of these outlier markers were strongly correlated with temperature and moisture availability at the site of origin, and with population differences in functional traits measured in two common gardens. Using the output from a canonical analysis of principal coordinates, we devised a metric that provides a holistic measure of genomic adaptation to aridity that could be used to guide assisted migration or genetic augmentation.     

Using mating-type gene sequences for improved phylogenetic resolution of Collectotrichum species complexes

Colletotrichum species are defined primarily on the basis of host preference and morphology of the organism in planta and in culture. However the genus contains several species complexes that encompass such a broad range of morphological and pathological variation that the species name is of relatively little use either to the taxonomist or plant pathologist. Phylogenetic analyses, primarily based on variable regions of the ribosomal DNA (rDNA) sequences, have indicated that these species complexes comprise a variable number of identifiable monophyletic clades. However rDNA sequences often are insufficiently diverse to fully resolve such closely related lineages. A group of isolates representing three species complexes (C. graminicola, C. gloeosporioides and C. acutatum) were analyzed by using the high mobility group (HMG)-encoding sequence of the MAT1-2 mating type sequence, which has been shown in other fungi to be especially suitable for distinguishing relationships among closely related groups. Results were compared with those obtained from analysis of variable regions of the rDNA as well as from standard morphological classification methods. Results achieved through analysis of MAT1-2 sequences correlated well with those obtained by analysis of rDNA sequences but provided significantly better resolution among the various lineages. Morphological traits, including hyphopodia size, colony appearance, spore size, appresorial shape and size and host preference, frequently were unreliable as indicators of phylogenetic association. Spore shape and hyphopodia shape more often were useful for this purpose.     

Benzodiazepine use in pregnancy and major malformations or oral cleft: meta-analysis of cohort and case-control studies

Objective: To determine if exposure to benzodiazepines during the first trimester of pregnancy increases risk of major malformations or cleft lip or palate. Design: Meta-analysis. Setting: Studies from 1966 to present. Subjects: Studies were located with Medline, Embase, Reprotox, and from references of textbooks, reviews, and included articles. Included studies were original, concurrently controlled studies in any language. Interventions: Data extraction and quality assessment were done independently and in duplicate. Main outcome measures: Maternal exposure to benzodiazepines in at least the first trimester; incidence of major malformations or oral cleft alone, measured as odds ratios and 95% confidence intervals with a random effects model. Results: Of over 1400 studies reviewed, 74 were retrieved and 23 included. In the analysis of cohort studies fetal exposure to benzodiazepine was not associated with major malformations (odds ratio 0.90; 95% confidence interval 0.61 to 1.35) or oral cleft (1.19; 0.34 to 4.15). Analysis of case-control studies showed an association between exposure to benzodiazepines and development of major malformations (3.01; 1.32 to 6.84) or oral cleft alone (1.79; 1.13 to 2.82). Conclusions: Pooled data from cohort studies showed no association between fetal exposure to benzodiazepines and the risk of major malformations or oral cleft. On the basis of pooled data from case-control studies, however, there was a significant increased risk for major malformations or oral cleft alone. Until more research is reported, level 2 ultrasonography should be used to rule out visible forms of cleft lip.

Key messages

• Pooled data from cohort studies showed no apparent association between fetal exposure to benzodiazepines and the risk for major malformations or oral cleft
• Data from case-control studies showed that risk for major malformations or oral cleft alone was increased
• Until more studies are done, it is prudent to perform level 2 ultrasonography to rule out visible forms of cleft lip

     

Phylogenetic reconstruction of vertebrate Hox cluster duplications

In vertebrates and the cephalochordate, amphioxus, the closest vertebrate relative, Hox genes are linked in a single cluster. Accompanying the emergence of higher vertebrates, the Hox gene cluster duplicated in either a single step or multiple steps, resulting in the four-cluster state present in teleosts and tetrapods. Mammalian Hox clusters (designated A, B, C, and D) extend over 100 kb and are located on four different chromosomes. Reconstructing the history of the duplications and its relation to vertebrate evolution has been problematic due to the lack of alignable sequence information. In this study, the problem was approached by conducting a statistical analysis of sequences from the fibrillar-type collagens (I, II, III, and IV), genes closely linked to each Hox cluster which likely share the same duplication history as the Hox genes. We find statistical support for the hypothesis that the cluster duplication occurred as multiple distinct events and that the four-cluster situation arose by a three- step sequential process.