Highly specific gene silencing by artificial microRNAs in the unicellular alga Chlamydomonas reinhardtii

MicroRNAs (miRNAs) are small RNAs, 21 to 22 nucleotides long, with important regulatory roles. They are processed from longer RNA molecules with imperfectly matched foldback regions and they function in modulating the stability and translation of mRNA. Recently, we and others have demonstrated that the unicellular alga Chlamydomonas reinhardtii , like diverse multicellular organisms, contains miRNAs. These RNAs resemble the miRNAs of land plants in that they direct site-specific cleavage of target mRNA with miRNA-complementary motifs and, presumably, act as regulatory molecules in growth and development. Utilizing these findings we have developed a novel artificial miRNA system based on ligation of DNA oligonucleotides that can be used for specific high-throughput gene silencing in green algae.     

Dipeptidyl nitrile inhibitors of Cathepsin L

A series of potent Cathepsin L inhibitors with good selectivity with respect to other cysteine Cathepsins is described and SAR is discussed with reference to the crystal structure of a protein-ligand complex.     

Designed Human Serum Hyaluronidase 1 Variant, HYAL1��L, Exhibits Activity up to pH 5.9

Hyaluronidases from diverse species and sources have different pH optima. Distinct mechanisms with regard to dynamic structural changes, which control hyaluronidase activity at varying pH, are unknown. Human serum hyaluronidase 1 (HYAL1) is active solely below pH 5.1. Here we report the design of a HYAL1 variant that degrades hyaluronan up to pH 5.9. Besides highly conserved residues in close proximity of the active site of most hyaluronidases, we identified a bulky loop formation located at the end of the substrate binding crevice of HYAL1 to be crucial for substrate hydrolysis. The stretch between cysteine residues 207 and 221, which normally contains 13 amino acids, could be replaced by a tetrapeptide sequence of alternating glycine serine residues, thereby yielding an active enzyme with an extended binding cleft. This variant exhibited hyaluronan degradation at elevated pH. This is indicative for appropriate substrate binding and proper positioning being decisively affected by sites far off from the active center.Hyaluronan (HA),³ a linear polysaccharide found in the extracellular matrix of most tissues and body fluids of vertebrates, is enzymatically degraded by hyaluronidases (1). Mammalian-type hyaluronidases are grouped into EC 3.2.1.35 (2, 3) or the glycoside hydrolase family 56 (4). Members of this enzyme family hydrolyze the 1,4-β-glycosidic linkage between N-acetyl-d-glucosamine and d-glucuronate within HA polymers (5). In mammalians, hyaluronidases have been found in testis, liver lysosomes, and serum. They are involved in controlling HA levels and are thus implicated in various diseases related to defects of HA metabolism (6).The crystal structures of hyaluronidase from bee (7), wasp (8), and only recently that of human serum hyaluronidase 1 (HYAL1) (9) have been deciphered. In addition to the N-terminal catalytic domain of the insect enzymes, which resembles a distorted (β/α)₈ barrel, HYAL1 contains yet another domain. HA hydrolysis is achieved by a pair of acidic amino acids via a retaining double displacement mechanism and a substrate-assisted catalysis, in which the carbonyl oxygen of the N-acetyl group of the cleaved HA subunit acts as the catalytic nucleophile (7).Mammalian-type hyaluronidases display different pH optima. HYAL1 (10) and hyaluronidase 2 (HYAL2) (11) exhibit highest activities at acidic conditions, whereas the hyaluronidase found in Xenopus laevis kidney is only active at neutral pH (12). Bee venom hyaluronidase (13), as well as sperm hyaluronidase, PH20 (SPAM1) (14), are capable of degrading HA over a broad pH range. Up to three PH20 isoforms with greatly different pH optima could be found in protein preparations from bovine testis (15). Extensive analysis of hyaluronidase structures did not bring forward any insights as to what residues or regions of the enzymes specify a specific pH optimum.Profiles of pH-dependent activities can be assigned by computing the electrostatic interactions of the enzyme, which are primarily determined by the ionization states of its amino acid side chains. The pK_a values of titratable groups of the enzyme reflect pH-dependent properties such as stability, enzymatic interaction, and substrate interactions (16). Here we present computational and experimental data on the replacement of a loop region located at the end of the substrate binding groove yielding a variant hyaluronidase with an altered pH profile.     

Environmental correlates for tropical tree diversity and distribution patterns in Borneo

Aim Identify environmental correlates for tropical tree diversity and composition. Location Borneo, Southeast Asia. Methods A GIS‐environmental database with 5 arc minute (c. 10 × 10 km) resolution was combined with tree inventory data. Tree diversity, phylogenetic diversity (PD) and the two main compositional gradients were determined for 46 tree inventories. Akaike's information criterion and a data jackknifing procedure were used to select 50 explanatory models for diversity and composition gradients. The average of these models was used as our final diversity and compositional model. We applied Moran's I to detect spatial autocorrelation of residuals. Results Tree diversity, PD and the two main compositional gradients in Borneo were all significantly correlated with the environment. Tree diversity correlated negatively with elevation, soil depth, soil coarseness (texture) and organic carbon content, whereas it correlated positively with soil C:N ratio, soil pH, moisture storage capacity and annual rainfall. Tree PD was correlated positively with elevation and temperature seasonality and was largely determined by gymnosperms. However, angiosperm PD also correlated positive with elevation. Compositional patterns were strongly correlated with elevation but soil texture, cation‐exchange‐capacity, C:N ratio, C and N content and drainage were also important next to rainfall seasonality and El Niño Southern Oscillation drought impact. Main conclusions Although elevation is the most important correlate for diversity and compositional gradients in Borneo, significant additional variability is explained by soil characteristics (texture, carbon content, pH, depth, drainage and nutrient status) and climate (annual rainfall, rainfall seasonality and droughts). The identified environmental correlates for diversity and composition gradients correspond to those found in other tropical regions of the world. Differences between the regions are mainly formed by differences in the relative importance of the environmental variables in explaining diversity and compositional gradients.     

Hedgerows as an environment for forest plants: a comparative case study of five species

Many areas in Europe are dominated by agricultural land use, and as a consequence, many typical forest plant species suffer from habitat loss and fragmentation. Hedgerows, one of the common elements of rural landscapes, have been considered as potential refuges for these species. The main objective of this study was to examine whether forests and hedgerows differ in environmental conditions, and whether important life-history attributes of the populations differ between the two habitat types. We selected five species commonly found in the region in both forests and hedgerows (Adoxa moschatellina, Anemone nemorosa, Circaea lutetiana, Polygonatum multiflorum and Stellaria holostea), and sampled data on 10 populations of each species in each habitat type, including measurements of light and various soil factors. Hedgerows had higher relative light availability and tended to have higher soil nutrient contents and lower soil water values than forests. The comparison of plant performance values between habitat types did not show consistent patterns across species. Anemone and Polygonatum performed equally well in hedgerows and forests, whereas Stellaria appeared to have a higher fitness in hedgerows. In contrast, Circaea showed a higher reproduction under forest conditions. For Adoxa, the results were somewhat contradictory: whereas the reproductive output of this species was higher in forests, population density was higher in hedgerows. The abiotic factors most closely related to the performance values were relative light and soil water availability. The majority of plant performance values did not differ between hedgerows and forests. We therefore conclude that the tested forest species are capable of growing also in hedgerows and will survive equally well in forest and its “surrogate” habitat.     

Semliki Forest Virus Expressing Interleukin-12 Induces Antiviral and Antitumoral Responses in Woodchucks with Chronic Viral Hepatitis and Hepatocellular Carcinoma

A vector based on Semliki Forest virus (SFV) expressing high levels of interleukin-12 (SFV-enhIL-12) has previously demonstrated potent antitumoral efficacy in small rodents with hepatocellular carcinoma (HCC) induced by transplantation of tumor cells. In the present study, the infectivity and antitumoral/antiviral effects of SFV vectors were evaluated in the clinically more relevant woodchuck model, in which primary HCC is induced by chronic infection with woodchuck hepatitis virus (WHV). Intratumoral injection of SFV vectors expressing luciferase or IL-12 resulted in high reporter gene activity within tumors and cytokine secretion into serum, respectively, demonstrating that SFV vectors infect woodchuck tumor cells. For evaluating antitumoral efficacy, woodchuck tumors were injected with increasing doses of SFV-enhIL-12, and tumor size was measured by ultrasonography following treatment. In five (83%) of six woodchucks, a dose-dependent, partial tumor remission was observed, with reductions in tumor volume of up to 80%, but tumor growth was restored thereafter. Intratumoral treatment further produced transient changes in WHV viremia and antigenemia, with ≥1.5-log₁₀ reductions in serum WHV DNA in half of the woodchucks. Antitumoral and antiviral effects were associated with T-cell responses to tumor and WHV antigens and with expression of CD4 and CD8 markers, gamma interferon, and tumor necrosis factor alpha in peripheral blood mononuclear cells, suggesting that immune responses against WHV and HCC had been induced. These experimental observations suggest that intratumoral administration of SFV-enhIL-12 may represent a strategy for treatment of chronic HBV infection and associated HCC in humans but indicate that this approach could benefit from further improvements.Hepatocellular carcinoma (HCC) is a major public health problem worldwide, representing the fifth most common type of cancer. HCC is also the third leading cause of cancer-related death, mainly because only surgical and local ablative therapeutic options have shown efficacy in patients with this type of cancer (21). Approximately 80% of all HCC cases are attributed to chronic infection with hepatitis C virus and/or hepatitis B virus (HBV). Chronic carriers of HBV have a greater than 100-fold-increased relative risk of developing HCC compared to HBV-uninfected humans, with an annual incidence rate of 2 to 6% in cirrhotic patients. The high incidence of HCC, together with its poor prognosis and limited therapeutic options, warrants the development of new treatment strategies for this disease.There is increasing evidence that stimulation of the immune system for subsequent recognition and killing of tumor cells may be a valuable treatment option for liver cancer. In general, HCC appears to be an attractive target for immunotherapy because cases of spontaneous tumor regression have been reported, HCC is often infiltrated with lymphocytes, and HCC-associated proteins such as alpha-fetoprotein may be used as targets for immune-mediated killing of tumors (5, 49).A promising strategy to stimulate the deficient antitumoral immune response is based on the transfer and subsequent expression of immunostimulatory genes in tumor cells using viral or nonviral delivery vectors. One of the most effective immunostimulatory cytokines is interleukin-12 (IL-12), a protein usually expressed by macrophages and dendritic cells. IL-12 has been demonstrated to induce strong antitumoral effects that are mediated by the stimulation of T-helper cell type 1 (Th1) responses, including the activation of cytolytic T lymphocytes (CTL) and natural killer cells, and by the inhibition of angiognesis (48, 50). All of these effects are dependent on the production of gamma interferon (IFN-γ). Viral vectors that are based on adenovirus have been used to deliver IL-12 into several animal models with transplantable HCC, resulting in a localized expression of this cytokine and usually leading to antitumoral effects (3, 14, 37). However, and despite successful treatment of HCC in preclinical studies, a phase I clinical trial with a first-generation adenoviral vector for delivery and expression of IL-12 in patients with primary and metastatic liver cancer produced only a modest antitumoral effect (41). This poor response was probably due to the low and transient IL-12 expression in tumors. These results in humans indicated a need for vectors with higher potency and for preclinical testing in relevant models of HCC (i.e., large animals with spontaneous tumors).Vectors based on Semliki Forest virus (SFV), a member of the alphavirus group, are highly efficient in inducing antitumoral responses in a variety of animal models (2, 9, 10, 39, 44, 53). The SFV vector used in the present study is based on a viral RNA genome in which the region coding for the structural proteins has been replaced by a heterologous gene (24). Recombinant SFV RNA can be transcribed in vitro and transfected into cells, resulting in viral replication and subsequent production of a subgenomic RNA from which the heterologous protein is expressed at very high levels. Recombinant SFV RNA can be packaged into viral particles (vp) by cotransfecting it into cells together with two helper RNAs coding for the capsid and the envelope proteins (43). Compared to adenoviral vectors expressing IL-12, tumor treatment with SFV vectors expressing the same cytokine resulted in greater antitumoral effects in a murine colon adenocarcinoma model and also in a rat orthotopic HCC model (16, 39). The greater antitumoral effect mediated by SFV vectors has been attributed to the higher expression of IL-12 and to the induction of apoptosis caused by SFV replication within tumor cells. Apoptosis leads to the release of tumor antigens that can be taken up by antigen-presenting cells, thereby potentiating the antitumoral response induced by IL-12 (54). Furthermore, SFV vectors have low immunogenicity when delivered intratumorally, allowing repetitive administrations into the same tumor, which is not possible with adenoviral vectors (38).In the present study, the antitumoral efficacy of an SFV vector expressing IL-12 (SFV-enhIL-12) was investigated in woodchucks with HCC. The Eastern woodchuck (Marmota monax) is frequently infected with the woodchuck hepatitis virus (WHV), which is closely related to the human HBV in its structure, genomic organization, mechanism of replication, and course of infection (29). The woodchuck has been used as a mammalian model for research on HBV, including the pathogenesis of acute and chronic HBV infection, and for preclinical evaluation of the safety and efficacy of candidate antiviral drugs and therapeutic immunomodulators for the treatment of chronic HBV infection (29) and prevention of HCC (47).All woodchucks chronically infected with WHV as neonates develop HCC, and the median time for tumor appearance is 24 months of age (34, 47). After identification of HCC, the median survival time of woodchucks is 6 months, a situation similar to that for patients with HCC. In addition, WHV-induced hepatocarcinogenesis shows strong similarity to HBV-induced carcinogenesis in humans (34, 47). These features of HCC that are associated with persistent hepatitis virus infection make the woodchuck model unique compared to other animal models, in which HCC is induced by a chemical carcinogen or by transplantation of established tumor cell lines into immune-deficient or immune-compatible hosts. Woodchucks with large liver tumors that acquire malignant characteristics in a stepwise process similar to HCC in humans are an attractive and suitable model for the preclinical evaluation of new treatment strategies for HBV-induced HCC in humans (47).The antitumoral efficacy of a SFV vector expressing high levels of IL-12 (SFV-enhIL-12) was investigated in six woodchucks with established chronic WHV infection and primary HCC. The results demonstrate that SFV-delivered IL-12 expression produced a dose-dependent, partial tumor remission that was associated with a general activation of cellular immune responses against HCC. The antitumoral activity, in addition to an antiviral activity against WHV, and the favorable safety profile in woodchucks suggest that a therapeutic approach based on SFV-enhIL-12 may represent a treatment strategy for HCC in patients with chronic HBV infection, but the overall results also indicate that this approach needs further improvement for inducing a complete tumor remission.