An efficient method for variable region assembly in the construction of scFv phage display libraries using independent strand amplification

Phage display library technology is a common method to produce human antibodies. In this technique, the immunoglobulin variable regions are displayed in a bacteriophage in a way that each filamentous virus displays the product of a single antibody gene on its surface. From the collection of different phages, it is possible to isolate the virus that recognizes specific targets. The most common form in which to display antibody variable regions in the phage is the single chain variable fragment format (scFv), which requires assembly of the heavy and light immunoglobulin variable regions in a single gene. In this work, we describe a simple and efficient method for the assembly of immunoglobulin heavy and light chain variable regions in a scFv format. This procedure involves a two-step reaction: (1) DNA amplification to produce the single strand form of the heavy or light chain gene required for the fusion; and (2) mixture of both single strand products followed by an assembly reaction to construct a complete scFv gene. Using this method, we produced 6-fold more scFv encoding DNA than the commonly used splicing by overlap extension PCR (SOE-PCR) approach. The scFv gene produced by this method also proved to be efficient in generating a diverse scFv phage display library. From this scFv library, we obtained phages that bound several non-related antigens, including recombinant proteins and rotavirus particles.     

Ethylene antagonizes the inhibition of germination in Arabidopsis induced by salinity by modulating the concentration of hydrogen peroxide

The capacity of plants to achieve successful germination and early seedling establishment under high salinity is crucial for tolerance of plants to salt. The gaseous hormone ethylene has been implicated in modulating salt tolerance, but the detailed role of how ethylene modulates the response of early seedling establishment to salt is unclear. To better understand the role of the ethylene signal transduction pathway during germination and seedling establishment, an ethylene insensitive mutation (ein2-5) and an ethylene sensitive mutation (ctr1-1) of Arabidopsis were analyzed under saline conditions and compared with the wild type plant (Col-0) as control. High salinity (>100?mM NaCl) inhibited and delayed germination. These effects were more severe in the ethylene insensitive mutants (ein2-5) and less severe in the constitutive ethylene sensitive plants (ctr1-1) compared with Col-0 plants. Addition of the ethylene precursor 1-aminocyclopropane-1-carboxylic acid (ACC) or inhibitors of ethylene action implied that ethylene was essential for early seedling establishment under normal and saline conditions. Salt stress increased the endogenous concentration of hydrogen peroxide (H₂O₂) in germinating seeds and ACC reduced its concentration. Our results suggest that ethylene promotes germination under salinity by modulating the endogenous concentration of H₂O₂ in germinating seeds. These findings demonstrate that ethylene is involved in regulating germination as an initiator of the process rather than consequence, and that ethylene promotes germination by modulating the endogenous concentration of H₂O₂ in germinating seeds under salinity.     

Historical ecology with real numbers: past and present extent and biomass of an imperilled estuarine habitat

Historic baselines are important in developing our understanding of ecosystems in the face of rapid global change. While a number of studies have sought to determine changes in extent of exploited habitats over historic timescales, few have quantified such changes prior to late twentieth century baselines. Here, we present, to our knowledge, the first ever large-scale quantitative assessment of the extent and biomass of marine habitat-forming species over a 100-year time frame. We examined records of wild native oyster abundance in the United States from a historic, yet already exploited, baseline between 1878 and 1935 (predominantly 1885-1915), and a current baseline between 1968 and 2010 (predominantly 2000-2010). We quantified the extent of oyster grounds in 39 estuaries historically and 51 estuaries from recent times. Data from 24 estuaries allowed comparison of historic to present extent and biomass. We found evidence for a 64 per cent decline in the spatial extent of oyster habitat and an 88 per cent decline in oyster biomass over time. The difference between these two numbers illustrates that current areal extent measures may be masking significant loss of habitat through degradation.     

Impacts of snow cover duration on vegetation spring phenology over the Tibetan Plateau

Aims Snow cover occupies large percentage of land surface in Tibetan Plateau. Snow cover duration (SCD) during non-growing seasons plays a critical role in regulating alpine vegetation’s phenology by affecting the energy budgets of land surface and soil moisture conditions. Different period’s snow cover during non-growing season may have distinct effect on the vegetation’s phenology. Start of season (SOS) has been observed advanced under the ongoing climate change in the plateau, but it still remains unclear how the SCD alters the SOS. This study attempts to answer the following questions: (i) What is the pattern of spatial and temporal variations for SCD and grassland SOS? (ii) Which period’s SCD plays a critical role in grassland’s SOS?     

Grazing alters environmental control mechanisms of evapotranspiration in an alpine meadow of the Tibetan Plateau

Aims Evapotranspiration (ET) is an important component of the terrestrial water cycle and is easily affected by external disturbances, such as climate change and grazing. Identifying ET responses to grazing is instructive for determining grazing activity and informative for understanding the water cycle.     

Complex-type-dependent scoring functions in protein-protein docking

A major challenge in the field of protein-protein docking is to discriminate between the many wrong and few near-native conformations, i.e. scoring. Here, we introduce combinatorial complex-type-dependent scoring functions for different types of protein-protein complexes, protease/inhibitor, antibody/antigen, enzyme/inhibitor and others. The scoring functions incorporate both physical and knowledge-based potentials, i.e. atomic contact energy (ACE), the residue pair potential (RP), electrostatic and van der Waals' interactions. For different type complexes, the weights of the scoring functions were optimized by the multiple linear regression method, in which only top 300 structures with ligand root mean square deviation (L_RMSD) less than 20 A from the bound (co-crystallized) docking of 57 complexes were used to construct a training set. We employed the bound docking studies to examine the quality of the scoring function, and also extend to the unbound (separately crystallized) docking studies and extra 8 protein-protein complexes. In bound docking of the 57 cases, the first hits of protease/inhibitor cases are all ranked in the top 5. For the cases of antibody/antigen, enzyme/inhibitor and others, there are 17/19, 5/6 and 13/15 cases with the first hits ranked in the top 10, respectively. In unbound docking studies, the first hits of 9/17 protease/inhibitor, 6/19 antibody/antigen, 1/6 enzyme/inhibitor and 6/15 others' complexes are ranked in the top 10. Additionally, for the extra 8 cases, the first hits of the two protease/inhibitor cases are ranked in the top for the bound and unbound test. For the two enzyme/inhibitor cases, the first hits are ranked 1st for bound test, and the 119th and 17th for the unbound test. For the others, the ranks of the first hits are the 1st for the bound test and the 12th for the 1WQ1 unbound test. To some extent, the results validated our divide-and-conquer strategy in the docking study, which might hopefully shed light on the prediction of protein-protein interactions.     

Mechanism of saikosaponin-d in the regulation of rat mesangial cell proliferation and synthesis of extracellular matrix proteins.

Glomerulosclerosis is a common disorder in many types of chronic kidney diseases. Previous studies have shown that glomerular mesangial cells (MCs) play an important role in the pathogenesis of glomerulosclerosis. The ability of saikosaponin-d (SSd) to reduce the damage of kidney in progressive glomerulosclerosis has been demonstrated. In this study, the effects of saikosaponin-d on MC proliferation and synthesis of extracellular matrix proteins were investigated. Rat MCs were isolated from Wistar rats and cultured in Dulbecco's modified Eagle's medium. MCs were challenged with lipopolysacchorides and incubated with different concentrations of SSd. Cell proliferation and cytotoxicity were determined by 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), flow cytometry, and lactate dehydrogenase assays. Type IV collagen, fibronectin, and TGF-beta1 in the conditioned medium were measured. The expression of cyclin-dependent kinase 4, c-Jun, and c-Fos was determined by immunohistochemistry. At a concentration of 4 microg/mL or lower, SSd inhibited MC proliferation but did not cause cell death. SSd also inhibited lipopolysaccharide-induced secretion of type IV collagen, fibronectin, and TGF-beta1 in MCs. Additionally, SSd reduced the expression of CDK4, c-Jun, and c-Fos in MCs. We conclude that SSd inhibited MC proliferation and synthesis of extracullular matrix proteins through the downregulation of the CDK4, c-Jun, and c-Fos genes.