High-throughput retrieval of physical DNA for NGS-identifiable clones in phage display library

In antibody discovery, in-depth analysis of an antibody library and high-throughput retrieval of clones in the library are crucial to identifying and exploiting rare clones with different properties. However, existing methods have technical limitations, such as low process throughput from the laborious cloning process and waste of the phenotypic screening capacity from unnecessary repetitive tests on the dominant clones. To overcome the limitations, we developed a new high-throughput platform for the identification and retrieval of clones in the library, TrueRepertoire?. This new platform provides highly accurate sequences of the clones with linkage information between heavy and light chains of the antibody fragment. Additionally, the physical DNA of clones can be retrieved in high throughput based on the sequence information. We validated the high accuracy of the sequences and demonstrated that there is no platform-specific bias. Moreover, the applicability of TrueRepertoire? was demonstrated by a phage-displayed single-chain variable fragment library targeting human hepatocyte growth factor protein.     

Amino acid modified chitosan beads: Improved polymer supports for immobilization of lipase from Candida rugosa

Amino acid modified chitosan beads (CBs) for immobilization of lipases from Candida rugosa were prepared by activation of a chitosan backbone with epichlorohydrin followed by amino acid coupling. The beads were analyzed by elemental analysis and solid state NMR with coupling yields of the amino acids ranging from 15 to 60%. The immobilized lipase on unmodified chitosan beads showed the highest immobilization yield (92.7%), but its activity was relatively low (10.4%). However, in spite of low immobilization yields (15–50%), the immobilized lipases on the amino acid modified chitosan beads showed activities higher than that of the unmodified chitosan beads, especially on Ala or Leu modified chitosan beads (Ala-CB or Leu-CB) with 49% activity for Ala-CB and 51% for Leu-CB. The immobilized lipases on Ala-CB improved thermal stability at 55 °C, compared to free and immobilized lipases on unmodified chitosan beads and the immobilized lipase on Ala-CB retained 93% of the initial activity when stored at 4 °C for 4 weeks. In addition, the activity of the immobilized lipase on Ala-CB retained 77% of its high initial activity after 10 times of reuse. The kinetic data (k_cat/K_m) supports that the immobilized lipase on Ala-CB can give better substrate specificity than the unmodified chitosan beads.     

The Novel Role of Platelet-Activating Factor in Protecting Mice against Lipopolysaccharide-Induced Endotoxic Shock

Background

Platelet-activating factor (PAF) has been long believed to be associated with many pathophysiological processes during septic shock. Here we present novel activities for PAF in protecting mice against LPS-mediated endotoxic shock.

Principal Findings

In vivo PAF treatment immediately after LPS challenge markedly improved the survival rate against mortality from endotoxic shock. Administration of PAF prominently attenuated LPS-induced organ injury, including profound hypotension, excessive polymorphonuclear neutrophil infiltration, and severe multiple organ failure. In addition, PAF treatment protects against LPS-induced lymphocytes apoptosis. These protective effects of PAF was correlated with significantly decreases in the production of the inflammatory mediators such as TNF-α, IL-1β, IL-12, and IFN-γ, while increasing production of the anti-inflammatory cytokine IL-10 in vivo and in vitro.

Conclusions

Taken together, these results suggest that PAF may protect mice against endotoxic shock via a complex mechanism involving modulation of inflammatory and anti-inflammatory mediators.     

Allergen-specific B cell subset responses in cow’s milk allergy of late eczematous reactions in atopic dermatitis

B cells have regulatory functions in immune responses. Antigen-specific responses of B cell subsets by allergen stimulation ex vivo were examined in milk allergy of late eczematous reactions. Eight milk allergy subjects and 13 milk tolerant subjects were selected by DBPCFC. PBMCs were stimulated by casein ex vivo and stained for B cell subsets using monoclonal antibodies. CD19+ B cells unchanged from 8.7 ± 3.8% to 8.0 ± 5.1% (p = 0.504, n = 8) in the milk allergy group and decreased in the milk tolerant group from 8.5 ± 3.2% to 5.0 ± 1.6% (p = 0.001, n = 13). The fraction of apoptotic B cells in B cells significantly decreased 4.4 ± 3.1% to 1.3 ± 0.4% (p = 0.027, n = 4) in the allergy group and insignificantly increased from 2.8 ± 0.6% to 5.4 ± 2.6% (p = 0.059, n = 6) in the milk tolerant group. CD5+ regulatory B1 cell% in B cells decreased in milk allergy subjects from 36.2 ± 5.0% to 31.0 ± 5.7% (p = 0.010) and unchanged in milk tolerant subjects from 41.6 ± 10.2% to 43.8 ± 10.0% (p = 0.413). IL-10 producing CD19+CD5+ regulatory B cell% in CD19+CD5+ regulatory B cells significantly decreased from 24.9 ± 6.5% to 13.8 ± 5.6% (p = 0.002, n = 5) by casein stimulation in milk allergy group and unchanged from 44.8 ± 11.3% to 43.9 ± 10.0% (p = 0.297, n = 5) in the milk tolerant group. B cell subset responses to IL-4 and IL-5 were also similar in both groups. B cell subset changes seemed to have diagnostic value. Exact immunologic roles of regulatory CD5+ B1 cells need further investigation.     

Seasonal variation in soil CO<Subscript>2</Subscript> efflux in evergreen coniferous and broad-leaved deciduous forests in a cool-temperate forest,central Korea

We measured the soil surface CO₂ efflux (R _S) from January 2005 to December 2006 in two neighboring stands in Gwangneung Forest, central Korea: evergreen coniferous forest (Abies holophylla, stand A) and broad-leaved deciduous forest (Quercus-dominated, stand Q). Regarding seasonal variation, R _S rate was low during the winter and early spring months in each stand and peaked in late July [1170 (stand A) and 1130 (stand Q) in 2005, and 1000 (stand A) and 740 (stand Q) mg CO₂ m⁻² h⁻¹ in 2006]. R _S rate was higher in stand A than in stand Q during most of the growing season. The pattern of summer rainfall differed between 2005 and 2006. R _S rate for both stands was suppressed significantly by the droughts in June 2005 and September 2006. After the heavy rainfall of July 2006, R _S rate was lower than in July 2005 in both stands, but this decrement was much greater in stand Q than in stand A. In midsummer (August) 2006, under higher soil temperature (ST) and lower soil water content (SWC) conditions than in August 2005, R _S rate of stand A was lower than that in August 2005, whereas stand Q showed no marked change. The exponential relationship between ST and R _S accounted for approximately 91–97% of the R _S variability in each stand and in each year. In stand A, the application of a second-order polynomial function indicated a significant correlation between SWC and R _S when the soil was warm (ST > 15°C). Our results suggest that the seasonality of R _S is strongly affected by the pattern of summer rainfall even in an Asia monsoon climate regime. In addition, the vegetation type (i.e., evergreen coniferous forest vs. broad-leaved deciduous forest) plays a significant role in response of R _S to various environmental fluctuations such as drought, heavy rainfall, and hot-dry condition.     

Carbon and nitrogen storage in an age-sequence of <Emphasis Type="Italic">Pinus densiflora</Emphasis> stands in Korea

The carbon (C) and nitrogen (N) storage capabilities of Pinus densiflora in six different stand ages (10, 27, 30, 32, 44, and 71 years old) were investigated in Korea. Thirty sample trees were destructively harvested and 12 were excavated. Samples from the above and belowground tree components, coarse woody debris (CWD), forest floor, and mineral soil (0–30 cm) were collected. Tree biomass was highest in the 71-year-old stand (202.8 t ha⁻¹) and lowest in the 10-year-old stand (18.4 t ha⁻¹). C and N storage in the mineral soil was higher in the 71-year-old stand than in the other stands, mainly due to higher soil C and N concentrations. Consequently, the total ecosystem C and N storage (tree+forest floor+CWD+soil) was positively correlated with stand age: increasing from a minimum in the 10 year old stand (18.8 t C ha⁻¹ and 1.3 t N ha⁻¹) to a maximum in the 71-year-old stand (201.4 t C ha⁻¹ and 8.5 t N ha⁻¹). The total ecosystem C storage showed a similar sigmoidal pattern to that of tree C storage as a function of the age-sequence, while N storage in the CWD, forest floor and mineral soil showed no significant temporal trends. Our results provide important insights that will increase our understanding of C and N storage in P. densiflora stands and our ability to predict changes according to stand age in the region.     

Cloning and expression pattern of a hemolin homologue from the diamondback moth, Plutella xylostella

Hemolin has been known to play a key role in insect innate immunity. In an attempt to examine expression pattern of the Hemolin gene in the diamondback moth, Plutellea xylostella, the full-length cDNA of Hemolin was cloned using 5′-RACE PCR technique. The cDNA contained a 5′ untranslated region of 48 nucleotides and a 3′ untranslated region of 198 nucleotides, including a stop codon (TAA) and a poly (A) tail. It consists of 1,401 bp with an open reading frame of 1,245 bp, encoding 414 amino acids. The deduced amino acid sequence of PxHemolin has relatively low identities (35?42%) to various insect Hemolins. However, it has high three-dimensional structural similarity to Hemolin. Interestingly, analysis of spatial expression pattern of PxHemolin shows that it was highly expressed in the Malpighian tubule and the silk gland although it was also detected in fat body and gut. Furthermore, PxHemolin mRNA was highly induced 3 hr after immune-challenging with lipopolysaccharide and was gradually up-regulated after laminarin treatment. These data suggest that PxHemolin may play a role in innate immune responses although it remains to further elucidate the precise biological functions in P. xylostella.