Application of phage display to high throughput antibody generation and characterization

We have created a high quality phage display library containing over 10¹⁰ human antibodies and describe its use in the generation of antibodies on an unprecedented scale. We have selected, screened and sequenced over 38,000 recombinant antibodies to 292 antigens, yielding over 7,200 unique clones. 4,400 antibodies were characterized by specificity testing and detailed sequence analysis and the data/clones are available online. Sensitive detection was demonstrated in a bead based flow cytometry assay. Furthermore, positive staining by immunohistochemistry on tissue microarrays was found for 37% (143/381) of antibodies. Thus, we have demonstrated the potential of and illuminated the issues associated with genome-wide monoclonal antibody generation.     

New Pedal Remains of Megaladapis and Their Functional Significance. Am J Phys Anthropol 100:115–139

Erratum: Wunderlich RE, Simons EL, Jungers WL. 1996. New Pedal Remains of Megaladapis and Their Functional Significance. Am J Phys Anthropol 100:115–139.     

Quality indexes to assess the reliability of genotypes in studies using noninvasive sampling and multiple‐tube approach

In noninvasive studies, the intersample variance in DNA quality and quantity is large, and produces multilocus genotypes of highly variable quality. Here we propose a standardized method for testing the reliability of the genotyping procedure when using the multiple‐tube approach. The quality indexes generated will allow reliable comparisons among samples, loci, studies, and field and/or laboratory protocols. These indexes represent a powerful tool for the quality management of noninvasive studies.     

Why western spruce budworms travel so far for the winter

1. Conifer‐feeding budworms (Choristoneura) hibernate in sheltered locations on their host trees from late summer of 1 year to spring of the next. During this period, they do not feed but rely on sustenance provided in the egg. Overwinter survival is dependent on the rate of consumption of these limited reserves. 2. A process model was developed that quantifies the relationship between the rate of consumption and survival at variable temperatures and exposure times for western spruce budworm. The model supported physiological evidence that warm weather conditions early in the diapause period have a dominant influence on overwinter survival. Output compared favourably with field observations of poorer budworm survival at lower elevations where late‐summer and autumn temperatures were warmer compared to those overwintering at cooler, higher elevations. 3. Field experiments demonstrated these weather‐dependent rates of survival were modulated significantly by the degree of shelter experienced by hibernating budworms. 4. Dissection of whole trees harbouring overwintering western spruce budworms showed a significant portion of the population had travelled a considerable distance from the periphery of the tree canopy where eggs were laid to overwinter successfully on the tree bole where sheltered niches are common. 5. Thus, budworms will travel relatively long distances and risk increased mortality during this dispersal to find adequate shelter to overwinter.     

Metagenomic analysis of the viromes of three North American bat species: viral diversity among different bat species that share a common habitat

Effective prediction of future viral zoonoses requires an in-depth understanding of the heterologous viral population in key animal species that will likely serve as reservoir hosts or intermediates during the next viral epidemic. The importance of bats as natural hosts for several important viral zoonoses, including Ebola, Marburg, Nipah, Hendra, and rabies viruses and severe acute respiratory syndrome-coronavirus (SARS-CoV), has been established; however, the large viral population diversity (virome) of bats has been partially determined for only a few of the ～1,200 bat species. To assess the virome of North American bats, we collected fecal, oral, urine, and tissue samples from individual bats captured at an abandoned railroad tunnel in Maryland that is cohabitated by 7 to 10 different bat species. Here, we present preliminary characterization of the virome of three common North American bat species, including big brown bats (Eptesicus fuscus), tricolored bats (Perimyotis subflavus), and little brown myotis (Myotis lucifugus). In samples derived from these bats, we identified viral sequences that were similar to at least three novel group 1 CoVs, large numbers of insect and plant virus sequences, and nearly full-length genomic sequences of two novel bacteriophages. These observations suggest that bats encounter and disseminate a large assortment of viruses capable of infecting many different animals, insects, and plants in nature.     

抗黄体酮联合Aromatase抑制剂或iNOS终止恒河猴妊娠

[目的]评价抗黄体酮(mifepristone)联合Aromatase抑制剂(letrozole或aminoglutethimide)或iNOS抑制剂(aminoguandine)是否能有效终止恒河猴早期妊娠。[方法]将30只猴子随机分为5组(治疗组每组6只,对照组6只),并在妊娠30,31和32天进行如下处理:对照组,每只动物1ml安慰剂;A组,Mifepristone(1mg/kg,sc.);B组,Mifepristone(sc.)+Letrozole(2.5mg/只sc.);C组,Mifepristone(1mg/kg,sc.)+aminoglute-chimide(50mg/kgsc.,bid);D组,Mifepristone(1mg/kg,sc.)+aminoguanidine(150mg/kg,sc.,bid)。所有妊娠猴在妊娠29天通过超声波确认。[结果]在B、C、D组,所有的动物的妊娠都在妊娠早期被终止(6/6)。A组和对照组的妊娠终止率分别为3/6和2/6。同时,联合用药能够有效排空子宫腔和减少出血。[结论]该处理能有效地终止恒河猴早期妊娠。联合用药比用于女人的妊娠治疗更有效,并减少了流血时间,或许可以代替目前的终止妊娠的医疗方法。     

Sequence and functional analyses of Haemophilus spp. genomic islands

Background

A major part of horizontal gene transfer that contributes to the diversification and adaptation of bacteria is facilitated by genomic islands. The evolution of these islands is poorly understood. Some progress was made with the identification of a set of phylogenetically related genomic islands among the Proteobacteria, recognized from the investigation of the evolutionary origins of a Haemophilus influenzae antibiotic resistance island, namely ICEHin1056. More clarity comes from this comparative analysis of seven complete sequences of the ICEHin1056 genomic island subfamily.

Results

These genomic islands have core and accessory genes in approximately equal proportion, with none demonstrating recent acquisition from other islands. The number of variable sites within core genes is similar to that found in the host bacteria. Furthermore, the GC content of the core genes is similar to that of the host bacteria (38% to 40%). Most of the core gene content is formed by the syntenic type IV secretion system dependent conjugative module and replicative module. GC content and lack of variable sites indicate that the antibiotic resistance genes were acquired relatively recently. An analysis of conjugation efficiency and antibiotic susceptibility demonstrates that phenotypic expression of genomic island-borne genes differs between different hosts.

Conclusion

Genomic islands of the ICEHin1056 subfamily have a longstanding relationship with H. influenzae and H. parainfluenzae and are co-evolving as semi-autonomous genomes within the 'supragenomes' of their host species. They have promoted bacterial diversity and adaptation through becoming efficient vectors of antibiotic resistance by the recent acquisition of antibiotic resistance transposons.     

Sulphur stable isotopes can distinguish trophic dependence on sediments and plankton in boreal lakes

1. Stable isotopes of carbon are useful for differentiating between freshwater food chains based on planktonic algae or benthic algae, but are reported to be of limited use for identifying food chains based on sedimentary detritus. Because data from marine systems suggest that stable isotopes of sulphur (δ³⁴S values) have potential in this regard, we tested their utility in freshwater lakes.
2. We found that sulphate in the water column of four boreal lakes was enriched in ³⁴S compared to the sulphur in bulk sediments from these lakes. Furthermore, within a given lake, insects known to feed on sediment (directly or via predation) had δ³⁴S values similar to those of sediment, whereas planktonic and benthic invertebrates known to feed on suspended particles had δ³⁴S values similar to those of sulphate in the water column.
3. Using the stable S isotope values of invertebrates that obtain their S from either the sediment or the water column as end members in a two-source mixing model, we show that two fish species obtain their food from both planktonic and sedimentary sources. Furthermore, model results suggest that, as expected, the more benthic-feeding fish species obtains more of its S from the sediment compartment than does the species that feeds in the water-column.
4. Our results suggest that measurements of stable sulphur isotopes provide a means of distinguishing between members of food chains that are based in the water column from those based on sedimentary detritus. As such, they would be a useful complement to stable C isotopes that are used to distinguish between food chains based on planktonic or benthic algae.