Data on vegetation across forest edges from the FERN (Forest Edge Research Network).

Many studies have focused on vegetation across forest edges to study impacts of edges created by human activities on forest structure and composition, or patterns of vegetation at inherent natural edges. Our objective was to create a database of plant-related variables across different types of edges from various studies (mainly from across Canada, but also in Brazil and Belize) to facilitate edge research. We compiled data on vegetation along more than 300 transects perpendicular to forest edges adjacent to clear-cuts, burned areas, bogs, lakes, barrens, insect disturbances, and riparian areas from 24 studies conducted over the past three decades. Data were compiled for more than 400 plant species and forest structure variables (e.g., trees, logs, canopy cover). All data were collected with a similar sampling design of quadrats along transects perpendicular to forest edges, but with varying numbers of transects and quadrats, and distances from the edge. The purpose for most of the studies was either to determine the distance of edge influence (edge width) or to explore the pattern of vegetation along the edge to interior gradient. We provide data tables for the cover of plant species and functional groups, the species and size of live and dead trees, the density of saplings, maximum height of functional groups and shrub species, and the cover of functional groups at different heights (vertical distribution of vegetation). The Forest Edge Research Network (FERN) database provides extensive data on many variables that can be used for further study including meta-analyses and can assist in answering questions important to conservation efforts (e.g., how is distance of edge influence from created edges affected by different factors?). We plan to expand this database with subsequent studies from the authors and we invite others to contribute to make this a more global database. The data are released under a CC0 license. When using these data, we ask that you cite this data paper and any relevant publications listed in our metadata file. We also encourage you to contact the first author if you are planning to use or contribute to this database.

Carboxypeptidase D is the only enzyme responsible for antibody C-terminal lysine cleavage in Chinese hamster ovary (CHO) cells.

Heterogeneity of C-terminal lysine levels often observed in therapeutic monoclonal antibodies is believed to result from the proteolysis by endogenous carboxypeptidase(s) during cell culture production. Identifying the responsible carboxypeptidase(s) for C-terminal lysine cleavage in CHO cells would provide valuable insights for antibody production cell culture processes development and optimization. In this study, five carboxypeptidases, CpD, CpM, CpN, CpB, and CpE, were studied for message RNA (mRNA) expression by qRT-PCR analysis in two most commonly used blank hosts (DUXB-11 derived DHFR-deficient DP12 host and DHFR-positive CHOK1 host), used for therapeutic antibody production, as well an antibody-expressing cell line derived from each host. Our results showed that CpD had the highest mRNA expression. When CpD mRNA levels were reduced by RNAi (RNA interference) technology, C-terminal lysine levels increased, whereas there was no obvious change in C-terminal lysine levels when a different carboxypeptidase mRNA level was knocked down suggesting that carboxypeptidase D is the main contributor for C-terminal lysine processing. Most importantly, when CpD expression was knocked out by CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology, C-terminal lysine cleavage was completely abolished in CpD knockout cells based on mass spectrometry analysis, demonstrating that CpD is the only endogenous carboxypeptidase that cleaves antibody heavy chain C-terminal lysine in CHO cells. Hence, our work showed for the first time that the cleavage of antibody heavy chain C-terminal lysine is solely mediated by the carboxypeptidase D in CHO cells and our finding provides one solution to eliminating C-terminal lysine heterogeneity for therapeutic antibody production by knocking out CpD gene expression. Biotechnol. Bioeng. 2016;113: 2100-2106. © 2016 Wiley Periodicals, Inc.

High resolution separation of recombinant monoclonal antibodies by size-exclusion ultra-high performance liquid chromatography (SE-UHPLC).

Size-exclusion chromatography (SEC) is an important mode of separation used in monoclonal antibody (mAb) characterization and quality control. SEC separates mAbs into three major species: high molecular weight species, main peak (predominantly monomer), and low molecular weight species. However, mAb SEC separations have low resolution between the different sized species, and the analysis is slow with low sample throughput. The introduction of size-exclusion ultra-high performance liquid chromatography (SE-UHPLC) columns offers a new opportunity to improve both the resolution and throughput of SEC analysis. This study demonstrates that SE-UHPLC columns deliver better resolution of size variants in a shorter period of time than conventional SEC columns. For example, an SE-UHPLC column 300-mm in length produced separation of mAb Fab/c fragments in less than 10min, in comparison to a conventional SEC column output, where these fragments co-elute with the main peak. Furthermore, we observed that high back pressure does not generate HMWS under optimized mobile phase conditions for mAbs. The platform SE-UHPLC method has been demonstrated to be suitable for the analysis of multiple mAbs, with greatly improved sample throughput and peak resolution of mAb size variants.

The prevalence and pathogenicity of Propionibacterium acnes keratitis.

PURPOSE: To study the prevalence, pathogenicity, and virulence of Propionibacterium acnes keratitis. METHODS: All cases of infectious keratitis submitted to the microbiologic laboratory of the New York Eye and Ear Infirmary between January 1, 2003, and April 6, 2006, were reviewed. Those cases in which P. acnes was recovered from culture were collected, and the medical records studied in depth. RESULTS: Of 1555 cultures submitted to the microbiology laboratory, 1329 (85.5%) were positive for growth. One hundred twenty four (9.3%) of the 1329 cases yielded P. acnes in at least 1 culture medium. Seventy eight (62.9%) of 124 cases had not been pretreated with antibiotics before culture, and 66.7% of the nonpretreated ulcers were monomicrobial (P. acnes only). Fifty one (65.4%) of 78 cases of the nonpretreated corneal ulcers presented with a cellular reaction in anterior chamber, 12 (15.4%) with a hypopyon (6 were monomicrobial), 21 (26.9%) had stromal thinning (12 of which were monomicrobial), and 2 (2.6%) progressed to perforation (both polymicrobial). Corneal ulcers associated with P. acnes tended to be small (66.7%) and were widely distributed: central (n = 17, 21.8%), paracentral (n = 44, 56.4%), and peripheral (n = 17, 21.8%). The most common risk factors were contact lens wear and previous history of ocular surgery. Three of the 78 nonpretreated patients were unresponsive to medical treatment and required surgery for keratitis. CONCLUSION: This study provides evidence that P. acnes is a frequent cause of bacterial keratitis and may cause significant morbidity.

Efficacy and safety of voriconazole as an additive in Optisol GS: a preservation medium for corneal donor tissue.

PURPOSE: To assess the endothelial toxicity and the microbiological efficacy of voriconazole (100 microg/mL) as an antimicrobial additive to Optisol GS. METHODS: A total of 533 donor rims were studied. One half of each donor rim was placed in standard Optisol GS and the other half rim in Optisol GS fortified with voriconazole (100 microg/mL). All rims were refrigerated for 24 hours at 3 degrees C and placed in thioglycolate broth and incubated at 37 degrees C for 7 days. A pair of donor buttons not used in transplantation was stored for 2 days in each solution and examined for endothelial changes with electron microscopy (EM). A second pair of cornea buttons was examined for toxicity by endothelial staining with 0.3% trypan blue and 0.2% alizarin red. RESULTS: Seven of 533 corneal rim cultures were positive for fungal organisms in the Optisol GS group. No rims were positive for fungal growth in the voriconazole-fortified Optisol GS medium. The difference was statistically significant (P = 0.015; Fisher exact test). There was no difference in the cellular morphology of the button stored in voriconazole fortified Optisol GS compared with Optisol GS using EM. In the bioassay, the percentage of nonviable cells in the voriconazole-fortified medium compared with the control medium was nonsignificant (P < 0.05, Student t test). CONCLUSIONS: Voriconazole seems to be safe as a fortifying agent for cornea storage medium. It significantly reduces the rate of positive fungal rim cultures and shows no signs of endothelial cytotoxicity as viewed by EM and by a bioassay of trypan blue and alizarin red.