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101.
Michelle Wille 《Molecular ecology》2020,29(1):23-25
The spillover of viruses from wildlife into agricultural animals or humans has profound socioeconomic and public health impact. Vampire bats, found throughout South America, feed directly on humans and other animals and are an important reservoir for zoonotic viruses, including rabies virus. This has resulted in considerable effort in understanding both the ecology of bat‐borne viruses and the composition and associated correlates of the structure of entire virus communities in wildlife, particularly in the context of disease control interventions. In a From the Cover article in this issue of Molecular Ecology, Bergner et al. (2019) set out to reveal virus community dynamics in vampire bats by interrogating factors that affect the structure, diversity and richness of these communities. Due to the linkage of metagenomic sequence data with community ecology, this study represents an important advance in the field of virus ecology. 相似文献
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Devon R. O'Rourke Nicholas A. Bokulich Michelle A. Jusino Matthew D. MacManes Jeffrey T. Foster 《Ecology and evolution》2020,10(18):9721-9739
Metabarcoding studies provide a powerful approach to estimate the diversity and abundance of organisms in mixed communities in nature. While strategies exist for optimizing sample and sequence library preparation, best practices for bioinformatic processing of amplicon sequence data are lacking in animal diet studies. Here we evaluate how decisions made in core bioinformatic processes, including sequence filtering, database design, and classification, can influence animal metabarcoding results. We show that denoising methods have lower error rates compared to traditional clustering methods, although these differences are largely mitigated by removing low‐abundance sequence variants. We also found that available reference datasets from GenBank and BOLD for the animal marker gene cytochrome oxidase I (COI) can be complementary, and we discuss methods to improve existing databases to include versioned releases. Taxonomic classification methods can dramatically affect results. For example, the commonly used Barcode of Life Database (BOLD) Classification API assigned fewer names to samples from order through species levels using both a mock community and bat guano samples compared to all other classifiers (vsearch‐SINTAX and q2‐feature‐classifier's BLAST + LCA, VSEARCH + LCA, and Naive Bayes classifiers). The lack of consensus on bioinformatics best practices limits comparisons among studies and may introduce biases. Our work suggests that biological mock communities offer a useful standard to evaluate the myriad computational decisions impacting animal metabarcoding accuracy. Further, these comparisons highlight the need for continual evaluations as new tools are adopted to ensure that the inferences drawn reflect meaningful biology instead of digital artifacts. 相似文献
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Joe Carver Domingos Ng Michelle Zhou Peggy Ko Dejin Zhan Mandy Yim David Shaw Brad Snedecor Michael W. Laird Steven Lang Amy Shen Zhilan Hu 《Biotechnology progress》2020,36(4):e2967
Historically, therapeutic protein production in Chinese hamster ovary (CHO) cells has been accomplished by random integration (RI) of expression plasmids into the host cell genome. More recently, the development of targeted integration (TI) host cells has allowed for recombination of plasmid DNA into a predetermined genomic locus, eliminating one contributor to clone-to-clone variability. In this study, a TI host capable of simultaneously integrating two plasmids at the same genomic site was used to assess the effect of antibody heavy chain and light chain gene dosage on antibody productivity. Our results showed that increasing antibody gene copy number can increase specific productivity, but with diminishing returns as more antibody genes are added to the same TI locus. Random integration of additional antibody DNA copies in to a targeted integration cell line showed a further increase in specific productivity, suggesting that targeting additional genomic sites for gene integration may be beneficial. Additionally, the position of antibody genes in the two plasmids was observed to have a strong effect on antibody expression level. These findings shed light on vector design to maximize production of conventional antibodies or tune expression for proper assembly of complex or bispecific antibodies in a TI system. 相似文献
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Phukuntsi Metlholo A. Du Plessis Morne Dalton Desiré L. Jansen Raymond Sauther Michelle L. Cuozzo Frank P. Kotze Antoinette 《Primates; journal of primatology》2021,62(4):667-675
Primates - The habitats of Galago moholi are suspected to be largely fragmented, while the species is thought to be expanding further into the southernmost fringe of its range, as well as into... 相似文献
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Background and AimsLeaf functional traits are strongly tied to growth strategies and ecological processes across species, but few efforts have linked intraspecific trait variation to performance across ontogenetic and environmental gradients. Plants are believed to shift towards more resource-conservative traits in stressful environments and as they age. However, uncertainty as to how intraspecific trait variation aligns with plant age and performance in the context of environmental variation may limit our ability to use traits to infer ecological processes at larger scales.MethodsWe measured leaf physiological and morphological traits, canopy volume and flowering effort for Artemisia californica (California sagebrush), a dominant shrub species in the coastal sage scrub community, under conditions of 50, 100 and 150 % ambient precipitation for 3 years.Key ResultsPlant age was a stronger driver of variation in traits and performance than water availability. Older plants demonstrated trait values consistent with a more conservative resource-use strategy, and trait values were less sensitive to drought. Several trait correlations were consistent across years and treatments; for example, plants with high photosynthetic rates tended to have high stomatal conductance, leaf nitrogen concentration and light-use efficiency. However, the trade-off between leaf construction and leaf nitrogen evident in older plants was absent for first-year plants. While few traits correlated with plant growth and flowering effort, we observed a positive correlation between leaf mass per area and performance in some groups of older plants.ConclusionsOverall, our results suggest that trait sensitivity to the environment is most visible during earlier stages of development, after which intraspecific trait variation and relationships may stabilize. While plant age plays a major role in intraspecific trait variation and sensitivity (and thus trait-based inferences), the direct influence of environment on growth and fecundity is just as critical to predicting plant performance in a changing environment. 相似文献
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Albert L. Harting Michelle M. Barbieri Jason D. Baker Tracy A. Mercer Thea C. Johanos Stacie J. Robinson Charles L. Littnan Katie M. Colegrove Dave S. Rotstein 《Marine Mammal Science》2021,37(1):235-250
Identifying, assessing, and ranking the impact of individual threats is fundamental to the conservation and recovery of rare and endangered species. In this analysis, we quantify not only the frequency of specific causes-of-death (CODs) among Main Hawaiian Island (MHI) monk seals, but also assess the impact of individual CODs on the intrinsic growth rate, λ, of the MHI population. We used gross necropsy results, histopathology, and other evidence to assign probabilities of 11 COD types to each mortality and then used Monte Carlo sampling to evaluate the influence of each COD on λ. By right censoring realizations involving specific CODs, we were able to estimate λ (and its associated uncertainty) when CODs were selectively removed from influencing survival. Applying the analysis to all known and inferred deaths believed to have occurred 2004–2019, the CODs with the largest influence on λ were anthropogenic trauma, anthropogenic drowning, and protozoal disease. In aggregate, anthropogenic CODs had a larger effect on the growth rate than either natural or disease CODs. Possible bias associated with differential carcass detection, recovery, and COD classification are discussed. 相似文献