Drawing Shadows to Stone

Drawing Shadows to Stone: Photographing North Pacific Peoples (1897-1902). American Museum of Natural History, New York, New York, November 14, 1997- March 1, 1998.
Drawing Shadows to Stone: The Photography of the Jesup North Pacific Expedition, 1897-1902. Laurel Kendall. Barbara Mathé. and Thomas Ross Miller. with Stanley A. Freed. Ruth S. Freed. and Laila Williamson. New York: American Museum of Natural History, 1997, and Seattle: University of Washington Press, 1997. 112 pp., 97 illust.     

Assessment of Blood Collection from the Lateral Saphenous Vein for Microfilaria Counts in Mongolian Gerbils (Meriones unguiculatus) Infected with Brugia pahangi

The NIH guidelines for survival bleeding of mice and rats note that using the retroorbital plexus has a greater potential for complications than do other methods of blood collection and that this procedure should be performed on anesthetized animals. Lateral saphenous vein puncture has a low potential for complications and can be performed without anesthesia. Mongolian gerbils (Meriones unguiculatus) are the preferred rodent model for filarial parasite research. To monitor microfilaria counts in the blood, blood sampling from the orbital plexus has been the standard. Our goal was to refine the blood collection technique. To determine whether blood collection from the lateral saphenous vein was a feasible alternative to retroorbital sampling, we compared microfilaria counts in blood samples collected by both methods from 21 gerbils infected with the filarial parasitic worm Brugia pahangi. Lateral saphenous vein counts were equivalent to retroorbital counts at relatively high counts (greater than 50 microfilariae per 20 µL) but were significantly lower than retroorbital counts when microfilarial concentrations were lower. Our results indicate that although retroorbital collection may be preferable when low concentrations of microfilariae need to be enumerated, the lateral saphenous vein is a suitable alternative site for blood sampling to determine microfilaremia and is a feasible refinement that can benefit the wellbeing of gerbils.Abbreviations: FR3, Filariasis Research Reagent Resource CenterLymphatic filariasis a major threat to human health worldwide. More than one billion people in more than 90 countries around the globe are at risk from lymphatic filariasis, and between 120 and 150 million people are infected.^9,11,25 Infection with the filarioid parasitic worms Brugia malayi and Wuchereria bancrofti can result in severe sequelae, including elephantiasis and hydrocoele formation.^3,11,15,25 In addition to the clinical manifestations of filariasis are the potential associated psychologic, social, and cultural effects in persons exhibiting visible signs of infection.^9,23,34The life cycle of filarioid nematodes requires an arthropod intermediate host and a definitive vertebrate host. Within the definitive host, dioecious adult filarial nematodes reproduce sexually. Inseminated adult female worms then release live, sheathed microfilariae into the lymph that circulate in the peripheral blood.²¹ In the case of B. malayi and W. bancrofti, the intermediate host is the mosquito.²¹ When an uninfected mosquito ingests a blood meal from an infected human, ingested microfilariae unsheathe to penetrate the midgut of the mosquito to reach the thoracic muscles and molt twice, to become the infectious third-stage larvae. The third-stage larvae then migrate to the mosquito''s proboscis and can infect another human when the mosquito takes a blood meal.^10,11 The third-stage larvae enter the new host''s lymphatic system which is their final location, where they undergo 2 molts into adults.Because of the complexity of filarioid life cycles, research involving these parasites can be logistically challenging. Although mice can be infected with W. bancrofti, they do not maintain the infection.³⁵ Furthermore, there is no suitable nonhuman host that can maintain a patent infection, with the exception of the silvered leaf monkey (Trachypithecus cristatus).⁹ Because the closely related parasites B. malayi and B. pahangi have more extensive host ranges than does W. bancrofti, they are easier to maintain in a research setting. Domestic cats (Felis catus) can be experimentally infected with B. malayi and develop a patent infection, and both domestic cats and dogs (Canis familiaris) can be experimentally infected with B. pahangi^13,29,37 and are suitable for obtaining microfilaremic blood for experimental feeding of mosquitoes. The Mongolian gerbil can be infected with B. pahangi. Because replacing a phylogenetically higher species with a lower species is preferable³⁶ and because performing experiments involving dogs and cats can be logistically difficult and cost-prohibitive, many researchers prefer a rodent model, specifically gerbils.The Filariasis Research Reagent Resource Center (FR3) is an NIH center whose mandate is to support filariasis research worldwide. The FR3 provides parasitic and molecular resources, as well as training in animal procedures, to researchers from many nations. The FR3 maintains both B. malayi and B. pahangi, and researchers occasionally require gerbils with patent infections. Because the required level of microfilaria counts varies among investigators, an accurate microfilaria count must be obtained prior to the shipment of gerbils. For example, some experiments require that live mosquitoes feed directly on infected gerbils, and when the microfilaria level is too low, the mosquitoes do not become infected. Conversely when the level is too high, the migration of microfilariae and the later larval stages can kill the mosquitoes. Historically, the FR3 has used retroorbital sampling under general anesthesia to obtain the blood for microfilaria counts.²⁸ Although this method has been fairly successful, the FR3 has encountered occasional complications secondary to the procedure, including exophthalmia and, rarely, death under anesthesia. The NIH guidelines for survival bleeding of mice and rats notes that compared with other blood collection methods, retroorbital sampling has a greater potential for complications. The guidelines recommend a 10- to 14-d period between retroorbital blood collections and state that the procedure is “…best conducted under general anesthesia.”³¹ By comparison, collecting blood from the lateral saphenous vein is considered to have a low potential for complications or tissue damage, can be performed without general anesthesia,^12,18,31 and can be performed repeatedly, even daily.³¹In the current study, we proposed to refine the blood collection method being used by FR3 by developing sampling from the lateral saphenous vein as the new standard blood-collection method for monitoring microfilaremia. Our goal was to assess blood collection from the lateral saphenous vein as a feasible refinement technique to potentially replace retroorbital sampling by determining whether the microfilaria counts in blood collected from the lateral saphenous vein without anesthesia were sufficiently similar to those from retroorbital blood sampling with anesthesia to provide adequate information about the microfilaremia level.     

High-Specificity Targeted Functional Profiling in Microbial Communities with ShortBRED

Profiling microbial community function from metagenomic sequencing data remains a computationally challenging problem. Mapping millions of DNA reads from such samples to reference protein databases requires long run-times, and short read lengths can result in spurious hits to unrelated proteins (loss of specificity). We developed ShortBRED (Short, Better Representative Extract Dataset) to address these challenges, facilitating fast, accurate functional profiling of metagenomic samples. ShortBRED consists of two components: (i) a method that reduces reference proteins of interest to short, highly representative amino acid sequences (“markers”) and (ii) a search step that maps reads to these markers to quantify the relative abundance of their associated proteins. After evaluating ShortBRED on synthetic data, we applied it to profile antibiotic resistance protein families in the gut microbiomes of individuals from the United States, China, Malawi, and Venezuela. Our results support antibiotic resistance as a core function in the human gut microbiome, with tetracycline-resistant ribosomal protection proteins and Class A beta-lactamases being the most widely distributed resistance mechanisms worldwide. ShortBRED markers are applicable to other homology-based search tasks, which we demonstrate here by identifying phylogenetic signatures of antibiotic resistance across more than 3,000 microbial isolate genomes. ShortBRED can be applied to profile a wide variety of protein families of interest; the software, source code, and documentation are available for download at http://huttenhower.sph.harvard.edu/shortbred     

Reproductive Isolation of Hybrid Populations Driven by Genetic Incompatibilities

Despite its role in homogenizing populations, hybridization has also been proposed as a means to generate new species. The conceptual basis for this idea is that hybridization can result in novel phenotypes through recombination between the parental genomes, allowing a hybrid population to occupy ecological niches unavailable to parental species. Here we present an alternative model of the evolution of reproductive isolation in hybrid populations that occurs as a simple consequence of selection against genetic incompatibilities. Unlike previous models of hybrid speciation, our model does not incorporate inbreeding, or assume that hybrids have an ecological or reproductive fitness advantage relative to parental populations. We show that reproductive isolation between hybrids and parental species can evolve frequently and rapidly under this model, even in the presence of substantial ongoing immigration from parental species and strong selection against hybrids. An interesting prediction of our model is that replicate hybrid populations formed from the same pair of parental species can evolve reproductive isolation from each other. This non-adaptive process can therefore generate patterns of species diversity and relatedness that resemble an adaptive radiation. Intriguingly, several known hybrid species exhibit patterns of reproductive isolation consistent with the predictions of our model.     

A Regression-Based Differential Expression Detection Algorithm for Microarray Studies with Ultra-Low Sample Size

Global gene expression analysis using microarrays and, more recently, RNA-seq, has allowed investigators to understand biological processes at a system level. However, the identification of differentially expressed genes in experiments with small sample size, high dimensionality, and high variance remains challenging, limiting the usability of these tens of thousands of publicly available, and possibly many more unpublished, gene expression datasets. We propose a novel variable selection algorithm for ultra-low-n microarray studies using generalized linear model-based variable selection with a penalized binomial regression algorithm called penalized Euclidean distance (PED). Our method uses PED to build a classifier on the experimental data to rank genes by importance. In place of cross-validation, which is required by most similar methods but not reliable for experiments with small sample size, we use a simulation-based approach to additively build a list of differentially expressed genes from the rank-ordered list. Our simulation-based approach maintains a low false discovery rate while maximizing the number of differentially expressed genes identified, a feature critical for downstream pathway analysis. We apply our method to microarray data from an experiment perturbing the Notch signaling pathway in Xenopus laevis embryos. This dataset was chosen because it showed very little differential expression according to limma, a powerful and widely-used method for microarray analysis. Our method was able to detect a significant number of differentially expressed genes in this dataset and suggest future directions for investigation. Our method is easily adaptable for analysis of data from RNA-seq and other global expression experiments with low sample size and high dimensionality.     

HOW COMMON IS HOMOPLOID HYBRID SPECIATION?

Hybridization has long been considered a process that prevents divergence between species. In contrast to this historical view, an increasing number of empirical studies claim to show evidence for hybrid speciation without a ploidy change. However, the importance of hybridization as a route to speciation is poorly understood, and many claims have been made with insufficient evidence that hybridization played a role in the speciation process. We propose criteria to determine the strength of evidence for homoploid hybrid speciation. Based on an evaluation of the literature using this framework, we conclude that although hybridization appears to be common, evidence for an important role of hybridization in homoploid speciation is more circumscribed.     

Marine biological community baselines in unimpacted tropical ecosystems: spatial and temporal analysis of reefs at Howland and Baker Islands

Howland and Baker Islands are two small, isolated reef and sand islets located near the equator in the central Pacific Ocean that are situated approximately 60 km apart. In 2004 and 2006, species-level monitoring at multiple sites, coupled with towed-diver surveys in 2002, 2004, and 2006 on both of these federally protected islands, revealed diverse fish, coral, macroinvertebrate, and algal assemblages. This study examines inter- and intra-island spatial and temporal differences in community composition among sites and presents baseline biological community parameters for two of the least impacted reef systems in the world. Despite similarities in species composition, permutational multivariate analysis of variance (PERMANOVA) and multidimensional scaling ordinations (nMDS) suggest biological communities at the two islands are distinct with Baker Island containing a greater percent cover of branched Acroporid corals and turf algae and Howland Island containing a greater percent cover of crustose coralline red algae and small, compact genera of coral. Both islands also contained considerable cover of non-invasive macroalgae. PERMANOVA further revealed benthic and fish species composition to differ between forereef and reef shelf sites from different sides of each island. When islands were considered as a whole, temporal changes were not noted between 2004 and 2006; however, temporal changes at select sites did occur, with coral cover decreasing significantly along the west side of Baker Island from 2004 to 2006.