Long-read powered viral metagenomics in the oligotrophic Sargasso Sea

Dominant microorganisms of the Sargasso Sea are key drivers of the global carbon cycle. However, associated viruses that shape microbial community structure and function are not well characterised. Here, we combined short and long read sequencing to survey Sargasso Sea phage communities in virus- and cellular fractions at viral maximum (80 m) and mesopelagic (200 m) depths. We identified 2,301 Sargasso Sea phage populations from 186 genera. Over half of the phage populations identified here lacked representation in global ocean viral metagenomes, whilst 177 of the 186 identified genera lacked representation in genomic databases of phage isolates. Viral fraction and cell-associated viral communities were decoupled, indicating viral turnover occurred across periods longer than the sampling period of three days. Inclusion of long-read data was critical for capturing the breadth of viral diversity. Phage isolates that infect the dominant bacterial taxa Prochlorococcus and Pelagibacter, usually regarded as cosmopolitan and abundant, were poorly represented.

Ocean-wide comparisons of mesopelagic planktonic community structures

For decades, marine plankton have been investigated for their capacity to modulate biogeochemical cycles and provide fishery resources. Between the sunlit (epipelagic) layer and the deep dark waters, lies a vast and heterogeneous part of the ocean: the mesopelagic zone. How plankton composition is shaped by environment has been well-explored in the epipelagic but much less in the mesopelagic ocean. Here, we conducted comparative analyses of trans-kingdom community assemblages thriving in the mesopelagic oxygen minimum zone (OMZ), mesopelagic oxic, and their epipelagic counterparts. We identified nine distinct types of intermediate water masses that correlate with variation in mesopelagic community composition. Furthermore, oxygen, NO3- and particle flux together appeared as the main drivers governing these communities. Novel taxonomic signatures emerged from OMZ while a global co-occurrence network analysis showed that about 70% of the abundance of mesopelagic plankton groups is organized into three community modules. One module gathers prokaryotes, pico-eukaryotes and Nucleo-Cytoplasmic Large DNA Viruses (NCLDV) from oxic regions, and the two other modules are enriched in OMZ prokaryotes and OMZ pico-eukaryotes, respectively. We hypothesize that OMZ conditions led to a diversification of ecological niches, and thus communities, due to selective pressure from limited resources. Our study further clarifies the interplay between environmental factors in the mesopelagic oxic and OMZ, and the compositional features of communities.

Novel integrative elements and genomic plasticity in ocean ecosystems

Horizontal gene transfer accelerates microbial evolution. The marine picocyanobacterium Prochlorococcus exhibits high genomic plasticity, yet the underlying mechanisms are elusive. Here, we report a novel family of DNA transposons-"tycheposons"-some of which are viral satellites while others carry cargo, such as nutrient-acquisition genes, which shape the genetic variability in this globally abundant genus. Tycheposons share distinctive mobile-lifecycle-linked hallmark genes, including a deep-branching site-specific tyrosine recombinase. Their excision and integration at tRNA genes appear to drive the remodeling of genomic islands-key reservoirs for flexible genes in bacteria. In a selection experiment, tycheposons harboring a nitrate assimilation cassette were dynamically gained and lost, thereby promoting chromosomal rearrangements and host adaptation. Vesicles and phage particles harvested from seawater are enriched in tycheposons, providing a means for their dispersal in the wild. Similar elements are found in microbes co-occurring with Prochlorococcus, suggesting a common mechanism for microbial diversification in the vast oligotrophic oceans.

Diversity and ecological footprint of Global Ocean RNA viruses

DNA viruses are increasingly recognized as influencing marine microbes and microbe-mediated biogeochemical cycling. However, little is known about global marine RNA virus diversity, ecology, and ecosystem roles. In this study, we uncover patterns and predictors of marine RNA virus community- and "species"-level diversity and contextualize their ecological impacts from pole to pole. Our analyses revealed four ecological zones, latitudinal and depth diversity patterns, and environmental correlates for RNA viruses. Our findings only partially parallel those of cosampled plankton and show unexpectedly high polar ecological interactions. The influence of RNA viruses on ecosystems appears to be large, as predicted hosts are ecologically important. Moreover, the occurrence of auxiliary metabolic genes indicates that RNA viruses cause reprogramming of diverse host metabolisms, including photosynthesis and carbon cycling, and that RNA virus abundances predict ocean carbon export.

Cryptic and abundant marine viruses at the evolutionary origins of Earth's RNA virome

Whereas DNA viruses are known to be abundant, diverse, and commonly key ecosystem players, RNA viruses are insufficiently studied outside disease settings. In this study, we analyzed ≈28 terabases of Global Ocean RNA sequences to expand Earth's RNA virus catalogs and their taxonomy, investigate their evolutionary origins, and assess their marine biogeography from pole to pole. Using new approaches to optimize discovery and classification, we identified RNA viruses that necessitate substantive revisions of taxonomy (doubling phyla and adding >50% new classes) and evolutionary understanding. "Species"-rank abundance determination revealed that viruses of the new phyla "Taraviricota," a missing link in early RNA virus evolution, and "Arctiviricota" are widespread and dominant in the oceans. These efforts provide foundational knowledge critical to integrating RNA viruses into ecological and epidemiological models.

iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology

Microbes drive myriad ecosystem processes, but under strong influence from viruses. Because studying viruses in complex systems requires different tools than those for microbes, they remain underexplored. To combat this, we previously aggregated double-stranded DNA (dsDNA) virus analysis capabilities and resources into 'iVirus' on the CyVerse collaborative cyberinfrastructure. Here we substantially expand iVirus's functionality and accessibility, to iVirus 2.0, as follows. First, core iVirus apps were integrated into the Department of Energy's Systems Biology KnowledgeBase (KBase) to provide an additional analytical platform. Second, at CyVerse, 20 software tools (apps) were upgraded or added as new tools and capabilities. Third, nearly 20-fold more sequence reads were aggregated to capture new data and environments. Finally, documentation, as "live" protocols, was updated to maximize user interaction with and contribution to infrastructure development. Together, iVirus 2.0 serves as a uniquely central and accessible analytical platform for studying how viruses, particularly dsDNA viruses, impact diverse microbial ecosystems.

Environmental vulnerability of the global ocean epipelagic plankton community interactome

Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles and help regulate climate. Although global surveys are starting to reveal ecological drivers underlying planktonic community structure and predicted climate change responses, it is unclear how community-scale species interactions will be affected by climate change. Here, we leveraged Tara Oceans sampling to infer a global ocean cross-domain plankton co-occurrence network-the community interactome-and used niche modeling to assess its vulnerabilities to environmental change. Globally, this revealed a plankton interactome self-organized latitudinally into marine biomes (Trades, Westerlies, Polar) and more connected poleward. Integrated niche modeling revealed biome-specific community interactome responses to environmental change and forecasted the most affected lineages for each community. These results provide baseline approaches to assess community structure and organismal interactions under climate scenarios while identifying plausible plankton bioindicators for ocean monitoring of climate change.

efam: an expanded, metaproteome-supported HMM profile database of viral protein families

Motivation

Viruses infect, reprogram and kill microbes, leading to profound ecosystem consequences, from elemental cycling in oceans and soils to microbiome-modulated diseases in plants and animals. Although metagenomic datasets are increasingly available, identifying viruses in them is challenging due to poor representation and annotation of viral sequences in databases.

Results

Here, we establish efam, an expanded collection of Hidden Markov Model (HMM) profiles that represent viral protein families conservatively identified from the Global Ocean Virome 2.0 dataset. This resulted in 240 311 HMM profiles, each with at least 2 protein sequences, making efam >7-fold larger than the next largest, pan-ecosystem viral HMM profile database. Adjusting the criteria for viral contig confidence from ‘conservative’ to ‘eXtremely Conservative’ resulted in 37 841 HMM profiles in our efam-XC database. To assess the value of this resource, we integrated efam-XC into VirSorter viral discovery software to discover viruses from less-studied, ecologically distinct oxygen minimum zone (OMZ) marine habitats. This expanded database led to an increase in viruses recovered from every tested OMZ virome by ∼24% on average (up to ∼42%) and especially improved the recovery of often-missed shorter contigs (<5 kb). Additionally, to help elucidate lesser-known viral protein functions, we annotated the profiles using multiple databases from the DRAM pipeline and virion-associated metaproteomic data, which doubled the number of annotations obtainable by standard, single-database annotation approaches. Together, these marine resources (efam and efam-XC) are provided as searchable, compressed HMM databases that will be updated bi-annually to help maximize viral sequence discovery and study from any ecosystem.

Availability and implementation

The resources are available on the iVirus platform at (doi.org/10.25739/9vze-4143).

Supplementary information

Supplementary data are available at Bioinformatics online.

Expanding standards in viromics: in silico evaluation of dsDNA viral genome identification, classification, and auxiliary metabolic gene curation

BACKGROUND

Viruses influence global patterns of microbial diversity and nutrient cycles. Though viral metagenomics (viromics), specifically targeting dsDNA viruses, has been critical for revealing viral roles across diverse ecosystems, its analyses differ in many ways from those used for microbes. To date, viromics benchmarking has covered read pre-processing, assembly, relative abundance, read mapping thresholds and diversity estimation, but other steps would benefit from benchmarking and standardization. Here we use in silico-generated datasets and an extensive literature survey to evaluate and highlight how dataset composition (i.e., viromes vs bulk metagenomes) and assembly fragmentation impact (i) viral contig identification tool, (ii) virus taxonomic classification, and (iii) identification and curation of auxiliary metabolic genes (AMGs).

RESULTS

The in silico benchmarking of five commonly used virus identification tools show that gene-content-based tools consistently performed well for long (≥3 kbp) contigs, while k-mer- and blast-based tools were uniquely able to detect viruses from short (≤3 kbp) contigs. Notably, however, the performance increase of k-mer- and blast-based tools for short contigs was obtained at the cost of increased false positives (sometimes up to ∼5% for virome and ∼75% bulk samples), particularly when eukaryotic or mobile genetic element sequences were included in the test datasets. For viral classification, variously sized genome fragments were assessed using gene-sharing network analytics to quantify drop-offs in taxonomic assignments, which revealed correct assignations ranging from ∼95% (whole genomes) down to ∼80% (3 kbp sized genome fragments). A similar trend was also observed for other viral classification tools such as VPF-class, ViPTree and VIRIDIC, suggesting that caution is warranted when classifying short genome fragments and not full genomes. Finally, we highlight how fragmented assemblies can lead to erroneous identification of AMGs and outline a best-practices workflow to curate candidate AMGs in viral genomes assembled from metagenomes.

CONCLUSION

Together, these benchmarking experiments and annotation guidelines should aid researchers seeking to best detect, classify, and characterize the myriad viruses 'hidden' in diverse sequence datasets.

Spinal Cord Injury Changes the Structure and Functional Potential of Gut Bacterial and Viral Communities

Emerging data indicate that gut dysbiosis contributes to many human diseases, including several comorbidities that develop after traumatic spinal cord injury (SCI). To date, all analyses of SCI-induced gut dysbiosis have used 16S rRNA amplicon sequencing. This technique has several limitations, including being susceptible to taxonomic "blind spots," primer bias, and an inability to profile microbiota functions or identify viruses. Here, SCI-induced gut dysbiosis was assessed by applying genome- and gene-resolved metagenomic analysis of murine stool samples collected 21 days after an experimental SCI at the 4th thoracic spine (T4) or 10th thoracic spine (T10) spinal level. These distinct injuries partially (T10) or completely (T4) abolish sympathetic tone in the gut. Among bacteria, 105 medium- to high-quality metagenome-assembled genomes (MAGs) were recovered, with most (n = 96) representing new bacterial species. Read mapping revealed that after SCI, the relative abundance of beneficial commensals (Lactobacillus johnsonii and CAG-1031 spp.) decreased, while potentially pathogenic bacteria (Weissella cibaria, Lactococcus lactis _A, Bacteroides thetaiotaomicron) increased. Functionally, microbial genes encoding proteins for tryptophan, vitamin B6, and folate biosynthesis, essential pathways for central nervous system function, were reduced after SCI. Among viruses, 1,028 mostly novel viral populations were recovered, expanding known murine gut viral species sequence space ∼3-fold compared to that of public databases. Phages of beneficial commensal hosts (CAG-1031, Lactobacillus, and Turicibacter) decreased, while phages of pathogenic hosts (Weissella, Lactococcus, and class Clostridia) increased after SCI. Although the microbiomes and viromes were changed in all SCI mice, some of these changes varied as a function of spinal injury level, implicating loss of sympathetic tone as a mechanism underlying gut dysbiosis.IMPORTANCE To our knowledge, this is the first article to apply metagenomics to characterize changes in gut microbial population dynamics caused by a clinically relevant model of central nervous system (CNS) trauma. It also utilizes the most current approaches in genome-resolved metagenomics and viromics to maximize the biological inferences that can be made from these data. Overall, this article highlights the importance of autonomic nervous system regulation of a distal organ (gut) and its microbiome inhabitants after traumatic spinal cord injury (SCI). By providing information on taxonomy, function, and viruses, metagenomic data may better predict how SCI-induced gut dysbiosis influences systemic and neurological outcomes after SCI.

VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses

BACKGROUND

Viruses are a significant player in many biosphere and human ecosystems, but most signals remain "hidden" in metagenomic/metatranscriptomic sequence datasets due to the lack of universal gene markers, database representatives, and insufficiently advanced identification tools.

RESULTS

Here, we introduce VirSorter2, a DNA and RNA virus identification tool that leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection. When benchmarked against genomes from both isolated and uncultivated viruses, VirSorter2 uniquely performed consistently with high accuracy (F1-score > 0.8) across viral diversity, while all other tools under-detected viruses outside of the group most represented in reference databases (i.e., those in the order Caudovirales). Among the tools evaluated, VirSorter2 was also uniquely able to minimize errors associated with atypical cellular sequences including eukaryotic genomes and plasmids. Finally, as the virosphere exploration unravels novel viral sequences, VirSorter2's modular design makes it inherently able to expand to new types of viruses via the design of new classifiers to maintain maximal sensitivity and specificity.

CONCLUSION

With multi-classifier and modular design, VirSorter2 demonstrates higher overall accuracy across major viral groups and will advance our knowledge of virus evolution, diversity, and virus-microbe interaction in various ecosystems. Source code of VirSorter2 is freely available ( https://bitbucket.org/MAVERICLab/virsorter2 ), and VirSorter2 is also available both on bioconda and as an iVirus app on CyVerse ( https://de.cyverse.org/de ). Video abstract.

Genome-resolved viral ecology in a marine oxygen minimum zone

Oxygen minimum zones (OMZs) are critical to marine nitrogen cycling and global climate change. While OMZ microbial communities are relatively well-studied, little is known about their viruses. Here, we assess the viral community ecology of 22 deeply sequenced viral metagenomes along a gradient of oxygenated to anoxic waters (<0.02 μmol/l O₂ ) in the Eastern Tropical South Pacific (ETSP) OMZ. We identified 46 127 viral populations (≥5 kb), which augments the known viruses from ETSP by 10-fold. Viral communities clustered into six groups that correspond to oceanographic features. Oxygen concentration was the predominant environmental feature driving viral community structure. Alpha and beta diversity of viral communities in the anoxic zone were lower than in surface waters, which parallels the low microbial diversity seen in other studies. ETSP viruses were largely endemic, with the majority of shared viruses (87%) also present in other OMZ samples. We detected 543 putative viral-encoded auxiliary metabolic genes (AMGs), of which some have a distribution that reflects physico-chemical characteristics across depth. Together these findings provide an ecological baseline for viral community structure, drivers and population variability in OMZs that will help future studies assess the role of viruses in these climate-critical environments.

The Gut Virome Database Reveals Age-Dependent Patterns of Virome Diversity in the Human Gut

The gut microbiome profoundly affects human health and disease, and their infecting viruses are likely as important, but often missed because of reference database limitations. Here, we (1) built a human Gut Virome Database (GVD) from 2,697 viral particle or microbial metagenomes from 1,986 individuals representing 16 countries, (2) assess its effectiveness, and (3) report a meta-analysis that reveals age-dependent patterns across healthy Westerners. The GVD contains 33,242 unique viral populations (approximately species-level taxa) and improves average viral detection rates over viral RefSeq and IMG/VR nearly 182-fold and 2.6-fold, respectively. GVD meta-analyses show highly personalized viromes, reveal that inter-study variability from technical artifacts is larger than any "disease" effect at the population level, and document how viral diversity changes from human infancy into senescence. Together, this compact foundational resource, these standardization guidelines, and these meta-analysis findings provide a systematic toolkit to help maximize our understanding of viral roles in health and disease.

DRAM for distilling microbial metabolism to automate the curation of microbiome function

Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

Ocean microbial communities strongly influence the biogeochemistry, food webs, and climate of our planet. Despite recent advances in understanding their taxonomic and genomic compositions, little is known about how their transcriptomes vary globally. Here, we present a dataset of 187 metatranscriptomes and 370 metagenomes from 126 globally distributed sampling stations and establish a resource of 47 million genes to study community-level transcriptomes across depth layers from pole-to-pole. We examine gene expression changes and community turnover as the underlying mechanisms shaping community transcriptomes along these axes of environmental variation and show how their individual contributions differ for multiple biogeochemically relevant processes. Furthermore, we find the relative contribution of gene expression changes to be significantly lower in polar than in non-polar waters and hypothesize that in polar regions, alterations in community activity in response to ocean warming will be driven more strongly by changes in organismal composition than by gene regulatory mechanisms.

Video Abstract

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A catalog of 47 million genes was generated from 370 globally distributed metagenomes

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Meta-omics data integration disentangled the mechanisms of changes in transcript pools

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Transcript pool changes of metabolic marker genes show distinct mechanistic patterns

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Community turnover as a response to ocean warming may be strongest in polar regions

Global Trends in Marine Plankton Diversity across Kingdoms of Life

The ocean is home to myriad small planktonic organisms that underpin the functioning of marine ecosystems. However, their spatial patterns of diversity and the underlying drivers remain poorly known, precluding projections of their responses to global changes. Here we investigate the latitudinal gradients and global predictors of plankton diversity across archaea, bacteria, eukaryotes, and major virus clades using both molecular and imaging data from Tara Oceans. We show a decline of diversity for most planktonic groups toward the poles, mainly driven by decreasing ocean temperatures. Projections into the future suggest that severe warming of the surface ocean by the end of the 21^st century could lead to tropicalization of the diversity of most planktonic groups in temperate and polar regions. These changes may have multiple consequences for marine ecosystem functioning and services and are expected to be particularly significant in key areas for carbon sequestration, fisheries, and marine conservation.

Video Abstract

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Most epipelagic planktonic groups exhibit a poleward decline of diversity

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No latitudinal diversity gradient was observed below the photic zone

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Temperature emerges as the best predictor of epipelagic plankton diversity

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Global warming may increase plankton diversity, particularly at high latitudes

Phage-specific metabolic reprogramming of virocells

Ocean viruses are abundant and infect 20–40% of surface microbes. Infected cells, termed virocells, are thus a predominant microbial state. Yet, virocells and their ecosystem impacts are understudied, thus precluding their incorporation into ecosystem models. Here we investigated how unrelated bacterial viruses (phages) reprogram one host into contrasting virocells with different potential ecosystem footprints. We independently infected the marine Pseudoalteromonas bacterium with siphovirus PSA-HS2 and podovirus PSA-HP1. Time-resolved multi-omics unveiled drastically different metabolic reprogramming and resource requirements by each virocell, which were related to phage–host genomic complementarity and viral fitness. Namely, HS2 was more complementary to the host in nucleotides and amino acids, and fitter during infection than HP1. Functionally, HS2 virocells hardly differed from uninfected cells, with minimal host metabolism impacts. HS2 virocells repressed energy-consuming metabolisms, including motility and translation. Contrastingly, HP1 virocells substantially differed from uninfected cells. They repressed host transcription, responded to infection continuously, and drastically reprogrammed resource acquisition, central carbon and energy metabolisms. Ecologically, this work suggests that one cell, infected versus uninfected, can have immensely different metabolisms that affect the ecosystem differently. Finally, we relate phage–host genome complementarity, virocell metabolic reprogramming, and viral fitness in a conceptual model to guide incorporating viruses into ecosystem models.

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

Microbes drive most ecosystems and are modulated by viruses that impact their lifespan, gene flow, and metabolic outputs. However, ecosystem-level impacts of viral community diversity remain difficult to assess due to classification issues and few reference genomes. Here, we establish an ∼12-fold expanded global ocean DNA virome dataset of 195,728 viral populations, now including the Arctic Ocean, and validate that these populations form discrete genotypic clusters. Meta-community analyses revealed five ecological zones throughout the global ocean, including two distinct Arctic regions. Across the zones, local and global patterns and drivers in viral community diversity were established for both macrodiversity (inter-population diversity) and microdiversity (intra-population genetic variation). These patterns sometimes, but not always, paralleled those from macro-organisms and revealed temperate and tropical surface waters and the Arctic as biodiversity hotspots and mechanistic hypotheses to explain them. Such further understanding of ocean viruses is critical for broader inclusion in ecosystem models.

A new enrichment model for high sensitivity detection and downstream analyses of circulating tumor cells in breast cancer patients

Abstract #4162

The detection of circulating tumor cells (CTCs) in breast cancer patients have the potential to improve prognostication and the monitoring of response to treatment. Most CTC enrichment technologies are based on binding to anti-EpCAM antibodies. The sensitivity of such assays is limited by tumors that express no or undetectable levels of EpCAM. Improvements in CTC detection coupled with the development of systems to interrogate CTCs for therapeutic target expression could lead to novel applications for patient monitoring, clinical diagnosis and treatment. In this study, we describe a sensitive and reproducible enrichment method for CTCs. We defined cells as circulating tumor cells with three criteria: Positive for cytokeratin (CK+) and DAPI (nuclear) (DAPI+) and negative staining for CD45 (CD45-). We have previously reported that this system has a higher sensitivity for circulating tumor cell detection and provides a better platform for CTC downstream analyses compare to the methods currently available in the market. Herein, we describe the use of this platform for the evaluation of breast cancer biomarkers in CTCs. Blood samples from patients with metastatic breast cancer were used for CellSearch™ assay (Veridex , LLC ) and our CTC assay (A1000 CTC enrichment and detection kit, Genetix). We performed the CTC enrichment assay using the combination of anti-CK and anti-EpCAM antibodies. CTCs were identified with brightfield and fluorescence labeled anti-CK, anti-CD45 and DAPI (nuclear stain) images. The Ariol® system (Applied Imaging Corporation) was employed for automated cell image capture and analysis of CTCs on glass slides. CTCs enriched on the glass slides were used for CTC downstream analysis. Our CTC enrichment model is designed to have the capability to enrich all the three types of CTCs including CK+ & EpCAM+, CK+ & EpCAM-/low and CK-/low & EpCAM+ cells. Compared to the enrichment methods using anti-EpCAM or anti-cytokeratin antibody alone, a higher CTC detection rate and a larger dynamic CTC detected range were obtained with our new enrichment model. Interestingly there were clear CTC number differences with enrichment methods in the higher CTC count patient samples which indicate that the different enrichment methods may enrich different types of CTCs from patient blood samples.&#x2028; Results of DNA and RNA FISH analyses on enriched CTCs indicate that the CTCs on glass slides can be used for its downstream analyses directly or indirectly. Our method may have better performance on enrichment of heterogeneous CTCs and provide a better platform for CTCs profiling for biomarker evaluations and CTC downstream analyses.

Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 4162.

Characterization of midgut and salivary gland proteins of Hyalomma dromedarii females controlled by entomopathogenic nematodes

Biological control of hard ticks, Hyalomma dromedarii (Acari: Ixodidae) using entomopathogenic nematode of two families; Heterorhabditidae and Steinernematidae was studied. The protective effect of controlled ticks including haemolymph and haemocytes against these biological agents were also investigated. It was found that heterorhabditid strains cause a higher effect in biological control of engorged female H. dromedarii than those of stienernematid strains. It induced mortality rates ranged from 12-92% versus 4-88% for stienernematid strains. It was also found that these entomopathogenic nematodes can not reproduce within the exposed ticks. SDS-PAGE of proteins extracted from midguts and salivary glands infected with 4000 IJs tick(-1) separated 21 and 25 protein bands versus 13 and 19 protein bands from non-infected ones, respectively. It was concluded that entomopathogenic nematodes of family Heterorhabditidae proved to have a potential acaricidal effect in the control of hard ticks. Moreover, the controlled ticks released unknown proteins in their haemolymph that may promote the haemocytes to phagocyte the nematodes as a type of defense mechanism.

In vitro acaricidal effect of plant extract of neem seed oil (Azadirachta indica) on egg, immature, and adult stages of Hyalomma anatolicum excavatum (Ixodoidea: Ixodidae)

Effects of the plant extract of neem seed (Azadirachta indica) on eggs, immature, and adult stages of Hyalomma anatolicum excavatum was studied at concentrations of 1.6, 3.2, 6.4, and 12.8%. The extract was found to have a significant effect on the hatching rate of eggs. It significantly increased the hatching rate during the first 7 days post-treatment (DPT) giving incompletely developed and dead larvae; however, it cause hatching failure at DPT 15. Neem Azal F induced a significant increased in mortality rates of newly hatched larvae, unfed larvae, and unfed adults reaching 100% on 15th, 3rd, and 15th DPT, respectively. The mortality rates increased with the extract concentrations. Although, it had no significant effect on the moulting rates of fed nymphs, it caused malformation or deformities in 4% of adults moulted. It was concluded that the concentration of Neem Azal F which may be used for commercial control of this tick species were 1.6 and 3.2%.

Localization and migration route of Cephalopina titillator (Diptera: Oestridae) larvae in the head of infested camels (Camelus dromedarius)

The localization and migration routes of Cephalopina titillator larvae were studied in the heads of 45 naturally infested camels. Larvae were located in the pharyngeal cavity (95.6%), the labyrinth of the ethmoid bone (71.1%), the turbinates (28.9%) and the lower nasal meatus (6.7%). Out of 261 first-instar larvae, 73.7% were found in the labyrinth of the ethmoid bone and 26.3% in the turbinates, while 88.9% of second-instar larvae were observed in the pharyngeal cavity and 11.1% in the labyrinth of the ethmoid bone. Most third-instar larvae (91.9%) were found in the pharyngeal cavity, with a few larvae in the labyrinth of the ethmoid bone (6.5%) and lower nasal meatus (1.6%). The first moult occurred in the labyrinth of the ethmoid bone. The second moult was observed in both the labyrinth of ethmoid bone and the pharyngeal cavity. The migration route of these larvae in the infested head was discussed.

Pig, donkey and buffalo meat as a source of some coccidian parasites infecting dogs

Experimental infection of dogs with meat samples (oesophagus, heart and diaphragm) from each of 105 pigs, 11 donkeys and 17 Egyptian water buffaloes indicated that they contained the infective stages of some coccidian parasites of dogs. The dogs which were fed pig meat shed in their faeces Isospora ohioensis, I. canis oocysts and Sarcocystis miescheriana sporocysts after prepatent periods of 3-5, 4-7 and 9-10 days, respectively. The dogs which were fed donkey meat excreted only I. ohioensis oocysts and Sarcocystis bertrami sporocysts after prepatent periods of 3 and 11 days, respectively. However, the dogs which were fed buffalo meat shed in their faeces I. ohioensis, I. canis and Hammondia heydorni oocysts with prepatent periods of 1, 1 and 7 days, respectively.

Studies on Rhinoestrus purpureus (Diptera: Oestridae) larvae infesting donkeys (Equus asinus) in Egypt. III. Pupal duration under controlled conditions

The pupal duration of Rhinoestrus purpureus was studied under variable degrees of temperature and relative humidity (RH). It was found that pupal duration was affected by temperature but not by RH. An increase in the temperature above 22 degrees C decreased the pupal duration: 26-27 days at 22 degrees C, 16-24 days at 27 degrees C, 13-15 days at 32 degrees C. At 37 degrees C, the pupated larvae failed to pupate and died. The deformity ratio of emerged flies was 25-30% at 22-32 degrees C, but it was directly proportional to RH at a constant temperature of 32 degrees C: 26.1% at 75% RH, 16.7% at 50% RH, 6.7% at 30% RH. It was concluded that the optimum temperature and RH for obtaining normal active flies were 32 degrees C and 30%, respectively.

The bulbocavernosus reflex in urology: a prospective study of 299 patients

Bulbocavernosus reflex was evaluated clinically in 299 patients during a routine urodynamic evaluation and compared to the electromyographic demonstration of the reflex. The findings were correlated with the neurologic status of the patients. There were 127 patients who were normal neurologically, and 98 per cent of the male and 81 per cent of the female patients in this group had a normal bulbocavernosus reflex clinically. All of the male and 92 per cent of the female patients had a bulbocavernosus reflex demonstrated by electromyography. There were 73 patients with neurologic lesions involving the sacral spinal cord. All patients with a complete lesion had absent bulbocavernosus reflexes clinically and on electromyography, while 44 per cent of the patients with incomplete sacral lesions had an intact bulbocavernosus reflex clinically and 78 per cent had reflex demonstrated by electromyography. There were 99 patients with neurologic lesions of the spinal cord above the sacral outflow, and 90 per cent of this group had demonstrable bulbocavernosus reflexes clinically and 93 per cent had the reflex demonstrated by electromyography. It is concluded that the absence of a bulbocavernosus reflex in a male patient is indicative of a neurologic lesion involving the sacral spinal cord and is highly suggestive of such a lesion in a female patient. The presence of a normal bulbocavernosus reflex in either sex does not rule out the possibility of a significant lesion. The electromyographic demonstration of the bulbocavernosus reflex is more sensitive than the clinical one.

Detrusor-external sphincter dyssynergia

Detrusor-external sphincter dyssynergia is characterized by involuntary contractions of the external urethral sphincter during detrusor contractions. A review of 550 consecutive patients who underwent urodynamic evaluation revealed that this condition was found only in patients who had involuntary detrusor contractions owing to well defined neurologic lesions of the suprasacral spinal cord. All patients with supracervical neurologic lesions had synergistic voiding patterns. We conclude that bladder-external sphincter dyssynergia is a neurologic condition owing to interruption of the spinal pathways connecting the pontine mesencephalic and the sacral micturition centers. In the absence of such a neurologic lesion one should be extremely cautious in making this diagnosis.

Detrusor-external sphincter dyssynergia: a detailed electromyographic study

We reviewed 54 cases of detrusor-external sphincter dyssynergia following complete urodynamic evaluations. All patients had well defined neurologic lesions of the suprasacral spinal cord. On the basis of urodynamic findings 3 types of dyssynergia were encountered: type 1 (30 per cent) was characterized by a crescendo increase in electromyographic activity that reached a maximum at the peak of the detrusor contraction, type 2 (15 per cent) consisted of clonic sphincter contractions interspersed throughout the detrusor contraction and type 3 (55 per cent) was characterized by a sustained sphincter contraction that coincided with the detrusor contraction. There was no correlation between the clinical neurologic level and the type of dyssynergia.

Cystometric response to propantheline in detrusor hyperreflexia: therapeutic implications

We studied 42 patients with urinary incontinence who demonstrated uninhibited detrusor contractions during cystometry. Each patient underwent urodynamic evaluation before and after the parenteral administration of propantheline bromide. Of these 42 patients 33 (79 per cent) had a positive response to propantheline: total abolition of uninhibited bladder contractions or 200 per cent increase in bladder capacity. Of these 33 patients 26 were treated with the oral drug and all but 1 had complete clinical response. Urinary retention occurred in half of the patients. These patients were managed with intermittent self-catheterization in addition to oral propantheline. None of the patients who failed to respond to the parenteral medication had a favorable response to the orally administered drug.

Failure of bethanechol denervation supersensitivity as a diagnostic aid

A total of 33 patients who demonstrated detrusor areflexia during cystometry underwent the bethanechol denervation supersensitivity test. In each instance the presence or absence of a neurologic lesion was documented carefully by complete neurologic evaluation. Of the 21 patients with a neurogenic bladder there was a falsely negative rate of 24 per cent. Of the 12 patients without a neurogenic bladder the falsely positive rate was 50 per cent. It is concluded that a positive bethanechol test is not by itself indicative of neurogenic bladder nor does a negative test exclude this diagnosis.