Standard methods for Nosema research

Methods are described for working with Nosema apis and Nosema ceranae in the field and in the laboratory. For fieldwork, different sampling methods are described to determine colony level infections at a given point in time, but also for following the temporal infection dynamics. Suggestions are made for how to standardise field trials for evaluating treatments and disease impact. The laboratory methods described include different means for determining colony level and individual bee infection levels and methods for species determination, including light microscopy, electron microscopy, and molecular methods (PCR). Suggestions are made for how to standardise cage trials, and different inoculation methods for infecting bees are described, including control methods for spore viability. A cell culture system for in vitro rearing of Nosema spp. is described. Finally, how to conduct different types of experiments are described, including infectious dose, dose effects, course of infection and longevity tests

Standard methods for maintaining adult Apis mellifera in cages under in vitro laboratory conditions

Adult honey bees are maintained in vitro in laboratory cages for a variety of purposes. For example, researchers may wish to perform experiments on honey bees caged individually or in groups to study aspects of parasitology, toxicology, or physiology under highly controlled conditions, or they may cage whole frames to obtain newly emerged workers of known age cohorts. Regardless of purpose, researchers must manage a number of variables, ranging from selection of study subjects (e.g. honey bee subspecies) to experimental environment (e.g. temperature and relative humidity). Although decisions made by researchers may not necessarily jeopardize the scientific rigour of an experiment, they may profoundly affect results, and may make comparisons with similar, but independent, studies difficult. Focusing primarily on workers, we provide recommendations for maintaining adults under in vitro laboratory conditions, whilst acknowledging gaps in our understanding that require further attention. We specifically describe how to properly obtain honey bees, and how to choose appropriate cages, incubator conditions, and food to obtain biologically relevant and comparable experimental results. Additionally, we provide broad recommendations for experimental design and statistical analyses of data that arises from experiments using caged honey bees. The ultimate goal of this, and of all COLOSS BEEBOOK papers, is not to stifle science with restrictions, but rather to provide researchers with the appropriate tools to generate comparable data that will build upon our current understanding of honey bees.

Activation of heat shock and antioxidant responses by the natural product celastrol: transcriptional signatures of a thiol-targeted molecule.

Stress response pathways allow cells to sense and respond to environmental changes and adverse pathophysiological states. Pharmacological modulation of cellular stress pathways has implications in the treatment of human diseases, including neurodegenerative disorders, cardiovascular disease, and cancer. The quinone methide triterpene celastrol, derived from a traditional Chinese medicinal herb, has numerous pharmacological properties, and it is a potent activator of the mammalian heat shock transcription factor HSF1. However, its mode of action and spectrum of cellular targets are poorly understood. We show here that celastrol activates Hsf1 in Saccharomyces cerevisiae at a similar effective concentration seen in mammalian cells. Transcriptional profiling revealed that celastrol treatment induces a battery of oxidant defense genes in addition to heat shock genes. Celastrol activated the yeast Yap1 oxidant defense transcription factor via the carboxy-terminal redox center that responds to electrophilic compounds. Antioxidant response genes were likewise induced in mammalian cells, demonstrating that the activation of two major cell stress pathways by celastrol is conserved. We report that celastrol's biological effects, including inhibition of glucocorticoid receptor activity, can be blocked by the addition of excess free thiol, suggesting a chemical mechanism for biological activity based on modification of key reactive thiols by this natural product.

The COLOSS BEEBOOK Volume II: Standard methods for Apis mellifera pest and pathogen research

n recent years, declines of honey bee populations have received massive media attention worldwide, yet attempts to understand the causes have been hampered by a lack of standardisation of laboratory techniques. Published as a response to this, the COLOSS BEEBOOK is a unique collaborative venture involving 234 bee scientists from 34 countries, who have produced the definitive guide to how to carry out research on honey bees. It is hoped that these volumes will become the standards to be adopted by bee scientists worldwide. Volume II includes approximately 600 separate protocols dealing with the study of the pests and diseases of the honey bee, Apis mellifera. These cover epidemiology and surveying techniques, virus diseases, bacterial diseases such as European and American foulbrood, fungal and microsporidian diseases such as Nosema, mites such as Acarapis, Varroa and Tropilaelaps, and other pests such as the small hive beetle.

The COLOSS BEEBOOK Volume I: Standard Methods for Apis mellifera Research

In recent years, declines of honey bee populations have received massive media attention worldwide, yet attempts to understand the causes have been hampered by a lack of standardisation of laboratory techniques. Published as a response to this, the COLOSS BEEBOOK is a unique collaborative venture involving 234 bee scientists from 34 countries, who have produced the definitive guide to how to carry out research on honey bees. It is hoped that these volumes will become the standards to be adopted by bee scientists worldwide. Volume I includes approximately 1,100 separate protocols dealing with the study of the honey bee, Apis mellifera. These cover anatomy, behavioural studies, chemical ecology, breeding, genetics, instrumental insemination and queen rearing, pollination, molecular studies, statistics, toxicology and numerous other techniques

Spatial genomic heterogeneity within localized, multifocal prostate cancer

Herein we provide a detailed molecular analysis of the spatial heterogeneity of clinically localized, multifocal prostate cancer to delineate new oncogenes or tumor suppressors. We initially determined the copy number aberration (CNA) profiles of 74 patients with index tumors of Gleason score 7. Of these, 5 patients were subjected to whole-genome sequencing using DNA quantities achievable in diagnostic biopsies, with detailed spatial sampling of 23 distinct tumor regions to assess intraprostatic heterogeneity in focal genomics. Multifocal tumors are highly heterogeneous for single-nucleotide variants (SNVs), CNAs and genomic rearrangements. We identified and validated a new recurrent amplification of MYCL, which is associated with TP53 deletion and unique profiles of DNA damage and transcriptional dysregulation. Moreover, we demonstrate divergent tumor evolution in multifocal cancer and, in some cases, tumors of independent clonal origin. These data represent the first systematic relation of intraprostatic genomic heterogeneity to predicted clinical outcome and inform the development of novel biomarkers that reflect individual prognosis.

Network Analysis Reveals Sex- and Antibiotic Resistance-Associated Antivirulence Targets in Clinical Uropathogens.

Increasing antibiotic resistance among uropathogenic Escherichia coli (UPEC) is driving interest in therapeutic targeting of nonconserved virulence factor (VF) genes. The ability to formulate efficacious combinations of antivirulence agents requires an improved understanding of how UPEC deploy these genes. To identify clinically relevant VF combinations, we applied contemporary network analysis and biclustering algorithms to VF profiles from a large, previously characterized inpatient clinical cohort. These mathematical approaches identified four stereotypical VF combinations with distinctive relationships to antibiotic resistance and patient sex that are independent of traditional phylogenetic grouping. Targeting resistance- or sex-associated VFs based upon these contemporary mathematical approaches may facilitate individualized anti-infective therapies and identify synergistic VF combinations in bacterial pathogens.

Isotope measurements from late Paleocene - early Eocene of 5 cores from Atlantic and Pacific Ocean

High-resolution stable carbon isotope records for upper Paleocene - lower Eocene sections at Ocean Drilling Program Sites 1051 and 690 and Deep Sea Drilling Project Sites 550 and 577 show numerous rapid (40 - 60 kyr duration) negative excursions of up to 1 per mill. We demonstrate that these transient decreases are the expected result of nonlinear insolation forcing of the carbon cycle in the context of a long carbon residence time. The transients occur at maxima in Earth's orbital eccentricity, which result in high-amplitude variations in insolation due to forcing by climatic precession. The construction of accurate orbital chronologies for geologic sections older than ~ 35 Ma relies on identifying a high-fidelity recorder of variations in Earth's orbital eccentricity. We use the carbon isotope records as such a recorder, establishing a robust orbitally tuned chronology for latest Paleocene-earliest Eocene events. Moreover, the transient decreases provide a means of precise correlation among the four sites that is independent of magnetostratigraphic and biostratigraphic data at the <10^5-year scale. While the eccentricity-controlled transient decreases bear some resemblance to the much larger-amplitude carbon isotope excursion (CIE) that marks the Paleocene/Eocene boundary, the latter event is found to occur near a minimum in the ~400-kyr eccentricity cycle. Thus the CIE occurred during a time of minimal variability in insolation, the dominant mechanism for forcing climate change on 104-year scales. We argue that this is inconsistent with mechanisms that rely on a threshold climate event to trigger the Paleocene/Eocene thermal maximum since any threshold would more likely be crossed during a period of high-amplitude climate variations.

Water chemistry, and biological traits and mercury content of Salvelinus alpinus and S. namaycush in Laflamme and Pingualuit lake

Pingualuk Lake fills a deep crater in the Parc National des Pingualuit on the Ungava Peninsula (Nunavik, Canada) and is isolated from nearby surface waters. The main objectives of this study were to determine and compare the concentrations of two atmospherically derived contaminants, mercury and perfluorinated chemicals (PFCs), in the lake water column and fish of Pingualuk Lake and to assess the physical and biological factors influencing contaminant concentrations. Mercury concentrations in arctic char muscle tissue were comparable to those of char in other Arctic lakes, while the total amount of PFCs was below reported levels for remote lakes in the Arctic and elsewhere. Stable isotope and stomach content analyses were made to investigate the feeding ecology of the Pingualuk Lake arctic char population and indicated the possibility of multiple feeding groups. Genetics characteristics (MH and mtDNA) of fish from Pingualuk Lake revealed that this population is likely distinct from that of nearby Laflamme Lake. However, both arctic char populations exhibit differential variation of their allele families. Physical characteristics determined for Lake Pingualuk revealed that the water column was inversely stratified beneath the ice and extremely transparent to visible and ultraviolet radiation. The highest mercury concentrations (3- 6 pg/mL THg) occurred just beneath the ice surface in each lake. Pingualuk Lake, given its near pristine state and exceptional limnological features, may serve as a most valuable reference ecosystem for monitoring environmental stressors, such as contaminants, in the Arctic.

Stable isotope record, Mg/Ca ratios and age model of St. Stephens Quarry, Alabama

In the largest global cooling event of the Cenozoic Era, between 33.8 and 33.5 Myr ago, warm, high-CO2 conditions gave way to the variable 'icehouse' climates that prevail today. Despite intense study, the history of cooling versus ice-sheet growth and sea-level fall reconstructed from oxygen isotope values in marine sediments at the transition has not been resolved. Here, we analyse oxygen isotopes and Mg/Ca ratios of benthic foraminifera, and integrate the results with the stratigraphic record of sea-level change across the Eocene-Oligocene transition from a continental-shelf site at Saint Stephens Quarry, Alabama. Comparisons with deep-sea (Sites 522 (South Atlantic) and 1218 (Pacific)) d18O and Mg/Ca records enable us to reconstruct temperature, ice-volume and sea-level changes across the climate transition. Our records show that the transition occurred in at least three distinct steps, with an increasing influence of ice volume on the oxygen isotope record as the transition progressed. By the early Oligocene, ice sheets were ~25% larger than present. This growth was associated with a relative sea-level decrease of approximately 105 m, which equates to a 67 m eustatic fall.

Palynological record and radiocarbon dates for sediment core T89-16, Congo River mouth

We present a high-resolution reconstruction of tropical palaeoenvironmental changes for the last deglacial transition (18 to 9 cal. kyr BP) based on integrated oceanic and terrestrial proxies from a Congo fan core. Pollen, grass cuticle, Pediastrum and dinoflagellate cyst fluxes, sedimentation rates and planktonic foraminiferal d18O ratios, uK37 sea-surface temperature and alkane/alkenone ratio data highlight a series of abrupt changes in Congo River palaeodischarge. A major discharge pulse is registered at around 13.0 cal. kyr BP which we attribute to latitudinal migration of the Intertropical Convergence Zone (ITCZ) during deglaciation. The data indicate abrupt and short-lived changes in the equatorial precipitation regime within a system of monsoonal dynamics forced by precessional cycles. The phases of enhanced Congo discharge stimulated river-induced upwelling and enhanced productivity in the adjacent ocean.

Nd-Sr isotopes in fossil fish debris from IODP Exp302

Strontium and neodymium radiogenic isotope ratios in early to middle Eocene fossil fish debris (ichthyoliths) from Lomonosov Ridge (Integrated Ocean Drilling Program Expedition 302) help constrain water mass compositions in the Eocene Arctic Ocean between 55 and 45 Ma. The inferred paleodepositional setting was a shallow, offshore marine to marginal marine environment with limited connections to surrounding ocean basins. The new data demonstrate that sources of Nd and Sr in fish debris were distinct from each other, consistent with a salinity-stratified water column above Lomonosov Ridge in the Eocene. The 87Sr/86Sr values of ichthyoliths (0.7079 - 0.7087) are more radiogenic than Eocene seawater, requiring brackish to fresh water conditions in the environment where fish metabolized Sr. The 87Sr/86Sr variations probably record changes in the overall balance of river Sr flux to the Eocene Arctic Ocean between 55 and 45 Ma and are used here to reconstruct surface water salinity values. The eNd values of ichthyoliths vary between -5.7 and -7.8, compatible with periodic (or intermittent) supply of Nd to Eocene Arctic intermediate water (AIW) from adjacent seas. Although the Norwegian-Greenland Sea and North Atlantic Ocean were the most likely sources of Eocene AIW Nd, input from the Tethys Sea (via the Turgay Strait in early Eocene time) and the North Pacific Ocean (via a proto-Bering Strait) also contributed.