Revealing the diversity of amber source plants from the Early Cretaceous Crato Formation, Brazil.

BACKGROUND: Amber has been reported from the Early Cretaceous Crato Formation, as isolated clasts or within plant tissues. Undescribed cones of uncertain gymnosperm affinity have also been recovered with amber preserved in situ. Here, we provide multiple lines of evidence to determine the botanical affinity of this enigmatic, conspicuous cone type, and to better understand the diversity of amber-source plants present in the Crato Formation and beyond. RESULTS: A new taxon of amber-bearing pollen cone Araripestrobus resinosus gen. nov. et sp. nov. is described here from complete cones and characteristic disarticulated portions. The best-preserved cone portion has both in situ amber infilling the resin canals inside the preserved microsporophyll tissues and pollen of the Eucommiidites-type. This places this genus within the Erdtmanithecales, an incompletely known gymnosperm group from the Mesozoic. FTIR analysis of the in situ amber indicates a potential araucariacean conifer affinity, although affinity with cupressacean conifers cannot be definitely ruled out. Pyr-GC-MS analysis of the Araripestrobus resinosus gen. nov. et sp. nov. in situ fossil resin shows that it is a mature class Ib amber, thought to indicate affinities with araucariacean and cupressacean, but not pinaceous, conifers. This is the first confirmed occurrence of this class of amber in the Crato Formation flora and in South America, except for an archaeological sample from Laguna Guatavita, Colombia. CONCLUSIONS: The combined results of the cones' novel gross morphology and the analyses of the in situ amber and pollen clearly indicate that the new taxon of resinous gymnosperm pollen cones from the Crato Formation is affiliated with Erdtmanithecales. The cone morphology is very distinct from all known pollen cone types of this extinct plant group. We therefore assume that the plant group that produced Eucommiidites-type pollen is much more diverse in habits than previously thought. Moreover, the diversity of potential amber source plants from the Crato Formation is now expanded beyond the Araucariaceae and the Cheirolepidiaceae to include this member of the Erdtmanithecales. Despite dispersed Eucommiidites pollen being noted from the Crato Formation, this is the first time macrofossils of Erdtmanithecales have been recognized from the Early Cretaceous of South America.

Prevalence, Persistence, and Antimicrobial Resistance of Campylobacter spp. from Eggs and Laying Hens Housed in Five Commercial Housing Systems.

Husbandry practices for laying hens in commercial egg production is a topic of interest from a social, economic, and regulatory standpoint. Animal welfare concerns regarding the use of conventional cages have arisen and consumer perceptions of hen welfare have led to a higher demand for cage-free eggs. The aim of this study was to assess the impact of housing systems on prevalence, persistence, and antimicrobial resistance (AMR) of Campylobacter from laying hens and shell eggs. A total of 425 samples were collected over a 10-month period from the North Carolina Layer Performance and Management Test and Campylobacter isolates were identified by serological, biochemical, and molecular tests. Genetic variability was evaluated using pulsed-field gel electrophoresis (PFGE) and AMR testing was performed. Prevalence of Campylobacter spp. ranged from 11.1% in the enrichable cages to 19.7% in the conventional systems. A greater prevalence of Campylobacter was found in the fecal swab samples from free-range birds compared with those of birds housed in the more intensive housing systems (p > 0.05). Overall, 72 isolates were confirmed as Campylobacter spp. by PCR. More than 90% of the isolates (n = 66) were identified as Campylobacter jejuni, followed by Campylobacter coli (n = 6). C. jejuni isolates displayed high levels of resistance to tetracycline (67%). Genetic variability of Campylobacter was high, with more than 20 PFGE patterns identified. Pattern "a" comprised 42% of isolates from all housing systems and was also the most persistent. This study suggests that housing systems of laying hens used for commercial shell egg production may impact the rate of Campylobacter shedding by layers. Isolation rates and tetracycline resistance levels of this pathogen are still of concern, emphasizing the need for well-implemented biosecurity measures on the farm.

Arbitrary GRIN component fabrication in optically driven diffusive photopolymers.

We introduce a maskless lithography tool and optically-initiated diffusive photopolymer that enable arbitrary two-dimensional gradient index (GRIN) polymer lens profiles. The lithography tool uses a pulse-width modulated deformable mirror device (DMD) to control the 8-bit gray-scale intensity pattern on the material. The custom polymer responds with a self-developing refractive index profile that is non-linear with optical dose. We show that this nonlinear material response can be corrected with pre-compensation of the intensity pattern to yield high fidelity, optically induced index profiles. The process is demonstrated with quadratic, millimeter aperture GRIN lenses, Zernike polynomials and GRIN Fresnel lenses.

Biogeographic and evolutionary implications of a diverse paleobiota in amber from the early Eocene of India.

For nearly 100 million years, the India subcontinent drifted from Gondwana until its collision with Asia some 50 Ma, during which time the landmass presumably evolved a highly endemic biota. Recent excavations of rich outcrops of 50-52-million-year-old amber with diverse inclusions from the Cambay Shale of Gujarat, western India address this issue. Cambay amber occurs in lignitic and muddy sediments concentrated by near-shore chenier systems; its chemistry and the anatomy of associated fossil wood indicates a definitive source of Dipterocarpaceae. The amber is very partially polymerized and readily dissolves in organic solvents, thus allowing extraction of whole insects whose cuticle retains microscopic fidelity. Fourteen orders and more than 55 families and 100 species of arthropod inclusions have been discovered thus far, which have affinities to taxa from the Eocene of northern Europe, to the Recent of Australasia, and the Miocene to Recent of tropical America. Thus, India just prior to or immediately following contact shows little biological insularity. A significant diversity of eusocial insects are fossilized, including corbiculate bees, rhinotermitid termites, and modern subfamilies of ants (Formicidae), groups that apparently radiated during the contemporaneous Early Eocene Climatic Optimum or just prior to it during the Paleocene-Eocene Thermal Maximum. Cambay amber preserves a uniquely diverse and early biota of a modern-type of broad-leaf tropical forest, revealing 50 Ma of stasis and change in biological communities of the dipterocarp primary forests that dominate southeastern Asia today.

Cretaceous African life captured in amber.

Amber is of great paleontological importance because it preserves a diverse array of organisms and associated remains from different habitats in and close to the amber-producing forests. Therefore, the discovery of amber inclusions is important not only for tracing the evolutionary history of lineages with otherwise poor fossil records, but also for elucidating the composition, diversity, and ecology of terrestrial paleoecosystems. Here, we report a unique find of African amber with inclusions, from the Cretaceous of Ethiopia. Ancient arthropods belonging to the ants, wasps, thrips, zorapterans, and spiders are the earliest African records of these ecologically important groups and constitute significant discoveries providing insight into the temporal and geographical origins of these lineages. Together with diverse microscopic inclusions, these findings reveal the interactions of plants, fungi and arthropods during an epoch of major change in terrestrial ecosystems, which was caused by the initial radiation of the angiosperms. Because of its age, paleogeographic location and the exceptional preservation of the inclusions, this fossil resin broadens our understanding of the ecology of Cretaceous woodlands.

Selective USP7 inhibition elicits cancer cell killing through a p53-dependent mechanism.

Ubiquitin specific peptidase 7 (USP7) is a deubiquitinating enzyme (DUB) that removes ubiquitin tags from specific protein substrates in order to alter their degradation rate and sub-cellular localization. USP7 has been proposed as a therapeutic target in several cancers because it has many reported substrates with a role in cancer progression, including FOXO4, MDM2, N-Myc, and PTEN. The multi-substrate nature of USP7, combined with the modest potency and selectivity of early generation USP7 inhibitors, has presented a challenge in defining predictors of response to USP7 and potential patient populations that would benefit most from USP7-targeted drugs. Here, we describe the structure-guided development of XL177A, which irreversibly inhibits USP7 with sub-nM potency and selectivity across the human proteome. Evaluation of the cellular effects of XL177A reveals that selective USP7 inhibition suppresses cancer cell growth predominantly through a p53-dependent mechanism: XL177A specifically upregulates p53 transcriptional targets transcriptome-wide, hotspot mutations in TP53 but not any other genes predict response to XL177A across a panel of ~500 cancer cell lines, and TP53 knockout rescues XL177A-mediated growth suppression of TP53 wild-type (WT) cells. Together, these findings suggest TP53 mutational status as a biomarker for response to USP7 inhibition. We find that Ewing sarcoma and malignant rhabdoid tumor (MRT), two pediatric cancers that are sensitive to other p53-dependent cytotoxic drugs, also display increased sensitivity to XL177A.

The nature and fate of natural resins in the geosphere XIII: a probable pinaceous resin from the early Cretaceous (Barremian), Isle of Wight.

Terpenoid resin is produced by all families and most genera of the order Coniferales (the conifers), and the distribution of terpenes present in most conifer resins is characteristic of the originating family. Analyses of early Cretaceous (Barremian) amber (fossil resin) from the English Wealden, Isle of Wight, southern England, by pyrolysis-gas chromatography-mass spectrometry (Py-GC-MS), indicate a terpene distribution dominated by abietane- and labdane-type terpenes. Similar distributions are observed in some species of the extant family Pinaceae. The Pinaceae are well represented within the Wealden deposits of southern England, by only one (known) species, Pityites solmsii (Seward) Seward, whereas the macro-fossil record of these deposits is dominated by the extinct conifer family Cheirolepidiaceae, for which no resin chemistry has been reported. By analogy with modern materials, it is probable that the ambers found in these deposits are derived from an extinct member of the Pinaceae, but given the absence of evidence concerning the chemotaxonomy of the Cheirolepidiaceae, this family cannot be excluded a priori as a possible paleobotanical source. These ambers may therefore be assigned to either the Pinaceae or to the Cheirolepidiaceae. These samples are the oldest ambers to date to yield useful chemotaxonomic data.

Chemical signatures of fossilized resins and recent plant exudates.

Amber is one of the few gemstones based on an organic structure. Found over most of the world, it is the fossil form of sticky plant exudates called resins. Investigation of amber by modern analytical techniques provides structural information and insight into the identity of the ancient plants that produced the source resin. Mass spectrometric analysis of materials separated by gas chromatography has identified specific compounds that are the basis of a reliable classification of the different types of amber. NMR spectroscopy of bulk, solid amber provides a complementary classification. NMR spectroscopy also can be used to characterize modern resins as well as other types of plant exudates such as gums, gum resins, and kinos, which strongly resemble resins in appearance but have very different molecular constitutions.

The nature and fate of natural resins in the geosphere. XII. Investigation of C-ring aromatic diterpenoids in Raritan amber by pyrolysis-GC-matrix isolation FTIR-MS.

Upper Cretaceous amber from the Raritan Formation (Sayerville, New Jersey) has been investigated by Pyrolysis-GC-MS and Pyrolysis-GC-matrix isolation FTIR-MS. Results establish the existence of two distinct forms of amber in this deposit. Both forms are Class Ib ambers, but they are unambiguously differentiated on the basis of their (intact) diterpenoid composition. The presence of callitrisate in both forms, and cupraene in samples designated form 1, strongly suggest that both derive from related-but-distinct species within the Cupressaceae. In addition to callitrisate, dehydroabietate and analogous 17-nor-, 16,17-dinor- and 15,16,17-trinor-analogues of these compounds are also observed. The distributions of these products in multiple samples suggest that they are the result of biological emplacement, rather than diagenetic modification of the parent compounds. This indicates that the distributions of diterpenes observed in these samples are representative of the original bioterpenoids and, hence, are useful for chemotaxonomic analyses.

Comparison of vitrified and unvitrified Eocene woody tissues by TMAH thermochemolysis - implications for the early stages of the formation of vitrinite.

Samples of vitrified and unvitrified Eocene woody plant tissues collected from the Fossil Forest site, Geodetic Hills, Axel Heiberg Island, have been characterized by TMAH thermochemolysis. All samples are gymnosperm-derived, are of very low maturity and all share the same post-depositional geologic history. Differences in the distributions of products observed from vitrified and unvitrified samples suggest that vitrification of woody tissue is associated with modification of the lignin C3 side chain, following loss of all or most of the carbohydrate present in the precursor woody tissues. The key driver of vitrification appears to be physical compression of the tissue following biological removal of cellulosic materials.

American Society of Clinical Oncology clinical practice guidelines: the role of bisphosphonates in multiple myeloma.

PURPOSE: To determine clinical practice guidelines for the use of bisphosphonates in the prevention and treatment of lytic bone disease in multiple myeloma and to determine their respective role relative to other conventional therapies for this condition. METHODS: An expert multidisciplinary Panel reviewed pertinent information from the published literature through January 2002. Values for levels of evidence and grade of recommendation were assigned by expert reviewers and approved by the Panel. Expert consensus was used if there were insufficient published data. The Panel addressed which patients to treat and when to treat them in the course of their disease. Additionally, specific drug delivery issues, duration of therapy, initiation of treatment and management of treatment of lytic bone disease was reviewed and compared with other forms of therapy for lytic bone lesions. Finally, the Panel discussed patient and physician expectations associated with this therapy for bony metastases, as well as public policy implications related to the use of bisphosphonates. The guidelines underwent external review by selected physicians, by the Health Services Research Committee members, and by the ASCO Board of Directors. RESULTS: The available evidence involving randomized controlled trials is modest but supports that oral clodronate, intravenous pamidronate, and intravenous zoledronic acid are superior to placebo in reducing skeletal complications. A reduction in vertebral fractures has consistently been seen across all studies. No agent has shown a definitive survival benefit. Intravenous zoledronic acid has recently been shown to be as effective as intravenous pamidronate. Because there are no direct comparisons between clodronate and pamidronate or zoledronic acid, the superiority of one agent cannot be definitively established. However, the panel recommends only intravenous pamidronate or zoledronic acid in light of the use of the time to first skeletal event as the primary end point and more complete assessment of bony complications in studies evaluating it. Additionally, clodronate is not available in the United States. The choice between pamidronate and zoledronic acid will depend on choosing between the higher drug cost of zoledronic acid, with its shorter, more convenient infusion time (15 minutes), versus the less expensive drug, pamidronate, with its longer infusion time (2 hours). CONCLUSION: Bisphosphonates provide a meaningful supportive benefit to multiple myeloma patients with lytic bone disease. However, further research on bisphosphonates is warranted, including the following: (1) when to start and stop therapy, (2) how to integrate their use with other treatments for lytic bone disease, (3) how to evaluate their role in myeloma patients without lytic bone involvement, (4) how to distinguish between symptomatic and asymptomatic bony events, and (5) how to better determine their cost-benefit consequence.

Identifying visual-vestibular contributions during target-directed locomotion.

The purpose of this experiment was to examine the potential interaction between visual and vestibular inputs as participants walked towards 1 of 3 targets located on a barrier 5m away. Visual and vestibular inputs were perturbed with displacing prisms and galvanic vestibular stimulation (GVS), respectively. For each target there were three vision conditions (no prisms, prisms left, and prisms right), and three GVS conditions (no GVS, anode left, and anode right). Participants were instructed to start with eyes closed, and to open the eyes at heel contact of the first step. GVS and target illumination were triggered by the first heel contact. This ensured that the upcoming visual condition and target were unknown and that both sensory perturbations occurred simultaneously. Lateral displacement was determined every 40 cm. Irrespective of target or direction, GVS or prism perturbation alone resulted in similar lateral deviations. When combined, the GVS and prism perturbations that had similar singular effects led to significantly larger deviations in the direction of the perturbations. The deviations were approximately equal to the sum of the single deviations indicating that the combined effects were additive. Conflicting GVS and prism perturbations led to significantly smaller deviations that were close to zero, indicating that opposite perturbations cancelled each other. These results show that when both visual and vestibular information remain important during task performance, the nervous system integrates the inputs equally.

Germination and elongation of flax in microgravity.

This experiment was conducted as part of a risk mitigation payload aboard the Space Shuttle Atlantis on STS-101. The objectives were to test a newly developed water delivery system, and to determine the optimal combination of water volume and substrate for the imbibition and germination of flax (Linum usitatissimum) seeds in space. Two different combinations of germination paper were tested for their ability to absorb, distribute, and retain water in microgravity. A single layer of thick germination paper was compared with one layer of thin germination paper under a layer of thick paper. Paper strips were cut to fit snugly into seed cassettes, and seeds were glued to them with the micropyle ends pointing outward. Water was delivered in small increments that traveled through the paper via capillary action. Three water delivery volumes were tested, with the largest (480 microliters) outperforming the 400 microliters and 320 microliters volumes for percent germination (90.6%) and root growth (mean=4.1 mm) during the 34-hour spaceflight experiment. The ground control experiment yielded similar results, but with lower rates of germination (84.4%) and shorter root lengths (mean=2.8 mm). It is not clear if the roots emerged more quickly in microgravity and/or grew faster than the ground controls. The single layer of thick germination paper generally exhibited better overall growth than the two layered option. Significant seed position effects were observed in both the flight and ground control experiments. Overall, the design of the water delivery system, seed cassettes and the germination paper strip concept was validated as an effective method for promoting seed germination and root growth under microgravity conditions.

Understanding and reducing the experimental variability of in vitro plasma protein binding measurements.

The experimental measurement of plasma protein binding is a useful in vitro Absorption Distribution Metabolism and Excretion(ADME) assay currently conducted in both screening and definitive early development candidate modes. The fraction unbound is utilized to calculate important pharmacokinetic (PK) parameters such as unbound clearance and unbound volume of distribution in animals that can be used to make human PK and dose predictions and estimate clinically relevant drug-drug interaction potential. Although these types of assays have been executed for decades, a rigorous statistical analysis of sources of variability has not been conducted because of the tedious nature of the manual experiment. Automated conduct of the incubations using a 96-well equilibrium dialysis device as well as high-throughput liquid chromatography-mass spectrometry quantitation has now made this level of rigor accessible and useful. Sources of variability were assessed including well position, day-to-day, and site-to-site reproducibility. Optimal pH conditions were determined using a design of experiments method interrogating buffer strength, CO2 % and device preparation conditions. Variability was minimized by implementing an in-well control that is concurrently analyzed with new chemical entity analytes. Data acceptance criteria have been set for both the in-well control and the range of analyte variability, with a sliding scale tied to analyte-binding characteristics. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association J Pharm Sci 103:3302-3309, 2014.

Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies.

Using a genome-scale, lentivirally delivered shRNA library, we performed massively parallel pooled shRNA screens in 216 cancer cell lines to identify genes that are required for cell proliferation and/or viability. Cell line dependencies on 11,000 genes were interrogated by 5 shRNAs per gene. The proliferation effect of each shRNA in each cell line was assessed by transducing a population of 11M cells with one shRNA-virus per cell and determining the relative enrichment or depletion of each of the 54,000 shRNAs after 16 population doublings using Next Generation Sequencing. All the cell lines were screened using standardized conditions to best assess differential genetic dependencies across cell lines. When combined with genomic characterization of these cell lines, this dataset facilitates the linkage of genetic dependencies with specific cellular contexts (e.g., gene mutations or cell lineage). To enable such comparisons, we developed and provided a bioinformatics tool to identify linear and nonlinear correlations between these features.

Review: description of the developmental patterns of epithelial cells and cancers originating from them will provide many sites for therapy.

Many types of cancers represent different forms of blocked differentiation, but the relationship with major, currently identified cancer driver mutational and epigenetic events is not well defined. Normal cellular differentiation depends upon hierarchically-organized sequences of control and synthetic events coupled with cellular proliferation. An ability to identify and possibly correct or otherwise modify defective cancer stem or daughter cell differentiation, or even non-malignant precursor cell differentiation occurring prior to the effect of oncogene and suppressor genomic activity should provide many new approaches to circumventing the oncogenic process. The use of whole-genome sequencing and related procedures coupled with computer-based analyses of developmental event trees, and with the numerous reports from the ENCODE (Encyclopedia of DNA elements) project that has uncovered the large number of potential underlying regulatory and other functions in the junk DNA of cells should eventually define the temporal progression of normal and aberrant differentiating events as they modulate cellular proliferation. This information should identify many new differentiation sites and their coupling with cellular proliferation as new potential targets susceptible to therapeutic manipulation.