Factors that drive the increasing use of FFPE tissue in basic and translational cancer research

The decision to use 10% neutral buffered formalin fixed, paraffin embedded (FFPE) archival pathology material may be dictated by the cancer research question or analytical technique, or may be governed by national ethical, legal and social implications (ELSI), biobank, and sample availability and access policy. Biobanked samples of common tumors are likely to be available, but not all samples will be annotated with treatment and outcomes data and this may limit their application. Tumors that are rare or very small exist mostly in FFPE pathology archives. Pathology departments worldwide contain millions of FFPE archival samples, but there are challenges to availability. Pathology departments lack resources for retrieving materials for research or for having pathologists select precise areas in paraffin blocks, a critical quality control step. When samples must be sourced from several pathology departments, different fixation and tissue processing approaches create variability in quality. Researchers must decide what sample quality and quality tolerance fit their specific purpose and whether sample enrichment is required. Recent publications report variable success with techniques modified to examine all common species of molecular targets in FFPE samples. Rigorous quality management may be particularly important in sample preparation for next generation sequencing and for optimizing the quality of extracted proteins for proteomics studies. Unpredictable failures, including unpublished ones, likely are related to pre-analytical factors, unstable molecular targets, biological and clinical sampling factors associated with specific tissue types or suboptimal quality management of pathology archives. Reproducible results depend on adherence to pre-analytical phase standards for molecular in vitro diagnostic analyses for DNA, RNA and in particular, extracted proteins. With continuing adaptations of techniques for application to FFPE, the potential to acquire much larger numbers of FFPE samples and the greater convenience of using FFPE in assays for precision medicine, the choice of material in the future will become increasingly biased toward FFPE samples from pathology archives. Recognition that FFPE samples may harbor greater variation in quality than frozen samples for several reasons, including variations in fixation and tissue processing, requires that FFPE results be validated provided a cohort of frozen tissue samples is available.     

Immunohistochemical expression of rabphilin-3A-like (Noc2) in normal and tumor tissues of human endocrine pancreas

Involvement of rabphilin-3A-like (RPH3AL), or Noc2, the potential effector of Ras-associated binding proteins Rab3A and Rab27A in the regulation of exocytotic processes in the endocrine pancreas has been demonstrated in experimental models. Noc2 expression together with other regulatory molecules of the exocytotic machinery in human tissues, however, has not been studied. We evaluated immunohistochemical expression of the key molecules of the exocytotic machinery, Noc2, Rab3A, Rab27A, and RIM2, together with the characteristic islet cell hormones, insulin and glucagon in normal and endocrine tumor tissues of human pancreas. Normal pancreatic islets were stained for all of these proteins and showed strong cytoplasmic localization. A similar pattern of strong cytoplasmic expression of these proteins was observed in the majority of endocrine tumors. By contrast, the exocrine portions of normal appearing pancreas completely lacked Rab27A staining and showed decreased expression of the proteins, Noc2, Rab3A, and RIM2. The staining pattern of Noc2 and Rab27A was similar to the staining pattern of glucagon-producing cells within the islets. The concomitant expression of Noc2 with these molecules suggests that Noc2 may serve as an effector for Rab3A and Rab27A and that it is involved in the regulation of exocytosis of the endocrine pancreas in humans.     

First records of the seven-gilled Notorynchus cepedianus and six-gilled Hexanchus griseus sharks (Chondrichthyes: Hexanchiformes: Hexanchidae) found in the Galápagos Marine Reserve

This study reports the first records of cowsharks (Hexanchidae) in the Galápagos Islands, in particular Notorynchus cepedianus and Hexanchus griseus, observed between depths of 210 and 418 m on footage from free-falling autonomous deep-ocean cameras. These sightings provide new information on the habitat preferences and range distribution for N. cepedianus and the first records of H. griseus in Ecuadorian waters. The findings support the formulation of regional conservation strategies for these large apex predator species and highlight the limited biological knowledge of Galápagos' deep-water ecosystems.     

Structural Characterization of Anti-Inflammatory Immunoglobulin G Fc Proteins

Immunoglobulin G (IgG) is a central mediator of host defense due to its ability to recognize and eliminate pathogens. The recognition and effector responses are encoded on distinct regions of IgGs. The diversity of the antigen recognition Fab domains accounts for IgG's ability to bind with high specificity to essentially any antigen. Recent studies have indicated that the Fc effector domain also displays considerable heterogeneity, accounting for its complex effector functions of inflammation, modulation, and immune suppression. Therapeutic anti-tumor antibodies, for example, require the pro-inflammatory properties of the IgG Fc to eliminate tumor cells, while the anti-inflammatory activity of intravenous IgG requires specific Fc glycans for activity. In particular, the anti-inflammatory activity of intravenous IgG is ascribed to a small population of IgGs in which the Asn297-linked complex N-glycans attached to each Fc C_H2 domain include terminal α2,6-linked sialic acids. We used chemoenzymatic glycoengineering to prepare fully disialylated IgG Fc and solved its crystal structure. Comparison of the structures of asialylated Fc, sialylated Fc, and F241A Fc, a mutant that displays increased glycan sialylation, suggests that increased conformational flexibility of the C_H2 domain is associated with the switch from pro-inflammatory to anti-inflammatory activity of the Fc.     

Stimulation of the autonomic nervous system in colorectal surgery: a study protocol for a randomized controlled trial

In this study we describe the sociodemographic characteristics of people participating in a clinical trial on the safety and immunogenicity of a H5N1 influenza vaccine and we identify the main motivations for joining it.     

Local hemodynamics affect monocytic cell adhesion to a three-dimensional flow model coated with E-selectin.

Monocyte adhesion to the endothelium depends on concentrations of receptors/ligands, local concentrations of chemoattractants, monocyte transport to the endothelial surface and hemodynamic forces. Monocyte adhesion to the inert surface of a three-dimensional perfusion model was shown to correlate inversely with wall shear stress, but was also affected by flow patterns which influenced the near-wall cell availability. We hypothesized that (a) under the same flow conditions, insolubilized E-selectin on the model's surface may mediate adhesive interactions at higher wall shear stresses, compared to an uncoated model, and (b) pulsatile flow may modify the adhesion profile obtained under steady flow. An axisymmetric flow model with a stenosis and a sudden expansion produced a range of wall shear stresses and a separated flow with recirculation and reattachment. Pre-activated U937 cells were perfused through the model under either steady (Re = 100, 140) or pulsatile (Remean = 107) flow. The velocity field was characterized through computational fluid dynamics and validated by inert particle tracking. Surface E-selectin greatly increased cell adhesion in all regions at Re = 100 and 140, compared to an uncoated model under the same flow conditions. In regions where the cells near the wall were abundant (taper and stenosis), adhesion to E-selectin correlated with the reciprocal of local wall shear stress when flow was steady. Pulsatile flow distributed the adherent cells more evenly throughout the coated model. Hence, characterizing both the local hemodynamics and the biological activity on the vessel wall is important in leukocyte adhesion.     

The toxicity of peach tree roots

Summary The HCN content of peach plants and the effect of this and other substances formed from peach root residues on growth of peach trees and on soil microorganisms were investigated. Peach root bark contained appreciable amounts of HCN. HCN was released from live roots after mechanical injury. Benzaldehyde and KCN were toxic to rooted peach trees in the greenhouse and they inhibited respiration of peach root tips. A similar suppression of respiration was caused by benzoic acid, mandelonitrile, and water extracts of peach root bark incubated in peach and non-peach soils. Extracts from peach soil caused greater inhibition to respiration of peach root tips than extracts from non-peach soil.KCN, mandelonitrile, benzaldehyde, peach root bark, and amygdalin reduced the total micro-organism, actinomycete, pythium, and pathogenic nematode population of an old peach soil.     

Phylogenetic analysis of cichlid fishes using nuclear DNA markers

The recent explosive adaptive radiation of cichlids in the great lakes of Africa has attracted the attention of both morphologists and molecular biologists. To decipher the phylogenetic relationships among the various taxa within the family Cichlidae is a prerequisite for answering some fundamental questions about the nature of the speciation process. In the present study, we used the random amplification of polymorphic DNA (RAPD) technique to obtain sequence differences between selected cichlid species. We then designed specific primers based on these sequences and used them to amplify template DNA from a large number of species by the polymerase chain reaction (PCR). We sequenced the amplified products and searched the sequences for indels and shared substitutions. We identified a number of such characters at three loci-- DXTU1, DXTU2, and DXTU3--and used them for phylogenetic and cladistic analysis of the relationships among the various cichlid groups. Our studies assign an outgroup position to Neotropical cichlids in relation to African cichlids, provide evidence for a sister-group relationship of tilapiines to the haplochromines, group Cyphotilapia frontosa with the lamprologines of Lake Tanganyika, place Astatoreochromis alluaudi to an outgroup position with respect to other haplochromines of Lakes Victoria and Malawi, and provide additional support for the monophyly of the remaining Lake Victoria haplochromines and the Lake Malawi haplochromines. The described approach holds great promise for further resolution of cichlid phylogeny.      

Salmonellosis in laboratory-housed iguanid lizards (Sceloporus spp.).

Fifteen wild-caught iguanid lizards (14 Sceloporus variabilis and one S. malachiticus) were used in a 3 mo study on thermal acclimation. Over a 2 mo period, five of the lizards showed decreased activity, anorexia and enlarged joints, and were either found moribund or were euthanatized due to their poor condition. Specimens taken from lesions in four of the five lizards were cultured and were infected with Salmonella spp. Salmonella spp. was cultured from cloacal swabs in six of the 10 surviving lizards. Standard metabolic rates of those that were infected did not differ significantly from those that were not infected. We postulate that the lizards were inapparent carriers of Salmonella spp. at the time of capture and, as a result of stress, five developed active overwhelming systemic infections.     

On the discrimination between band-limited coherent and random apparent stresses in transitional pulsatile flow

A frequency domain approach that incorporates a matched filter was examined for discriminating between ordered velocity fluctuations with band-limited frequency content and random velocity variations in pulsatile disturbed flows. Fluctuations at pseudo-discrete frequencies may yield a significant contribution to the apparent stress tensor computed from the unsteady Navier Stokes equations, and an estimate of the stresses arising from these ordered structures can be obtained once the velocity variations have been decomposed. This type of decomposition permits the estimation of the apparent stresses in turbulent flows, consisting of coherent and random parts, in blood flow applications such as diseased constricted arteries or downstream of artificial heart valves.