Colorectal cancer screening: a new strategy for the demonstration of occult intestinal bleeding

The topic of colorectal cancer screening is discussed with special emphasis on its history and improvement of its methodology. The author's own results are evaluated in terms of international data published in literature in order to put forward his proposals for a new strategy. The devastating power and endemic character of colorectal cancers is stressed and the development of screening activities is recommended to accomplish within the frame of the complex health service.     

A mass spectrometric strategy for the rapid screening of homologous proteins: studies on a Pseudomonas azurin.

We describe a mass spectrometric strategy for the rapid screening of homologous proteins. The method involves non-specific enzymic digestion followed by a single ion-exchange purification step. Mixtures of peptides are then sequenced by low resolution electron impact mass spectrometry. Peptides are aligned by homology with a type sequence thus obviating the necessity for obtaining overlap information. The procedure, which is rapid and reliable, is illustrated by work on a $\text{Pseudomonas}$ azurin.     

CoagVDb: a comprehensive database for coagulation factors and their associated SAPs

The current state of the art in medical genetics is to identify and classify the functional (deleterious) or non-functional (neutral) single amino acid substitutions (SAPs), also known as non-synonymous SNPs (nsSNPs). The primary goal is to elucidate the mechanisms through which functional SAPs exert their effects, and ultimately interrogating this information for association with complex phenotypes. This work focuses on coagulation factors involved in the coagulation cascade pathway which plays a vital role in the maintenance of homeostasis in the human system. We developed an integrated coagulation variation database, CoagVDb, which makes use of the biological information from various public databases such as NCBI, OMIM, UniProt, PDB and SAPs (rsIDs/variant). CoagVDb enriched with computational prediction scores classify SAPs as either deleterious or tolerated. Also, various other properties are incorporated such as amino acid composition, secondary structure elements, solvent accessibility, ordered/disordered regions, conservation, and the presence of disulfide bonds. This specialized database provides integration of various prediction scores from different computational methods along with gene, protein, and disease information. We hope our database will act as a useful reference resource for hematologists to reveal protein structure–function relationship and disease genotype–phenotype correlation.

Electronic supplementary material

The online version of this article (doi:10.1186/s40659-015-0028-5) contains supplementary material, which is available to authorized users.     

A comprehensive approach for drug safety assessment

A comprehensive, multidisciplinary approach is proposed here for the development of a drug with an acceptable safety profile. Key parameters to be considered for drug safety evaluation based on this comprehensive approach include the following: (1) Pharmacology: Possible toxicity due to drug-target interactions, including interactions with unintended molecular targets, or with molecular targets in unintended organs. (2) Chemistry: Chemical scaffolding and side-chains with safety concerns. (3) Toxicology: Toxicity in animals in vivo, and in relevant animal and human cells in culture. (4) Drug metabolism and pharmacokinetics: Safety concerns due to toxification or detoxification, organ distribution, clearance and pharmacokinetic drug-drug interactions. (5) Risk factors: Physiological, environmental and genetic factors that may enhance a patient's susceptibility. It is proposed that this integrated, multidisciplinary approach to safety evaluation may enhance the accuracy of the prediction of drug safety and thereby the efficiency of drug development.     

The minisequencing method: a simple strategy for genetic screening of MEN 2 families

Background  

Multiple endocrine neoplasia type 2 is an autosomal dominant disorder. MEN 2A is characterized by medullary thyroid carcinoma, pheochromocytoma and hyperparathyroidism; MEN 2B by medullary thyroid carcinoma, pheochromocytoma and characteristic stigmata. Activating germline mutations of the RET proto oncogene are responsible for this hereditary syndrome. Codon 634 mutations are the most common mutations occurring in MEN 2A families whereas a specific mutation at codon 918 is observed in the great majority of MEN 2B families. Analysis of these codons will provide a final diagnosis in the great majority of affected families making unnecessary further studies. To specifically study the codons 634 and 918 we used a minisequencing method as an alternative method to complete sequencing.     

Geomorphic dynamics of floodplains: ecological implications and a potential modelling strategy

1.  The dynamics of channel migration and floodplain renewal constitute an important control of the ecological diversity of river corridors. Restoration initiatives should therefore assess whether these dynamics must be reinstated in order to address the cause rather than the symptoms of floodplain biodiversity decline.
2.  Restoration of reach-scale dynamism in rivers where this is a natural behavioural process will restore smaller-scale geomorphological and sedimentological processes that encourage vegetation regeneration, but may require catchment-scale management of material flows.
3.  Channel dynamics depend on the style of river–floodplain interaction, and this may be summarised in qualitative, classificatory, sedimentological models of floodplain architecture that have been somewhat neglected in the ecological literature.
4.  One approach to the assessment of floodplain biodiversity and its restoration would be through the development of simulation models based on specified channel styles, and involving simplified hydrodynamics and successional changes. Such models, currently the subject of research as a spin-off from modelling studies of landscape evolution, would permit evaluation of the consequences for ecological diversity of implementing various management options that may affect the dynamics of channel migration.     

Development of a strategy for the screening of α-glucosidase-producing microorganisms

α-Glucosidase is a crucial enzyme for the production of isomaltooligosaccharide. In this study, a novel method comprising eosin Y (EY) and α-d-methylglucoside (AMG) in glass plates was tested for the primary screening of α-glucosidaseproducing strains. First, α-glucosidase-producing Aspergillus niger strains were selected on plates containing EY and AMG based on transparent zone formation resulting from the solubilization of EY by the hydrolyzed product. Conventional methods that use trypan blue (TB) and p-nitrophenyl-α-d-glucopyranoside (pPNP) as indicators were then compared with the new strategy. The results showed that EY-containing plates provide the advantages of low price and higher specificity for the screening of α-glucosidase-producing strains. We then evaluated the correlation between the hydrolytic activity of α-glucosidase and diffusion distance, and found that good linearity could be established within a 6–75 U/ml enzyme concentration range. Finally, the hydrolytic and transglycosylation activities of α-glucosidase obtained from the target isolates were determined by EY plate assay and 3,5-dinitrosalicylic acid-Saccharomyces cerevisiae assay, respectively. The results showed that the diameter of the transparent zone varied among isolates was positively correlated with α-glucosidase hydrolytic activity, while good linearity could also be established between α-glucosidase transglycosylation activity and non-fermentable reducing sugars content. With this strategy, 7 Aspergillus niger mutants with high yield of α-glucosidase from 200 obvious single colonies on the primary screen plate were obtained.     

A new pooling strategy for high-throughput screening: the Shifted Transversal Design

Background  

In binary high-throughput screening projects where the goal is the identification of low-frequency events, beyond the obvious issue of efficiency, false positives and false negatives are a major concern. Pooling constitutes a natural solution: it reduces the number of tests, while providing critical duplication of the individual experiments, thereby correcting for experimental noise. The main difficulty consists in designing the pools in a manner that is both efficient and robust: few pools should be necessary to correct the errors and identify the positives, yet the experiment should not be too vulnerable to biological shakiness. For example, some information should still be obtained even if there are slightly more positives or errors than expected. This is known as the group testing problem, or pooling problem.     

MeTaDoR: a comprehensive resource for membrane targeting domains and their host proteins

MOTIVATION: Protein-lipid interactions play a central role in cellular signaling and membrane trafficking and at the core of these interactions are domains specialized in lipid binding and membrane targeting. Considering the importance of these domains, we have created MeTaDoR, a comprehensive resource dedicated to membrane targeting domains (MTDs). RESULT: MeTaDoR begins with a brief introduction about all the important MTDs including their subcellular localization and structural features. Sequences of all known MTDs are then provided in two formats: standard Prosite format and a parsed tab-delimited format that provides a manually curated classification into binding or non-binding. Structures of all MTDs and host proteins known so far are provided with links to PDB and Pfam databases. Membrane-binding orientation of these proteins, whether experimentally determined or proposed, is also provided with links to the appropriate literature. To facilitate molecular dynamics studies of these proteins, the force-field parameters for many non-standard lipids that commonly interact with these proteins are also provided. Finally, an online server for predicting membrane-binding proteins and a search function with various search fields are included. The resource is publicly available and will be updated on a regular basis.     

Biodegradation of pig manure by the housefly, Musca domestica: a viable ecological strategy for pig manure management

The technology for biodegradation of pig manure by using houseflies in a pilot plant capable of processing 500-700 kg of pig manure per week is described. A single adult cage loaded with 25,000 pupae produced 177.7±32.0 ml of eggs in a 15-day egg-collection period. With an inoculation ratio of 0.4-1.0 ml eggs/kg of manure, the amount of eggs produced by a single cage can suffice for the biodegradation of 178-444 kg of manure. Larval development varied among four different types of pig manure (centrifuged slurry, fresh manure, manure with sawdust, manure without sawdust). Larval survival ranged from 46.9±2.1%, in manure without sawdust, to 76.8±11.9% in centrifuged slurry. Larval development took 6-11 days, depending on the manure type. Processing of 1 kg of wet manure produced 43.9-74.3 g of housefly pupae and the weight of the residue after biodegradation decreased to 0.18-0.65 kg, with marked differences among manure types. Recommendations for the operation of industrial-scale biodegradation facilities are presented and discussed.     

The key elements of a comprehensive global mammal conservation strategy

A global strategy is necessary to achieve the level of coordination, synergy and therefore optimization of resources to achieve the broad goal of conserving mammals worldwide. Key elements for the development of such a strategy include: an institutional subject that owns the strategy; broad conservation goals, quantitative targets derived from them and appropriate indicators; data on the distribution of species, their threats, the cost-effectiveness of conservation actions; and a set of methods for the identification of conservation priorities. Previous global mammal research investigated phylogeny, extinction risk, and the species and areas that should be regarded as global conservation priorities. This theme issue presents new key elements: an updated Red List Index, a new list of evolutionarily distinct and globally endangered species, new high-resolution mammal distribution models, a global connectivity analysis and scenarios of future mammal distribution based on climate and land-cover change. Area prioritization schemes account for mammalian phylogeny, governance and cost-benefit of measures to abate habitat loss. Three discussion papers lay the foundations for the development of a global unifying mammal conservation strategy, which should not be further deterred by the knowledge gaps still existing.     

A comprehensive review of the screening methodology for anaerobic biodegradability of surfactants

A biodegradability assay should mimic in situ conditions as closely as possible. If this is not entirely possible, the assayshould at least include inoculum from the site. This review attemptsto condense current literature on anaerobic biodegradability assayand propose a clear assessment methodology to determine the fatesurfactants in anaerobic environments. It has been well documentedthat surfactant concentrations toxic to the microflora can lead tounwarranted failure of biodegradability assays. Thus, an important recommendation is to first perform a toxicity evaluation with relevant controls. Based on the results of this evaluation, a Tier 1biodegradability assay that assesses the rate of formation of reducedendproducts or the consumption of a particular terminal electron acceptor is recommended and supported by current literature. Balancedchemical equations for the complete mineralization of the substrateare then used to compare the amount of transformation that actuallyoccurred with that theoretically expected. When required, resultsshould be confirmed by Tier 2 testing, which includes monitoring ofsubstrate disappearance over time using a variety of analytical tools.These recommended procedures are scientifically defensible and havethe potential of providing environmentally relevant information on thefate of surfactant materials in the environment.     

The use of SAX-HPLC-CD as a heparin screening strategy

Heparin, a heterogeneous polysaccharide, has been widely used as an anticoagulant for decades. Recently, however, international events involving the sudden onset of allergic-type reactions following heparin administration led to numerous fatalities, and demanded the use of multiple laborious, time consuming techniques to identify an economically motivated adulterant. Using these methods cooperatively, the semi-synthetic molecule known as oversulfated chondroitin sulfate (OSCS), was found to be present at significant concentrations. Since the discovery of this adulterant, several analytical methods have been put forth or updated to advance the process of screening pharmaceutical heparins; of these, strong anion exchange high performance liquid chromatography (SAX-HPLC) methods have now become routine. In this preliminary work, we report the use of circular dichroism (CD) detection in conjunction with existing SAX-HPLC methods to quantitate various sulfated polysaccharides. The proposed strategy exploits the selectivity associated with CD detection of heparin and heparin-like polysaccharides, while taking advantage of the method's insensitivity to the use of mobile phase additives and programmed gradients. The limit of detection of heparin by CD was found to be ～0.22 mg/mL, whereas traditional UV/Vis detection yielded a detection limit of ～1.09 mg/mL. The success of CD detection varied for other polymers, however no significant modifications were made to the separations method to capitalize on the advantages of CD detection.     

A strategy for evaluating the safety of organisms for biological weed control

A strategy for establishing the specificity and safety of an organism as a biological weed control agent is described. A critical first step is to expose to its attack a small group of plants very closely related and exhibiting morphological and biochemical similarities to the weed. To prevent an erroneous negative result tests are also made on selected cultivated plants, including those closely related to the weed, those of which the associated insects and fungi are little known, those that have evolved apart from or been little exposed to the agent, those attacked by closely related organisms and those already recorded as hosts. The circumstances under which the strategy might fail to indicate safety are discussed, i.e. polyphagous organisms attacking plants irregularly distributed throughout many families, organisms highly specific to two alternate hosts, and those attacking two or three phylogenetically widely separated plant groups. The additional crop plant testing, included in the overall strategy to deal with such possible failures, is discussed. It is shown that the strategy would have included Sesamum tndicum in the list of plants challenged by the bug Teleonemia scrupulosa in biological testing for control of Lantana camara, thereby forewarning of the attack that was subsequently observed in Africa.     

An NMR strategy for fragment-based ligand screening utilizing a paramagnetic lanthanide probe

A nuclear magnetic resonance-based ligand screening strategy utilizing a paramagnetic lanthanide probe is presented. By fixing a paramagnetic lanthanide ion to a target protein, a pseudo-contact shift (PCS) and a paramagnetic relaxation enhancement (PRE) can be observed for both the target protein and its bound ligand. Based on PRE and PCS information, the bound ligand is then screened from the compound library and the structure of the ligand–protein complex is determined. PRE is an isotropic paramagnetic effect observed within 30 Å from the lanthanide ion, and is utilized for the ligand screening in the present study. PCS is an anisotropic paramagnetic effect providing long-range (~40 Å) distance and angular information on the observed nuclei relative to the paramagnetic lanthanide ion, and utilized for the structure determination of the ligand–protein complex. Since a two-point anchored lanthanide-binding peptide tag is utilized for fixing the lanthanide ion to the target protein, this screening method can be generally applied to non-metal-binding proteins. The usefulness of this strategy was demonstrated in the case of the growth factor receptor-bound protein 2 (Grb2) Src homology 2 (SH2) domain and its low- and high-affinity ligands.     

The safety problem and a physiological strategy for using glucocorticoid hormones]

Principal problems of glucocorticoid hormone application in non-endocrine diseases are discussed proceeding from the mechanism of their action and the role in organism's life. It appeared that the hazard of glucocorticoid therapy is mainly due to the absence of a test for sufficiency and real needs in these hormones. It was shown that the test has to be introduced reflecting on the whole body level the glucocorticoid activity in the cell, that is similar to blood glucose in relation to insulin. The introduction of free blood tyrosine as such test appears to allow the development of safe individual strategy for the usage of glucocorticoids.     

Molecular genetic testing for familial hypercholesterolemia in the Netherlands: a stepwise screening strategy enhances the mutation detection rate

Familial hypercholesterolemia (FH) has been identified as a major risk factor for coronary vascular disease and is associated with mutations in the low-density liporotein receptor (LDLR) and apolipoprotein B (APOB) gene. The molecular basis of FH in the Dutch population is well understood. Approximately 160 different LDLR and APOB gene defects have been identified with a panel of 9 LDLR gene and 1 APOB gene frequently occurring mutations accounting for approximately 30% of all clinically diagnosed FH cases. As molecular diagnosis of FH is becoming increasingly widely applied, a variety of mutation detection rates is reported, ranging from as low as 30% and up to 80%. This variability appears to depend on the clinical criteria applied to identify patients with FH and on the strategies and methodologies used for mutation screening. In this study we describe the application of a stepwise screening approach, combining different methodologies, to detect mutations of the LDLR gene and APOB gene in 1465 patients with FH. A mutation was found in approximately 44% of the patients, which demonstrates that this is an effective strategy for the molecular diagnosis of FH.