Modelling an outbreak of an emerging pathogen

To illustrate the usefulness of mathematical models to the microbiology and medical communities, we explain how to construct and apply a simple transmission model of an emerging pathogen. We chose to model, as a case study, a large (>8,000 reported cases) on-going outbreak of community-acquired meticillin-resistant Staphylococcus aureus (CA-MRSA) in the Los Angeles County Jail. A major risk factor for CA-MRSA infection is incarceration. Here, we show how to design a within-jail transmission model of CA-MRSA, parameterize the model and reconstruct the outbreak. The model is then used to assess the severity of the outbreak, predict the epidemiological consequences of a catastrophic outbreak and design effective interventions for outbreak control.     

Adaptation of an introduced host to an indigenous parasite

Introduction of striped bass to the west coast from the east coast of the U.S.A. provided the opportunity to study a recent host-parasite association in a marine system. An indigenous species of parasite was known to induce pathological changes in the introduced population. Because the west coast population has been in association with this pathogenic parasite more than 20 generations, we predicted that the host reaction of the west coast population would be less severe compared to that of the naive east coast stock of striped bass. This prediction was tested by conducting reciprocal infection experiments with east and west coast hosts and parasites. The group of west coast striped bass had a lower intensity of infection and exhibited less tissue damage compared to the group of east coast striped bass. We suggest that selection has acted only on the host and is driven by parasite-induced host mortality. This type of 1-sided selection is in contrast to present models of the evolution of host-parasite associations.     

Inheritance of an oviposition behavior by an egg parasitoid

A quantitative genetic study revealed genetic and environmental sources of variance in percentage parasitism of European corn borer egg masses and secondary sex ratios by Trichogramma nubilale. Full and half-sib groups of T. nubilale were obtained from a nested mating design, which permitted the partitioning of the variance of T. nubilale parasitism of European corn borer egg masses into additive genetic variance, maternal/dominant variance and environmental variance. A mother-daughter regression of the percentage of an egg mass parasitized allowed a determination of the direction of a potential response to selection in the event of maternal effects. No or very little additive genetic effects were associated with the percentage of eggs within a mass parasitized and secondary sex ratios, but a significant amount of the variance for both traits had a maternal and/or dominant genetic source. The relationship between mothers and daughters in egg mass parasitism was positive, and 55.4% of the progeny of a given mother had behaviors that resemble their mother. Most of the variance had an environmental and/or unknown genetic source implying potentially high phenotypic plasticity associated with all these traits. The presence of maternal effects and phenotypic plasticity could have multiple and complex effects on progeny characters and potential responses to selection.     

Implementation of an AI-assisted fragment-generator in an open-source platform

We recently reported a deep learning model to facilitate fragment library design, which is critical for efficient hit identification. However, our model was implemented in Python. We have now created an implementation in the KNIME graphical pipelining environment which we hope will allow experimentation by users with limited programming knowledge.

We report a deep learning model to facilitate fragment library design, which is critical for efficient hit identification, and an implementation in the KNIME graphical workflow environment which should facilitate a more codeless use.     

Development of an STS map of an interspecific progeny of Malus

Simple sequence repeat (SSR) markers developed from Malus, as well as Prunus, Pyrus and Sorbus, and some other sequence-tagged site (STS) loci were analysed in an interspecific F₁ apple progeny from the cross ‘Fiesta’ × ‘Totem’ that segregated for several agronomic characters. A linkage map was constructed using 259 STS loci (247 SSRs, four SCARs and eight known-function genes) and five genes for agronomic traits—scab resistance (Vf), mildew resistance (Pl-2), columnar growth habit (Co), red tissues (Rt) and green flesh background colour (Gfc). Ninety SSR loci and three genes (ETR1, Rt and Gfc) were mapped for the first time in apple. The transferability of markers from other Maloideae to Malus was found to be around 44%. The loci are spread across 17 linkage groups, corresponding to the basic chromosome number of Malus and cover 1,208 cM, approximately 85% of the estimated length of the apple genome. Interestingly, we have extended the top of LG15 with eight markers covering 25 cM. The average map density is 4.7 cM per marker; however, marker density varies greatly between linkage groups, from 2.5 in LG14 to 8.9 in LG7, with some areas of the genome still in need of further STS markers for saturation. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. An erratum to this article can be found at     

Tauchbeobachtungen an Plankton und an Echostreuschichten

Zusammenfassung 1. Das Tauchen als Methode zur Untersuchung von Plankton und Echostreuschichten wird durch vier Beispiele erläutert: (a) Visuelle Beobachtungen an Wasserschichtungen und Grenzschichten durch Schwimmtaucher. (b) Untersuchung von Echostreuschichten durch Freitaucher, wobei sich ergab, daß angesammeltes biogenes Material in den untersuchten Sprung- beziehungsweise Streuschichten die Schallreflektion nicht beeinflußt. (c) Beobachtung von Großplankton und Feststellung von Planktonund Sestonkonzentrationen beim Tauchen mit dem Bathyscaph. (d) Untersuchung der Tiefenstreuschicht (deep scattering layer) durch Beobachtung der Vertikalwanderung bestimmter Arten des Großplanktons mit den Tauchbooten Bathyscaph und Soucoupe Plongeante. Physonectide Siphonophoren und Myctophiden standen in deutlicher Beziehung zur Tiefenstreuschicht und wurden als Echogeber erkannt.2. Die Möglichkeiten, von Tauchbooten aus quantitative und qualitative Proben von Plankton und auch vom Benthos zu nehmen, sind zur Zeit noch unzureichend. Die Entwicklung entsprechender Geräte für den wahlweisen und mehrfachen Einsatz bei demselben Tauchgang wird empfohlen.

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Diving observations on plankton and on scattering layers

Diving techniques are employed as a research tool in plankton investigations carried out in shallow water of the western Baltic Sea. Observations and samplings were made by skin divers on scattering layers corresponding to the discontinuity layers. Biogene materials, sometimes concentrated at the thermocline, are not responsible for this special kind of scattering, but rather discontinuity of salinity and temperature (Lenz 1965). For observations in deep water the use of undersea vehicles is recommended. From the Bathyscaph and the diving saucer, single plankton organisms and plankton concentrations were observed (e. g.Bernard 1958); investigations on the deep scattering layer have shown physonectid siphonophores and myctophids to be scatterers (Barham 1966). The equipment for sampling plankton and benthos from undersea vehicles is poorly developed. We need urgently gear for quantitative and qualitative sampling and for manifold use during single dives, i. e., multiple sampling gear and magazins for storage of samples.

     

Solution structure of an oligonucleotide containing an abasic site: evidence for an unusual deoxyribose conformation

The antitumor antibiotic bleomycin causes two major lesions in the deoxyribose backbone of DNA: formation of 4′-keto abasic sites and formation of strand breaks with 3′-phosphoglycolate and 5′-phosphate ends. As a model for the 4′-keto abasic site, we have characterized an abasic site (X) in d(CCAAAGXACTGGG)·d(CCCAGTACTTTGG) by two-dimensional NMR spectroscopy. A total of 475 NOEs and 101 dihedral angles provided the restraints for molecular modeling. Four unusual NOEs were observed between each anomer of the abasic site and the neighboring bases. In addition, four coupling constants for adjacent protons of the deoxyribose of both the α and β anomers of the abasic site were observed. The modeling suggests that for both anomers the abasic site is extrahelical, without significant distortion of the backbone opposite the lesion. The coupling constants further allowed assignment of an unusual sugar pucker for each anomer. The unique position of the abasic site in our structural model for each anomer is discussed in terms of repair of such lesions in vivo.     

Isolation of an agent affecting the development of an internal parasitoid

The development of an internal braconid parasitoid, Glyptapanteles militaris, is adversely affected when its host, Pseudaletia unipuncta, is infected with the Hawaiian strain of granulosis virus. A plasma-derived agent, isolated from virus-infected hosts, was shown to elicit developmental aberrations in the parasitoid similar to those observed in virus-infected hosts. This agent was isolated by ammonium sulfate precipitation, gel filtration, and anion exchange chromatography, and its molecular weight, established by gel filtration and SDS-polyacrylamide gel electrophoresis, was determined to be about 64,000. The dilution end point of the agent and some stability properties were also established.     

Seprase: an overview of an important matrix serine protease

Seprase or Fibroblast Activation Protein (FAP) is an integral membrane serine peptidase, which has been shown to have gelatinase activity. Seprase has a dual function in tumour progression. The proteolytic activity of Seprase has been shown to promote cell invasiveness towards the ECM and also to support tumour growth and proliferation. Seprase appears to act as a proteolytically active 170-kDa dimer, consisting of two 97-kDa subunits. It is a member of the group type II integral serine proteases, which includes dipeptidyl peptidase IV (DPPIV/CD26) and related type II transmembrane prolyl serine peptidases, which exert their mechanisms of action on the cell surface. DPPIV and Seprase exhibit multiple functions due to their abilities to form complexes with each other and to interact with other membrane-associated molecules. Localisation of these protease complexes at cell surface protrusions, called invadopodia, may have a prominent role in processing soluble factors and in the degradation of extracellular matrix components that are essential to the cellular migration and matrix invasion that occur during tumour invasion, metastasis and angiogenesis.     

Synthetic peptide model of an essential region of an aminoacyl-tRNA synthetase

A 40 amino acid sequence of the unsolved structure of Escherichia coli alanine-tRNA synthetase is essential for tRNA binding and encodes an immunological determinant that cross-reacts with antibodies raised against a eukaryote (insect Bombyx mori) alanine enzyme. The secondary structure of this sequence is predicted to be an amphiphilic alpha-helix that includes one aspartyl and eight glutamyl side chain carboxyl groups. The antibody reactivity and the conformation of a synthetic peptide model of this region (Glu346 to Ser385) were investigated. In addition, double Arg----Gln and Leu----Ala substitutions were separately placed in the enzyme on the hydrophilic and hydrophobic face, respectively, of the predicted helix. These mutations conserve the polar/nonpolar character of each face and retain the potential for helix formation. Circular dichroism spectra of the synthetic peptide model demonstrate the potential for amphiphilic helix formation for the segment from Glu346 to Ser385. The behavior of the mutations in the enzyme, together with earlier data and immunological assays presented here, suggests that one face of the putative helix is an antigenic region of the surface of the enzyme where it contributes to the interaction with alanine tRNA and that the specific sequence of the helix is an important determinant of enzyme stability.     

Properties of an unusual DNA primase from an archaeal plasmid

Primases are specialized DNA-dependent RNA polymerases that synthesize a short oligoribonucleotide complementary to single-stranded template DNA. In the context of cellular DNA replication, primases are indispensable since DNA polymerases are not able to start DNA polymerization de novo.

The primase activity of the replication protein from the archaeal plasmid pRN1 synthesizes a rather unusual mixed primer consisting of a single ribonucleotide at the 5′ end followed by seven deoxynucleotides. Ribonucleotides and deoxynucleotides are strictly required at the respective positions within the primer. Furthermore, in contrast to other archaeo-eukaryotic primases, the primase activity is highly sequence-specific and requires the trinucleotide motif GTG in the template. Primer synthesis starts outside of the recognition motif, immediately 5′ to the recognition motif. The fidelity of the primase synthesis is high, as non-complementary bases are not incorporated into the primer.

     

Obesity and microbiota: an example of an intricate relationship

It is widely accepted that metabolic disorders, such as obesity, are closely linked to lifestyle and diet. Recently, the central role played by the intestinal microbiota in human metabolism and in progression of metabolic disorders has become evident. In this context, animal studies and human trials have demonstrated that alterations of the intestinal microbiota towards enhanced energy harvest is a characteristic of the obese phenotype. Many publications, involving both animal studies and clinical trials, have reported on the successful exploitation of probiotics and prebiotics to treat obesity. However, the molecular mechanisms underlying these observed anti-obesity effects of probiotics and prebiotic therapies are still obscure. The aim of this mini-review is to discuss the intricate relationship of various factors, including diet, gut microbiota, and host genetics, that are believed to impact on the development of obesity, and to understand how modulation of the gut microbiota with dietary intervention may alleviate obesity-associated symptoms.     

Comparative larval energetics of an ophiuroid and an echinoid echinoderm

The morphologically convergent larvae of the echinoderm classes Ophiuroidea and Echinoidea have been suggested to be functionally dissimilar when it comes to their capacities to feed, but little is known about whether these larvae are similar in terms of energetics. Here, we compare the energetics of early development of a tropical ophiuroid, Ophiocoma alexandri, and a temperate to tropical echinoid, Arbacia punctulata, two species with similarly sized eggs. Measurements of respiration and constituent analyses were performed on eggs and unfed larvae of both species. Members of both species showed an increase in oxygen consumption during morphogenesis followed by a lower, static rate once morphogenesis was complete (3 d for O. alexandri and 1.3 d for A. punctulata). Compared to the echinoid larvae, the ophiuroid larvae developed more slowly and had peak respiration rates that were 3.1× lower. Eggs of O. alexandri contained significantly more protein and significantly less triacylglycerol than eggs of A. punctulata. Energy utilization, as calculated via respiration measurements, closely matched decreases in energy content from the eggs to larvae as measured with biochemical constituent assays. Larvae of A. punctulata used 1.4× more energy to reach the pluteus stage than larvae of O. alexandri, and used 4× more energy during the first 9 d of larval life. These data suggest that echinoid larvae require more energy to develop to the feeding stage than ophiuroid larvae, and likewise have higher requirements for maintenance metabolism. Ophiuroid larvae may be more tolerant of low food levels due to their very low metabolic rates, but this advantage may be offset by their slower rate of development.     

Multipole representation of an eccentric dipole and an eccentric double-layer

Recently a theorem for representing current generators in a volume conductor by the superposition of a central dipole, quadrupole, octopole, etc., has been established by G. C. K. Yeh, J. Martinek, and H. de Beaumont (Bull. Math. Biophysics,20, 203–16, 1958). This theorem makes possible the representation of any discrete or line, surface- or volume-distributed current source by a unique model which can be determined for each given case by surface potential measurements and closed form analysis. In this paper the multipole representations of an eccentric dipole and an eccentric double-layer are obtained in terms of the various parameters of the assumed singularities, and the contributions to surface potentials due to each of the multipoles are compared. Certain numerical results corresponding to those of E. Frank (Amer. Heart J.,46, 364–78, 1953) are carried out and compared. Furthermore, the multipole representation of a partially damaged double-layer is also determined and compared with that of an undamaged one. It is concluded that within the range of parameters corresponding to human subjects the higher-order multipoles can contribute significantly to the surface potentials compared with the dipole. This investigation was supported by the National Heart Institute under a research grant H-2263(c).     

Incidence of an electron layer on an electrically insulated body with an unsteady self-consistent positive charge

Dynamics of an electron layer incident on the surface of an electrically insulated conducting body with an unsteady self-consistent positive charge is investigated. At the initial instant, the electron velocity is directed toward the body and the electron layer is not adjacent to the body surface. One-dimensional plane, cylindrical, and spherical electron motions in vacuum and against the background of motionless ions and neutral particles are considered. Exact analytical solutions to the set of nonlinear plasma hydrodynamics equations with absorbing boundary conditions for electrons are obtained. The spatial and time dependences of the electric field, electron density, and electron velocity are found. The time evolution of the surface charge density is determined.     

Carbon as an indicator of Daphnia condition in an alpine lake

Carbon–length relationships can be used to indicate the condition of daphnids in natural situations. We examined the Daphnia galeata population of an alpine lake (Oberer, Arosasee, Switzerland), where most individuals display diel vertical migration behaviour (DVM). Normally, migrating daphnids face a trade-off between `predator safe areas' in the hypolimnion and `food rich areas' with high predation risk. However, in alpine lakes, with chlorophyll a and POC maxima typically in deeper layers and weak temperature gradients, migrating species are confronted less with this trade-off. We investigated the seasonal changes in carbon content of D. galeata in different depth strata in relation to environmental parameters of the lake. The carbon content of D. galeata was high in spring, but declined considerably in summer and increased slightly in autumn. The low values indicate that D. galeata are food limited for much of the year. The slopes of the regression lines between carbon content and body length varied seasonally, but were not significantly different among depths on a given date. In summer, D. galeata individuals residing in the deep layers during the day had a significantly higher carbon content than individuals in the surface layers. During the rest of the year, the carbon content of individuals was similar among all depth strata. We conclude that migrating D. galeata and individuals remaining in deep layer had better body conditions compared to non-migrating D. galeata in this alpine lake during summer, when migration amplitudes were highest.     

Induction of an epithelial-mesenchymal transition by an in vivo adheron-like complex

The embryonic vertebrate heart consists of two epithelia: the myocardium and endothelium, separated by the myocardial basement membrane (MBM). The myocardium has been shown to induce endothelial transformation into prevalvular mesenchyme in a temporally and site restricted manner. Previously, we hypothesized that the myocardial-endothelial interaction is mediated in vivo by aggregates of 30-nm particles in the MBM which can be removed by EDTA extraction. These MBM extracts contain fibronectin and other lower Mr proteins and can initiate an epithelial-mesenchymal transition in the AV (atrioventricular canal) endothelium of embryonic chick heart in collagen gel culture. These and other data suggested that the 30-nm multicomponent particles are similar, structurally and compositionally, to multimolecular complexes, termed adherons, secreted by L6 muscle cells in culture. The purpose of this study was to (1) test whether the removal of the 30-nm particles from MBM extracts of embryonic chick hearts would remove the in vitro biological activity and (2) determine if the fractionated MBM extracts can cause AV endothelial cells to follow the same differentiation pathway observed in vivo by monitoring immunohistochemically the cell surface expression of N-CAM. Results showed that centrifugation of extract at 100,000g for 1 hr produced a supernatant fraction that was unable to initiate mesenchyme formation from AV endothelium. However, the resuspended pellet fraction did initiate differentiation of endothelium into mesenchyme. Conditioned medium from L6 skeletal muscle cultures could not substitute for the EDTA extract of embryonic heart. Endothelial cells undergoing the transition to form mesenchyme, both in vivo and in vitro, showed a concomitant decrease in N-CAM staining. This suggested that the pellet-induced formation of migrating cells in the collagen gels is not the result a novel in vitro phenomenon.     

Development of an Fn14 agonistic antibody as an anti-tumor agent

TNF-like weak inducer of apoptosis (TWEAK), a tumor necrosis factor (TNF) family ligand with pleiotropic cellular functions, was originally described as capable of inducing tumor cell death in vitro. TWEAK functions by binding its receptor, Fn14, which is upregulated on many human solid tumors. Herein, we show that intratumoral administration of TWEAK, delivered either by an adenoviral vector or in an immunoglobulin Fc-fusion form, results in significant inhibition of tumor growth in a breast xenograft model. To exploit the TWEAK-Fn14 pathway as a therapeutic target in oncology, we developed an anti-Fn14 agonistic antibody, BIIB036. Studies described herein show that BIIB036 binds specifically to Fn14 but not other members of the TNF receptor family, induces Fn14 signaling and promotes tumor cell apoptosis in vitro. In vivo, BIIB036 effectively inhibits growth of tumors in multiple xenograft models, including colon (WiDr), breast (MDA-MB-231) and gastric (NCI-N87) tumors, regardless of tumor cell growth inhibition response observed to BIIB036 in vitro. The anti-tumor activity in these cell lines is not TNF-dependent. Increasing the antigen-binding valency of BIIB036 significantly enhances its anti-tumor effect, suggesting the contribution of higher order cross-linking of the Fn14 receptor. Full Fc effector function is required for maximal activity of BIIB036 in vivo, likely due to the cross-linking effect or tumor killing activity caused by antibody-dependent cell-mediated cytotoxicity. Taken together, the anti-tumor properties of BIIB036 validate Fn14 as a promising target in oncology and demonstrate its potential therapeutic utility in multiple solid tumor indications.Key words: TWEAK, Fn14, monoclonal antibody, agonist, xenograft, apoptosis     

Periphyton growth as an indicator of eutrophication; an experimental approach

Growth of periphyton was studied in the Archipelago Sea (Finland) during summer 1994 as a part of the annual monitoring control of fish farms. Experimental growth plates (Whatman GF/C filters) were incubated (two weeks) at 213 sites in different parts of the Archipelago Sea and in the coastal area north of the Archipelago Sea. At each site incubations were repeated two or three times during the summer (July 4- -September 1). The growth of periphyton was measured as the amount of chlorophyll a (mg m-2) extracted from the incubation plates. The growth varied significantly among different parts of the study area. The strongest growth was observed in the inner archipelago and in areas with high fish production and relatively slow water exchange. In the outer archipelago, rapid water exchange ensured good mixing of nutrients from fish farms and other sources into relatively large water volumes. The local impacts of nutrient loading thus remained too low to be detected by measuring nutrient concentrations or periphyton growth. Periphyton growth was positively correlated with concentrations of total nitrogen, total phosphorus and chlorophyll a in the productivity layer (approximately 2 × Secchi depth). A significant inverse correlation was also shown between periphyton growth and Secchi depth. Archipelago areas with different levels of eutrophication could satisfactorily be distinguished in this study. The results were consequent with previous classifications of the eutrophication levels in the Archipelago Sea. Periphyton studies thus are a useful addition to conventional monitoring programs. This revised version was published online in July 2006 with corrections to the Cover Date.     

Development of an Fn14 agonistic antibody as an anti-tumor agent

TWEAK, a TNF family ligand with pleiotropic cellular functions, was originally described as capable of inducing tumor cell death in vitro. TWEAK functions by binding its receptor, Fn14, which is up-regulated on many human solid tumors. Herein, we show that intratumoral administration of TWEAK, delivered either by an adenoviral vector or in an immunoglobulin Fc-fusion form, results in significant inhibition of tumor growth in a breast xenograft model. To exploit the TWEAK-Fn14 pathway as a therapeutic target in oncology, we developed an anti-Fn14 agonistic antibody, BIIB036. Studies described herein show that BIIB036 binds specifically to Fn14 but not other members of the TNF receptor family, induces Fn14 signaling, and promotes tumor cell apoptosis in vitro. In vivo, BIIB036 effectively inhibits growth of tumors in multiple xenograft models, including colon (WiDr), breast (MDA-MB-231), and gastric (NCI-N87) tumors, regardless of tumor cell growth inhibition response observed to BIIB036 in vitro. The anti-tumor activity in these cell lines is not TNF-dependent. Increasing the antigen-binding valency of BIB036 significantly enhances its anti-tumor effect, suggesting the contribution of higher order cross-linking of the Fn14 receptor. Full Fc effector function is required for maximal activity of BIIB036 in vivo, likely due to the cross-linking effect and/or ADCC mediated tumor killing activity. Taken together, the anti-tumor properties of BIIB036 validate Fn14 as a promising target in oncology and demonstrate its potential therapeutic utility in multiple solid tumor indications.