An integrative simulation model linking major biochemical reactions of actin-polymerization to structural properties of actin filaments

We report on an advanced universal Monte Carlo simulation model of actin polymerization processes offering a broad application panel. The model integrates major actin-related reactions, such as assembly of actin nuclei, association/dissociation of monomers to filament ends, ATP-hydrolysis via ADP-Pi formation and ADP-ATP exchange, filament branching, fragmentation and annealing or the effects of regulatory proteins. Importantly, these reactions are linked to information on the nucleotide state of actin subunits in filaments (ATP hydrolysis) and the distribution of actin filament lengths. The developed stochastic simulation modelling schemes were validated on: i) synthetic theoretical data generated by a deterministic model and ii) sets of our and published experimental data obtained from fluorescence pyrene-actin experiments. Build on an open-architecture principle, the designed model can be extended for predictive evaluation of the activities of other actin-interacting proteins and can be applied for the analysis of experimental pyrene actin-based or fluorescence microscopy data. We provide a user-friendly, free software package ActinSimChem that integrates the implemented simulation algorithms and that is made available to the scientific community for modelling in silico any specific actin-polymerization system.     

Phenotypic changes in the regenerating rabbit bladder muscle. Role of interstitial cells and innervation on smooth muscle cell differentiation

 We have studied the phenotypic changes in regenerating smooth muscle (SM) tissue of detrusor muscle after local application of a necrotizing, freeze–thaw injury to the serosal surface of rabbit bladder. Bromo-deoxyuridine (BrdU) incorporation and immunofluorescence studies were performed on bladder cryosections from day 2 up to day 15 after surgery with monoclonal antibodies specific for some cytoskeletal markers [desmin, vimentin, non-muscle (NM) myosin] and for SM-specific proteins (α-actin, myosin, and SM22). Four days after lesion, some clls incorporated in regenerating SM bundles are BrdU positive, but all display a phenotypic pattern identical to that of the interstitial, highly proliferating cells, i.e., expression of vimentin. By days 7–15 the differentiation profile of regenerating SM returns to that of uninjured SM tissue (appearance of desmin, SM-type α-actin, and SM myosin). A chemical denervation achieved by 6-hydroxydopamine treatment for 2 weeks induces the formation of vimentin/SM α-actin/NM myosin/SM22-containing myofibroblasts in the interstitial, fibroblast-like cells of uninjured bladder. In the bladder wall, alteration of reinnervation during the regenerating SM process produces: (1) in the outer region, the activation of vimentin/SM α-actin/desmin myofibroblasts in the de novo SM cell bundles; and (2) in the inner region of bladder, including the muscularis mucosae, the formation of proliferating, fully differentiated SM cells peripherally to newly formed SM cell bundles. These findings suggest that: (1) the de novo SM tissue formation in the bladder can occur via incorporation of interstitial cells into growing SM bundles; and (2) the alteration of reinnervation during the regenerating process induces a spatial-specific differentiation of interstitial myofibroblasts in SM cells before SM cell bundling. Accepted: 14 May 1997     

High Log-Scale Expansion of Functional Human Natural Killer Cells from Umbilical Cord Blood CD34-Positive Cells for Adoptive Cancer Immunotherapy

Immunotherapy based on natural killer (NK) cell infusions is a potential adjuvant treatment for many cancers. Such therapeutic application in humans requires large numbers of functional NK cells that have been selected and expanded using clinical grade protocols. We established an extremely efficient cytokine-based culture system for ex vivo expansion of NK cells from hematopoietic stem and progenitor cells from umbilical cord blood (UCB). Systematic refinement of this two-step system using a novel clinical grade medium resulted in a therapeutically applicable cell culture protocol. CD56⁺CD3⁻ NK cell products could be routinely generated from freshly selected CD34⁺ UCB cells with a mean expansion of >15,000 fold and a nearly 100% purity. Moreover, our protocol has the capacity to produce more than 3-log NK cell expansion from frozen CD34⁺ UCB cells. These ex vivo-generated cell products contain NK cell subsets differentially expressing NKG2A and killer immunoglobulin-like receptors. Furthermore, UCB-derived CD56⁺ NK cells generated by our protocol uniformly express high levels of activating NKG2D and natural cytotoxicity receptors. Functional analysis showed that these ex vivo-generated NK cells efficiently target myeloid leukemia and melanoma tumor cell lines, and mediate cytolysis of primary leukemia cells at low NK-target ratios. Our culture system exemplifies a major breakthrough in producing pure NK cell products from limited numbers of CD34⁺ cells for cancer immunotherapy.     

Modelling the ability of mass drug administration to interrupt soil-transmitted helminth transmission: Community-based deworming in Kenya as a case study

The World Health Organization has recommended the application of mass drug administration (MDA) in treating high prevalence neglected tropical diseases such as soil-transmitted helminths (STHs), schistosomiasis, lymphatic filariasis, onchocerciasis and trachoma. MDA—which is safe, effective and inexpensive—has been widely applied to eliminate or interrupt the transmission of STHs in particular and has been offered to people in endemic regions without requiring individual diagnosis. We propose two mathematical models to investigate the impact of MDA on the mean number of worms in both treated and untreated human subpopulations. By varying the efficay of drugs, initial conditions of the models, coverage and frequency of MDA (both annual and biannual), we examine the dynamic behaviour of both models and the possibility of interruption of transmission. Both models predict that the interruption of transmission is possible if the drug efficacy is sufficiently high, but STH infection remains endemic if the drug efficacy is sufficiently low. In between these two critical values, the two models produce different predictions. By applying an additional round of biannual and annual MDA, we find that interruption of transmission is likely to happen in both cases with lower drug efficacy. In order to interrupt the transmission of STH or eliminate the infection efficiently and effectively, it is crucial to identify the appropriate efficacy of drug, coverage, frequency, timing and number of rounds of MDA.     

Fulminant cryptosporidiosis associated with digestive adenocarcinoma in SCID mice infected with Cryptosporidium parvum TUM1 strain

We recently demonstrated that Cryptosporidium parvum IOWA strain induces in situ ileo-caecal adenocarcinoma in an animal model. Herein, the ability of another C. parvum strain to induce digestive neoplasia in dexamethasone-treated SCID mice was explored. SCID mice infected with C. parvum TUM1 strain developed a fulminant cryptosporidiosis associated with intramucosal adenocarcinoma, which is considered an early histological sign of invasive cancer. Both evidence of a role of C. parvum in adenocarcinoma induction and the extended prevalence of cryptosporidiosis worldwide, suggest that the risk of C. parvum-induced gastro-intestinal cancer in humans should be assessed.     

Mitosis-specific kinesins in Arabidopsis

Kinesins are a class of microtubule-associated proteins that possess a motor domain for binding to microtubules and, in general, allows movement along microtubules. In animal mitosis, they function in spindle formation, chromosome movement and in cytokinesis. In addition to the spindle, plants develop a preprophase band and a phragmoplast that might require multiple kinesins for construction and functioning. Indeed, several kinesins play a role in phragmoplast and cell plate dynamics. Surprisingly few kinesins have been associated with the spindle and the preprophase band. Analysis of expression datasets from synchronized cell cultures indicate that at least 23 kinesins are in some way implicated in mitosis-related processes. In this review, the function of kinesins in animal and plant mitoses are compared, and the divergence that originates from plant-specific aspects is highlighted.     

Is diatom size selection by harpacticoid copepods related to grazer body size?

Copepods are known as important consumers of primary production and are eaten by larger animals. They therefore form a main link to higher trophic levels. While feeding pathways and specificity of planktonic copepods have been well studied, the selectivity of the benthic harpacticoid copepods is far less documented. A better knowledge of the functional ecology of harpacticoids as important grazers on primary producers may have consequences for the re-evaluation of basic energy flow in benthic ecosystems.We tested whether size selectivity for diatoms exists in harpacticoid copepods. We hypothesized that size selectivity of harpacticoid copepod species is strongly related to body size. Because of morphological constraints, we expected smaller copepods to prefer smaller diatoms while larger copepods should be able to consume both small and large diatoms. We tested this hypothesis in four harpacticoid copepod species of varied body size: Tigriopus brevicornis, Harpacticus obscurus, Amphiascus minutus and Paramphiascella fulvofasciata. As food source we used two ¹³C labelled strains of the benthic diatom Seminavis robusta with a four-fold difference in cell biovolume.Three out of four harpacticoid species showed size selectivity: H. obscurus and A. minutus preferred the larger Seminavis cells, while P. fulvofasciata selected the smaller Seminavis cells. Based on monoclonal treatments, there was no clear preference found for T. brevicornis although there was a small preference for large cells in the mixed treatments. Except for P. fulvofasciata, all species showed a lower uptake when offered the mixed diet (both small and large cells). Although most species showed a size selectivity, our results suggest that this selectivity was not related to their body size. However, the only species that ate significantly more of small diatoms was characterised by comparatively small mouthparts in relation to its body size.     

Molecular cytogenetics and DNA sequence analysis of an apomixis-linked BAC in Paspalum simplex reveal a non pericentromere location and partial microcolinearity with rice

Apomixis in plants is a form of clonal reproduction through seeds. A BAC clone linked to apomictic reproduction in Paspalum simplex was used to locate the apomixis locus on meiotic chromosome preparations. Fluorescent in situ hybridisation revealed the existence of a single locus embedded in a heterochromatin-poor region not adjacent to the centromere. We report here for the first time information regarding the sequencing of a large DNA clone from the apomixis locus. The presence of two genes whose rice homologs were mapped on the telomeric part of the long arm of rice chromosome 12 confirmed the strong synteny between the apomixis locus of P. simplex with the related area of the rice genome at the map level. Comparative analysis of this region with rice as representative of a sexual species revealed large-scale rearrangements due to transposable elements and small-scale rearrangements due to deletions and single point mutations. Both types of rearrangements induced the loss of coding capacity of large portions of the “apomictic” genes compared to their rice homologs. Our results are discussed in relation to the use of rice genome data for positional cloning of apomixis genes and to the possible role of rearranged supernumerary genes in the apomictic process of P. simplex. Ornella Calderini and Song B. Chang have contributed equally to this article     

Ontogeny of the chondrocranium in Corydoras aeneus (Gill, 1858) (Callichthyidae, Siluriformes)

Callichthyids take a basal position in the loricarioid evolutionary lineage leading up to an algae scraping feeding mechanism in the loricariid family. Therefore, the study of the morphology and development of a callichthyid representative would contribute to a better knowledge on the differences in cranial morphology and their impact on feeding ecology within this superfamily. Therefore, development in the chondrocranium of Corydoras aeneus was studied based on 22 cleared and stained specimens and 6 series of serial sections. The latter sections were also digitized and used for 3D reconstructions. Development overall follows the typical siluriform trends in chondrocranial development. Even the low complexity of the chondrocranium at hatching fits the trend observed in other siluriforms, although other studies showed loricarioid hatchlings to generally show more complex chondrocrania. In contrast to other catfish, in C. aeneus, the notochord was never found to protrude into the hypophyseal fenestra. In addition, also differing from other siluriforms, a commissura lateralis is present, a state also reported for Ancistrus cf. triradiatus (Geerinckx et al., [2005] J Morphol 266:331-355). The splanchnocranium again has the typical siluriform shape during its ontogeny, with the presence of a compound hyosymplectic-pterygoquadrate plate, although not fused to the neurocranium or interhyal at any time during ontogeny, a state described earlier for Callichthys callichthys (Hoedeman, [1960a] Bull Aquat Biol 1:73-84; Howes and Teugels, [1989] J Zool Lond 219:441-456). The most striking difference found in comparison to other catfishes, however, involves thebranchial basket, which arises as a single element with a further differentiation from the middle arches on in both a rostral and caudal direction.