Development and mechanistic explanation

Within modern philosophy of biology the topic of mechanistic explanation has become a central theme for critical discussion. The neo-mechanical philosophers have developed accounts that emphasize intervention and manipulation as the central epistemic tools that allow gaining epistemic access upon the mechanisms and have argued that the processes of inter-field integration across disciplines can be understood through the analysis of mechanisms spanning multiple levels. In this paper I revisit current proposals on mechanistic explanation in order to show some of their limitations when dealing with developmental mechanisms. I basically argue that (i) developmental mechanisms cannot be accommodated within a framework centered upon the mutual manipulation principle, (ii) the distinction between causal relations vs. constitutive relations cannot be easily demarcated within developmental biology and (iii) the notion of "part" underlying the neo-mechanical accounts on explanation is not suitable for developmental biology.     

Detection of Bacterial 16S rRNA and Identification of Four Clinically Important Bacteria by Real-Time PCR

Within the paradigm of clinical infectious disease research, Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa represent the four most clinically relevant, and hence most extensively studied bacteria. Current culture-based methods for identifying these organisms are slow and cumbersome, and there is increasing need for more rapid and accurate molecular detection methods. Using bioinformatic tools, 962,279 bacterial 16S rRNA gene sequences were aligned, and regions of homology were selected to generate a set of real-time PCR primers that target 93.6% of all bacterial 16S rRNA sequences published to date. A set of four species-specific real-time PCR primer pairs were also designed, capable of detecting less than 100 genome copies of A. baumannii, E. coli, K. pneumoniae, and P. aeruginosa. All primers were tested for specificity in vitro against 50 species of Gram-positive and –negative bacteria. Additionally, the species-specific primers were tested against a panel of 200 clinical isolates of each species, randomly selected from a large repository of clinical isolates from diverse areas and sources. A comparison of culture and real-time PCR demonstrated 100% concordance. The primers were incorporated into a rapid assay capable of positive identification from plate or broth cultures in less than 90 minutes. Furthermore, our data demonstrate that current targets, such as the uidA gene in E.coli, are not suitable as species-specific genes due to sequence variation. The assay described herein is rapid, cost-effective and accurate, and can be easily incorporated into any research laboratory capable of real-time PCR.     

Uniform light delivery in volumetric optoacoustic tomography

Accurate image reconstruction in volumetric optoacoustic tomography implies the efficient generation and collection of ultrasound signals around the imaged object. Non‐uniform delivery of the excitation light is a common problem in optoacoustic imaging often leading to a diminished field of view, limited dynamic range and penetration, as well as impaired quantification abilities. Presented here is an optimized illumination concept for volumetric tomography that utilizes additive manufacturing via 3D printing in combination with custom‐made optical fiber illumination. The custom‐designed sample chamber ensures convenient access to the imaged object along with accurate positioning of the sample and a matrix array ultrasound transducer used for collection of the volumetric image data. Ray tracing is employed to optimize the positioning of the individual fibers in the chamber. Homogeneity of the generated light excitation field was confirmed in tissue‐mimicking agar spheres. Applicability of the system to image entire mouse organs ex vivo has been showcased. The new approach showed a clear advantage over conventional, single‐sided illumination strategies by eliminating the need to correct for illumination variances and resulting in enhancement of the effective field of view, greater penetration depth and significant improvements in the overall image quality.      

Detecting de novo insulin synthesis in embryonic stem cell-derived populations

Several studies in recent years have described protocols, both genetic- and culture-based, that induce the differentiation of embryonic stem (ES) cells towards a pancreatic beta-cell type. The success of previous protocols in generating insulin-producing beta-cells has been questioned due in part to uncertainty regarding cell lineage but also due to the controversy regarding the source of any insulin detected in these cells. In an attempt to address the latter, we designed a novel assay that can identify de novo insulin synthesis. The method is based on metabolic labeling combined with a modified radio-immunoassay and will routinely detect less than 5 pg/microl of de novo insulin synthesis in lysates from the insulinoma cell line MIN6. This assay failed to detect any newly translated insulin in an ES cell-derived population generated using an adapted version of a previously published, 5-stage differentiation protocol. In combination with other techniques, including immunofluorescent staining and western blot analysis to detect and quantify C-peptide, we conclude that the majority of the insulin found in these differentiated ES cell cultures is medium-derived.     

Methotrexate in chronic-recurrent calcium pyrophosphate deposition disease: no significant effect in a randomized crossover trial

Introduction

Calcium pyrophosphate deposition (CPPD) may cause severe arthropathy, major joint destruction and treatment options are limited. The aim of this study was to test the therapeutic efficacy of methotrexate (MTX) in chronic or recurrent CPPD arthropathy.

Methods

Patients with CPPD arthropathy were randomized to receive either weekly subcutaneous injections of 15 mg/week of MTX or placebo (PBO) for three months, in a double-blind, crossover randomized controlled trial. Inclusion criteria comprised definite CPPD disease, recurrent arthritis or persistent polyarthritis, and an insufficient response to NSAIDs, glucocorticoids or colchicine. The primary outcome was an improvement in the disease activity scores based on 44 joints (DAS44). The analysis was performed on an intent-to-treat basis.

Results

We randomized 26 patients, and compared 25 treatment periods on MTX with 21 treatment periods on PBO. Baseline characteristics were balanced between the groups. The evolution of the DAS44 was not statistically significantly different between groups (median DAS44 decreased by −0.08 on MTX versus −0.13 on PBO, after three months, P = 0.44). Furthermore, pain levels remained stable in both groups (median change in VAS Pain −1 unit on MTX and 0 on PBO, P = 0.43), and none of the secondary outcomes was significantly different between the two groups. Minor adverse events (AE) did not differ in frequency between the groups, but the only serious AE occurred on MTX (bicytopenia).

Conclusions

The results of this trial with MTX in this older population with chronic or recurrent CPPD arthropathy suggest no strong effect of MTX on disease activity.

Trial registration

EudraCT No: 2007-003479-37. Registered 26 April 2008     

Targeting cyclin B1 through peptide-based delivery of siRNA prevents tumour growth

The development of short interfering RNA (siRNA), has provided great hope for therapeutic targeting of specific genes responsible for patholological disorders. However, the poor cellular uptake and bioavailability of siRNA remain a major obstacle to their clinical development and most strategies that propose to improve siRNA delivery remain limited for in vivo applications. In this study, we report a novel peptide-based approach, MPG-8 an improved variant of the amphipathic peptide carrier MPG, that forms nanoparticles with siRNA and promotes their efficient delivery into primary cell lines and in vivo upon intra-tumoral injection. Moreover, we show that functionalization of this carrier with cholesterol significantly improves tissue distribution and stability of siRNA in vivo, thereby enhancing the efficiency of this technology for systemic administration following intravenous injection without triggering any non-specific inflammatory response. We have validated the therapeutic potential of this strategy for cancer treatment by targeting cyclin B1 in mouse tumour models, and demonstrate that tumour growth is compromised. The robustness of the biological response achieved through this approach, infers that MPG 8-based technology holds a strong promise for therapeutic administration of siRNA.     

Checklist and Scoring System for the Assessment of Soft Tissue Preservation in CT Examinations of Human Mummies

The purpose of this study was to develop a checklist for standardized assessment of soft tissue preservation in human mummies based on whole-body computed tomography examinations, and to add a scoring system to facilitate quantitative comparison of mummies. Computed tomography examinations of 23 mummies from the Capuchin Catacombs of Palermo, Sicily (17 adults, 6 children; 17 anthropogenically and 6 naturally mummified) and 7 mummies from the crypt of the Dominican Church of the Holy Spirit of Vilnius, Lithuania (5 adults, 2 children; all naturally mummified) were used to develop the checklist following previously published guidelines. The scoring system was developed by assigning equal scores for checkpoints with equivalent quality. The checklist was evaluated by intra- and inter-observer reliability. The finalized checklist was applied to compare the groups of anthropogenically and naturally mummified bodies. The finalized checklist contains 97 checkpoints and was divided into two main categories, “A. Soft Tissues of Head and Musculoskeletal System” and “B. Organs and Organ Systems”, each including various subcategories. The complete checklist had an intra-observer reliability of 98% and an inter-observer reliability of 93%. Statistical comparison revealed significantly higher values in anthropogenically compared to naturally mummified bodies for the total score and for three subcategories. In conclusion, the developed checklist allows for a standardized assessment and documentation of soft tissue preservation in whole-body computed tomography examinations of human mummies. The scoring system facilitates a quantitative comparison of the soft tissue preservation status between single mummies or mummy collections.     

Conservation implications of grazing practices on the plant and dipteran communities of a turlough in Co. Mayo,Ireland

Turloughs, which are classified as priority habitats under the European Habitats Directive, are seasonally flooded depressions found almost exclusively in Ireland. In 2001, three adjacent fields with different stocking densities were selected and plant/dipteran communities within the same vegetation zone of each field (site) were investigated using quadrats and sweep netting, respectively. There was a significant positive relationship between Diptera morphospecies richness/Diptera abundance and mean vegetation height (P < 0.001). However, no significant relationship between Diptera morphospecies richness and plant species richness was found. Median Diptera morphospecies richness per sweep was lower at the site with the highest stocking density (17) than at the other two sites (22 and 31, respectively). Total species richness of Sciomyzidae was greater at the least grazed site (7) than at the more heavily grazed sites (2 and 1, respectively). The results suggest that an evaluation of turlough management practices based on plant communities alone is not sufficient and that at least some areas within the turlough basin remain ungrazed on a rotational basis to ensure maximum diversity of Diptera.     

Field and laboratory studies to determine the suitability of Cissoanthonomus tuberculipennis (Coleoptera: Curculionidae) for release against Cardiospermum grandiflorum (Sapindaceae) in South Africa

Cardiospermum grandiflorum is an invasive creeper that was targeted for biological control in South Africa in 2003. To determine ecological host range of its natural enemies, surveys were conducted on C. grandiflorum and 11 other Sapindaceae at 40 sites in the weed's native range (Argentina). These surveys indicated that the seed-feeding weevil Cissoanthonomus tuberculipennis was restricted to C. grandiflorum, and that it was among the common natural enemies, occurring at most sites where C. grandiflorum was recorded. Open-field tests were conducted under natural conditions in Argentina to determine the host preference of C. tuberculipennis and other natural enemies of C. grandiflorum among three Cardiospermum species. These tests revealed that C. tuberculipennis and the bug Gargaphia sp. were restricted to C. grandiflorum though the latter subsequently developed on non-target Cardiospermum species in the laboratory. C. tuberculipennis was found to be highly damaging, destroying up to 44% of the seeds per plant in Argentina. In all the host-specificity tests, including no-choice, paired-choice and multi-choice tests, C. tuberculipennis only fed and developed on C. grandiflorum. Failure of C. tuberculipennis to feed and develop on all congeners of C. grandiflorum shows that the weevil is highly host-specific to the target weed. Results of host-specificity tests, open field tests and long-term monitoring of C. tuberculipennis populations demonstrate that the weevil poses no threat to non-target plant species, and therefore safe for release against C. grandiflorum in South Africa. Permission to release C. tuberculipennis in South Africa has been granted by the relevant regulatory authorities.