Menoci: lightweight extensible web portal enhancing data management for biomedical research projects.

BACKGROUND: Biomedical research projects deal with data management requirements from multiple sources like funding agencies' guidelines, publisher policies, discipline best practices, and their own users' needs. We describe functional and quality requirements based on many years of experience implementing data management for the CRC 1002 and CRC 1190. A fully equipped data management software should improve documentation of experiments and materials, enable data storage and sharing according to the FAIR Guiding Principles while maximizing usability, information security, as well as software sustainability and reusability. RESULTS: We introduce the modular web portal software menoci for data collection, experiment documentation, data publication, sharing, and preservation in biomedical research projects. Menoci modules are based on the Drupal content management system which enables lightweight deployment and setup, and creates the possibility to combine research data management with a customisable project home page or collaboration platform. CONCLUSIONS: Management of research data and digital research artefacts is transforming from individual researcher or groups best practices towards project- or organisation-wide service infrastructures. To enable and support this structural transformation process, a vital ecosystem of open source software tools is needed. Menoci is a contribution to this ecosystem of research data management tools that is specifically designed to support biomedical research projects.

Morphological development of Pleurochrysis carterae coccoliths examined by cryo-electron tomography.

Coccolithophores are single-celled marine algae that produce calcified scales called coccoliths. Each scale is composed of anvil-shaped single crystals of calcite that are mechanically interlocked, constituting a remarkable example of the multi-level construction of mineralized structures. Coccolith formation starts with the nucleation of rhombohedral crystals on an organic substrate called base plate. The crystals then grow preferentially along specific directions to generate the mature structure, which is then transported to the outside of the cells. Here, we extracted forming coccoliths from Pleurochrysis carterae cells and used cryo-electron tomography to characterize, in their native, hydrated state, the three-dimensional morphology and arrangement of the crystals. Comparing the crystal morphology across three different stages of coccolith formation, we show that competition for space between adjacent crystals contributes significantly to regulation of morphology by constraining growth in certain directions. We further demonstrate that crystals within a coccolith ring develop at different rates and that each crystalline unit rests directly in contact with the base plate and overgrow the rim of the organic substrate during development.

Three-dimensional architecture and surface functionality of coccolith base plates.

Coccolithophores are marine phytoplankton that are among the most prolific calcifiers widespread in Earth's oceans, playing a crucial role in the carbon cycle and in the transport of organic matter to the deep sea. These organisms produce highly complex mineralized scales that are composed of hierarchical assemblies of nano-crystals of calcium carbonate in the form of calcite. Coccolith formation in vivo occurs within compartmentalized mineralisation vesicles derived from the Golgi body, which contain coccolith-associated polysaccharides ('CAPs') providing polymorph selection and mediating crystal growth kinetics, and oval organic mineralisation templates, also known as base plates, which promote heterogenous nucleation and further mechanical interlocking of calcite single crystals. Although the function of coccolith base plates in controlling crystal nucleation have been widely studied, their 3D spatial organization and the chemical functional groups present on the crystal nucleation sites, which are two crucial features impacting biomineralization, remain unsolved. Utilising cryo-electron tomography we show that base plates derived from an exemplary coccolithophore Pleurochrysis carterae (Pcar) in their native hydrated state have a complex 3-layered structure. We further demonstrate, for the first time, the edge and rim of the base plate - where the crystals nucleate - are rich in primary amine functionalities that provide binding targets for negatively charged complexes composed of synthetic macromolecules and Ca2+ ions. Our results indicate that electrostatic interactions between the negatively charged biogenic CAPs and the positively charged rim of the base plate are sufficient to mediate the transport of Ca2+ cations to the mineralization sites.

Formation of Fluorohydroxyapatite with Silver Diamine Fluoride.

Silver diamine fluoride (SDF) is found to promote remineralization and harden the carious lesion. Hydroxyapatite crystallization is a crucial process in remineralization; however, the role of SDF in crystal formation is unknown. We designed an in vitro experiment with calcium phosphate with different SDF concentrations (0.38, 1.52, 2.66, 3.80 mg/mL) to investigate the effect of this additive on the nucleation and growth of apatite crystals. Two control groups were also prepared-calcium phosphate (CaCl2·2H2O + K2HPO4 in buffer solution) and SDF (Ag[NH3]2F in buffer solution). After incubation at 37 oC for 24 h, the shape and organization of the crystals were examined by bright-field transmission electron microscopy and electron diffraction. Unit cell parameters of the obtained crystals were determined with powder X-ray diffraction. The vibrational and rotational modes of phosphate groups were analyzed with Raman microscopy. The transmission electron microscopy and selected-area electron diffraction confirmed that all solids precipitated within the SDF groups were crystalline and that there was a positive correlation between the increased percentage of crystal size and the concentration of SDF. The powder X-ray diffraction patterns indicated that fluorohydroxyapatite and silver chloride were formed in all the SDF groups. Compared with calcium phosphate control, a contraction of the unit cell in the a-direction but not the c-direction in SDF groups was revealed, which suggested that small localized fluoride anions substituted the hydroxyl anions in hydroxyapatite crystals. This was further evidenced by the Raman spectra, which displayed up-field shift of the phosphate band in all the SDF groups and confirmed that the chemical environment of the phosphate functionalities indeed changed. The results suggested that SDF reacted with calcium and phosphate ions and produced fluorohydroxyapatite. This preferential precipitation of fluorohydroxyapatite with reduced solubility could be one of the main factors for arrest of caries lesions treated with SDF.

K-ras exon 2 point mutations in human endometrial cancer.

In the present study, we screened for the K-ras exon 2 point mutations in a group of 87 gynecological neoplasms (82 endometrial carcinomas, four carcinomas of the uterine cervix and one uterine carcinosarcoma) using the non-isotopic PCR-SSCP-direct sequencing techniques. Direct sequencing analysis revealed CAA-->CAC (Gln-->His) K-ras codon 61 point mutations in two (2.4%) of the 82 endometrial carcinomas mentioned above. These two cases were endometrial endometrioid carcinomas at an early clinical stage of disease (stage IB and IC due to FIGO). Those endometrial carcinomas that showed K-ras exon 2 point mutations revealed a strong positivity for heterogeneous nuclear retinoblastoma protein staining; none of these, however, have had the K-ras codon 12 point mutation. In addition, there were no K-ras gene point mutations in three endometrial carcinomas lacking the Rb protein immunohistochemically. None of the cervical carcinomas tested had K-ras gene point mutations, whereas one carcinosarcoma harbored K-ras codon 61 point mutation (CAA-->CAC). In conclusion, our data support the view that K-ras exon 2 point mutations are rare events in human endometrial cancer. Rb and K-ras gene abnormalities may occur independently of each other during endometrial carcinogenesis in humans.

Effect of tyrphostins on programmed cell death in colon adenocarcinoma cell line LS-180.

Programmed cell death is an important process in the regulation of cellular proliferation, rest, differentiation and death. It is a genetically controlled process with characteristic biochemical and morphological features. Apoptosis directly regulates tumorigenesis and its induction could be a useful method of cancer therapy. Cancer cells could be influenced by some factors which induce apoptosis. We investigated the influence of tyrphostins, that specifically inhibits protein tyrosine kinases and stops the cell cycle in apoptosis of the colon adenocarcinoma cell line LS180. We used them at the concentration of 1-10 microM for 24 and 48 hours. We detected apoptosis using techniques that monitor either biochemical and morphological features of this process, such as staining with 7-amino-actinomycin D, staining with Grünwald-Giemsa, TUNEL reaction, in situ hybridization and with immunoperoxidase staining procedures. We examined the expression of genes and proteins connected with programmed cell death (p53, c-myc, p21, bcl-2). We estimated the results by cytophotometry and documented them by colour photography. We found that tyrphostin rapidly inhibits the cell cycle, particularly at the concentration of 5 microM. The expression of genes and proteins was strongly correlated with the increased apoptotic cell death conforming to the results of TUNEL and staining methods.

Analysis of p53 and K-ras genes and their proteins in a sarcoma botryoides of the uterine cervix.

Several data indicate that the activation of oncogenes and growth factors as well as inactivation of the tumor suppressor genes are implicated in the development of human neoplasms, including sarcomas. In the present study we described a case of the extremely rare, but highly malignant neoplasm of the female genital tract known as sarcoma botryoides of the uterine cervix and assessed, using molecular and an immunohistochemical analysis, p53 and K-ras alterations in the tumor. A point mutation in exon 6 of the p53 tumor suppressor gene was found but no K-ras gene point mutations at codons 12, 13 and 61 were detected using molecular analysis. p53 protein was overexpressed in more than half of the neoplastic cells, however, ras p21 protein expression was not immunohistochemically detected. Our data indicate that p53, but not K-ras gene alterations may play a role in the development and progression of sarcoma botryoides of the uterine cervix.

[Prognostic value of amniotic fluid index estimated during labor during chronic fetal acidosis]. / Wartosc prognostyczna indeksu plynu owodniowego AFI oznaczanego w trakcie porodu przy przewidywaniu plodowej kwasicy.

There were performed measurements of AFI in 32 women during labour and they were referred to pH of neonatal umbilical vein. It was proved by significant statistic relation p = 0.034 (r = 0.375) between AFI and pH of umbilical vein blood. In anticipation of fetal acidosis with AFI < or = 5 cm with pH < or = 7.25 it was determined that: sensitivity 66.7%, specificity 58.6%, positive predictive value 14.3%, negative predictive value 94.4%, false positive 85.7%, false negative 5.6%, accuracy 59.4%. Obtained data do not differ from those given in literature. Measurements of AFI < or = 5 cm help in identification of the risk group (fetus in danger, of acidosis during labour) but due to low specificity and low positive predictive value (66.7% and 14.3% respectively). Clinical decisions should be made after consideration the result of the other tests of fetal well-being.

[A case of neoplastic diathesis]. / Przypadek skazy nowotworowej.

A female patient is described who during 7 years had three operations for neoplasms situated in various sites and exhibiting different histological structure. Seven years ago malignant melanoma was excised from her left thigh, three years later hysterectomy was done for carcinoma, 18 months later an epithelioid carcinoma was removed from the retroperitoneal space.