Data Model for the Comprehensive Management of Biobanks and Its Contribution to Personalized Medicine.

Biobanks are infrastructures essential for research involving multi-disciplinary teams and an increasing number of stakeholders. In the field of personalized medicine, biobanks play a key role through the provision of well-characterized and annotated samples protecting at the same time the right of donors. The Andalusian Public Health System Biobank (SSPA Biobank) has implemented a global information management system made up of different modules that allow for the recording, traceability and monitoring of all the information associated with the biobank operations. The data model, designed in a standardized and normalized way according to international initiatives on data harmonization, integrates the information necessary to guarantee the quality of results from research, benefiting researchers, clinicians and donors.

Green and sustainable approaches for the Friedel-Crafts reaction between aldehydes and indoles.

The synthesis of indoles and their derivatives, more specifically bis(indolyl)methanes (BIMs), has been an area of great interest in organic chemistry, since these compounds exhibit a range of interesting biological and pharmacological properties. BIMs are naturally found in cruciferous vegetables and have been shown to be effective antifungal, antibacterial, anti-inflammatory, and even anticancer agents. Traditionally, the synthesis of BIMs has been achieved upon the acidic condensation of an aldehyde with indole, utilizing a variety of protic or Lewis acids. However, due to the increased environmental awareness of our society, the focus has shifted towards the development of greener synthetic technologies, like photocatalysis, organocatalysis, the use of nanocatalysts, microwave irradiation, ball milling, continuous flow, and many more. Thus, in this review, we summarize the medicinal properties of BIMs and the developed BIM synthetic protocols, utilizing the reaction between aldehydes with indoles, while focusing on the more environmentally friendly methods developed over the years.

Effect of phage vB_EcoM_FJ1 on the reduction of ETEC O9:H9 infection in a neonatal pig cell line.

Enterotoxigenic Escherichia coli (ETEC) colonizes the intestine of young pigs causing severe diarrhoea and consequently bringing high production costs. The rise of antibiotic selective pressure together with ongoing limitations on their use, demands new strategies to tackle this pathology. The pertinence of using bacteriophages as an alternative is being explored, and in this work, the efficacy of phage vB_EcoM_FJ1 (FJ1) in reducing the load of ETEC EC43-Ph (serotype O9:H9 expressing the enterotoxin STa and two adhesins F5 and F41) was assessed. Foreseeing the oral application on piglets, FJ1 was encapsulated on calcium carbonate and alginate microparticles, thus preventing phage release under adverse conditions of the simulated gastric fluid (pH 3.0) and allowing phage availability in simulated intestinal fluid (pH 6.5). A single dose of encapsulated FJ1, provided to IPEC-1 cultured cells (from intestinal epithelium of piglets) previously infected by EC43, provided bacterial reductions of about 99.9% after 6 h. Although bacteriophage-insensitive mutants (BIMs) have emerged from treatment, the consequent fitness costs associated with this new phenotype were demonstrated, comparatively to the originating strain. The higher competence of the pig complement system to decrease BIMs' viability, the lower level of colonization of IPEC-1 cells observed with these mutants, and the increased survival rates and health index recorded in infected Galleria mellonella larvae supported this observation. Most of all, FJ1 established a proof-of-concept of the efficiency of phages to fight against ETEC in piglet intestinal cells.

Utilizing Modular Biobanking Software in Different Types of Biobanking Activities.

Biobanking defines all activities linked to bioresource management-whether of human, animal, microbial, or environmental origin-which means that any biobank information management system should take into account the multistep life cycle of the samples: from acquisition, through preparation, storage, to distribution to the end users (medical or research teams). Different types of biobanks can use diverse approaches, making it difficult to find software that can handle all types of scenarios. Modul-Bio has developed MBioLIMS BioBanking®, a software dedicated to biobanking, as a modular solution so that our various clients can access the functionalities and scale in a system to match their needs. These projects range from biobanks setup and managed by academic institutions, hospitals, and private companies to small and large clinical trials across different countries, as well as to whole campus or organization solutions for multiple biorepositories. Each solution differs in size, requirements, and number of users, from small biobanks with a few members of staff accessing the software to large operations with multiple sites that can collect and ship samples to a centralized site. This article explores different projects that use Modul-Bio's software in a myriad of ways to manage the complete life cycle of biospecimens and associated data.

How Well Does the Brief Interview for Mental Status Identify Risk for Cognition Mediated Functional Impairment in a Community Sample?

OBJECTIVE: To determine the adequacy of the Brief Interview for Mental Status (BIMS) compared with other screening tools in identifying individuals with limitations in functional cognition and instrumental activities of daily living (IADL). DESIGN: Cross-sectional observational study. SETTING: Midsized midwestern city. PARTICIPANTS: We assessed a convenience sample of community dwelling individuals (N=197) aged 55 years and older who were living independently. MAIN OUTCOME MEASURES: Participant scores on the BIMS, Mini-Cog, Menu Task, and Montreal Cognitive Assessment (MoCA) were compared with the Performance Assessment of Self-Care Skills Checkbook Balancing and Shopping tasks (PCST), which are known to predict impairment in complex IADLs associated with a diagnosis of mild cognitive impairment. Multiple logistic regression analyses controlling for participant demographics, as well as sensitivity and specificity, were computed for each screening measure using the PCST as the criterion measure. RESULTS: The Mini-Cog, Menu Task, and MoCA identified 25.89%, 32.49%, and 47.21% more individuals, respectively, as impaired than the BIMS. In multiple logistical regression analyses, the BIMS correctly identified 58% of those impaired on the PCST. However, each of the alternate screening measures correctly identified at least 70% of individuals as impaired on the PCST. CONCLUSIONS: In this community sample, the BIMS was insensitive to subtle impairments with the potential to compromise community living, suggesting that the BIMS may be inappropriate for use outside nursing home settings.

Automatic Indoor as-Built Building Information Models Generation by Using Low-Cost RGB-D Sensors.

To generate indoor as-built building information models (AB BIMs) automatically and economically is a great technological challenge. Many approaches have been developed to address this problem in recent years, but it is far from being settled, particularly for the point cloud segmentation and the extraction of the relationship among different elements due to the complicated indoor environment. This is even more difficult for the low-quality point cloud generated by low-cost scanning equipment. This paper proposes an automatic as-built BIMs generation framework that transforms the noisy 3D point cloud produced by a low-cost RGB-D sensor (about 708 USD for data collection equipment, 379 USD for the Structure sensor and 329 USD for iPad) to the as-built BIMs, without any manual intervention. The experiment results show that the proposed method has competitive robustness and accuracy, compared to the high-quality Terrestrial Lidar System (TLS), with the element extraction accuracy of 100%, mean dimension reconstruction accuracy of 98.6% and mean area reconstruction accuracy of 93.6%. Also, the proposed framework makes the BIM generation workflows more efficient in both data collection and data processing. In the experiments, the time consumption of data collection for a typical room, with an area of 45-67 m 2 , is reduced to 4-6 min with an RGB-D sensor from 50-60 min with TLS. The processing time to generate BIM models is about half minutes automatically, from around 10 min with a conventional semi-manual method.

Synthesis of novel antiproliferative hybrid bis-(3-indolyl)methane phosphonate derivatives.

An efficient synthetic methodology for the preparation of phosphorus substituted bis-(3-indolyl)methane through a double nucleophilic addition of indole derivatives to an in situ generated α-iminophosphonate is reported. In addition, bis-(3-indolyl)methane substrates showed in vitro cytotoxicity, inhibiting the growth of carcinoma human tumor cell lines A549 (carcinomic human alveolar basal epithelial cell) and SKOV03 (human ovarian carcinoma).

Propylsulfonic acid-anchored isocyanurate-based periodic mesoporous organosilica (PMO-ICS-Pr-SO3H): A new and highly efficient recoverable nanoporous catalyst for the one-pot synthesis of bis(indolyl)methane derivatives.

A new propylsulfonic acid-anchored isocyanurate bridging periodic mesoporous organosilica (PMO-ICS-Pr-SO3H) was prepared and shown to be a highly efficient recyclable nanoporous catalyst for the one-pot synthesis of bis(indolyl)methane derivatives in good to excellent yields from indole and different aldehydes in EtOH under mild reaction conditions in short reaction times. Moreover, the nanoporous catalyst was recovered and reused at least four times without significant decrease in its catalytic activity. The PMO-ICS-Pr-SO3H catalyst was characterizred by Fourier transform infrared (FTIR) spectroscopy, thermogravimetry analysis (TGA) and N2 adsorption-desorption isotherms techniques as well as field emission scanning electron microscopy (FESEM) and energy-dispersive X-ray (EDX) spectroscopy. Compared to the classical methodologies, this method illustrated significant advantages including low loading of the catalyst, high to excellent yields, short reaction times, avoiding the use of toxic transition metals or reactive reagents for modification of the catalytic activity, easy separation and purification of the products, and reusability of the catalyst.

Construction and the infection efficiency of BimS lentivirus RNA interference vector / 实用口腔医学杂志

Objective:To construct BimS lentivirus RNA interference(RNAi) vector and to study its infection efficiency by using RNAi technique.Methods:Three interference targets were designed according to the BimS sequence.The single chain primer was annealed into double-stranded oligo sequences,and then connected with vector linearized with Age Ⅰ and EcoR Ⅰ enzyme.The recombinant plasmid was packaged,and the infection efficiency was observed by infecting ACC-2 cells.Results:After amplification,a 337 bp band was appeared in the electrophoresis results of positive clones.Sequence of inserted fragments were identical with the result of DNA sequencing.Restructuring lentivirus was packed in 293T cells,the virus titer was 2 × 108 TU/ml,MOI =20,and the transfection efficiency was 85％.The BmS mRNA relative expression of pFU-GV-BmS-1,pFU-GV-BMS-2 and control group was 0.743 ±0.025,0.466 ±0.023 and 1.266 ±0.042 respectively(between each 2 groups,P ＜0.05).Conclusion:BimS lentivirus virus RNA interference vectors can be constructed,and can efficiently infect ACC-2 cells.

MCL-1 inhibition provides a new way to suppress breast cancer metastasis and increase sensitivity to dasatinib.

BACKGROUND: Metastatic disease is largely resistant to therapy and accounts for almost all cancer deaths. Myeloid cell leukemia-1 (MCL-1) is an important regulator of cell survival and chemo-resistance in a wide range of malignancies, and thus its inhibition may prove to be therapeutically useful. METHODS: To examine whether targeting MCL-1 may provide an effective treatment for breast cancer, we constructed inducible models of BIMs2A expression (a specific MCL-1 inhibitor) in MDA-MB-468 (MDA-MB-468-2A) and MDA-MB-231 (MDA-MB-231-2A) cells. RESULTS: MCL-1 inhibition caused apoptosis of basal-like MDA-MB-468-2A cells grown as monolayers, and sensitized them to the BCL-2/BCL-XL inhibitor ABT-263, demonstrating that MCL-1 regulated cell survival. In MDA-MB-231-2A cells, grown in an organotypic model, induction of BIMs2A produced an almost complete suppression of invasion. Apoptosis was induced in such a small proportion of these cells that it could not account for the large decrease in invasion, suggesting that MCL-1 was operating via a previously undetected mechanism. MCL-1 antagonism also suppressed local invasion and distant metastasis to the lung in mouse mammary intraductal xenografts. Kinomic profiling revealed that MCL-1 antagonism modulated Src family kinases and their targets, which suggested that MCL-1 might act as an upstream modulator of invasion via this pathway. Inhibition of MCL-1 in combination with dasatinib suppressed invasion in 3D models of invasion and inhibited the establishment of tumors in vivo. CONCLUSION: These data provide the first evidence that MCL-1 drives breast cancer cell invasion and suggests that MCL-1 antagonists could be used alone or in combination with drugs targeting Src kinases such as dasatinib to suppress metastasis.

Adenovirus mediated BIMS transfer induces growth supression and apoptosis in Raji lymphoma cells.

OBJECTIVE: To transfer pro-apoptotic BIM directly into tumor cells bypass the complicated biological processes of BIM activation so as to reverse the chemoresistance of cancer cells. METHODS: BIMS was specifically amplified from HL-60 cells by RT-PCR, confirmed to be correct by sequencing and cloned into shuttle vector pAdTrack-CMV carrying a green fluorescence protein gene to generate a recombinant plasmid pAdTrack-CMV-BIMS. This plasmid and adenovirus backbone plasmid pAdEasy-1 were linearized and electroporated into E.coli BJ5183 host bacteria to mediate homologous recombination. The positive clone was identified by restrict endonuclease digestion. The recombinant pAdEasy-CMV-BIMS was transferred into HEK293 cells for packaging and amplification. The successful construction of recombinant human BIMS adenovirus (Ad-BIMS) was demonstrated by Western blot. To test whether Ad-BIMS has the capability of inducing apoptosis of tumor cells, Ad-BIMS was used to infect GC resistant Burkitt lymphoma Raji cells. RESULTS: After infected for 2-5 days, BIMS expression in Raji cells was detected by RT-PCR and Western blot. The significant growth retardation and apoptosis of Raji cells were also observed by MTT and flow cytometry. CONCLUSION: These results indicated that BIMS might be a potential candidate of gene therapy for chemoresistant tumor cells.

An electronic specimen collection protocol schema (eSCPS). Document architecture for specimen management and the exchange of specimen collection protocols between biobanking information systems.

BACKGROUND: The integrity of collection protocols in biobanking is essential for a high-quality sample preparation process. However, there is not currently a well-defined universal method for integrating collection protocols in the biobanking information system (BIMS). Therefore, an electronic schema of the collection protocol that is based on Extensible Markup Language (XML) is required to maintain the integrity and enable the exchange of collection protocols. MATERIALS AND METHODS: The development and implementation of an electronic specimen collection protocol schema (eSCPS) was performed at two institutions (Muenster and Cologne) in three stages. First, we analyzed the infrastructure that was already established at both the biorepository and the hospital information systems of these institutions and determined the requirements for the sufficient preparation of specimens and documentation. Second, we designed an eSCPS according to these requirements. Finally, a prospective study was conducted to implement and evaluate the novel schema in the current BIMS. RESULTS: We designed an eSCPS that provides all of the relevant information about collection protocols. Ten electronic collection protocols were generated using the supplementary Protocol Editor tool, and these protocols were successfully implemented in the existing BIMS. Moreover, an electronic list of collection protocols for the current studies being performed at each institution was included, new collection protocols were added, and the existing protocols were redesigned to be modifiable. The documentation time was significantly reduced after implementing the eSCPS (5 ± 2 min vs. 7 ± 3 min; p = 0.0002). CONCLUSION: The eSCPS improves the integrity and facilitates the exchange of specimen collection protocols in the existing open-source BIMS.

Adenovirus mediated BIMS transfer induces growth supression and apoptosis in Raji lymphoma cells / 生物医学与环境科学（英文）

<p><b>OBJECTIVE</b>To transfer pro-apoptotic BIM directly into tumor cells bypass the complicated biological processes of BIM activation so as to reverse the chemoresistance of cancer cells.</p><p><b>METHODS</b>BIMS was specifically amplified from HL-60 cells by RT-PCR, confirmed to be correct by sequencing and cloned into shuttle vector pAdTrack-CMV carrying a green fluorescence protein gene to generate a recombinant plasmid pAdTrack-CMV-BIMS. This plasmid and adenovirus backbone plasmid pAdEasy-1 were linearized and electroporated into E.coli BJ5183 host bacteria to mediate homologous recombination. The positive clone was identified by restrict endonuclease digestion. The recombinant pAdEasy-CMV-BIMS was transferred into HEK293 cells for packaging and amplification. The successful construction of recombinant human BIMS adenovirus (Ad-BIMS) was demonstrated by Western blot. To test whether Ad-BIMS has the capability of inducing apoptosis of tumor cells, Ad-BIMS was used to infect GC resistant Burkitt lymphoma Raji cells.</p><p><b>RESULTS</b>After infected for 2-5 days, BIMS expression in Raji cells was detected by RT-PCR and Western blot. The significant growth retardation and apoptosis of Raji cells were also observed by MTT and flow cytometry.</p><p><b>CONCLUSION</b>These results indicated that BIMS might be a potential candidate of gene therapy for chemoresistant tumor cells.</p>

The bHLH proteins BEE and BIM positively modulate the shade avoidance syndrome in Arabidopsis seedlings.

The shade avoidance syndrome (SAS) refers to a set of plant responses initiated after perception by the phytochromes of light with a reduced red to far-red ratio, indicative of vegetation proximity or shade. These responses, including elongation growth, anticipate eventual shading from potential competitor vegetation by overgrowing neighboring plants or flowering to ensure production of viable seeds for the next generation. In Arabidopsis thaliana seedlings, the SAS includes dramatic changes in gene expression, such as induction of PHYTOCHROME RAPIDLY REGULATED 1 (PAR1), encoding an atypical basic helix-loop-helix (bHLH) protein that acts as a transcriptional co-factor to repress hypocotyl elongation. Indeed, PAR1 has been proposed to act fundamentally as a dominant negative antagonist of conventional bHLH transcription factors by forming heterodimers with them to prevent their binding to DNA or other transcription factors. Here we report the identification of PAR1-interacting factors, including the brassinosteroid signaling components BR-ENHANCED EXPRESSION (BEE) and BES1-INTERACTING MYC-LIKE (BIM), and characterize their role as networked positive regulators of SAS hypocotyl responses. We provide genetic evidence that these bHLH transcriptional regulators not only control plant growth and development under shade and non-shade conditions, but are also redundant in the control of plant viability. Our results suggest that SAS responses are initiated as a consequence of a new balance of transcriptional regulators within the pre-existing bHLH network triggered by plant proximity, eventually causing hypocotyls to elongate.