Molecular Biological Data Research Articles

Evidence for the functional involvement of members of the TRP channel family in the uptake of Na(+) and NH4 (+) by the ruminal epithelium.

Large quantities of protein are degraded in the fermentative parts of the gut to ammonia, which is absorbed, detoxified to urea, and excreted, leading to formation of nitrogenous compounds such as N2O that are associated with global warming. In ruminants, channel-mediated uptake of NH4 (+) from the rumen predominates. The molecular identity of these channels remains to be clarified. Ruminal cells and epithelia from cows and sheep were investigated using patch clamp, Ussing chamber, microelectrode techniques, and qPCR. In patch clamp experiments, bovine ruminal epithelial cells expressed a conductance for NH4 (+) that could be blocked in a voltage-dependent manner by divalent cations. In the native epithelium, NH4 (+) depolarized the apical potential, acidified the cytosol and induced a rise in short-circuit current (I sc) that persisted after the removal of Na(+), was blocked by verapamil, enhanced by the removal of divalent cations, and was sensitive to certain transient receptor potential (TRP) channel modulators. Menthol or thymol stimulated the I sc in Na(+) or NH4 (+) containing solutions in a dose-dependent manner and modulated transepithelial Ca(2+) fluxes. On the level of messenger RNA (mRNA), ovine and bovine ruminal epithelium expressed TRPA1, TRPV3, TRPV4, TRPM6, and TRPM7, with any expression of TRPV6 marginal. No bands were detected for TRPV1, TRPV5, or TRPM8. Functional and molecular biological data suggest that the transport of NH4 (+), Na(+), and Ca(2+) across the rumen involves TRP channels, with TRPV3 and TRPA1 emerging as prime candidate genes. TRP channels may also contribute to the transport of NH4 (+) across other epithelia.

Pituitary Adenylate Cyclase Activating Polypeptide, A Potential Therapeutic Agent for Diabetic Retinopathy in Rats: Focus on the Vertical Information Processing Pathway.

Pituitary adenylate cyclase activating polypeptide (PACAP) is a neurotrophic and neuroprotective peptide that has been shown to exert protective effects in different neuronal injuries, such as retinal degenerations. Diabetic retinopathy (DR), the most common complication of diabetes, affects the microvasculature and neuronal architecture of the retina. We have proven earlier that PACAP is also protective in a rat model of DR. In this study, streptozotocin-induced DR was treated with intravitreal PACAP administration in order to further analyze the synaptic structure and proteins of PACAP-treated diabetic retinas, primarily in the vertical information processing pathway. Streptozotocin-treated Wistar rats received intravitreal PACAP injection three times into the right eye 2weeks after the induction of diabetes. Morphological and molecular biological (qRT-PCR; Western blot) methods were used to analyze retinal synapses (ribbons, conventional) and related structures. Electron microscopic analysis revealed that retinal pigment epithelium, the ribbon synapses and other synaptic profiles suffered alterations in diabetes. However, in PACAP-treated diabetic retinas more bipolar ribbon synapses were found intact in the inner plexiform layer than in DR animals. The ribbon synapse was marked with C-terminal binding protein 2/Bassoon and formed horseshoe-shape ribbons, which were more retained in PACAP-treated diabetic retinas than in DR rats. These results are supported by molecular biological data. The selective degeneration of related structures such as bipolar and ganglion cells could be ameliorated by PACAP treatment. In summary, intravitreal administration of PACAP may have therapeutic potential in streptozotocin-induced DR through maintaining synapse integrity in the vertical pathway.

Wikidata as a semantic framework for the Gene Wiki initiative.

Open biological data are distributed over many resources making them challenging to integrate, to update and to disseminate quickly. Wikidata is a growing, open community database which can serve this purpose and also provides tight integration with Wikipedia. In order to improve the state of biological data, facilitate data management and dissemination, we imported all human and mouse genes, and all human and mouse proteins into Wikidata. In total, 59 721 human genes and 73 355 mouse genes have been imported from NCBI and 27 306 human proteins and 16 728 mouse proteins have been imported from the Swissprot subset of UniProt. As Wikidata is open and can be edited by anybody, our corpus of imported data serves as the starting point for integration of further data by scientists, the Wikidata community and citizen scientists alike. The first use case for these data is to populate Wikipedia Gene Wiki infoboxes directly from Wikidata with the data integrated above. This enables immediate updates of the Gene Wiki infoboxes as soon as the data in Wikidata are modified. Although Gene Wiki pages are currently only on the English language version of Wikipedia, the multilingual nature of Wikidata allows for usage of the data we imported in all 280 different language Wikipedias. Apart from the Gene Wiki infobox use case, a SPARQL endpoint and exporting functionality to several standard formats (e.g. JSON, XML) enable use of the data by scientists.In summary, we created a fully open and extensible data resource for human and mouse molecular biology and biochemistry data. This resource enriches all the Wikipedias with structured information and serves as a new linking hub for the biological semantic web.Database URL: https://www.wikidata.org/

Transcriptome Analysis and Development of SSR Molecular Markers in Glycyrrhiza uralensis Fisch.

Licorice is an important traditional Chinese medicine with clinical and industrial applications. Genetic resources of licorice are insufficient for analysis of molecular biology and genetic functions; as such, transcriptome sequencing must be conducted for functional characterization and development of molecular markers. In this study, transcriptome sequencing on the Illumina HiSeq 2500 sequencing platform generated a total of 5.41 Gb clean data. De novo assembly yielded a total of 46,641 unigenes. Comparison analysis using BLAST showed that the annotations of 29,614 unigenes were conserved. Further study revealed 773 genes related to biosynthesis of secondary metabolites of licorice, 40 genes involved in biosynthesis of the terpenoid backbone, and 16 genes associated with biosynthesis of glycyrrhizic acid. Analysis of unigenes larger than 1 Kb with a length of 11,702 nt presented 7,032 simple sequence repeats (SSR). Sixty-four of 69 randomly designed and synthesized SSR pairs were successfully amplified, 33 pairs of primers were polymorphism in in Glycyrrhiza uralensis Fisch., Glycyrrhiza inflata Bat., Glycyrrhiza glabra L. and Glycyrrhiza pallidiflora Maxim. This study not only presents the molecular biology data of licorice but also provides a basis for genetic diversity research and molecular marker-assisted breeding of licorice.

C3-P-06Structome analysis of freeze-substituted virulentMycobacterium tuberculosisbased on direct enumeration of the serial ultrathin sections with TEM

Serial ultrathin sections of virulent Mycobacterium tuberculosis H37Rv (ATCC 27294) were examined by transmission electron microscope and “structome” analysis (i.e., the quantitative three-dimensional structural analysis of a whole cell through direct enumeration and measurement at the electron microscopic level) was performed [ 1 ]. Five M. tuberculosis cells were cut into 24, 36, 69, 55, and 63 serial ultrathin cross sections, respectively. On average, the cells were 2.71 ± 1.05 μm in length, and the average diameter of the cell was 0.345 ± 0.029 μm. The outer membrane and plasma membrane surface areas were 3.04 ± 1.33 μm 2 and 2.67 ± 1.19 μm 2 , respectively. The cell and cytoplasm volumes were 0.293 ± 0.113 fl (= μm 3 ) and 0.210 ± 0.091 fl, respectively. The average total ribosome number per cell was 1,672 ± 568, and the ribosome density was 716.5 ± 171.4/0.1 fl. This is the first report of a structome analysis of M. tuberculosis cells prepared as serial ultrathin sections following cryofixation and rapid freeze substitution. These data are based on the direct measurement and enumeration of exquisitely preserved single-cell structures in transmission electron microscopy images rather than calculations or assumptions from indirect biochemical or molecular biological data, and may explain the slow growth of M. tuberculosis and enhance understanding of the structural properties related to the expression of antigenicity, acid-fastness, and the mechanism of drug resistance, particularly in regard to the ratio of target to drug concentrations.

METB-07CLASSIFICATION OF HIGH GRADE GLIOMA USING MATRIX-ASSISTED LASER DESORPTION/IONIZATION MASS SPECTROMETRY IMAGING (MALDI MSI): INTERIM RESULTS OF THE GLIOMIC STUDY

Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) allows to determine spatial localization of molecules along tissue sections. The aim of the Gliomic study is to classify high-grade gliomas (HGG) by MALDI-MSI according to their prognosis. Until now, samples from 13 patients have been analyzed after tumor resection. According to the OMS 2007 classification, 3 tumors were grade 3 (2 oligoastrocytoma and 1 astrocytoma) and 10 were grade 4. An isocitrate dehydrogenase 1 (IDH1) mutation was found in 31% of the cases, a O(6)-methylguanine-DNA methyltransferase (MGMT) promoter methylation in 20% (median value: 5%, range 2-93%). Frozen tissue sections of 12 µm thickness were realized and matrix was then deposited homogeneously with a manual sprayer to cover the entire surface. Tissues were prepared for analysis of low-weighted molecules, particularly lipids. Tumor-specific mass spectra were acquired with 70 µm spatial resolution. After molecular image acquisition, matrix was removed, tissues were stained and annotated by a pathologist. The imaging datasets were spatially segmented by clustering all spectra by their molecular profiles similarity. Individual tissue segmentations were compared with histological annotations and revealed new regions of interest. A low concordance between the histological annotations and the MS imaging data was found for tumor regions. Global segmentations were generated using all the tissues and revealed 3 molecularly different groups. Known low infiltrated regions and necrotic regions were still grouped together respectively after this global segmentation. Pre-necrotic regions were divided between necrotic and tumor regions. Moreover, we highlighted sub-regions within the tumor area which were not histologically annotated. This analysis provided new insights into HGG tissue organization. The data obtained from MALDI MSI analysis may provide specific information and allow a more accurate diagnosis. A total of 21 patients have been enrolled and updated results will be presented taking account histological and molecular biology data.

Description and phylogeny of a new prostomatid, Metacystis similis nov. spec. (Protista, Ciliophora) from the East China Sea

The living morphology and infraciliature of a new marine prostomatid, Metacystis similis nov. spec., have been observed and investigated. Based on both morphological and molecular biological data, several closely-related and easily confused taxa were compared. The diagnosis for this new taxon: cylindrical marine Metacystis with a slightly blunt anterior end, in vivo 50-70 x 18-23 μm; body not loricate, uniformly cinctured by 16-18 transverse rings of cilia, which are also arranged in 32-36 longitudinal kineties; oral apparatus consisting of one circumoral dikinety and six girdles of densely packed monokinetids; single spherical macronucleus located in the center of the body; caudal region possessing one transparent, protruding hemicycle terminal vacuole. Information concerning the small-subunit rRNA gene sequence of the new species was also provided.

The early history of the metazoa—a paleontologist’s viewpoint

The molecular biology success, which became influential for a revision of principal views on the relationships and evolutionary pathways of major groups ("phyla") of multicellular animals, were much more appreciated by palaeontologists rather than by neontologists. This is not surprising because this is the fossil record that serves as a firm test for molecular biological hypotheses. The fossil record indicates that the different "phyla" united nowadays into the Ecdysozoa, namely, arthropods, onychophorans, tardigrades, priapulids, nematomorphs, comprise a number of transitional forms having become extinct already in the early Palaeozoic. The very appearance of those organisms fits entirely to hypothetical ancestral forms which have to exist in accordance with some data on ontogeny. There are no even tentative intermediates between arthropods and annelids in the fossil record. The oldest Deuterostomia, which is the only branch of the Bilateria being agreed upon by all the biological disciplines, allow us, although in less details, to present their early history and point to agile bilaterally-symmetrical forms at the dawn of chordates, hemichordates, and echinoderms. The interpretation of the early history of the Lophotrochozoa is even more difficult because in comparison to other bilaterians, their oldest fossils are preserved as mineralized skeletons only. However, a unity of microstructures of molluscs, brachiopods, and bryozoans, absent in other metazoans, is indicative of the presence of close relatives among different earliest lophotrochozoans some of which are sedentary filterers while others are motile epibenthic detritophages. In the aggregate, modern data of molecular biology, palaeontology, and comparative embryology/morphology, having got a second wind with an introduction of new microscopy techniques, imply that the suggestion of a planktotrophic gastraea-like common ancestor is the least possible among diverse suggestions on the Metazoa origins. The common ancestor of the Bilateria had to be a motile epibenthic animal and the explosive metazoan diversification embracing the late Ediacaran--early Cambrian interval (c. 40 Ma) was probably a real event, which was predated by a long (c. a billion years) assembly of the metazoan genome within unicellular and colonial common ancestors of the Opisthokonta and even the Unikonta as a whole.

The Arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome.

The Arabidopsis Information Resource (TAIR) is a continuously updated, online database of genetic and molecular biology data for the model plant Arabidopsis thaliana that provides a global research community with centralized access to data for over 30,000 Arabidopsis genes. TAIR's biocurators systematically extract, organize, and interconnect experimental data from the literature along with computational predictions, community submissions, and high throughput datasets to present a high quality and comprehensive picture of Arabidopsis gene function. TAIR provides tools for data visualization and analysis, and enables ordering of seed and DNA stocks, protein chips, and other experimental resources. TAIR actively engages with its users who contribute expertise and data that augments the work of the curatorial staff. TAIR's focus in an extensive and evolving ecosystem of online resources for plant biology is on the critically important role of extracting experimentally based research findings from the literature and making that information computationally accessible. In response to the loss of government grant funding, the TAIR team founded a nonprofit entity, Phoenix Bioinformatics, with the aim of developing sustainable funding models for biological databases, using TAIR as a test case. Phoenix has successfully transitioned TAIR to subscription-based funding while still keeping its data relatively open and accessible.

Molecular and clinical support for a four-tiered grading system for bladder cancer based on the WHO 1973 and 2004 classifications

Currently, the use of two classification systems for bladder cancer grade is advocated in clinical guidelines because the WHO2004 classification has not been sufficiently validated with biological markers and follow-up. The slides of 325 primary non-muscle invasive bladder cancers from three hospitals were reviewed by one uro-pathologist in two separate sessions for the WHO1973 (G1, G2 and G3) and 2004 (papillary urothelial neoplasm of low malignant potential (LMP), low-grade (LG) and high-grade (HG)) classifications. FGFR3 status was examined with PCR-SNaPshot analysis. Expression of Ki-67, P53 and P27 was analyzed by immuno-histochemistry. Clinical recurrence and progression were determined. We performed validation and cross-validation of the two systems for grade with molecular markers and clinical outcome. Multivariable analyses were done to predict prognosis and pT1 bladder cancer. Grade review resulted in 88 G1, 149 G2 and 88 G3 lesions (WHO1973) and 79 LMP, 101 LG and 145 HG lesions (WHO2004). Molecular validation of both grading systems showed that FGFR3 mutations were associated with lower grades whereas altered expression (Ki-67, P53 and P27) was found in higher grades. Clinical validation showed that the two classification systems were both significant predictors for progression but not for recurrence. Cross-validation of both WHO systems showed a significant stepwise increase in biological (molecular markers) and clinical (progression) potential along the line: G1—LG—G2—HG—G3. The LMP and G1 categories had a similar clinical and molecular profile. On the basis of molecular biology and multivariable clinical data, our results support a four-tiered grading system using the 1973 and 2004 WHO classifications with one low-grade (LMP/LG/G1) category that includes LMP, two intermediate grade (LG/G2 and HG/G2) categories and one high-grade (HG/G3) category.

The origin of the variola virus.

The question of the origin of smallpox, one of the major menaces to humankind, is a constant concern for the scientific community. Smallpox is caused by the agent referred to as the variola virus (VARV), which belongs to the genus Orthopoxvirus. In the last century, smallpox was declared eradicated from the human community; however, the mechanisms responsible for the emergence of new dangerous pathogens have yet to be unraveled. Evolutionary analyses of the molecular biological genomic data of various orthopoxviruses, involving a wide range of epidemiological and historical information about smallpox, have made it possible to date the emergence of VARV. Comparisons of the VARV genome to the genomes of the most closely related orthopoxviruses and the examination of the distribution their natural hosts’ ranges suggest that VARV emerged 3000 to 4000 years ago in the east of the African continent. The VARV evolution rate has been estimated to be approximately 2 × 10−6 substitutions/site/year for the central conserved genomic region and 4 × 10−6 substitutions/site/year for the synonymous substitutions in the genome. Presumably, the introduction of camels to Africa and the concurrent changes to the climate were the particular factors that triggered the divergent evolution of a cowpox-like ancestral virus and thereby led to the emergence of VARV.

Hybrid sterility of the yeast Schizosaccharomyces pombe: Genetic genus and many species in statu nascendi?

A phenomenon of ascospore death was observed in a number of Schizosaccharomyces pombe interstrain hybrids. Meiotic recombination of the control parental auxotrophic markers was, however, observed in a random ascospore analysis. Genetic and molecular biological data indicated existence of at least geographical divergence of the genomes in Sch. pombe populations. Classification of the genus, species, and varieties of these yeasts is discussed.

Pharmacologically distinct nicotinic acetylcholine receptors drive efferent-mediated excitation in calyx-bearing vestibular afferents.

Electrical stimulation of vestibular efferent neurons rapidly excites the resting discharge of calyx/dimorphic (CD) afferents. In turtle, this excitation arises when acetylcholine (ACh), released from efferent terminals, directly depolarizes calyceal endings by activating nicotinic ACh receptors (nAChRs). Although molecular biological data from the peripheral vestibular system implicate most of the known nAChR subunits, specific information about those contributing to efferent-mediated excitation of CD afferents is lacking. We sought to identify the nAChR subunits that underlie the rapid excitation of CD afferents and whether they differ from α9α10 nAChRs on type II hair cells that drive efferent-mediated inhibition in adjacent bouton afferents. We recorded from CD and bouton afferents innervating the turtle posterior crista during electrical stimulation of vestibular efferents while applying several subtype-selective nAChR agonists and antagonists. The α9α10 nAChR antagonists, α-bungarotoxin and α-conotoxin RgIA, blocked efferent-mediated inhibition in bouton afferents while leaving efferent-mediated excitation in CD units largely intact. Conversely, 5-iodo-A-85380, sazetidine-A, varenicline, α-conotoxin MII, and bPiDDB (N,N-dodecane-1,12-diyl-bis-3-picolinium dibromide) blocked efferent-mediated excitation in CD afferents without affecting efferent-mediated inhibition in bouton afferents. This pharmacological profile suggested that calyceal nAChRs contain α6 and β2, but not α9, nAChR subunits. Selective blockade of efferent-mediated excitation in CD afferents distinguished dimorphic from calyx afferents by revealing type II hair cell input. Dimorphic afferents differed in having higher mean discharge rates and a mean efferent-mediated excitation that was smaller in amplitude yet longer in duration. Molecular biological data demonstrated the expression of α9 in turtle hair cells and α4 and β2 in associated vestibular ganglia.

Recommandations de l’Anocef pour la prise en charge des métastases cérébrales

The incidence of brain metastases is increasing because of the use of new therapeutic agents, which allow an improvement of overall survival, but with only a poor penetration into the central nervous system brain barriers. The management of brain metastases has changed due to a better knowledge of immunohistochemical data and molecular biological data, the development of new surgical, radiotherapeutic approaches and improvement of systemic treatments. Most of the time, the prognosis is still limited to several months, nevertheless, prolonged survival may be now observed in some sub-groups of patients. The main prognostic factors include the type and subtype of the primitive, age, general status of the patient, number and location of brain metastases, extracerebral disease. The multidisciplinary discussion should take into account all of these parameters. We should notice also that treatments including surgery or radiotherapy may be proposed in a symptomatic goal in advanced phases of the disease underlying the multidisciplinary approach until late in the evolution of the disease. This article reports on the ANOCEF (French neuro-oncology association) guidelines. The management of brain metastases of breast cancers and lung cancers are discussed in the same chapter, while the management of melanoma brain metastases is reported in a separate chapter due to different responses to the brain radiotherapy.

Orchestrating high-throughput genomic analysis with Bioconductor.

Bioconductor is an open-source, open-development software project for the analysis and comprehension of high-throughput data in genomics and molecular biology. The project aims to enable interdisciplinary research, collaboration and rapid development of scientific software. Based on the statistical programming language R, Bioconductor comprises 934 interoperable packages contributed by a large, diverse community of scientists. Packages cover a range of bioinformatic and statistical applications. They undergo formal initial review and continuous automated testing. We present an overview for prospective users and contributors.

Structome analysis of virulent Mycobacterium tuberculosis, which survives with only 700 ribosomes per 0.1 fl of cytoplasm.

We previously reported the exquisite preservation of the ultrastructures of virulent Mycobacterium tuberculosis cells processed through cryofixation and rapid freeze substitution. Here, we report the “structome” analysis (i.e., the quantitative three-dimensional structural analysis of a whole cell at the electron microscopic level) of virulent M. tuberculosis using serial ultrathin sections prepared after cryofixation and rapid freeze substitution and analyzed by transmission electron microscopy. Five M. tuberculosis cells, which were contained in the serial ultrathin cross sections encompassing from one end to the other, were cut into 24, 36, 69, 55, and 63 serial ultrathin sections, respectively. On average, the cells were 2.71 ± 1.05 μm in length, and the average diameter of the cell was 0.345 ± 0.029 μm. The outer membrane and plasma membrane surface areas were 3.04 ± 1.33 μm2 and 2.67 ± 1.19 μm2, respectively. The cell, outer membrane, periplasm, plasma membrane, and cytoplasm volumes were 0.293 ± 0.113 fl (= μm3), 0.006 ± 0.003 fl, 0.060 ± 0.021 fl, 0.019 ± 0.008 fl, and 0.210 ± 0.091 fl, respectively. The average total ribosome number was 1,672 ± 568, and the ribosome density was 716.5 ± 171.4/0.1 fl. This is the first report of a structome analysis of M. tuberculosis cells prepared as serial ultrathin sections following cryofixation and rapid freeze substitution and examined by transmission electron microscopy. These data are based on the direct measurement and enumeration of exquisitely preserved single-cell structures in transmission electron microscopy images rather than calculations or assumptions from indirect biochemical or molecular biological data. In addition, these data may explain the slow growth of M. tuberculosis and enhance understanding of the structural properties related to the expression of antigenicity, acid-fastness, and the mechanism of drug resistance, particularly in regard to the ratio of target to drug concentrations.

Therapeutic Management of Acute Myeloid Leukemia Patients after Stratification on Age, Prognosis and Allogeneic Hematopoietic Stem Cell Transplantation Eligibility

We evaluated in this study the therapeutic management of all newly diagnosed acute myeloid leukemia (AML) patients followed in our center between July 2007 and September 2013, after stratification on age, prognostic factors, whether they were candidate to allogeneic hematopoietic stem cell transplantation (allo-HSCT), transplanted or not with the evaluation of each therapeutic strategy and its impact on overall survival. A total of 572 consecutive newly diagnosed AML patients were included; there were 311 (54%) males and 261 females with a median age of 63 years (range: 20-92), 406 (71%) were de novo AML and 166 (29%) secondary AML. Complete cytogenetic and molecular biology data were collected for all patients and prognosis was differentiated according to the European LeukemiaNet classification (Dohner et al. Blood 2010). Accordingly, 335 (59%) patients were unfavorable, 83 (15%) favorable, 48 (8%) intermediate I and 106 (18%) were in intermediate II category. Following the Acute Leukemia French Association (ALFA) guidelines for allo-HSCT in AML, patients with intermediate II and unfavorable prognosis ≤ 65 years should receive intensive chemotherapy followed by allo-HSCT in the presence of related or unrelated HSCT donors. We divided the population into two sub-populations, the first was considered as “young” with age ≤ 65 years (N=318, 56%) and the second considered as “old” with age > 65 years (N=254, 44%). In the young population, there was 4 groups, group 1: patients with good prognosis (favorable/intermediate1) who received intensive chemotherapy within or according to ALFA protocols (N=105, median age= 47 years); group 2: patients with poor prognosis (intermediate2 /unfavorable) who received intensive chemotherapy within or according to ALFA protocols followed by allo-HSCT (N=126, median age= 50 years), group 3: patients with poor prognosis who received only intensive chemotherapy without allo-HSCT (N=69, median age= 57 years), and group 4: patients with poor prognosis who could not be treated due to early death (N=18). In the old population we distinguished, group 1: patients with good prognosis who received moderate intensity chemotherapy within or according to ALFA protocols (N=25, median age=73 years); group 2: patients with poor prognosis who received azacitidine (N=25, median age=76 years), group 3: patients with poor prognosis who received moderate intensity chemotherapy (N=89, median age=76 years), group 4: patients with poor prognosis who received low dose Ara-C (N=28, median age=76 years), group 5: patients with poor prognosis who received other treatment (N=38, median age=77 years) and finally group 6: patients with poor prognosis considered as palliative or who did not receive any treatment (N=49, median age=77 years). After a median follow-up of 34 months (range: 4-77) for surviving patients, the 2-years probability of overall survival (OS) in the “young” population for groups 1,2,3 and 4 was 84%, 56%, 31% and 0% respectively; and in the “old” group it was 71%, 37%, 31%, 5%, 21% and 0% for groups 1,2,3,4,5 and 6 respectively (figure).We showed that newly diagnosed AML patients with good prognosis all ages included could achieve very good survival rates after intensive chemotherapy; allo-HSCT after induction chemotherapy remains the best therapeutic option for fit patients with poor prognosis while the same fit patients with no donor have significantly lower survival (p<0.001) and for whom allo-HSCT could be proposed by using haploidentical donors in case of cord blood or unrelated donors absence. Interestingly, in the “old” population, we showed that poor prognosis patients receiving azacytidine had a significantly better survival compared to those receiving low dose Ara-C (p=0.015), with a comparable outcome to those receiving induction chemotherapy. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Allogeneic Hematopoietic Stem Cell Transplantation for Therapy-Related Acute Myeloid Leukemia

Background:With the expanding pool of cancer survivors, therapy-related AML (t-AML) is increasingly encountered and constitutes approximately 10%-20% of newly diagnosed patients with AML. These patients have a poor prognosis with conventional anti-leukemia therapies with median survival of less than 1 year. This outcome is related to several factors including older age, worse performance score, comorbidities, therapy resistance, and bone marrow failure. Allogeneic hematopoietic stem cell transplantation, when feasible, represents a potential promising treatment for patients with t-AML.Objective:The aim of this study is to evaluate the different treatment options and outcomes of patients with t-AML followed at our center between year 2007 and 2013.Patients and methods:Between July 2007 and September 2013, we evaluated 166 consecutive newly diagnosed t-AML patients among a total of 572 AML diagnosed and followed in our center during this period; there were 95 (57%) males and 71 (43%) females with a median age of 66 years (range: 18-92), 48 (29%) were less than 60 years old, 83 (50%) were between 60 and 75 years, and 35 (21%) were older than 75 years; 128 (77%) were secondary AML after hematological malignancies [66 (56%) myelodysplastic syndrome (MDS) and 44 (34%) myeloproliferative syndromes and 18 (14%) lymphoid malignancies], and 38 (23%) after solid tumors. At diagnosis, the patients were evaluated according to both cytogenetic and molecular biology data as proposed by the European LeukemiaNet (Dohner et al. Blood 2010), accordingly, 160 (96%) patients were unfavorable [having one or more of the following: -5, -7, 5q-, 7q-,11q23 or MLL+ including MLL-PTD (except 9;11), t(6;9) Complex karyotype (≥ 3 abnormalities), 3q26 abnormalities or EVI-1+], and only 6 (4%) had favorable prognosis [t(8;21), in(16) or t(16;16)]. Following the Acute Leukemia French Association (ALFA) guidelines for allo-HSCT in AML, all patients in this study should be candidate for transplantation after induction chemotherapy because of t-AML only if the patient condition is suitable (age, co-morbidities) and hematopoietic stem cell donor is available.Results:Among 166 patients, only 42 (25%) have been treated according to the ALFA recommendations and received induction chemotherapy followed by allo-HSCT, 36 (86%) were in first complete remission (CR1) and 6 were in less than CR1, 18 (43%) received hematopoietic stem cells from identical siblings (15 peripheral blood stem cells, 3 bone marrow) and 24 (57%) from unrelated donors (16 peripheral blood stem cells, 3 bone marrow and 5 cord blood cells); 31 (74%) received reduced intensity conditioning, 6 (14%) myeloablative and 5 (12%) sequential chemotherapy conditioning. For the rest of 124 (75%) patients, they could not benefit from allo-HSCT, they received either induction chemotherapy ± consolidation treatment or chemo/palliative treatment, among them 91 (73%) were ineligible to allo-HSCT due to age > 65 years and 33 (27%) could not be transplanted due to either non-availability of stem cells donor (N=12), early death before donor search (N=6), early death despite availability of stem cells donor (N=8), other comorbidities (N=7).The probability of overall survival (OS) at 2 years was 55% (range: 47-63) for patients who received allo-HSCT and it was 18% (range: 14-22) for those who received induction or palliative treatment without allo-HSCT with a median OS of 33 and 7 months respectively. The probability of progression-free survival for patients who received allo-HSCT was 68% (range: 60-76) at two years with a median not reached, and the cumulative incidence of transplant-related mortality was 24% (range: 17-31) at two years.Conclusion:Therapy-related acute myeloid leukemia remains having a poor prognosis with conventional therapy. Allogeneic HCT represents the only curative approach. We obtained encouraging results in eligible patients who received allogeneic transplantation especially that the majority of patients had unfavorable prognosis factors according to molecular biology and cytogenetics. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

The development and implementation of an instrument to assess students' data analysis skills in molecular biology.

Developing visual literacy skills is an important component of scientific literacy in undergraduate science education. Comprehension, analysis, and interpretation are parts of visual literacy that describe related data analysis skills important for learning in the biological sciences. The Molecular Biology Data Analysis Test (MBDAT) was developed to measure students’ data analysis skills connected with scientific reasoning when analyzing and interpreting scientific data generated from experimental research. The skills analyzed included basic skills, such as identification of patterns and trends in data and connecting a method that generated the data, and advanced skills, such as distinguishing positive and negative controls, synthesizing conclusions, determining if data supports a hypothesis, and predicting alternative or next-step experiments. Construct and content validity were established and calculated statistical parameters demonstrate that the MBDAT is valid and reliable for measuring students’ data analysis skills in molecular and cell biology contexts. The instrument also measures students’ perceived confidence in their data interpretation abilities. As scientific research continues to evolve in complexity, interpretation of scientific information in visual formats will continue to be an important component of scientific literacy. Thus science education will need to support and assess students’ development of these skills as part of students’ scientific training.

Molecular characteristics of pediatric high-grade gliomas.

High-grade gliomas (HGGs) are extremely lethal tumors. Survival has not changed significantly in the past decades. The only known prognostic factors in pediatric HGGs (pHGGs) are extent of resection and histologic grade. Treatment has historically been based on adult trials because of the rarity of pHGGs and the lack of genomic tools to explore their unique molecular characteristics. The recent advances in molecular biological data helped divide these tumors into distinct subgroups. In this review, the authors focus on major molecular targets of alterations in pHGGs: histone H3.3, telomeres, PDGFRA, IDH, BRAF (V600E), ACVR1 and NTRK and briefly highlight the difference with the adult counterpart.