Highlights of meiotic genes in Arabidopsis thaliana

Meiosis is a fascinating and complex phenomenon and, despite its central role in sexual plant reproduction, little is known on the molecular mechanisms involved in this process. We review the progress made in recent years using Arabidopsis thaliana mutants for isolating meiotic genes. In particular, emphasis is given on the description of mutants affecting either the regular commitment to meiosis, or the mechanisms of synapsis, recombination, and cytokinesis. We believe that the isolation of genes affecting some crucial meiotic events may represent the first step towards the practical use of meiotic genes in plant breeding. The introduction of deviations in the meiotic pathway into sexual crops will have important implications for the exploitation of apomixis and sexual polyploidization. Key words: Arabidopsis, meiosis, mutants, fertility. African Journal of Biotechnology Vol. 2 (12), pp.516-520, December 200

Appropriateness of internal digital phantoms for monitoring the stability of the UBIS 5000 quantitative ultrasound device in clinical trials

In bone status assessment, proper quality assurance/quality control is crucial since changes due to disease or therapeutic treatment are very small, in the order of 2-5%. Unlike for dual X-ray absorptiometry, quality control procedures have not been extensively developed and validated for quantitative ultrasound technology, limiting its use in longitudinal monitoring. While the challenge of developing an ideal anthropometric phantom is still open, some manufacturers use the concept of the internal digital phantom mimicking human characteristics to check the stability of their device. The objective of the study was to develop a sensitive model of quality control suitable for the correction of QUS patient data. In order to achieve this goal, we simulated a longitudinal device lifetime with both correct and malfunctioning behaviors. Then, we verified the efficiency of digital phantoms in detecting those changes and subsequently established the in vitro/in vivo relationship. This is the first time that an attempt to validate an internal digital phantom has made, and that this type of validation approach is used. The digital phantom (DP) was designed to mimic normal bone (BUAP2) and osteoporotic bone (BUAP1) properties. The DP was studied using the UBIS 5000 ultrasound device (DMS, France). Diverse malfunctions of the UBIS-5000 were simulated. Several series of measurements were performed on both BUAP1 and 2 and on 12 volunteers at each grade of malfunction. The effect of each simulated malfunction on in vivo and in vitro results was presented graphically by plotting the average BUA values against the percentage change from baseline. The change from baseline in BUA was modeled using linear regression, and the in vivo/in vitro ratio was obtained from the model. All experimentations influenced the measure of BUAP1 and 2 as well as the measure of our 12 volunteers. However, the degree of significance varied as a function of the severity of the malfunction, and the results also differed substantially in magnitude between in vivo and in vitro. Indeed, the DP was about 10 times more sensitive to variations of the transfer function than was the in vivo measurement, which is very reassuring. The sensitivity of the digital phantoms was reliable in the determination of simulated malfunctions of the UBIS-5000. The digital phantoms provided an accurate evaluation of the acoustic performance of the scanner, including the fidelity of transducers. In light of these results, the QC approach of the UBIS-5000 will be extremely simple to implement compared with other devices. Indeed, since the digital phantom was automatically measured during every patient measurement, the QC approach could be built on an individual level basis rather than on an average basi

A multipurpose X-ray fluorescence scanner developed for in situ analysis

Abstract: Over the time, instrument transportability has become more and more important, especially in Cultural Heritage, as often artworks cannot be moved from their site, either because of the size or due to problems with permission issues, or simply because moving them to a laboratory is physically impossible, as e.g. in the case of mural paintings. For this reason, the INFN-CHNet, the network for Cultural Heritage studies of the Italian National Institute of Nuclear Physics (INFN), has developed an XRF scanner for in situ analyses. The instrument is the result of a wide collaboration, where different units of the network have been developing the diverse parts, then merged in a single system. The XRF scanner has been designed to be a four-season and green instrument. The control/acquisition/analysis software has been fully developed by our group, using only open-source software. Other strong points of the system are easiness of use, high portability, good performances and ultra-low radiation dispersion, which allows us to use even when the public can be present. It can run both with mains or on batteries, in the latter case with a maximum runtime longer than 10 h. It has a very low cost, when compared to commercial systems with equivalent performances, and easily replaceable components, which makes it accessible for a much wider portion of the interested community. The system has been thought and designed as an open system, suitable for further development/improvements, that can result interesting for non-conventional XRF analysis. The CHNet XRF scanner has proved to be really very well suited for applications in the Cultural Heritage field, as testified by the many recent applications. This paper describes the present version of our instrument and reports on the tests performed to characterise its main features.Fil: Taccetti, F.. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Castelli, L.. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Czelusniak, C.. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Gelli, N.. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Mazzinghi, A.. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Palla, L.. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Ruberto, C.. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Censori, C.. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Lo Giudice, A.. Università di Torino; Italia. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Re, A.. Università di Torino; Italia. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Zafiropulos, D.. Istituto Nazionale di Fisica Nucleare; ItaliaFil: Arneodo, F.. New York University Abu Dhab; Emiratos Arabes UnidosFil: Conicella, V.. New York University Abu Dhab; Emiratos Arabes UnidosFil: Di Giovanni, A.. New York University Abu Dhab; Emiratos Arabes UnidosFil: Torres, R.. New York University Abu Dhab; Emiratos Arabes UnidosFil: Castella, F.. Universidad Nacional de San Martín. Instituto de Investigaciones sobre el Patrimonio Cultural; ArgentinaFil: Mastrangelo, Noemi Elisa. Universidad Nacional de San Martín. Instituto de Investigaciones sobre el Patrimonio Cultural; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Gallegos, D.. Universidad Nacional de San Martín. Instituto de Investigaciones sobre el Patrimonio Cultural; ArgentinaFil: Tascon, Marcos. Universidad Nacional de San Martín. Instituto de Investigaciones sobre el Patrimonio Cultural; Argentina. Universidad Nacional de San Martín. Instituto de Investigación e Ingeniería Ambiental. - Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigación e Ingeniería Ambiental; ArgentinaFil: Marte, F.. Universidad Nacional de San Martín. Instituto de Investigaciones sobre el Patrimonio Cultural; ArgentinaFil: Giuntini, L.. Università degli Studi di Firenze; Itali

RAAD: LIGHT-1 CubeSat's Payload for the Detection of Terrestrial Gamma-Ray Flashes

The Rapid Acquisition Atmospheric Detector (RAAD), onboard the LIGHT-1 3U CubeSat, detects photons between hard X-rays and soft gamma-rays, in order to identify and characterize Terrestrial Gamma Ray Flashes (TGFs). Three detector configurations are tested, making use of Cerium Bromide and Lanthanum BromoChloride scintillating crystals coupled to photomultiplier tubes or Multi-Pixel Photon Counters, in order to identify the optimal combination for TGF detection. High timing resolution, a short trigger window, and the short decay time of its electronics allow RAAD to perform accurate measurements of prompt, transient events. Here we describe the overview of the detection concept, the development of the front-end acquisition electronics, as well as the ground testing and simulation the payload underwent prior to its launch on December 21st, 2021. We further present an analysis of the detector's in-orbit system behavior and some preliminary results.Comment: 19 pages, 15 figure

Atomic structures of TDP-43 LCD segments and insights into reversible or pathogenic aggregation.

The normally soluble TAR DNA-binding protein 43 (TDP-43) is found aggregated both in reversible stress granules and in irreversible pathogenic amyloid. In TDP-43, the low-complexity domain (LCD) is believed to be involved in both types of aggregation. To uncover the structural origins of these two modes of β-sheet-rich aggregation, we have determined ten structures of segments of the LCD of human TDP-43. Six of these segments form steric zippers characteristic of the spines of pathogenic amyloid fibrils; four others form LARKS, the labile amyloid-like interactions characteristic of protein hydrogels and proteins found in membraneless organelles, including stress granules. Supporting a hypothetical pathway from reversible to irreversible amyloid aggregation, we found that familial ALS variants of TDP-43 convert LARKS to irreversible aggregates. Our structures suggest how TDP-43 adopts both reversible and irreversible β-sheet aggregates and the role of mutation in the possible transition of reversible to irreversible pathogenic aggregation

Evolution of Parallel Spindles Like genes in plants and highlight of unique domain architecture#

<p>Abstract</p> <p>Background</p> <p>Polyploidy has long been recognized as playing an important role in plant evolution. In flowering plants, the major route of polyploidization is suggested to be sexual through gametes with somatic chromosome number (2<it>n</it>). <it>Parallel Spindle1 </it>gene in <it>Arabidopsis thaliana </it>(<it>AtPS1</it>) was recently demonstrated to control spindle orientation in the 2nd division of meiosis and, when mutated, to induce 2<it>n </it>pollen. Interestingly, <it>AtPS1 </it>encodes a protein with a FHA domain and PINc domain putatively involved in RNA decay (i.e. Nonsense Mediated mRNA Decay). In potato, 2<it>n </it>pollen depending on parallel spindles was described long time ago but the responsible gene has never been isolated. The knowledge derived from <it>AtPS1 </it>as well as the availability of genome sequences makes it possible to isolate potato <it>PSLike </it>(<it>PSL</it>) and to highlight the evolution of <it>PSL </it>family in plants.</p> <p>Results</p> <p>Our work leading to the first characterization of <it>PSLs </it>in potato showed a greater <it>PSL </it>complexity in this species respect to <it>Arabidopsis thaliana</it>. Indeed, a genomic <it>PSL </it>locus and seven cDNAs affected by alternative splicing have been cloned. In addition, the occurrence of at least two other <it>PSL </it>loci in potato was suggested by the sequence comparison of alternatively spliced transcripts.</p> <p>Phylogenetic analysis on 20 <it>Viridaeplantae </it>showed the wide distribution of <it>PSLs </it>throughout the species and the occurrence of multiple copies only in potato and soybean.</p> <p>The analysis of PSL^FHAand PSL^PINcdomains evidenced that, in terms of secondary structure, a major degree of variability occurred in PINc domain respect to FHA. In terms of specific active sites, both domains showed diversification among plant species that could be related to a functional diversification among <it>PSL </it>genes. In addition, some specific active sites were strongly conserved among plants as supported by sequence alignment and by evidence of negative selection evaluated as difference between non-synonymous and synonymous mutations.</p> <p>Conclusions</p> <p>In this study, we highlight the existence of PSLs throughout <it>Viridaeplantae</it>, from mosses to higher plants. We provide evidence that <it>PSLs </it>occur mostly as singleton in the analyzed genomes except in soybean and potato both characterized by a recent whole genome duplication event. In potato, we suggest the candidate <it>PSL </it>gene having a role in 2<it>n </it>pollen that should be deeply investigated.</p> <p>We provide useful insight into evolutionary conservation of FHA and PINc domains throughout plant PSLs which suggest a fundamental role of these domains for PSL function.</p

An examination of periodontal treatment and per member per month (PMPM) medical costs in an insured population

BACKGROUND: Chronic medical conditions have been associated with periodontal disease. This study examined if periodontal treatment can contribute to changes in overall risk and medical expenditures for three chronic conditions [Diabetes Mellitus (DM), Coronary Artery Disease (CAD), and Cerebrovascular Disease (CVD)]. METHODS: 116,306 enrollees participating in a preferred provider organization (PPO) insurance plan with continuous dental and medical coverage between January 1, 2001 and December 30, 2002, exhibiting one of three chronic conditions (DM, CAD, or CVD) were examined. This study was a population-based retrospective cohort study. Aggregate costs for medical services were used as a proxy for overall disease burden. The cost for medical care was measured in Per Member Per Month (PMPM) dollars by aggregating all medical expenditures by diagnoses that corresponded to the International Classification of Diseases, 9(th )Edition, (ICD-9) codebook. To control for differences in the overall disease burden of each group, a previously calculated retrospective risk score utilizing Symmetry Health Data Systems, Inc. Episode Risk Groups™ (ERGs) were utilized for DM, CAD or CVD diagnosis groups within distinct dental services groups including; periodontal treatment (periodontitis or gingivitis), dental maintenance services (DMS), other dental services, or to a no dental services group. The differences between group means were tested for statistical significance using log-transformed values of the individual total paid amounts. RESULTS: The DM, CAD and CVD condition groups who received periodontitis treatment incurred significantly higher PMPM medical costs than enrollees who received gingivitis treatment, DMS, other dental services, or no dental services (p < .001). DM, CAD, and CVD condition groups who received periodontitis treatment had significantly lower retrospective risk scores (ERGs) than enrollees who received gingivitis treatment, DMS, other dental services, or no dental services (p < .001). CONCLUSION: This two-year retrospective examination of a large insurance company database revealed a possible association between periodontal treatment and PMPM medical costs. The findings suggest that periodontitis treatment (a proxy for the presence of periodontitis) has an impact on the PMPM medical costs for the three chronic conditions (DM, CAD, and CVD). Additional studies are indicated to examine if this relationship is maintained after adjusting for confounding factors such as smoking and SES

WHOLE-GENOME RE-SEQUENCING OF TWO TOMATO LANDRACES REVEALS SEQUENCE VARIATIONS UNDERPINNING KEY ECONOMICALLY IMPORTANT TRAITS

In the post-genomic era, one of the major challenges is the identification of alleles directly responsible for phenotype variation among different genotypes within the same species. Tomato is a model crop for understanding the development and ripening of climacteric fleshy fruits, and it is also known to be an important source of health-promoting compounds. In addition, cultivated tomato germplasm shows a high phenotypic variation despite its very low genetic diversity. Toward the identification of sequence variations responsible for stress tolerance, high fruit quality and long shelf life, we re-sequenced the genomes of two traditional landraces grown in the Campania region (Southern Italy). Crovarese, belonging to the Corbarino type (COR), and Lucariello (LUC) are typically grown under low water regimes and produce highly appreciated fruits, which can be stored up to 4-8 months. We generated 65.8M and 56.4M of paired-end 30-150 bp reads with an average insert size of 380 bp (± 52bp) and 364 bp (± 49bp) for COR and LUC, respectively. A referenceguided assembly was performed using 'Heinz 1706' as a reference genome. We estimated a mean coverage depth of ~15X for COR and 13X for LUC. Comparing the genomes of COR and LUC with that of 'Heinz 1706' we found a similar distribution of SNPs (68.8% vs. 69.9%, respectively), small deletions (8.9% vs. 8.6%) and small insertions (22.1% vs. 21.3%). Through a de novo assembly of the unmapped reads we identified 29 and 36 new contigs in COR and LUC, respectively. The new contigs could be assigned to the chromosomes thanks to the use of a splitread approach. On average, the contigs inserted in COR were 654bp, whereas those inserted in LUC were 616bp. Using custom RNA-seq data, a total of 43054 and 44576 gene loci were annotated in COR and LUC, corresponding to 62369 and 65094 transcripts, respectively. Among the genes showing a similar structure in COR and LUC compared to 'Heinz 1706', we identified ~2000 and 1700 SNPs causing potentially disruptive effects on the function of 1371 and 1201 genes in COR and LUC, respectively. Interesting GO categories highly represented in genes affected by sequence changes were identified. Major variations were present in stress-responsive genes as well as in fruit quality and development-related genes. From a practical perspective, the identified SNPs and InDels are candidate polymorphisms to track DNA variations associated to key traits of economic interest