bluuebunny/crossref_metadata_2025_split huggingface dataset:
Linked-read sequencing of gametes allows efficient genome-wide analysis of meiotic recombination
Authors: Sun Hequan , Rowan Beth A. , Flood Pádraic J. , Brandt Ronny , Fuss Janina , Hancock Angela M. , Michelmore Richard W. , Huettel Bruno , Schneeberger Korbinian 
Published: December 2018

ABSTRACTMeiotic crossovers (COs) ensure proper chromosome segregation and redistribute the genetic variation that is transmitted to the next generation. Existing methods for CO identification are challenged by large populations and the demand for genome-wide and fine-scale resolution. Taking advantage of linked-read sequencing, we developed a highly efficient method for genome-wide identification of COs at kilobase resolution in pooled recombinants. We first tested this method using a pool of Arabidopsis F2 recombinants, and obtained results that recapitulated those identified from the same plants using individual whole-genome sequencing. By applying this method to a pool of pollen DNA from a single F1 plant, we established a highly accurate CO landscape without generating or sequencing a single recombinant plant. The simplicity of this approach now enables the simultaneous generation and analysis of multiple CO landscapes and thereby allows for efficient comparison of genotypic and environmental effects on recombination, accelerating the pace at which the mechanisms for the regulation of recombination can be elucidated.
Who’s who in the western Hermann’s tortoise conservation: a STR toolkit and reference database for wildlife forensic genetic analyses
Authors: Roberto Biello , Mauro Zampiglia , Claudia Corti , Gianluca Deli , Marta Biaggini , Michel Delaugerre , Luciano Di Tizio , Luigi Leonetti Francesco , Oliviero Olivieri , Francesco Pellegrino , Antonio Romano , Emilio Sperone , Massimo Trabalza-Marinucci , Giorgio Bertorelle , Daniele Canestrelli 
Published: December 2018

ABSTRACTIllegal trade is threatening tortoise populations worldwide since decades. Nowadays, however, DNA typing and forensic genetic approaches allow to investigate geographic origin of confiscated animals and to relocate them into the wild, provided that suitable molecular tools and reference data are available. Here we assess the suitability of a small panel of microsatellite markers to investigate patterns of illegal translocations and to assist forensic genetic applications in the endangered Mediterranean land tortoiseTestudo hermanni hermanni. We used the microsatellite panel to (i) increase the understanding of the population genetic structure in wild populations with new data from previously unsampled geographic areas (overall 461 wild individuals from 28 sampling sites); (ii) detect the presence of non-native individuals in wild populations; and (iii) identify the most likely geographic area of origin of 458 confiscated individuals hosted in Italian seizure and recovery centers. Our analysis initially identified six major genetic clusters corresponding to different geographic macro-areas along the Mediterranean range. Long-distance migrants among wild populations, due to translocations, were found and removed from the reference database. Assignment tests allowed us to allocate approximately 70% of confiscated individuals of unknown origin to one of the six Mediterranean macro-areas. Most of the assigned tortoises belonged to the genetic cluster corresponding to the area where the respective captivity center was located. However, we also found evidence of long-distance origin of confiscated individuals, especially in centers along the Adriatic coast and facing the Balkan regions, a well-known source of illegally traded individuals. Our results clearly show the role for reintroduction projects of the microsatellite panel, which was useful to re-assign most of the confiscated individuals to the respective macro-area of origin. At the same time, the microsatellite panel can assist future forensic genetic applications to detect illegal trade and possess ofTestudo hermanniindividuals.
Genetic, structural, and functional analysis of mutations causing methylmalonyl-CoA epimerase deficiency
Authors: Heuberger Kathrin , Bailey Henry J. , Burda Patricie , Chaikuad Apirat , Krysztofinska Ewelina , Suormala Terttu , Bürer Céline , Lutz Seraina , Fowler Brain , Froese D. Sean , Yue Wyatt W. , Baumgartner Matthias R. 
Published: December 2018

AbstractHuman methylmalonyl-CoA epimerase (MCEE) catalyzes the interconversion of D-methylmalonyl-CoA and L-methylmalonyl-CoA in propionate catabolism. Autosomal recessive mutations inMCEEreportedly cause methylmalonic aciduria (MMAuria) in eleven patients. We investigated a cohort of 150 individuals suffering from MMAuria of unknown origin, identifying ten new patients with mutations inMCEE. Nine patients were homozygous for the known nonsense mutation p.Arg47* (c.139C>T), and one for the novel missense mutation p.Ile53Arg (c.158T>G). To understand better the molecular basis of MCEE deficiency, we mapped p.Ile53Arg, and two previously described patient mutations p.Lys60Gln and p.Arg143Cys, onto our 1.8 Å structure of wild-type (wt) human MCEE. This revealed potential dimeric assembly disruption by p.Ile53Arg, but no clear defects from p.Lys60Gln or p.Arg143Cys. Functional analysis of MCEE-Ile53Arg expressed in a bacterial recombinant system as well as patient-derived fibroblasts revealed nearly undetectable soluble protein levels, defective globular protein behavior, and using a newly developed assay, lack of enzymatic activity - consistent with misfolded protein. By contrast, soluble protein levels, unfolding characteristics and activity of MCEE-Lys60Gln were comparable to wt, leaving unclear how this mutation may cause disease. MCEE-Arg143Cys was detectable at comparable levels to wt MCEE, but had slightly altered unfolding kinetics and greatly reduced activity. We solved the structure of MCEE-Arg143Cys to 1.9 Å and found significant disruption of two important loop structures, potentially impacting surface features as well as the active-site pocket. These studies reveal ten new patients with MCEE deficiency and rationalize misfolding and loss of activity as molecular defects in MCEE-type MMAuria.
Soil microbial communities in diverse agroecosystems exposed to glyphosate
Authors: Kepler Ryan M. , Epp Schmidt Dietrich J. , Yarwood Stephanie A. , Reddy Krishna N. , Duke Stephen O. , Bradley Carl A. , Williams Martin M. , Buyer Jeffery , Cavigelli Michel A. , Maul Jude E. 
Published: December 2018

AbstractIn spite of glyphosate’s wide use in agriculture, questions remain about effects of the herbicide on soil microbial communities. Conflicting scientific literature reports divergent results; from no observable effect of glyphosate to the enrichment of common agricultural pathogens such as Fusarium. We conducted a comprehensive field-based study to compare treatments that did and did not receive foliar application of glyphosate spray. The study included two field sites, Maryland and Mississippi; two crops, soybean and corn; four site years, 2013 and 2014; and a variety of organic and conventional farming systems. Using amplicon sequencing, the prokaryotic (16S rRNA) and fungal (ITS) communities were described along with chemical and physical properties of the soil. Sections of corn and soy roots were plated to screen for the presence of plant pathogens. Geography, farming system, and seasonal progression were significant factors determining composition of fungal and bacterial communities. Plots treated with or without glyphosate did not differ in overall microbial community composition after controlling for these factors. No differential effect of glyphosate treatment was found in the relative abundance of organisms such as Fusarium spp. or putative growth-promoting bacteria Pseudomonas spp.
Coupling and Decoupling between Brain and Body Oscillations
Authors: Rassi Elie , Dorffner Georg , Gruber Walter , Klimesch Wolfgang 
Published: December 2018

AbstractCross frequency coupling is used intensively to study the cross talk between brain oscillations. In this paper we focus on a special type of frequency coupling between brain and body oscillations, which is reflected by the numerical ratio (r) between two frequencies (m and n; n > m). This approach is motivated by theoretical considerations indicating that an integer relationship (r = n/m = integer number) reflects coupling, whereas an irrational relationship (r = n/m = irrational number) reflects decoupling. We analyzed alpha frequency, heart rate, breathing frequency and spindle frequency from data collected by the SIESTA research group. Our results show a 1:4 frequency relationship between heart rate and breathing frequency both during wakefulness and sleep. During wakefulness we expected but did not find an integer relationship between alpha frequency and heart rate or alpha frequency and breathing frequency. During sleep, we observed an irrational relationship between spindle frequency and heart rate as well as spindle frequency and breathing frequency–suggesting decoupling.
Single cell derived organoids capture the self-renewing subpopulations of metastatic ovarian cancer
Authors: Velletri Tania , Villa Emanuele Carlo , Lupia Michela , Riso Pietro Lo , Luongo Raffaele , Tobon Alejandro Lopez , Simone Marco De , Bonnal Raoul J.P. , Minucci Saverio , Piccolo Stefano , Colombo Nicoletta , Pagani Massimiliano , Cavallaro Ugo , Testa Giuseppe 
Published: December 2018

AbstractHigh Grade Serous Ovarian cancer (HGSOC) is a major unmet need in oncology, due to its precocious dissemination and the lack of meaningful human models for the investigation of disease pathogenesis in a patient-specific manner. To overcome this roadblock, we present a new method to isolate and grow single cells directly from patients’ ascites, establishing the conditions for propagating them as single-cell derived ovarian cancer organoids (scOCOs). By single cell RNA sequencing (scRNAseq) we define the cellular composition of metastatic ascites and trace its propagation in 2D and 3D culture paradigms, finding that scOCOs retain and amplify key subpopulations from the original patients’ samples and recapitulate features of the original metastasis that do not emerge from classical 2D culture, including retention of individual patients’ specificities. By enabling the enrichment of uniquely informative cell subpopulations from HGSOC metastasis and the clonal interrogation of their diversity at the functional and molecular level, this method transforms the prospects of precision oncology for ovarian cancer.
Hierarchical Stem Cell Topography Splits Growth and Homeostatic Functions in the Fish Gill
Authors: Stolper Julian , Ambrosio Elizabeth , Danciu Diana-P , Elliot David A. , Naruse Kiyoshi , Czochra Anna Marciniak , Centanin Lazaro 
Published: December 2018

AbstractWhile lower vertebrates contain adult stem cells (aSCs) that maintain homeostasis and drive un-exhaustive organismal growth, mammalian aSCs display mainly the homeostatic function. Understanding aSC-driven growth is of paramount importance to promote organ regeneration and prevent tumor formation in mammals. Here we present a clonal approach to address common or dedicated populations of aSCs for homeostasis and growth. Our functional assays on medaka gills demonstrate the existence of separate homeostatic and growth aSCs, which are clonal but differ in their topology. While homeostatic aSCs are fixed, embedded in the tissue, growth aSCs locate at the expanding peripheral zone. Modifications in tissue architecture can convert the homeostatic zone into a growth zone, indicating a leading role for the physical niche defining stem cell output. We hypothesize that physical niches are main players to restrict aSCs to a homeostatic function in animals with a fixed adult size.
Science Family skills: An Alexa Assistant Tailored for Laboratory Routine
Authors: Lubiana-Alves Tiago , Gonçalves André A.N.A. , Nakaya Helder I 
Published: December 2018

ABSTRACTVoice User Interfaces such as Amazon Alexa and Google Home are already widely available and used for personal purposes. These services could be used to improve experimental biology laboratory routine, facilitate troubleshooting and increase efficiency. Till date, no applications that are tailored to enhance laboratory routine have been made available. Here, we present a set of free-to-use, open source tools adapted to Alexa for application in the laboratory environment, with prospects of enhancing productivity and reducing work-related stress. All skills, 3D printer model and source codes are freely available in the Alexa app store and in GitHub.
MLL-AF9 Initiates Transformation From Fast-Proliferating Myeloid Progenitors
Authors: Chen Xinyue , Hartman Amaleah , Hu Xiao , Eastman Anna E. , Wang Xujun , Zhong Mei , Guo Shangqin 
Published: December 2018

AbstractCancer is a hyper-proliferative clonal disease. Whether the proliferative state originates from the cell-of-origin or emerges later remains elusive. By tracking de novo transformation from normal hematopoietic progenitors expressing an acute myeloid leukemia (AML) oncogene MLL-AF9, we reveal that the cell cycle rate heterogeneity among granulocyte-macrophage progenitors (GMPs) determines their probability of transformation. An intrinsic fast cell cycle kinetics at the time of oncogene expression provide permissiveness for transformation, with the fastest cycling 3% of GMPs (∼0.006% of bone marrow nucleated cells) acquiring malignancy with nearly 100% efficiency. Molecularly, we propose that MLL-AF9 preserves the gene expression of the cellular states in which it is expressed. As such, when expressed in the naturally-existing, rapidly-cycling myeloid progenitors, this cell state is perpetuated, yielding malignancy. Our work elucidates one of the earliest steps toward malignancy and suggests that modifying the cycling state of the cell-of-origin could be an effective approach to prevent malignancy.
Usefulness Criterion and post-selection Parental Contributions in Multi-parental Crosses: Application to Polygenic Trait Introgression
Authors: Allier Antoine , Moreau Laurence , Charcosset Alain , Teyssèdre Simon , Lehermeier Christina 
Published: December 2018

ABSTRACTPredicting the usefulness of crosses in terms of expected genetic gain and genetic diversity is of interest to secure performance in the progeny and to maintain long-term genetic gain in plant breeding. A wide range of crossing schemes are possible including large biparental crosses, backcrosses, four-way crosses, and synthetic populations.In silicoprogeny simulations together with genome-based prediction of quantitative traits can be used to guide mating decisions. However, the large number of multi-parental combinations can hinder the use of simulations in practice. Analytical solutions have been proposed recently to predict the distribution of a quantitative trait in the progeny of biparental crosses using information of recombination frequency and linkage disequilibrium between loci. Here, we extend this approach to obtain the progeny distribution of more complex crosses including two to four parents. Considering agronomic traits and parental genome contribution as jointly multivariate normally distributed traits, the usefulness criterion parental contribution (UCPC) enables to (i) evaluate the expected genetic gain for agronomic traits, and at the same time (ii) evaluate parental genome contributions to the selected fraction of progeny. We validate and illustrate UCPC in the context of multiple allele introgression from a donor into one or several elite recipients in maize (Zea maysL.). Recommendations regarding the interest of two-way, three-way, and backcrosses were derived depending on the donor performance. We believe that the computationally efficient UCPC approach can be useful for mate selection and allocation in many plant and animal breeding contexts.
Cardiac afferent activity modulates early neural signature of error detection during skilled performance
Authors: Bury Gabriela , Huesca Marta García , Bhattacharya Joydeep , Ruiz María Herrojo 
Published: December 2018

AbstractBehavioral adaptations during performance rely on predicting and evaluating the consequences of our actions through action monitoring. Previous studies revealed that proprioceptive and exteroceptive signals contribute to error-monitoring processes, which are implemented in the posterior medial frontal cortex. Interestingly, errors also trigger changes in autonomic nervous system activity such as pupil dilation or heartbeat deceleration. Yet, the contribution of implicit interoceptive signals of bodily states to error-monitoring during ongoing performance has been overlooked.This study investigated whether cardiovascular interoceptive signals influence the neural correlates of error processing during performance, with an emphasis on the early stages of error processing. We recorded musicians’ electroencephalography and electrocardiogram signals during the performance of highly-trained music pieces. Previous event-related potential (ERP) studies revealed that pitch errors during skilled musical performance are preceded by an error detection signal, the pre-error-negativity (preERN), and followed by a later error positivity (PE). In this study, by combining ERP, source localization and multivariate pattern classification analysis, we found that the error-minus-correct ERP waveform had an enhanced amplitude within 40-100 ms following errors in the systolic period of the cardiac cycle. This component could be decoded from singletrials, was dissociated from the preERN and PE, and stemmed from the inferior parietal cortex, which is a region implicated in cardiac autonomic regulation. In addition, the phase of the cardiac cycle influenced behavioral alterations resulting from errors, with a smaller post-error slowing and less perturbed velocity in keystrokes following pitch errors in the systole relative to the diastole phase of the cardiac cycle. Lastly, changes in the heart rate anticipated the upcoming occurrence of errors. This study provides the first evidence of preconscious visceral information modulating neural and behavioral responses related to early error monitoring during skilled performance.
An individual-based mechanical model of cell movement in heterogeneous tissues and its coarse-grained approximation
Authors: Murphy R. J. , Buenzli P. R. , Baker R. E. , Simpson M. J. 
Published: December 2018

AbstractMechanical heterogeneity in biological tissues, in particular stiffness, can be used to distinguish between healthy and diseased states. However, it is often difficult to explore relationships between cellular-level properties and tissue-level outcomes when biological experiments are performed at a single scale only. To overcome this difficulty we develop a multi-scale mathematical model which provides a clear framework to explore these connections across biological scales. Starting with an individual-based mechanical model of cell movement, we subsequently derive a novel coarse-grained system of partial differential equations governing the evolution of the cell density due to heterogeneous cellular properties. We demonstrate that solutions of the individual-based model converge to numerical solutions of the coarse-grained model, for both slowly-varying-in-space and rapidly-varying-in-space cellular properties. Applications of the model are discussed, including determining relative cellular-level properties and an interpretation of data from a breast cancer detection experiment.
Arabidopsis TRM5 encodes a nuclear-localised bifunctional tRNA guanine and inosine-N1-methyltransferase that is important for growth
Authors: Guo Q. , Ng PQ. , Shi S. , Fan D. , Li J. , Wang H. , Do T. , David R. , Mittal P. , Bock R. , Zhao M. , Zhou W. , Searle I. R. 
Published: December 2018

AbstractModified nucleosides in tRNAs are critical for protein translation. N1-methylguanosine-37 and N1-methylinosine-37 in tRNAs, both located at the 3’-adjacent to the anticodon, are formed by Trm5 and here we describe Arabidopsis thaliana AtTrm5 (At3g56120) as a Trm5 ortholog. We show that AtTrm5 complements the yeast trm5 mutant, and in vitro methylates tRNA guanosine-37 to produce N1-methylguanosine (m1G). We also show in vitro that AtTRM5 methylates tRNA inosine-37 to produce N1-methylinosine (m1I) and in Attrm5 mutant plants, we show a reduction of both N1-methylguanosine and N1-methylinosine. We also show that AtTRM5 is localized to the nucleus in plant cells. Attrm5 mutant plants have overall slower growth as observed by slower leaf initiation rate, delayed flowering and reduced primary root length. In Attrm5 mutants, mRNAs of flowering time genes are less abundant and correlated with delayed flowering. Finally, proteomics data show that photosynthetic protein abundance is affected in mutant plants. Our findings highlight the bifunctionality of AtTRM5 and the importance of the post-transcriptional tRNA modifications m1G and m1I at tRNA position 37 in general plant growth and development.
An experiential approach to learning about change management
Authors: Vandangeon-Derumez Isabelle , Djedidi Amina , Szendy Eila 
Published: December 2018

PurposeThe purpose of this paper is to focus on the role of experience in learning about, and preparing for, change management.Design/methodology/approachA course with a different approach to teaching about change management has been proposed to learners. It uses drawing, simulation and exploration of case studies. Learners wrote reports on change management before and after the course and these reports were then thematically analyzed.FindingsResults show the specific ways in which the course places learners in a position to: experience change, use their collective experiences, acquire and develop practical knowledge, and prepare themselves for change. Capitalizing on such experiences of change could arguably become an integral part of an organization’s “readiness to change” strategy.Research limitations/implicationsIt would be useful to further investigate what happens after this experience by interviewing learners, later on, in order to analyze how they subsequently use, in a real professional environment, such knowledge and skills acquired during the learning process.Practical implicationsUsing this approach, future managers are arguably better prepared to implement change. Capitalizing on such experiences of change could become part of an organization’s “readiness for change” strategy.Social implicationsThe benefits of experiencing change management in a learning environment will only be reaped when firms allocate time and space to such experiential learning. This entails going beyond managing this change to a deeper perspective by identifying key elements to maintain and/or enhance one’s experience of managing change.Originality/valueThe value of the present paper lies in individual and collective experience as a key element to prepare managers to change management.