bluuebunny/crossref_metadata_2025 huggingface dataset:
A study of factors affecting torque transmission in permanent magnet-based magnetorheological fluid clutch
Authors: Fernández Manuel Alejandro , Chang Jen-Yuan (James)
Published: April 2021

In this article, the study of several factors affecting the torque transmission capability of a permanent magnet-based, drum-type magnetorheological fluid (MRF) clutch is presented. These factors are: number of magnetic poles in the magnet assembly, material of the clutch, MRF layer thickness, and relative rotational velocity between the input and output stages of the clutch. For this purpose, a special single-MRF layer clutch was designed and fabricated, one which allows the convenient assembly and disassembly to reduce preparation time for testing. The average transmitted torque of this clutch under several combinations of the aforementioned factors was recorded and analyzed. Additionally, several magnetostatic simulations of the clutch were carried out, and both the magnetic flux density and transmittable torque calculated from the results of these simulation were compared against experimental measurements. It was found that magnet assemblies with lower number of magnetic poles resulted in higher torque outputs, however, the effectiveness of the utilized torque variation mechanism was reduced due to magnetic saturation of the components of the clutch. The material of the clutch was found to have a significant effect at low relative rotational velocities, resulting in a nonlinear relationship between transmitted torque and relative angular velocity. This nonlinear effect was more significant when aluminum was used in the components which interact directly with the MR fluid whereas the use of ferromagnetic components reduced this effect. Finally, the thickness of the MRF layer was found to have a significant effect on the transmitted torque of the MRF clutch, although not according to what magnetostatic simulations predict.
Refined circuit model for current distribution of the no-insulation HTS insert magnet
Authors: Qin Lang , Wang Lei , Liu Jianhua , Wang Kangshuai , Zhou Benzhe , Sun Hongbo , Wang Qiuliang
Published: April 2021

Detailed simulation can play a fundamental role in the design, manufacture, and operation of high-field magnets. This study introduces a new equivalent circuit simulation method for the no-insulation (NI) superconducting magnet. The refined circuit model (RCM) can describe the current distribution inside the REBa2Cu3O7-δ
(RE, rare earth elements) tapes in the equivalent circuit model. A single turn of REBCO tape was divided in both the width and length directions to achieve better results. A simulation model for a NI REBCO insert magnet was established through the RCM. Simulation results show that the screen current starts to saturate within 500 s during the excitation of the HTS magnet. The refined circuit model can help to make a more detailed mechanical analysis of the REBCO magnets. It can also guide the excitation of the HTS magnet and screen current reduction through real-time simulation.
Propagation of cosine beam in uniaxial crystal orthogonal to optical axis
Authors: Bayraktar Mert
Published: April 2021

In this paper, we analyze the intensity and phase changes of cosine beam(CB) propagating uniaxial crystal orthogonal to optical axis. Received field is derived based upon Huygens–Fresnel integration. Main objective of this paper is to present intensity and phase evolution of cosine beam in uniaxial crystals first time in the literature. However, behavior of other untraditional beams is studied, reaction of cosine beam against uniaxial crystal is not studied previously. We analyze the results considering source beam settings, crystal structure, and propagation distance. Our results indicate that matrix view in intensity profile evolves into straight lines along propagation axis. In other point of view, symmetric cosine beam has constant phase at close distance and periodic oscillation is observed at middle at far distance. We believe that results of this study will be beneficial for optical tracking and other optical applications.
Hyperfine structures and the field effects of IBr molecule in its rovibronic ground state*
Authors: Wang Defu , Shao Xuping , Huang Yunxia , Li Chuanliang , Yang Xiaohua
Published: April 2021

Hyperfine structures and the field effects of IBr molecule in its rovibronic ground state are theoretically studied by diagonalizing the effective Hamiltonian matrix. Perturbations of high-J levels up to 4 are taken into account when studying the hyperfine sub-levels of the J = 0 level, and thus, an 80 × 80 matrix is constructed and solved. Some of the experimentally absent molecular constants are computed using Dalton program. Our results will be helpful in the experimental investigation of manipulation and further cooling of cold IBr molecules.
Design and performance tests of a modular 166.6-MHz 50-kW compact solid-state power amplifier for the HEPS-TF project
Authors: Luo Y. , Zhang P. , Lin H. , Wang Q. , Ma Q. , Pan W.
Published: April 2021

A 166.6-MHz 50-kW power transmitter is required to drive the
dressed superconducting radio-frequency (RF) cavity during
horizontal tests and to condition the fundamental power couplers as
well as higher-order-mode ferrite absorbers. A highly modular yet
compact amplifier adopting solid-state technologies was therefore
developed in the framework of High Energy Photon Source - Test
Facility. All power amplifier and power supply modules are pluggable
from the front panel of the amplifier system. A 3-stage power
combining topology was realized by using 32 power amplifier modules,
4 eight-way stripline power combiners, 2 two-way 35-kW coaxial power
combiners, and 1 two-way 65-kW coaxial power combiner. Each power
amplifier module is equipped with individual circulator and load
utilizing an optimized cooling circuit design to ensure the entire
amplifier system to be operational in both full-transmission and
full-reflection scenarios. No final-stage high-power circulator or
load is needed. The amplifier system is tunable in pulsed mode for
any duty factors and fully functional in the continuous-wave mode as
required. Excellent noise suppression and high wall-plug-to-RF
efficiency were achieved at nominal power. Comfortable redundancies
for both power amplifier and power supply modules were reserved to
compensate for any hardware degradations during
operations. Temperature, current, voltage, and RF signal of each
module as well as cooling were monitored and managed by using EPICS
in the control system of the amplifier. An interlock system was also
integrated as well as an event logging system for post-mortem
analysis. The system has accumulated over 2000 hours of
operation. The design and performance tests of the first 166.6-MHz
50-kW modular solid-state power amplifier are presented.
Measurement of neutrino source activity in the experiment BEST by calorimetric method
Authors: Gavrin V.N. , Ibragimova T.V. , Kozlova J.P. , Tarasov V.A. , Veretenkin E.P. , Zvir A.I.
Published: April 2021

Experiments to study non-standard properties of neutrinos using high-intensity artificial neutrino sources require high accuracy in determining their activity. A calorimetric system to determine the activity of a ^51Cr neutrino source in the experiment BEST with an accuracy better than 1% was created. The design of the calorimetric system and the main factors affecting the accuracy of measurements are considered. The results of measurements of the activity of the source made for the BEST experiment are presented. The value of the source activity from calorimetric measurements was 3.41 MCi at the beginning of the experiment.
A perfusable vascularized full-thickness skin model for potential topical and systemic applications
Authors: Salameh Sacha , Tissot Nicolas , Cache Kevin , Lima Joaquim , Suzuki Itaru , Marinho Paulo André , Rielland Maité , Soeur Jérémie , Takeuchi Shoji , Germain Stéphane , Breton Lionel
Published: April 2021

Vascularization of reconstructed tissues is one of the remaining hurdles to be considered to improve both the functionality and viability of skin grafts and the relevance of in vitro applications. Our study, therefore, sought to develop a perfusable vascularized full-thickness skin equivalent that comprises a more complex blood vasculature compared to existing models. We combined molding, auto-assembly and microfluidics techniques in order to create a vascularized skin equivalent representing (a) a differentiated epidermis with a physiological organization and correctly expressing K14, K10, Involucrin, TGM1 and Filaggrin, (b) three perfusable vascular channels with angiogenic sprouts stained with VE-Caderin and Collagen IV, (c) an adjacent microvascular network created via vasculogenesis and connected to the sprouting macrovessels. Histological analysis and immunostaining of CD31, Collagen IV, Perlecan and Laminin proved the integrity of vascular constructs. In order to validate the vascularized skin potential of topical and systemic applications, caffeine and minoxidil, two compounds with different chemical properties, were topically applied to measure skin permeability and benzo[a]pyrene pollutant was systemically applied to evaluate systemic delivery. Our results demonstrated that perfusion of skin reconstructs and the presence of a complex vascular plexus resulted in a more predictive and reliable model to assess respectively topical and systemic applications. This model is therefore aimed at furthering drug discovery and improving clinical translation in dermatology.
Fast approximate inference for multivariate longitudinal data
Authors: Hughes David M , García-Fiñana Marta , Wand Matt P
Published: April 2021

Collecting information on multiple longitudinal outcomes is increasingly common in many clinical settings. In many cases, it is desirable to model these outcomes jointly. However, in large data sets, with many outcomes, computational burden often prevents the simultaneous modeling of multiple outcomes within a single model. We develop a mean field variational Bayes algorithm, to jointly model multiple Gaussian, Poisson, or binary longitudinal markers within a multivariate generalized linear mixed model. Through simulation studies and clinical applications (in the fields of sight threatening diabetic retinopathy and primary biliary cirrhosis), we demonstrate substantial computational savings of our approximate approach when compared to a standard Markov Chain Monte Carlo, while maintaining good levels of accuracy of model parameters.
O2: TOWARDS A LIVING BIOBANK OF SURGICALLY-RELEVANT 3-DIMENSIONAL GLIOBLASTOMA STEM CELL MODELS TO EVALUATE NOVEL THERAPEUTICS AND INTERROGATE INTRATUMOURAL HETEROGENEITY
Authors: Rominiyi O , Vanderlinden A , Myers K , Gomez-Roman N , Dar D , Bagga V , Jellinek DA , Chalmers AJ , Carroll TA , Al-Tamimi Y , Collis SJ
Published: April 2021

Introduction

Glioblastoma is the most common cancer arising within the brain. Despite surgery, followed by DNA-damaging chemoradiotherapy, average survival remains between 12-15 months. Unacceptable survival rates underline the need to develop preclinical research models which recapitulate features underpinning therapeutic resistance in patients, such as intratumoural heterogeneity and treatment resistant glioblastoma stem cell (GSC) subpopulations which demonstrate elevated DNA damage response (DDR) activity.

Method

Tumour specimens from patients were used to generate 2D and 3D scaffold-based GSC models, with a range of preclinical survival and molecular assays used to interrogate cancer biology and assess therapeutic responses.

Result

We have developed a ‘living biobank’ of 20+ ex-vivo GSC models which reflect key clinicopathological diversity. These models include residual disease models based on careful macrodissection of rare en-blocpartial lobectomy specimens to liberate parallel GSC lines from the tumour core and adjacent infiltrated brain, to represent cells typically left behind after surgery. Therapeutic strategies targeting fundamental DDR processes demonstrate preclinical efficacy, for example dual inhibition of ATR and the FA DNA damage repair pathways elicits profound radiosensitisation (sensitiser enhancement ratio of 3.23 (3.03-3.49, 95%-CI)) with evidence of delayed DNA damage repair on single-cell gel electrophoresis. Finally, characterisation of our surgically-relevant resected and residual models reveals numerous divergent properties including elevated stem cell marker expression in residual models (p=0.0021), which may partially explain treatment resistance in disease left behind after surgery.

Conclusion

Our living biobank represents a useful resource for preclinical glioblastoma research and demonstrates the value of partnership between surgeons and laboratory-based scientists.

Take-home message

Our living biobank represents a useful resource for preclinical glioblastoma research and demonstrates the value of partnership between surgeons and laboratory-based scientists.
O5: THE CLIFF AND CONOR STUDIES NOVEL ASSESSMENT TOOLS IN COLORECTAL LIVER METASTASES (CLIFF STUDY - CHANGE IN LIVER FUNCTION AND FAT IN PRE-OPERATIVE CHEMOTHERAPY FOR COLORECTAL LIVER METASTASES, CONOR STUDY
Authors: Parmar KL , Slawinski C , Malcomson L , OReilly D , Valle JW , Braun M , Naish JH , Williams SR , Renehan AG
Published: April 2021

Introduction

Hepatic resection is the only potentially curative treatment for patients with colorectal liver metastases (CLM). Patient selection is key, but there is wide variation in practice. Pre-operative chemotherapy can improve oncological outcomes, however chemotherapy-associated liver injury (CALI) may hinder liver regenerative capacity. Standard pre-operative assessments fail to accurately capture factors such as CALI and future liver remnant (FLR) function. The CLiFF and CoNoR studies utilise two novel assessment techniques, aiming to improve patient outcomes.

Method

The CLiFF study prospectively assesses two primary outcomes in 35 patients undergoing pre-operative chemotherapy for CLM: 1) change in liver function (via LiMAx test: direct assessment of hepatic functional capacity), and 2) change in liver fat (via advanced MR imaging (in-house spectroscopy and modified Dixon technique, scaled up via Perspectum LiverMultiScan)). The CoNoR study assesses potential added benefit of these novel tools in CLM resectability decision-making via sequential workstreams: a systematic review and international hepatobiliary expert interviews inform the online survey, assessing added benefit via online MDT scenarios.

Result

Preliminary CLiFF analysis suggests that CALI changes in liver fat and function are unrelated. Liver fat analysis techniques are compared and correlated with digital histological analysis. The CoNoR systematic review identifies key factors influencing CLM resectability decision-making and informs the international expert interviews, scheduled to occur during a February 2020 international hepatobiliary conference.

Conclusion

These studies are the first to assess where these novel tools might be utilised to maximal patient benefit within the Hepatobiliary MDT, and the first systematic review in CLM resectability decision-making.

Take-home message

These two linked studies evaluate the use of two novel assessment tools in the treatment of colorectal liver metastases, with the potential to improve patient selection for curative resection and patient outcomes.

PATEY PRIZE SESSION
O45: DEFINING CELL-ENRICHED MICRORNAS TO SUPPORT RATIONAL BIOMARKER SELECTION IN HUMAN RENAL TRANSPLANTATION
Authors: Connor K , Teenan O , Thomas R , Banwell V , Finnie S , Monaghan ML , Cairns C , Tannahill G , Harrison E , Conway B , Marson L , Denby L , Wigmore S
Published: April 2021

Introduction

MicroRNAs are promising biomarkers of renal disease, however the cellular origin of their expression is usually unclear limiting their interpretation when measured in renal biopsies and urine. We hypothesised that by first defining renal cell-enriched microRNAs, we could select biomarkers based on the expected histopathological profile.

Method

Small RNA-sequencing of cortical, proximal tubular (LTL), macrophage (F480), endothelial (CD31) and fibroblast (PDGFRb) populations from the reversible unilateral ureteric obstruction (rUUO) murine model was performed. Hierarchical clustering was used to identify clusters. Findings were translated into an ischaemia reperfusion injury (IRI) model and then into urine samples from renal transplant recipients (n=16) with delayed graft function (DGF) vs. those with primary function.

Result

Kidney injury resulted in significant macrophage infiltration and tubular injury which improved upon reversal. We characterised novel microRNA clusters enriched for each cell type. With injury there was a significant increase in macrophage (p<0.0001), fibroblast (p<0.01) and decrease in proximal tubule (p<0.0001) enriched microRNAs vs. non-enriched microRNAs. We validated macrophage enriched miR-18a, miR-16 and tubular enriched miR-194 in the IRI model, demonstrating that microRNA expression reflected the histological profile. In humans, urinary miR-16 (FC 16.9; p<0.05) and miR-18a (FC 10: p=0.06) were upregulated at day 2 in patients with DGF; outperforming the traditional injury marker KIM1.

Conclusion

This is the first study to characterise cell-enriched microRNAs during renal injury and repair. By defining the source of microRNA expression we were able to rationally select miR-16 and miR-18a as promising urinary biomarkers of renal injury.

Take-home message

We have found that microRNAs have differences in expression between cell types and renal injury states which is important when considering microRNA expression in samples composed of varying cellular composition. By defining the cellular origins of microRNA expression we were able to rationally select microRNA biomarkers of human renal injury.
Sleep Leads to Brain-Wide Neural Changes Independent of Allocentric and Egocentric Spatial Training in Humans and Rats
Authors: Samanta Anumita , van Rongen Laurens S , Rossato Janine I , Jacobse Justin , Schoenfeld Robby , Genzel Lisa
Published: April 2021

Sleep is important for memory consolidation and systems consolidation in particular, which is thought to occur during sleep. While there has been a significant amount of research regarding the effect of sleep on behavior and certain mechanisms during sleep, evidence that sleep leads to consolidation across the system has been lacking until now. We investigated the role of sleep in the consolidation of spatial memory in both rats and humans using a watermaze task involving allocentric- and egocentric-based training. Analysis of immediate early gene expression in rodents, combined with functional magnetic resonance imaging in humans, elucidated similar behavioral and neural effects in both species. Sleep had a beneficial effect on behavior in rats and a marginally significant effect in humans. Interestingly, sleep led to changes across multiple brain regions at the time of retrieval in both species and in both training conditions. In rats, sleep led to increased gene expression in the hippocampus, striatum, and prefrontal cortex. In the humans, sleep led to an activity increase in brain regions belonging to the executive control network and a decrease in activity in regions belonging to the default mode network. Thus, we provide cross-species evidence for system-level memory consolidation occurring during sleep.
The Recovery of the Anglo-Saxon Past, c.1770–1850
Authors: Sweet Rosemary
Published: April 2021

Between the eighteenth and the nineteenth centuries, a remarkable shift took place in the reception of England’s Anglo-Saxon past. During the eighteenth century the contributions of the Anglo-Saxons to English traditions of political liberty and the common law were acknowledged—and highly prized—but as a people, they were also indelibly associated with the barbarism of the Dark Ages. By the mid-nineteenth century, however, attitudes had shifted substantively. While the debt to Anglo-Saxon legal and political institutions was still acknowledged, it was, relatively speaking, diminished and the focus was rather upon their role in the development of the nation and the shaping of English national character. They were rendered more conformable forebears for the increasingly urban, domestic and commercial society of nineteenth-century England. This article analyses how such a reconceptualisation came about. Rather than concentrating on the emergence of a discourse of race or national character or tracing the emergence of rigorous philological inquiry into Old English, it focuses upon the production of historical knowledge that permitted the development of a more varied, nuanced and fuller history of the Anglo-Saxon period. In doing so, the article illuminates the porosity of the boundaries between antiquarian and historical activity, and argues that the recovery of the Anglo-Saxon past in this period was shaped by a complex set of influences, which an emphasis upon the emergence of a discourse of race alone obscures.
A Performance Analysis of Sawmills in Oregon from 2003 to 2017
Authors: Sun Changyou , Marcille Kate C , Daniels Jean M
Published: April 2021

The number of mills and employees in Oregon’s sawmill sector has continuously declined from 2003 to 2017, but the amount of lumber produced has stabilized in recent years. In this study, the performance of individual sawmills is evaluated by applying data envelopment analysis on a unique dataset for 146 mills over four survey years of 2003, 2008, 2013, and 2017. The scale efficiency of these mills is generally high, but their overall technical efficiency is only 85%. In 2017, the most efficient mills as a group used 14% fewer employees, processed 18% more sawlogs, and produced 32% more lumber than an average mill in Oregon. Across the four survey years, productivity growth over time is small at only 0.14% per year, and most of the growth can be attributed to changes in technology. The catch-up effect by individual mills is actually negative at −0.07% per year. These findings reveal that the growth of production efficiency in Oregon’s sawmill sector has been slow, and the direction for future improvement relies on better management of operations and resources by individual mills.
Gene Silencing by DNA Methylation and Dual Inheritance in Chinese Hamster Ovary Cells
Authors: Paulin R P , Ho T , Balzer H J , Holliday R
Published: April 2021

Chinese hamster ovary (CHO) cells strain D422, which has one copy of the adenine phosphoribosyl transferase (APRT) gene, were permeabilized by electroporation and treated with 5-methyl deoxycytidine triphosphate. Cells with a silenced APRT gene were selected on 2, 6-diaminopurine. Colonies were isolated and shown to be reactivated to APRT+ by 5-aza-cytidine and by selection in medium containing adenine, aminopterin and thymidine. Genomic DNA was prepared from eight isolates of independent origin and subjected to bisulphite treatment. This deaminates cytosine to uracil in single-stranded DNA but does not deaminate 5-methyl cytosine. PCR, cloning and sequencing revealed the methylation pattern of CpG doublets in the promoter region of the APRT− gene, whereas the active APRT gene had nonmethylated DNA. CHO strain K1, which has two copies of the APRT+ gene, could also be silenced by the same procedure but at a lower frequency. The availability of the 5-methyl dCTP-induced silencing, 5-aza-CR and a standard mutagen, ethyl methane sulphonate, makes it possible to follow concomitantly the inheritance of active, mutant or silenced gene copies. This analysis demonstrates “dual inheritance” at the APRT locus in CHO cells.
Gametocidal Genes Induce Chromosome Breakage in the Interphase Prior to the First Mitotic Cell Division of the Male Gametophyte in Wheat
Authors: Nasuda Shuhei , Friebe Bernd , Gill Bikram S
Published: April 2021

Male gametogenesis was cytologically analyzed in wheat lines homozygous or hemizygous for gametocidal (Gc) factors with different modes of action. The first and second meiotic divisions in all lines were cytologically normal. The postmeiotic mitoses were normal in the homozygous lines; however, chromosome fragments and bridges were observed in the mitoses of the hemizygous lines. The morphology of the chromosome fragments suggests that the Gc genes induce chromosome breaks in the G1 phase prior to DNA synthesis of the first postmeiotic mitosis. The age of an anther was correlated with the frequency of aberrant second mitosis. Younger anthers contained a higher number of pollen undergoing normal second mitosis. This observation suggests that the arresting of the cell cycle occurs as the result of chromosome breaks during the first mitosis. Because chromosome bridges were more frequent than fragments in the second mitosis, breakage-fusion-bridge cycles possibly occurred during gametogenesis, which led to further chromosomal rearrangements. The Gc factors located on chromosomes 2S of Aegilops speltoides and 4Ssh of Ae. sharonensis induce severe chromosome breakage in pollen lacking them. However, the Gc factor on telosome 2CcL of Ae. cylindrica only induced chromosome breaks at a low frequency. The observed partial fertility of Gc lines is presumably due to cell cycle arrest and the competition among gametes with and without chromosome breakage.
One-Locus Two-Allele Models With Maternal (Parental) Selection
Authors: Gavrilets Sergey
Published: April 2021

I formulate and study a series of simple one-locus two-allele models for maternal (parental) selection. I show that maternal (parental) selection can result in simultaneous stability of equilibria of different types. Thus, in the presence of maternal (parental) selection the outcome of population evolution can significantly depend on initial conditions. With maternal selection, genetic variability can be maintained in the population even if none of the offspring of heterozygous mothers survive. I demonstrate that interactions of maternal and paternal selection can result in stable oscillations of genotype frequencies. A necessary condition for cycling is strong selection.
Evidence for a Role for AtMYB2 in the Induction of the Arabidopsis Alcohol Dehydrogenase Gene (ADH1) by Low Oxygen
Authors: Hoeren Frank U , Dolferus Rudy , Wu Yingru , Peacock W James , Dennis Elizabeth S
Published: April 2021

The transcription factor AtMYB2 binds to two sequence motifs in the promoter of the Arabidopsis ADH1 gene. The binding to the GT-motif (5′-TGGTTT-3′) is essential for induction of ADH1 by low oxygen, while binding to the second motif, MBS-2, is not essential for induction. We show that AtMYB2 is induced by hypoxia with kinetics compatible with a role in the regulation of ADH1. Like ADH1, AtMYB2 has root-limited expression. When driven by a constitutive promoter, AtMYB2 is able to transactivate ADH1 expression in transient assays in both Arabidopsis and Nicotiana plumbaginifolia protoplasts, and in particle bombardment of Pisum sativum leaves. Mutation of the GT-motif abolished binding of AtMYB2 and caused loss of activity of the ADH1 promoter in both transient assays and transgenic Arabidopsis plants. These results are consistent with AtMYB2 being a key regulatory factor in the induction of the ADH1 promoter by low oxygen.
Genetics of the Deflagellation Pathway in Chlamydomonas
Authors: Finst Rip J , Kim Peter J , Quarmby Lynne M
Published: April 2021

Signal-induced deflagellation in Chlamydomonas involves Ca2+-activated breakage of the nine outer-doublet axonemal microtubules at a specific site in the flagellar transition zone. In this study, we isolated 13 new deflagellation mutants that can be divided into two phenotypic classes, the Adf class and the Fa class. Cells with the Adf deflagellation phenotype are defective in acid-stimulated Ca2+ influx, but can be induced to deflagellate by treatment with nonionic detergent and Ca2+. Genetic analyses show that the five new Adf mutations, as well as the previously identified adf1 mutation, are alleles of the ADF1 gene. Mutants in the second phenotypic class, the Fa mutants, fail to deflagellate in response to any known chemical stimulus and are defective in Ca2+-activated microtubule severing. Genetic analysis of these eight new Fa strains demonstrated that they define two complementation groups, and one of these contains the previously identified fa1 mutation. Diploid analysis showed that five alleles map to the FA1 gene, whereas four alleles define a novel gene that we have named FA2. The isolation of multiple mutant alleles of each gene, generated by either ultraviolet irradiation or insertional mutagenesis, indicates that ADF1, FA1, and FA2 may be the only genes that can be identified in a loss-of-function screen. These alleles should provide a better understanding of the regulation of microtubule severing by Ca2+.
Allele-Specific Population Structure of Drosophila melanogaster Alcohol Dehydrogenase at the Molecular Level
Authors: Veuille Michel , Bénassi Véronique , Aulard Sylvie , Depaulis Frantz
Published: April 2021

The history of the Drosophila melanogaster alcohol dehydrogenase (ADH) Fast/Slow polymorphism was studied by recording molecular variation and inversion polymorphism in 233 chromosomes from European and African populations. Silent molecular variation in the Slow allele was very different between standard chromosomes and chromosomes bearing the In(2L)t inversion. Within populations, inverted Slow haplotypes were more variable than standard Slow haplotypes. Between populations, geographical structure was almost nonexistent for inverted Slow haplotypes and highly significant for standard Slow. All Fast haplotypes occurred on standard chromosomes. They showed little variation within and between populations. They were highly significantly closer to standard Slow haplotypes from Europe. These results suggest that the current range of Fast and In(2L)t Slow haplotypes is recent and that an older genetic differentiation between populations was followed by allele-specific gene flow.
Effects of DNA Double-Strand and Single-Strand Breaks on Intrachromosomal Recombination Events in Cell-Cycle-Arrested Yeast Cells
Authors: Galli Alvaro , Schiestl Robert H
Published: April 2021

Intrachromosomal recombination between repeated elements can result in deletion (DEL recombination) events. We investigated the inducibility of such intrachromosomal recombination events at different stages of the cell cycle and the nature of the primary DNA lesions capable of initiating these events. Two genetic systems were constructed in Saccharomyces cerevisiae that select for DEL recombination events between duplicated alleles of CDC28 and TUB2. We determined effects of double-strand breaks (DSBs) and single-strand breaks (SSBs) between the duplicated alleles on DEL recombination when induced in dividing cells or cells arrested in G1 or G2. Site-specific DSBs and SSBs were produced by overexpression of the I-Sce I endonuclease and the gene II protein (gIIp), respectively. I-Sce I-induced DSBs caused an increase in DEL recombination frequencies in both dividing and cell-cycle-arrested cells, indicating that G1- and G2-arrested cells are capable of completing DSB repair. In contrast, gIIp-induced SSBs caused an increase in DEL recombination frequency only in dividing cells. To further examine these phenomena we used both γ-irradiation, inducing DSBs as its most relevant lesion, and UV, inducing other forms of DNA damage. UV irradiation did not increase DEL recombination frequencies in G1 or G2, whereas γ-rays increased DEL recombination frequencies in both phases. Both forms of radiation, however, induced DEL recombination in dividing cells. The results suggest that DSBs but not SSBs induce DEL recombination, probably via the single-strand annealing pathway. Further, DSBs in dividing cells may result from the replication of a UV or SSB-damaged template. Alternatively, UV induced events may occur by replication slippage after DNA polymerase pausing in front of the damage.
Identification of Heterochronic Mutants in Caenorhabditis elegans: Temporal Misexpression of a Collagen::Green Fluorescent Protein Fusion Gene
Authors: Abrahante Juan E , Miller Eric A , Rougvie Ann E
Published: April 2021

The heterochronic genes lin-4, lin-14, lin-28, and lin-29 specify the timing of lateral hypodermal seam cell terminal differentiation in Caenorhabditis elegans. We devised a screen to identify additional genes involved in this developmental timing mechanism based on identification of mutants that exhibit temporal misexpression from the col-19 promoter, a downstream target of the heterochronic gene pathway. We fused the col-19 promoter to the green fluorescent protein gene (gfp) and demonstrated that hypodermal expression of the fusion gene is adult-specific in wild-type animals and temporally regulated by the heterochronic gene pathway. We generated a transgenic strain in which the col-19::gfp fusion construct is not expressed because of mutation of lin-4, which prevents seam cell terminal differentiation. We have identified and characterized 26 mutations that restore col-19::gfp expression in the lin-4 mutant background. Most of the mutations also restore other aspects of the seam cell terminal differentiation program that are defective in lin-4 mutant animals. Twelve mutations are alleles of three previously identified genes known to be required for proper timing of hypodermal terminal differentiation. Among these are four new alleles of lin-42, a heterochronic gene for which a single allele had been described previously. Two mutations define a new gene, lin-58. When separated from lin-4, the lin-58 mutations cause precocious seam cell terminal differentiation and thus define a new member of the heterochronic gene pathway.
Mitochondrial DNA Haplotype Frequencies in Natural and Experimental Populations of Drosophila subobscura
Authors: García-Martínez José , Castro José Aurelio , Ramón Misericordia , Latorre Amparo , Moya Andrés
Published: April 2021

The evolution of Drosophila subobscura mitochondrial DNA has been studied in experimental populations, founded with flies from a natural population from Esporles (Majorca, Balearic Islands, Spain). This population, like other European ones, is characterized by the presence of two very common (>96%) mitochondrial haplotypes (called I and II) and rare and endemic haplotypes that appear at very low frequencies. There is no statistical evidence of positive Darwinian selection acting on the mitochondrial DNA variants according to Tajima's neutrality test. Two experimental populations, with one replicate each, were established with flies having a heterogeneous nuclear genetic background, which was representative of the composition of the natural population. Both populations were started with the two most frequent mitochondrial haplotypes, but at different initial frequencies. After 13 to 16 generations, haplotype II reached fixation in three cages and its frequency was 0.89 by generation 25 in the fourth cage. Random drift can be rejected as the force responsible for the observed changes in haplotype frequencies. There is not only statistical evidence of a linear trend favoring a mtDNA (haploid) fitness effect, but also of a significant nonlinear deviation that could be due to a nuclear component.
Correlation Between the Substitution Rate and Rate Variation Among Sites in Protein Evolution
Authors: Zhang Jianzhi , Gu Xun
Published: April 2021

It is well known that the rate of amino acid substitution varies among different proteins and among different sites of a protein. It is, however, unclear whether the extent of rate variation among sites of a protein and the mean substitution rate of the protein are correlated. We used two approaches to analyze orthologous protein sequences of 51 nuclear genes of vertebrates and 13 mitochondrial genes of mammals. In the first approach, no assumptions of the distribution of the rate variation among sites were made, and in the second approach, the gamma distribution was assumed. Through both approaches, we found a negative correlation between the extent of among-site rate variation and the average substitution rate of a protein. That is, slowly evolving proteins tend to have a high level of rate variation among sites, and vice versa. We found this observation consistent with a simple model of the neutral theory where most sites are either invariable or neutral. We conclude that the correlation is a general feature of protein evolution and discuss its implications in statistical tests of positive Darwinian selection and molecular time estimation of deep divergences.
Analysis of a Drosophila cyclin E Hypomorphic Mutation Suggests a Novel Role for Cyclin E in Cell Proliferation Control During Eye Imaginal Disc Development
Authors: Secombe Julie , Pispa Johanna , Saint Robert , Richardson Helena
Published: April 2021

We have generated and characterized a Drosophila cyclin E hypomorphic mutation, DmcycEJP, that is homozygous viable and fertile, but results in adults with rough eyes. The mutation arose from an internal deletion of an existing P[w+lacZ] element inserted 14 kb upstream of the transcription start site of the DmcycE zygotic mRNA. The presence of this deleted P element, but not the P[w+lacZ] element from which it was derived, leads to a decreased level of DmcycE expression during eye imaginal disc development. Eye imaginal discs from DmcycEJP larvae contain fewer S phase cells, both anterior and posterior to the morphogenetic furrow. This results in adults with small rough eyes, largely due to insufficient numbers of pigment cells. Altering the dosage of the Drosophila cdk2 homolog, cdc2c, retinoblastoma, or p21CIP1 homolog dacapo, which encode proteins known to physically interact with Cyclin E, modified the DmcycEJP rough eye phenotype as expected. Decreasing the dosage of the S phase transcription factor gene, dE2F, enhanced the DmcycEJP rough eye phenotype. Surprisingly, mutations in G2/M phase regulators cyclin A and string (cdc25), but not cyclin B1, B3, or cdc2, enhanced the DmcycE JP phenotype without affecting the number of cells entering S phase, but by decreasing the number of cells entering mitosis. Our analysis establishes the DmcycE JP allele as an excellent resource for searching for novel cyclin E genetic interactors. In addition, this analysis has identified cyclin A and string as DmcycEJP interactors, suggesting a novel role for cyclin E in the regulation of Cyclin A and String function during eye development.
Identification and Mapping of Two Divergent, Unlinked Major Histocompatibility Complex Class II B Genes in Xiphophorus Fishes
Authors: McConnell Thomas J , Godwin Ulla B , Norton Stephen F , Nairn Rodney S , Kazianis Steven , Morizot Donald C
Published: April 2021

We have isolated two major histocompatibility complex (MHC) class II B genes from the inbred fish strain Xiphophorus maculatus Jp 163 A. We mapped one of these genes, designated here as DXB, to linkage group III, linked to a malic enzyme locus, also syntenic with human and mouse MHC. Comparison of genomic and cDNA clones shows the gene consists of six exons and five introns. The encoded β1 domain has three amino acids deleted and a cytoplasmic tail nine amino acids longer than in other teleost class II β chains, more similar to HLA-DRB, clawed frog Xela-F3, and nurse shark Gici-B. Key residues for disulfide bonds, glycosylation, and interaction with α chains are conserved. These same features are also present in a swordtail (Xiphophorus helleri) genomic DXB PCR clone. A second type of class II B clone was amplified by PCR from X. maculatus and found to be orthologous to class II genes identified in other fishes. This DAB-like gene is 63% identical to the X. maculatus DXB sequence in the conserved β2-encoding exon and was mapped to new unassigned linkage group LG U24. The DXB gene, then, represents an unlinked duplicated locus not previously identified in teleosts.
Analysis of Genetic Structure and Dispersal Patterns in a Population of Sea Beet
Authors: Tufto Jarle , Raybould Alan F , Hindar Kjetil , Engen Steinar
Published: April 2021

A model of the migration pattern in a metapopulation of sea beet (Beta vulgaris L. ssp. maritima), based on the continuous distributions of seed and pollen movements, is fitted to gene frequency data at 12 isozyme and RFLP loci by maximum likelihood by using an approximation of the simultaneous equilibrium distribution of the gene frequencies generated by the underlying multivariate stochastic process of genetic drift in the population. Several alternative restrictions of the general model are fitted to the data, including the island model, a model of complete isolation, and a model in which the seed and pollen dispersal variances are equal. Several likelihood ratio tests between these alternatives are performed, and median bias in the estimated parameters is corrected by using parametric bootstrapping. To assess the fit of the selected model, the predicted covariances are compared with covariances computed from the data directly. The dependency of estimated parameters on the ratio between effective and absolute subpopulation sizes, which is treated as a known parameter in the analysis, is also examined. Finally, we note that the data also appear to contain some information about this ratio.
A Microsatellite Map of Wheat
Authors: Röder Marion S , Korzun Victor , Wendehake Katja , Plaschke Jens , Tixier Marie-Hélène , Leroy Philippe , Ganal Martin W
Published: April 2021

Hexaploid bread wheat (Triticum aestivum L. em. Thell) is one of the world's most important crop plants and displays a very low level of intraspecific polymorphism. We report the development of highly polymorphic microsatellite markers using procedures optimized for the large wheat genome. The isolation of microsatellite-containing clones from hypomethylated regions of the wheat genome increased the proportion of useful markers almost twofold. The majority (80%) of primer sets developed are genome-specific and detect only a single locus in one of the three genomes of bread wheat (A, B, or D). Only 20% of the markers detect more than one locus. A total of 279 loci amplified by 230 primer sets were placed onto a genetic framework map composed of RFLPs previously mapped in the reference population of the International Triticeae Mapping Initiative (ITMI) Opata 85 × W7984. Sixty-five microsatellites were mapped at a LOD >2.5, and 214 microsatellites were assigned to the most likely intervals. Ninety-three loci were mapped to the A genome, 115 to the B genome, and 71 to the D genome. The markers are randomly distributed along the linkage map, with clustering in several centromeric regions.
An AFLP-Based Procedure for the Efficient Mapping of Mutations and DNA Probes in Barley
Authors: Castiglioni P , Pozzi C , Heun M , Terzi V , Müller K J , Rohde W , Salamini F
Published: April 2021

A strategy based upon AFLP markers for high-efficiency mapping of morphological mutations and DNA probes to linkage groups in barley is presented. First, 511 AFLP markers were placed on the linkage map derived from the cross Proctor × Nudinka. Second, loci controlling phenotypic traits were assigned to linkage groups by AFLP analysis, using F2 populations consisting of 30–50 mutant plants derived from crosses of the type “mutant × Proctor” and “mutant × Nudinka.” To map DNA probes, 67 different wild-type barley lines were selected to generate F2 populations by crossing with Proctor and Nudinka. F2 plants that were polymorphic for a given RFLP fragment were classified into genotypic classes. Linkage of the RFLP polymorphism to 1 of the 511 AFLP loci was indicated by cosegregation. The use of the strategy is exemplified by the mapping of the mutation branched-5 to chromosome 2 and of the DNA probes Bkn2 and BM-7 to chromosomes 5 and 1, respectively. Map expansion and marker order in map regions with dense clustering of markers represented a particular problem. A discussion considering the effect of noncanonical recombinant products on these two parameters is provided.
Canalization, Genetic Assimilation and Preadaptation: A Quantitative Genetic Model
Authors: Eshel Ilan , Matessi Carlo
Published: April 2021

We propose a mathematical model to analyze the evolution of canalization for a trait under stabilizing selection, where each individual in the population is randomly exposed to different environmental conditions, independently of its genotype. Without canalization, our trait (primary phenotype) is affected by both genetic variation and environmental perturbations (morphogenic environment). Selection of the trait depends on individually varying environmental conditions (selecting environment). Assuming no plasticity initially, morphogenic effects are not correlated with the direction of selection in individual environments. Under quite plausible assumptions we show that natural selection favors a system of canalization that tends to repress deviations from the phenotype that is optimal in the most common selecting environment. However, many experimental results, dating back to Waddington and others, indicate that natural canalization systems may fail under extreme environments. While this can be explained as an impossibility of the system to cope with extreme morphogenic pressure, we show that a canalization system that tends to be inactivated in extreme environments is even more advantageous than rigid canalization. Moreover, once this adaptive canalization is established, the resulting evolution of primary phenotype enables substantial preadaptation to permanent environmental changes resembling extreme niches of the previous environment.
Two Pleiotropic Classes of daf-2 Mutation Affect Larval Arrest, Adult Behavior, Reproduction and Longevity in Caenorhabditis elegans
Authors: Gems David , Sutton Amy J , Sundermeyer Mark L , Albert Patrice S , King Kevin V , Edgley Mark L , Larsen Pamela L , Riddle Donald L
Published: April 2021

The nematode Caenorhabditis elegans responds to overcrowding and scarcity of food by arresting development as a dauer larva, a nonfeeding, long-lived, stress-resistant, alternative third-larval stage. Previous work has shown that mutations in the genes daf-2 (encoding a member of the insulin receptor family) and age-1 (encoding a PI 3-kinase) result in constitutive formation of dauer larvae (Daf-c), increased adult longevity (Age), and increased intrinsic thermotolerance (Itt). Some daf-2 mutants have additional developmental, behavioral, and reproductive defects. We have characterized in detail 15 temperature-sensitive and 1 nonconditional daf-2 allele to investigate the extent of daf-2 mutant defects and to examine whether specific mutant traits correlate with each other. The greatest longevity seen in daf-2 mutant adults was approximately three times that of wild type. The temperature-sensitive daf-2 mutants fell into two overlapping classes, including eight class 1 mutants, which are Daf-c, Age, and Itt, and exhibit low levels of L1 arrest at 25.5°. Seven class 2 mutants also exhibit the class 1 defects as well as some or all of the following: reduced adult motility, abnormal adult body and gonad morphology, high levels of embryonic and L1 arrest, production of progeny late in life, and reduced brood size. The strengths of the Daf-c, Age, and Itt phenotypes largely correlated with each other but not with the strength of class 2-specific defects. This suggests that the DAF-2 receptor is bifunctional. Examination of the null phenotype revealed a maternally rescued egg, L1 lethal component, and a nonconditional Daf-c component. With respect to the Daf-c phenotype, the dauer-defective (Daf-d) mutation daf-12(m20) was epistatic to daf-2 class 1 alleles but not the severe class 2 alleles tested. All daf-2 mutant defects were suppressed by the daf-d mutation daf-16(m26). Our findings suggest a new model for daf-2, age-1, daf-12, and daf-16 interactions.