bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of a control system for a mobile robot based on Markov processes
Authors: Fedorov A A , Orekhov S Y , Veysman P I , Vasilchuk N Y
Published: April 2021

The purpose of this work is to develop and study a control system for mobile robots based on Markov processes. The paper investigates the adequacy of the control system algorithms based on Markov processes as applied to a mobile tracked robot.
Magnetic memory. Mechanical tests and proposed mechanisms
Authors: Sklemina O Yu , Skvortsov A A , Pshonkin D E , Tsilenko L P
Published: April 2021

The article considers the issue of an attempt to experimentally study the effect of constant magnetic fields on the processes of plastic deformation of aluminum alloys. An analysis of the influence of a magnetic field on the creep of an Al alloy with iron inclusions is presented. Estimates of the supposed mechanisms of the influence of the magnetic field on the creep processes are given.
Urates of colubroid snakes are different from those of boids and pythonids
Authors: Thornton Alyssa M , Schuett Gordon W , Swift Jennifer A
Published: April 2021

Uricotelic species, such as squamate reptiles, birds and insects, effectively eliminate nitrogen as uric acid in a solid form commonly called urates. Observations made over a decade suggested that the voided urates produced by colubroids (modern snake species) exhibit remarkable differences from those of boids and pythons (ancient snake species). Here, we compare the urates generated by eight captive snake species fed the same diet. Although all fresh urates were wet at the time of excretion, those produced by modern snakes dried to a powdery solid, whereas those of ancient species dried to a rock-hard mass that was tightly adherent to surfaces. Powder X-ray diffraction and infrared spectroscopy analyses performed on voided urates produced by five modern and three ancient snakes confirmed their underlying chemical and structural differences. Urates excreted by ancient snakes were amorphous uric acid, whereas urates from modern snakes consisted primarily of ammonium acid urate, with some uric acid dihydrate. These compositional differences indicate that snakes have more than one mechanism to manage nitrogenous waste. Why different species use different nitrogen-handling pathways is not yet known, but the answer might be related to key differences in metabolism, physiology or, in the case of ancient snakes, the potential use of urates in social communication.
Acceptance and Perceived Control are Independently Associated With Quality of Life in Inflammatory Bowel Disease: Introduction of a New Segmentation Model
Authors: van Erp Liselot W , van Gerven Jop , Bloem Sjaak , Groenen Marcel J M , Wahab Peter J
Published: April 2021

Background and Aims

Segmentation of patients based on psychological determinants of subjective health may provide new ways to personalized care. The cross-disease segmentation model developed by Bloem & Stalpers discriminates patients based on disease acceptance and perceived control. We aimed to validate the segmentation model, compare segments and evaluate whether segments independently correlate with quality of life in inflammatory bowel disease [IBD].

Methods

A cross-sectional study of adult IBD patients was performed with questionnaires on quality of life [32-item inflammatory bowel disease questionnaire], acceptance and perceived control [six items with 7-point Likert scale]. Four segments were formed [cut-off > 5]: [I] high acceptance, high control; [II] high acceptance, low control [III]; low acceptance, high control and; [IV] low acceptance, low control.

Results

We included 686 patients. The acceptance and perceived control scales were unidimensionally structured and internally consistent. Segments differed significantly in age, smoking behaviour, diagnosis, disease duration, extra-intestinal manifestations, IBD medication, clinical disease activity and quality of life. High acceptance (standardized beta coefficient [ß] 0.25, p < 0.001), high perceived control [ß 0.12, p < 0.001] or both [ß 0.53, p < 0.001], were associated with a significantly better health-related quality of life compared with low acceptance and low perceived control. Sociodemographic and clinical factors explained 25% of the variance in quality of life. The explained variance significantly increased to 45% when the patients’ segment was added to the model [ΔR2 20%, p < 0.001].

Conclusions

The segmentation model based on disease acceptance and perceived control is valid in IBD patients and discriminates different segments that correlate independently with quality of life. This may open new strategies for patient care.
18F-fluorodeoxyglucose positron emission tomography/computed tomography imaging in atrial fibrillation: a pilot prospective study
Authors: Xie Boqia , Chen Bi-Xi , Nanna Michele , Wu Jiao-Yan , Zhou Yang , Shi Liang , Wang Yanjiang , Zeng Lijun , Wang Yuetao , Yang Xing , Liu Xingpeng , Yang Min-Fu
Published: April 2021

Aims

This prospective study explored relevant factors and clinical significance of atrial 18F-fluorodeoxyglucose (FDG) uptake in patients with atrial fibrillation (AF).

Methods and results

One hundred AF patients underwent baseline FDG imaging prior to radiofrequency catheter ablation (RFCA). Of those, 30 subjects underwent additional FDG imaging at 3 months post-RFCA. Voltage mapping of the left atrium was analysed as a voltage score. Patients who received RFCA were followed for 26 months (17–31 months) to assess recurrence. At baseline FDG imaging, 74% of patients with persistent AF (PsAF) and 24% of patients with paroxysmal AF showed increased atrial FDG uptake. The prevalence was higher in the right atrium (49%) than in the left atrium (15%, P < 0.001) or left atrial appendage (21%, P < 0.001). Multivariate analysis demonstrated that PsAF and elevated B-type natriuretic peptide (BNP) were related to enhanced right atrial (RA) activity, and increased epicardial adipose tissue (EAT) activity was predictive of left atrial (LA) activity. LA activity was inversely associated with voltage score, while increased FDG uptake in the right atrium was predictive of successful AF termination by RFCA. Atrial FDG activities decreased significantly post-RFCA, but none of the FDG parameters were predictive of AF recurrence.

Conclusions

Enhanced RA activity was associated with elevated BNP level, whereas LA activity was related to the increased activity of EAT and inversely correlated with LA fibrosis. Increased RA activity was predictive of successful AF termination by RFCA in PsAF patients.
A Caenorhabditis elegans Pheromone Antagonizes Volatile Anesthetic Action Through a Go-Coupled Pathway
Authors: van Swinderen Bruno , Metz Laura B , Shebester Laynie D , Crowder C Michael
Published: April 2021

Volatile anesthetics (VAs) disrupt nervous system function by an ill-defined mechanism with no known specific antagonists. During the course of characterizing the response of the nematode C. elegans to VAs, we discovered that a C. elegans pheromone antagonizes the VA halothane. Acute exposure to pheromone rendered wild-type C. elegans resistant to clinical concentrations of halothane, increasing the EC50 from 0.43 ± 0.03 to 0.90 ± 0.02. C. elegans mutants that disrupt the function of sensory neurons required for the action of the previously characterized dauer pheromone blocked pheromone-induced resistance (Pir) to halothane. Pheromone preparations from loss-of-function mutants of daf-22, a gene required for dauer pheromone production, lacked the halothane-resistance activity, suggesting that dauer and Pir pheromone are identical. However, the pathways for pheromone’s effects on dauer formation and VA action were not identical. Not all mutations that alter dauer formation affected the Pir phenotype. Further, mutations in genes not known to be involved in dauer formation completely blocked Pir, including those altering signaling through the G proteins Goα and Gqα. A model in which sensory neurons transduce the pheromone activity through antagonistic Go and Gq pathways, modulating VA action against neurotransmitter release machinery, is proposed.
A hobo Transgene That Encodes the P-Element Transposase in Drosophila melanogaster: Autoregulation and Cytotype Control of Transposase Activity
Authors: Simmons Michael J , Haley Kevin J , Grimes Craig D , Raymond John D , Niemi Jarad B
Published: April 2021

Drosophila were genetically transformed with a hobo transgene that contains a terminally truncated but otherwise complete P element fused to the promoter from the Drosophila hsp70 gene. Insertions of this H(hsp/CP) transgene on either of the major autosomes produced the P transposase in both the male and female germlines, but not in the soma. Heat-shock treatments significantly increased transposase activity in the female germline; in the male germline, these treatments had little effect. The transposase activity of two insertions of the H(hsp/CP) transgene was not significantly greater than their separate activities, and one insertion of this transgene reduced the transposase activity of P(ry+, Δ2-3)99B, a stable P transgene, in the germline as well as in the soma. These observations suggest that, through alternate splicing, the H(hsp/CP) transgene produces a repressor that feeds back negatively to regulate transposase expression or function in both the somatic and germline tissues. The H(hsp/CP) transgenes are able to induce gonadal dysgenesis when the transposase they encode has P-element targets to attack. However, this ability and the ability to induce P-element excisions are repressed by the P cytotype, a chromosomal/cytoplasmic state that regulates P elements in the germline.
A 160-bp Palindrome Is a Rad50·Rad32-Dependent Mitotic Recombination Hotspot in Schizosaccharomyces pombe
Authors: Farah Joseph A , Hartsuiker Edgar , Mizuno Ken-ichi , Ohta Kunihiro , Smith Gerald R
Published: April 2021

Palindromic sequences can form hairpin and cruciform structures that pose a threat to genome integrity. We found that a 160-bp palindrome (an inverted repeat of 80 bp) conferred a mitotic recombination hotspot relative to a control nonpalindromic sequence when inserted into the ade6 gene of Schizosaccharomyces pombe. The hotspot activity of the palindrome, but not the basal level of recombination, was abolished by a rad50 deletion, by a rad50S “separation of function” mutation, or by a rad32-D25A mutation in the nuclease domain of the Rad32 protein, an Mre11 homolog. We propose that upon extrusion of the palindrome the Rad50·Rad32 nuclease complex recognizes and cleaves the secondary structure thus formed and generates a recombinogenic break in the DNA.
The mcm5-bob1 Bypass of Cdc7p/Dbf4p in DNA Replication Depends on Both Cdk1-Independent and Cdk1-Dependent Steps in Saccharomyces cerevisiae
Authors: Sclafani Robert A , Tecklenburg Marianne , Pierce Angela
Published: April 2021

The roles in DNA replication of two distinct protein kinases, Cdc7p/Dbf4p and Cdk1p/Clb (B-type cyclin), were studied. This was accomplished through a genetic and molecular analysis of the mechanism by which the mcm5-bob1 mutation bypasses the function of the Cdc7p/Dbf4p kinase. Genetic experiments revealed that loss of either Clb5p or Clb2p cyclins suppresses the mcm5-bob1 mutation and prevents bypass. These two cyclins have distinct roles in bypass and presumably in DNA replication as overexpression of one could not complement the loss of the other. Furthermore, the ectopic expression of CLB2 in G1 phase cannot substitute for CLB5 function in bypass of Cdc7p/Dbf4p by mcm5-bob1. Molecular experiments revealed that the mcm5-bob1 mutation allows for constitutive loading of Cdc45p at early origins in arrested G1 phase cells when both kinases are inactive. A model is proposed in which the Mcm5-bob1 protein assumes a unique molecular conformation without prior action by either kinase. This conformation allows for stable binding of Cdc45p to the origin. However, DNA replication still cannot occur without the combined action of Cdk1p/Clb5p and Cdk1p/Clb2p. Thus Cdc7p and Cdk1p kinases catalyze the initiation of DNA replication at several distinct steps, of which only a subset is bypassed by the mcm5-bob1 mutation.
Genetic Analysis of Tissue Aging in Caenorhabditis elegans: A Role for Heat-Shock Factor and Bacterial Proliferation
Authors: Garigan Delia , Hsu Ao-Lin , Fraser Andrew G , Kamath Ravi S , Ahringer Julie , Kenyon Cynthia
Published: April 2021

The genetic analysis of life span has revealed many interesting genes and pathways; however, our understanding of aging has been limited by the lack of a way to assay the aging process itself. Here we show that the tissues of aging worms have a characteristic appearance that is easy to recognize and quantify using Nomarski optics. We have used this assay to determine whether life-span mutations affect the rate of aging, to identify animals that age more rapidly than normal, and to infer the cause of death in C. elegans. Mutations that reduce insulin/IGF-1 signaling double the life span of C. elegans, and we find that tissue decline is slowed in these mutants. Thus this endocrine system appears to influence the rate at which tissues age. This effect extends even to the germline, which is the only mitotically active tissue in the adult. We find that Nomarski microscopy also allows a ready distinction between short-lived mutants that age more rapidly than normal and those that are simply sick, and we have identified an RNAi clone that confers a dramatic rapid-aging phenotype. This clone encodes the C. elegans heat-shock factor (HSF), a transcription factor that regulates the response to heat and oxidative stress. This suggests that heat-shock proteins, many of which act as chaperones, may function in normal animals to slow the rate of aging. Finally, we have identified a cause of death of C. elegans: namely, proliferating bacteria. This suggests that increased susceptibility to bacterial infections contributes to mortality in these animals, just as it does in humans.
An α-Tubulin Mutant Demonstrates Distinguishable Functions Among the Spindle Assembly Checkpoint Genes inSaccharomyces cerevisiae
Authors: Abruzzi Katharine C , Magendantz Margaret , Solomon Frank
Published: April 2021

Cells expressing a mutant allele of α-tubulin, tub1-729, are cold sensitive and arrest as large-budded cells with microtubule defects. The cold sensitivity of tub1-729 is suppressed by extra copies of a subset of the mitotic checkpoint genes BUB1, BUB3, and MPS1, but not MAD1, MAD2, and MAD3. This suppression by checkpoint genes does not depend upon their role in the MAD2-dependent spindle assembly checkpoint. In addition, BUB1 requires an intact kinase domain as well as Bub3p to suppress tub1-729. The data suggest that tub1-729 cells are defective in microtubule-kinetochore attachments and that the products of specific checkpoint genes can act either directly or indirectly to affect these attachments.
Genomic Changes in Nucleotide and Dinucleotide Frequencies in Pasteurella multocida Cultured Under High Temperature
Authors: Xia Xuhua , Wei Ting , Xie Zheng , Danchin Antoine
Published: April 2021

We used 94 RAPD primers of different nucleotide composition to probe the genomic differences between a highly virulent P. multocida strain and an attenuated vaccine strain derived from the virulent strain after culturing the latter under increasing temperature for ∼14,400 generations. The GC content of the vaccine strain is significantly (P < 0.05) lower than that of the virulent strain, contrary to the popular hypothesis of covariation between the GC content and temperature. The frequencies of AA, TA, and TT dinucleotides were higher, and those of AT, GC, and CG dinucleotides were lower, in the vaccine strain than in the virulent strain. A statistic called genomic RAPD entropy is formulated to measure the randomness of the genome, and the genome of the vaccine strain is more random than that of the virulent strain. These differences between the virulent and vaccine strains are interpreted in terms of mutation and selection under increased culturing temperature. A method for estimating substitution rates is developed in the appendix.
The tRNA-Tyr Gene Family of Saccharomyces cerevisiae: Agents of Phenotypic Variation and Position Effects on Mutation Frequency
Authors: Ito-Harashima Sayoko , Hartzog Phillip E , Sinha Himanshu , McCusker John H
Published: April 2021

Extensive phenotypic diversity or variation exists in clonal populations of microorganisms and is thought to play a role in adaptation to novel environments. This phenotypic variation or instability, which occurs by multiple mechanisms, may be a form of cellular differentiation and a stochastic means for modulating gene expression. This work dissects a case of phenotypic variation in a clinically derived Saccharomyces cerevisiae strain involving a cox15 ochre mutation, which acts as a reporter. The ochre mutation reverts to sense at a low frequency while tRNA-Tyr ochre suppressors (SUP-o) arise at a very high frequency to produce this phenotypic variation. The SUP-o mutations are highly pleiotropic. In addition, although all SUP-o mutations within the eight-member tRNA-Tyr gene family suppress the ochre mutation reporter, there are considerable phenotypic differences among the different SUP-o mutants. Finally, and of particular interest, there is a strong position effect on mutation frequency within the eight-member tRNA-Tyr gene family, with one locus, SUP6, mutating at a much higher than average frequency and two other loci, SUP2 and SUP8, mutating at much lower than average frequencies. Mechanisms for the position effect on mutation frequency are evaluated.
A Role for the Saccharomyces cerevisiae RENT Complex Protein Net1 in HMR Silencing
Authors: Kasulke Daniela , Seitz Stefanie , Ehrenhofer-Murray Ann E
Published: April 2021

Silencing in the yeast Saccharomyces cerevisiae is known in three classes of loci: in the silent mating-type loci HML and HMR, in subtelomeric regions, and in the highly repetitive rDNA locus, which resides in the nucleolus. rDNA silencing differs markedly from the other two classes of silencing in that it requires a DNA-associated protein complex termed RENT. The Net1 protein, a central component of RENT, is required for nucleolar integrity and the control of exit from mitosis. Another RENT component is the NAD+-dependent histone deacetylase Sir2, which is the only silencing factor known to be shared among the three classes of silencing. Here, we investigated the role of Net1 in HMR silencing. The mutation net1-1, as well as NET1 expression from a 2μ-plasmid, restored repression at silencing-defective HMR loci. Both effects were strictly dependent on the Sir proteins. We found overexpressed Net1 protein to be directly associated with the HMR-E silencer, suggesting that Net1 could interact with silencer binding proteins and recruit other silencing factors to the silencer. In agreement with this, Net1 provided ORC-dependent, Sir1-independent silencing when artificially tethered to the silencer. In contrast, our data suggested that net1-1 acted indirectly in HMR silencing by releasing Sir2 from the nucleolus, thus shifting the internal competition for Sir2 from the silenced loci toward HMR.
A Heritable Structural Alteration of the Yeast Mitochondrion
Authors: Lockshon Daniel
Published: April 2021

Prions have revived interest in hereditary change that is due to change in cellular structure. How pervasive is structural inheritance and what are its mechanisms? Described here is the initial characterization of [LeuP], a heritable structural change of the mitochondrion of Saccharomyces cerevisiae that often but not always accompanies the loss of all or part of the mitochondrial genome. Three phenotypes are reported in [LeuP] vs. [Leu+] strains: twofold slower growth, threefold slower growth in the absence of leucine, and a marked delocalization of nuclear-encoded protein destined for the mitochondrion. Introduction of mitochondria from a [Leu+] strain by cytoduction can convert a [LeuP] strain to [Leu+] and vice versa. Evidence against the Mendelian inheritance of the trait is presented. The incomplete dominance of [LeuP] and [Leu+] and the failure of HSP104 deletion to have any effect suggest that the trait is not specified by a prion but instead represents a new class of heritable structural change.
The DSC1 Channel, Encoded by the smi60E Locus, Contributes to Odor-Guided Behavior in Drosophila melanogaster
Authors: Kulkarni Nalini H , Yamamoto Akihiko H , Robinson Kellie O , Mackay Trudy F C , Anholt Robert R H
Published: April 2021

Previously, we generated P-element insert lines in Drosophila melanogaster with impaired olfactory behavior. One of these smell-impaired (smi) mutants, smi60E, contains a P[lArB] transposon in the second intron of the dsc1 gene near a nested gene encoding the L41 ribosomal protein. The dsc1 gene encodes an ion channel of unknown function homologous to the paralytic (para) sodium channel, which mediates neuronal excitability. Complementation tests between the smi60E mutant and several EP insert lines map the smellimpaired phenotype to the P[lArB] insertion site. Wild-type behavior is restored upon P-element excision. Evidence that reduction in DSC1 rather than in L41 expression is responsible for the smell-impaired phenotype comes from a phenotypic revertant in which imprecise P-element excision restores the DSC1 message while further reducing L41 expression. Behavioral assays show that a threefold decrease in DSC1 mRNA is accompanied by a threefold shift in the dose response for avoidance of the repellent odorant, benzaldehyde, toward higher odorant concentrations. In situ hybridization reveals widespread expression of the dsc1 gene in the major olfactory organs, the third antennal segment and the maxillary palps, and in the CNS. These results indicate that the DSC1 channel contributes to processing of olfactory information during the olfactory avoidance response.
A Genetic Linkage Map of the Model LegumeLotus japonicusand Strategies for Fast Mapping of New Loci
Authors: Sandal Niels , Krusell Lene , Radutoiu Simona , Olbryt Magdalena , Pedrosa Andrea , Stracke Silke , Sato Shusei , Kato Tomohiko , Tabata Satoshi , Parniske Martin , Bachmair Andreas , Ketelsen Tina , Stougaard Jens
Published: April 2021

A genetic map for the model legume Lotus japonicus has been developed. The F2 mapping population was established from an interspecific cross between L. japonicus and L. filicaulis. A high level of DNA polymorphism between these parents was the source of markers for linkage analysis and the map is based on a framework of amplified fragment length polymorphism (AFLP) markers. Additional markers were generated by restriction fragment length polymorphism (RFLP) and sequence-specific PCR. A total of 524 AFLP markers, 3 RAPD markers, 39 gene-specific markers, 33 microsatellite markers, and six recessive symbiotic mutant loci were mapped. This genetic map consists of six linkage groups corresponding to the six chromosomes in L. japonicus. Fluorescent in situ hybridization (FISH) with selected markers aligned the linkage groups to chromosomes as described in the accompanying article by Pedrosa  et al. (2002, this issue). The length of the linkage map is 367 cM and the average marker distance is 0.6 cM. Distorted segregation of markers was found in certain sections of the map and linkage group I could be assembled only by combining colormapping and cytogenetics (FISH). A fast method to position genetic loci employing three AFLP primer combinations yielding 89 markers was developed and evaluated by mapping three symbiotic loci, Ljsym1, Ljsym5, and Ljhar1-3.
Mutation of a Novel Gene Results in Abnormal Development of Spermatid Flagella, Loss of Intermale Aggression and Reduced Body Fat in Mice
Authors: Campbell Patrick K , Waymire Katrina G , Heier Robb L , Sharer Catherine , Day Diane E , Reimann Heike , Jaje J Michael , Friedrich Glenn A , Burmeister Margit , Bartness Timothy J , Russell Lonnie D , Young Larry J , Zimmer Michael , Jenne Dieter E , MacGregor Grant R
Published: April 2021

ROSA22 male mice are sterile due to a recessive gene-trap mutation that affects development of the spermatid flagellum. The defect involves the flagellar axoneme, which becomes unstable around the time of its assembly. Despite a subsequent complete failure in flagellar assembly, development of the spermatid head appears normal and the spermatid head is released at the correct stage in spermatogenesis. The mutation is pleiotropic. Although ROSA22 homozygote males have normal levels of circulating testosterone and display normal mating behavior, they do not exhibit intermale aggressive behavior and have reduced body fat. The mutated gene (Gtrgeo22) maps to mouse chromosome 10 and is closely flanked by two known genes, Madcam1 and Cdc34. Ribonuclease protection analysis indicates that expression of the flanking genes is unaffected by the mutation. Gtrgeo22 is expressed at low levels in epithelial cells in several tissues, as well as in testis and brain. Analysis of the peptide coding sequence suggests that Gtrgeo22 encodes a novel transmembrane protein, which contains dileucine and tyrosine-based motifs involved in intracellular sorting of transmembrane proteins. Analysis of the Gtrgeo22 gene product should provide novel insight into the molecular basis for intermale aggression and sperm flagellar development.
The First Comprehensive Genetic Linkage Map of a Marsupial: The Tammar Wallaby (Macropus eugenii)
Authors: Zenger Kyall R , McKenzie Louise M , Cooper Desmond W
Published: April 2021

The production of a marsupial genetic linkage map is perhaps one of the most important objectives in marsupial research. This study used a total of 353 informative meioses and 64 genetic markers to construct a framework genetic linkage map for the tammar wallaby (Macropus eugenii). Nearly all markers (93.8%) formed a significant linkage (LOD > 3.0) with at least one other marker, indicating that the majority of the genome had been mapped. In fact, when compared with chiasmata data, >70% (828 cM) of the genome has been covered. Nine linkage groups were identified, with all but one (LG7; X-linked) allocated to the autosomes. These groups ranged in size from 15.7 to 176.5 cM and have an average distance of 16.2 cM between adjacent markers. Of the autosomal linkage groups (LGs), LG2 and LG3 were assigned to chromosome 1 and LG4 localized to chromosome 3 on the basis of physical localization of genes. Significant sex-specific distortions toward reduced female recombination rates were revealed in 22% of comparisons. When comparing the X chromosome data to closely related species it is apparent that they are conserved in both synteny and gene order.
A General Likelihood Approach to Trait-Based Multipoint Linkage Analysis in Large Groups of Half-Sibs and Super Sisters
Authors: Reinsch Norbert
Published: April 2021

The idea of trait-based linkage analysis in half-sibs is extended by comparing the frequency of parental marker haplotypes in animals with different phenotypes. This article first presents the likelihood of observing different classes of paternal haplotypes in a half-sib family, where only family members of a certain phenotype (e.g., affected) are genotyped and are fully informative. The likelihood function is then generalized to multiple phenotypic categories. A linear predictor allows for discontinuous as well as for continuous phenotypes and other explanatory variables. Finally, how to incorporate not fully informative offspring and how to analyze super sister families are shown. Maximum-likelihood estimates of all parameters can be found by a Newton-Raphson algorithm, which mimics an iteratively weighted least-squares procedure. The method allows for any multilocus feasible mapping function and, among others, for situations with selective or nonselective genotyping, single or multiple traits, and continuous or categorical traits. No parameters are required to describe the mode of inheritance and the method copes with virtually any family size. Fields of applications are therefore mapping experiments in species with a high reproductive capacity, such as cattle, pigs, horses, honey bees, trees, and fish.
Identification of 1088 New Transposon Insertions of Caenorhabditis elegans: A Pilot Study Toward Large-Scale Screens
Authors: Martin Edwige , Laloux Hélène , Couette Gaëlle , Alvarez Thierry , Bessou Catherine , Hauser Oliver , Sookhareea Satis , Labouesse Michel , Ségalat Laurent
Published: April 2021

We explored the feasibility of a strategy based on transposons to generate identified mutants of most Caenorhabditis elegans genes. A total of 1088 random new insertions of C. elegans transposons Tc1, Tc3, and Tc5 were identified by anchored PCR, some of which result in a mutant phenotype.
A Novel Yeast Silencer: The 2μ Origin of Saccharomyces cerevisiae Has HST3-, MIG1- and SIR-Dependent Silencing Activity
Authors: Grünweller Arnold , Ehrenhofer-Murray Ann E
Published: April 2021

Silencing in Saccharomyces cerevisiae is found at the mating-type loci HMR and HML, in subtelomeric regions, and at the rDNA locus. Repressed chromatin is built up by the recruitment of the Sir proteins via their interaction with DNA-binding proteins that bind to silencers. Here, we have performed a genetic screen for novel sequence elements within the yeast genome that display silencing activity. We isolated as a novel silencer element the origin of replication from the endogenous 2μ plasmid (2μARS). 2μARS-mediated silencing was dependent upon the Sir proteins, the origin recognition complex (ORC), and Hst3, a Sir2 histone deacetylase homolog, suggesting that it constituted a novel class of silencing in yeast. Moreover, 2μARS carried a binding site for Mig1, a transcriptional repressor of glucose-regulated genes. Both the Mig1-binding site and the MIG1 gene were necessary for full silencing activity of 2μARS. Furthermore, Hst3 was physically present at 2μARS in a silencing context as well as at the endogenous 2μ plasmid. Also, Hst3 regulated the repression of the flipase gene, although this was likely an indirect effect of HST3 on FLP1 expression.
Identification of RTG2 as a Modifier Gene for CTG·CAG Repeat Instability in Saccharomyces cerevisiae
Authors: Bhattacharyya Saumitri , Rolfsmeier Michael L , Dixon Michael J , Wagoner Kara , Lahue Robert S
Published: April 2021

Trinucleotide repeats (TNRs) undergo frequent mutations in families affected by TNR diseases and in model organisms. Much of the instability is conferred in cis by the sequence and length of the triplet tract. Trans-acting factors also modulate TNR instability risk, on the basis of such evidence as parent-of-origin effects. To help identify trans-acting modifiers, a screen was performed to find yeast mutants with altered CTG·CAG repeat mutation frequencies. The RTG2 gene was identified as one such modifier. In rtg2 mutants, expansions of CTG·CAG repeats show a modest increase in rate, depending on the starting tract length. Surprisingly, contractions were suppressed in an rtg2 background. This creates a situation in a model system where expansions outnumber contractions, as in humans. The rtg2 phenotype was apparently specific for CTG·CAG repeat instability, since no changes in mutation rate were observed for dinucleotide repeats or at the CAN1 reporter gene. This feature sets rtg2 mutants apart from most other mutants that affect genetic stability both for TNRs and at other DNA sequences. It was also found that RTG2 acts independently of its normal partners RTG1 and RTG3, suggesting a novel function of RTG2 that helps modify CTG·CAG repeat mutation risk.
Recombination at his-3 in Neurospora Declines Exponentially With Distance from the Initiator, cog
Authors: Yeadon P Jane , Koh L Y , Bowring F J , Rasmussen J P , Catcheside D E A
Published: April 2021

By deletion of 1.8 kb of sequence between cogL and his-3 and replacement with sequences of different lengths, we have generated a set of Neurospora strains in which the distance between cogL and the site at which recombination is selected varies from 1.7 to nearly 6 kb. Each of the manipulated strains includes cogL, a highly active recombination hotspot, and rec-2, thus allowing high-frequency recombination. In addition, each is a his-3 mutant, either K26 or K480. The frequency of His+ recombinants in progeny of these crosses is inversely proportional to the distance between his-3 and cog. Specifically, there is a linear relationship between log10 (recombination frequency) and the distance in base pairs, indicating that as distance decreases, the rate of interallelic recombination increases exponentially. An exponential relationship between distance separating markers and the chance of co-conversion has been found in both Drosophila and fission yeast, indicating that the extension of recombination events may be a stochastic process in most organisms. On the basis of these and additional data presented in this article, we conclude that recombination is initiated at cogL in >17% of meioses, that most conversion tracts are very short, and that few extend >14 kb.
Hague (Hag): A New Mouse Hair Mutation With an Unstable Semidominant Allele
Authors: Poirier Christophe , Yoshiki Atsushi , Fujiwara Kyoko , Guénet Jean-Louis , Kusakabe Moriaki
Published: April 2021

A spontaneous mouse hair mutation was identified in a C3H/HeN colony. The mode of inheritance of the mutation was semidominant, with incomplete penetrance when heterozygous. The trait is controlled by a single locus hague (Hag), which was mapped to the telomeric region of chromosome 15. This mutation was shown to be unstable, since its transmission could be switched from semidominant to recessive. To identify the causative gene and the nature of the mutation, hague was introduced into a high-resolution and high-density molecular genetic map. Over 2000 meioses were analyzed and the mutation was mapped to the keratin 2 complex genes. A YAC and BAC physical map of the critical region was then constructed and the gene involved was located in a 600- to 800-kb-long segment. Fourteen genes were mapped to this region; of these, 11 were expressed in the skin (5 epidermic cytokeratin and 6 hard keratin genes), but none were mutated in hague mice.
Excess Heterozygosity Contributes to Genetic Map Expansion in Pea Recombinant Inbred Populations
Authors: Knox M R , Ellis T H N
Published: April 2021

Several plant genetic maps presented in the literature are longer than expected from cytogenetic data. Here we compare F2 and RI maps derived from a cross between the same two parental lines and show that excess heterozygosity contributes to map inflation. These maps have been constructed using a common set of dominant markers. Although not generally regarded as informative for F2 mapping, these allowed rapid map construction, and the resulting data analysis has provided information not otherwise obvious when examining a population from only one generation. Segregation distortion, a common feature of most populations and marker systems, found in the F2 but not the RI, has identified excess heterozygosity. A few markers with a deficiency of heterozygotes were found to map to linkage group V (chromosome 3), which is known to form rod bivalents in this cross. Although the final map length was longer for the F2 population, the mapped order of markers was generally the same in the F2 and RI maps. The data presented in this analysis reconcile much of the inconsistency between map length estimates from chiasma counts and genetic data.
Coevolution of theS-Locus GenesSRK,SLGandSP11/SCRinBrassica oleraceaandB. rapa
Authors: Sato Keiichi , Nishio Takeshi , Kimura Ryo , Kusaba Makoto , Suzuki Tohru , Hatakeyama Katsunori , Ockendon David J , Satta Yoko
Published: April 2021

Brassica self-incompatibility (SI) is controlled by SLG and SRK expressed in the stigma and by SP11/SCR expressed in the anther. We determined the sequences of the S domains of 36 SRK alleles, 13 SLG alleles, and 14 SP11 alleles from Brassica oleracea and B. rapa. We found three S haplotypes lacking SLG genes in B. rapa, confirming that SLG is not essential for the SI recognition system. Together with reported sequences, the nucleotide diversities per synonymous and nonsynonymous site (πS and πN) at the SRK, SLG, and SP11 loci within B. oleracea were computed. The ratios of πN:πS for SP11 and the hypervariable region of SRK were significantly >1, suggesting operation of diversifying selection to maintain the diversity of these regions. In the phylogenetic trees of 12 SP11 sequences and their linked SRK alleles, the tree topology was not significantly different between SP11 and SRK, suggesting a tight linkage of male and female SI determinants during the evolutionary course of these haplotypes. Genetic exchanges between SLG and SRK seem to be frequent; three such recent exchanges were detected. The evolution of S haplotypes and the effect of gene conversion on self-incompatibility are discussed.
Molecular Evidence on the Origin and Evolution of Glutinous Rice
Authors: Olsen Kenneth M , Purugganan Michael D
Published: April 2021

Glutinous rice is a major type of cultivated rice with long-standing cultural importance in Asia. A mutation in an intron 1 splice donor site of the Waxy gene is responsible for the change in endosperm starch leading to the glutinous phenotype. Here we examine an allele genealogy of the Waxy locus to trace the evolutionary and geographical origins of this phenotype. On the basis of 105 glutinous and nonglutinous landraces from across Asia, we find evidence that the splice donor mutation has a single evolutionary origin and that it probably arose in Southeast Asia. Nucleotide diversity measures indicate that the origin of glutinous rice is associated with reduced genetic variation characteristic of selection at the Waxy locus; comparison with an unlinked locus, RGRC2, confirms that this pattern is specific to Waxy. In addition, we find that many nonglutinous varieties in Northeast Asia also carry the splice donor site mutation, suggesting that partial suppression of this mutation may have played an important role in the development of Northeast Asian nonglutinous rice. This study demonstrates the utility of phylogeographic approaches for understanding trait diversification in crops, and it contributes to growing evidence on the importance of modifier loci in the evolution of domestication traits.
Scanning Mutagenesis Identifies Amino Acid Residues Essential for the in Vivo Activity of the Escherichia coli DnaJ (Hsp40) J-Domain
Authors: Genevaux Pierre , Schwager Françoise , Georgopoulos Costa , Kelley William L
Published: April 2021

The DnaJ (Hsp40) cochaperone regulates the DnaK (Hsp70) chaperone by accelerating ATP hydrolysis in a cycle closely linked to substrate binding and release. The J-domain, the signature motif of the Hsp40 family, orchestrates interaction with the DnaK ATPase domain. We studied the J-domain by creating 42 mutant E. coli DnaJ variants and examining their phenotypes in various separate in vivo assays, namely, bacterial growth at low and high temperatures, motility, and propagation of bacteriophage λ. Most mutants studied behaved like wild type in all assays. In addition to the 33HisProAsp35 (HPD) tripeptide found in all known functional J-domains, our study uncovered three new single substitution mutations (Y25A, K26A, and F47A) that totally abolish J-domain function. Furthermore, two glycine substitution mutants in an exposed flexible loop (R36G, N37G) showed partial loss of J-domain function alone and complete loss of function as a triple (RNQ-GGG) mutant coupled with the phenotypically silent Q38G. Interestingly, all the essential residues map to a small region on the same solvent-exposed face of the J-domain. Engineered mutations in the corresponding residues of the human Hdj1 J-domain grafted in E. coli DnaJ also resulted in loss of function, suggesting an evolutionarily conserved interaction surface. We propose that these clustered residues impart critical sequence determinants necessary for J-domain catalytic activity and reversible contact interface with the DnaK ATPase domain.
The Gene for the Intermediate Chain Subunit of Cytoplasmic Dynein Is Essential in Drosophila
Authors: Boylan Kristin L M , Hays Thomas S
Published: April 2021

The microtubule motor cytoplasmic dynein powers a variety of intracellular transport events that are essential for cellular and developmental processes. A current hypothesis is that the accessory subunits of the dynein complex are important for the specialization of cytoplasmic dynein function. In a genetic approach to understanding the range of dynein functions and the contribution of the different subunits to dynein motor function and regulation, we have identified mutations in the gene for the cytoplasmic dynein intermediate chain, Dic19C. We used a functional Dic transgene in a genetic screen to recover X-linked lethal mutations that require this transgene for viability. Three Dic mutations were identified and characterized. All three Dic alleles result in larval lethality, demonstrating that the intermediate chain serves an essential function in Drosophila. Like a deficiency that removes Dic19C, the Dic mutations dominantly enhance the rough eye phenotype of Glued1, a dominant mutation in the gene for the p150 subunit of the dynactin complex, a dynein activator. Additionally, we used complementation analysis to identify an existing mutation, shortwing (sw), as an allele of the dynein intermediate chain gene. Unlike the Dic alleles isolated de novo, shortwing is homozygous viable and exhibits recessive and temperature-sensitive defects in eye and wing development. These phenotypes are rescued by the wild-type Dic transgene, indicating that shortwing is a viable allele of the dynein intermediate chain gene and revealing a novel role for dynein function during wing development.
How Intron Splicing Affects the Deletion and Insertion Profile in Drosophila melanogaster
Authors: Ptak Susan E , Petrov Dmitri A
Published: April 2021

Studies of “dead-on-arrival” transposable elements in Drosophila melanogaster found that deletions outnumber insertions ∼8:1 with a median size for deletions of ∼10 bp. These results are consistent with the deletion and insertion profiles found in most other Drosophila pseudogenes. In contrast, a recent study of D. melanogaster introns found a deletion/insertion ratio of 1.35:1, with 84% of deletions being shorter than 10 bp. This discrepancy could be explained if deletions, especially long deletions, are more frequently strongly deleterious than insertions and are eliminated disproportionately from intron sequences. To test this possibility, we use analysis and simulations to examine how deletions and insertions of different lengths affect different components of splicing and determine the distribution of deletions and insertions that preserve the original exons. We find that, consistent with our predictions, longer deletions affect splicing at a much higher rate compared to insertions and short deletions. We also explore other potential constraints in introns and show that most of these also disproportionately affect large deletions. Altogether we demonstrate that constraints in introns may explain much of the difference in the pattern of deletions and insertions observed in Drosophila introns and pseudogenes.
Mapping Unexplored Genomes: A Genetic Linkage Map of the Hawaiian Cricket Laupala
Authors: Parsons Y M , Shaw K L
Published: April 2021

As with many organisms of evolutionary interest, the Hawaiian cricket Laupala genome is not well characterized genetically. Mapping such an unexplored genome therefore presents challenges not often faced in model genetic organisms and not well covered in the literature. We discuss the evolutionary merits of Laupala as a model for speciation studies involving prezygotic change, our choice of marker system for detecting genetic variation, and the initial genetic expectations pertaining to the construction of any unknown genomic map in general and to the Laupala linkage map construction in particular. We used the technique of amplified fragment length polymorphism (AFLP) to develop a linkage map of Laupala. We utilized both EcoRI/MseI- and EcoRI/PstI-digested genomic DNA to generate AFLP bands and identified 309 markers that segregated among F2 interspecific hybrid individuals. The map is composed of 231 markers distributed over 11 and 7 species-specific autosomal groups together with a number of putative X chromosome linkage groups. The integration of codominant markers enabled the identification of five homologous linkage groups corresponding to five of the seven autosomal chromosomal pairs found in Laupala.
Estimation of Deleterious Genomic Mutation Parameters in Natural Populations by Accounting for Variable Mutation Effects Across Loci
Authors: Deng Hong-Wen , Gao Guimin , Li Jin-Long
Published: April 2021

The genomes of all organisms are subject to continuous bombardment of deleterious genomic mutations (DGM). Our ability to accurately estimate various parameters of DGM has profound significance in population and evolutionary genetics. The Deng-Lynch method can estimate the parameters of DGM in natural selfing and outcrossing populations. This method assumes constant fitness effects of DGM and hence is biased under variable fitness effects of DGM. Here, we develop a statistical method to estimate DGM parameters by considering variable mutation effects across loci. Under variable mutation effects, the mean fitness and genetic variance for fitness of parental and progeny generations across selfing/outcrossing in outcrossing/selfing populations and the covariance between mean fitness of parents and that of their progeny are functions of DGM parameters: the genomic mutation rate U, average homozygous effect s, average dominance coefficient h, and covariance of selection and dominance coefficients cov(h, s). The DGM parameters can be estimated by the algorithms we developed herein, which may yield improved estimation of DGM parameters over the Deng-Lynch method as demonstrated by our simulation studies. Importantly, this method is the first one to characterize cov(h, s) for DGM.
Positive Selection ofCaenorhabditis elegansMutants With Increased Stress Resistance and Longevity
Authors: Muñoz Manuel J , Riddle Donald L
Published: April 2021

We developed selective conditions for long-lived mutants of the nematode Caenorhabditis elegans by subjecting the first larval stage (L1) to thermal stress at 30° for 7 days. The surviving larvae developed to fertile adults after the temperature was shifted to 15°. A total of one million F2 progeny and a half million F3 progeny of ethyl-methanesulfonate-mutagenized animals were treated in three separate experiments. Among the 81 putative mutants that recovered and matured to the reproductive adult, 63 retested as thermotolerant and 49 (80%) exhibited a >15% increase in mean life span. All the known classes of dauer formation (Daf) mutant that affect longevity were found, including six new alleles of daf-2, and a unique temperature-sensitive, dauer-constitutive allele of age-1. Alleles of dyf-2 and unc-13 were isolated, and mutants of unc-18, a gene that interacts with unc-13, were also found to be long lived. Thirteen additional mutations define at least four new genes.