bluuebunny/crossref_metadata_2025 huggingface dataset:
O58: THE IMPACT OF RADIOTHERAPY ON PATIENT-REPORTED OUTCOMES OF IMMEDIATE IMPLANT-BASED BREAST RECONSTRUCTION: RESULTS OF A PROSPECTIVE MULTICENTRE COHORT STUDY
Authors: Sewart E , Turner N , Conroy EJ , Cutress R , Skillman J , Whisker L , Thrush S , Barnes N , Holcombe C , Potter S
Published: April 2021

Introduction

Post-mastectomy radiotherapy (PMRT) is increasing given to improve breast cancer outcomes but can increase complication rates following implant-based breast reconstruction (IBBR). Little, however, is known about the impact of PMRT on patient-reported outcomes (PROs) of IBBR, especially in the context of mesh-assisted techniques.

Method

2108 consecutive women undergoing IBBR at 81 UK centres were prospectively recruited between 2014 and 2016. Demographic, operative, oncological and 3-month complication data were collected, and patients who consented received post-operative questionnaires. An 18-month questionnaire assessed PROs using the validated BREAST-Q. The effect of IBBR on PROs was investigated using mixed-effects regression models adjusted for clinically relevant confounders and including a random effect to account for potential clustering by centre.

Result

1693 iBRA participants underwent mastectomy for malignancy, of whom 1187 (70%) consented to receive the 18-month questionnaire and 732 (43%) completed it. Patients undergoing PMRT (n=214) reported significantly worse scores across 3 BREAST-Q domains: satisfaction with breasts (-6.27 points, p=0.008, 95% confidence interval (CI)[-10.91,-1.63]), satisfaction with outcome (-7.53 points, p=0.002, CI[-12.20,-2.85]) and physical well-being (-6.55 points, p<0.001, CI[-9.43,-3.67]). Overall satisfaction was worse in the PMRT group (OR 0.497, p=0.002, CI[0.32,0.77]). Use of biological mesh did not ameliorate the impact of PMRT on patient satisfaction (interaction term p-values [0.173 - 0.826]).

Conclusion:

PMRT adversely affects PROs of IBBR. This should be discussed with patients considering IBBR, especially if PMRT is anticipated or indications are borderline, to enable informed decisions regarding oncological and reconstructive options.

Abbrev

PMRT: post-mastectomy radiotherapy, PRO: patient-reported outcome

Take-home message

This multicentre, prospective cohort study of 732 patients undergoing implant-based breast reconstruction demonstrates worse 18-month patient-reported outcomes in women who received post-mastectomy radiotherapy than those who did not. These data should be discussed with patients to help them make informed decisions about reconstructive surgery.
O75: SINGLE CENTRE EXPERIENCE OF SIROLIMUS THERAPY IN HEAD AND NECK VASCULAR MALFORMATIONS
Authors: Pang C , Evans N , Papadopoulou A , Khalifa M , Tsui J , Hamilton G , Lim CS , Brookes J
Published: April 2021

Introduction

To assess the efficacy and safety of Sirolimus in the treatment of low-flow head and neck (H&N) vascular malformations

Method

Patients who presented to our tertiary referral clinic were assessed for eligibility. Suitable patients were commenced on Sirolimus at 0.8 mg/m2, administered orally twice daily, which was approved by our trust Drug and Therapeutic Committee. Patients were reviewed on a monthly basis for a total of six months with an additional one-month review to check for effects upon ceasing treatment. Efficacy and safety were measured through functional and radiological response, laboratory investigations and quality of life questionnaire (36-Item Short Form Health Survey (SF-36), Hospital Anxiety and Depression Scale (HADS) and Visual Analogue Score for Pain (VAS-P)).

Result

Seven patients (mean age 39 years, range 23-65 years) were recruited. One patient did not complete treatment due to intolerable side effects. All patients had a partial response with no patients showing disease progression or complete response. All post-treatment MRI scans showed stable disease with five patients demonstrating a decrease in lesion volume. Five patients reported return of symptoms at one-month post review upon discontinuation of treatment. No statistical significance (P>0.05) in all eight domains of SF-36, HADS, VAS-P and radiological vascular lesion volume between pre- and post-treatment. Most common reported side effects were mouth ulcers (n=2) and metabolic/laboratory abnormality (n=2)

Conclusion

Sirolimus is an effective and safe treatment for patients with complicated low-flow H&N vascular malformations. This provides an alternative treatment where interventional therapy is considered to be limited or challenging.

Take-home message

Sirolimus is an effective and safe treatment option for patients with complicated low-flow head and neck vascular malformations where interventional therapy is limited or challenging.
O77: DOES MESH IMPROVE PATIENT SATISFACTION AND HEALTH-RELATED QUALITY OF LIFE AFTER IMPLANT-BASED BREAST RECONSTRUCTION? A MULTICENTRE PROSPECTIVE COHORT STUDY
Authors: Sewart E , Turner N , Conroy EJ , Cutress R , Skillman J , Whisker L , Thrush S , Barnes N , Holcombe C , Potter S
Published: April 2021

Introduction

Biological and synthetic meshes may improve outcomes of immediate IBBR by facilitating single-stage direct-to-implant procedures. However, high-quality supporting evidence is limited, particularly regarding PROs.

Method

2108 consecutive women undergoing IBBR at 81 centres were prospectively recruited between 2014-2016. Demographic, operative, oncological and 3-month complication data were collected. An 18-month questionnaire assessed PROs using the validated BREAST-Q and a five-point Likert scale rating of overall reconstructive outcome.

The impacts of different IBBR techniques on PROs were explored using mixed-effects regression models adjusted for clinically-relevant confounders and including a random effect to account for clustering by centre. The reference group was two- stage submuscular reconstruction without mesh.

Result

1470 participants consented to receive the questionnaire and 891 completed it. 67 patients underwent two-stage submuscular reconstruction; 764 patients received subpectoral reconstructions with biological mesh (n=495) synthetic mesh (n=95) or dermal sling (n=174). 14 patients underwent prepectoral reconstructions (introduced late in the study).

Compared with two-stage reconstructions, no differences in PROs were seen in biological or synthetic mesh-assisted or dermal sling procedures (p>0.05). However, prepectoral IBBR patients reported better satisfaction with breasts (difference=6.63, 95% confidence interval[1.65–11.61], p=0.009). Outcomes were similar to those in the NMBRA 2008/9 cohort, which included submuscular procedures only.

Conclusion

This study does not suggest that mesh improves PROs of IBBR. It provides early data supporting improved satisfaction with breasts following prepectoral reconstructions. Future trials are needed to robustly evaluate prepectoral techniques.

Abbrev

IBBR: implant-based breast reconstruction, PRO: patient-reported outcome, NMBRA: National Mastectomy and Breast Reconstruction Audit

Take-home message

Although mesh-assisted techniques have become widely adopted, this large, prospective, multicentre cohort study does not suggest that mesh improves patient-reported outcomes of implant-based breast reconstruction compared with standard submuscular techniques. However, it provides early data to support improved satisfaction with breasts in the prepectoral setting, which now requires robust evaluation.
P9: MANAGEMENT OF ESOPHAGEAL FOOD BOLUS OBSTRUCTION AT A UNIVERSITY TEACHING HOSPITAL – A RETROSPECTIVE ANALYSIS
Authors: Hashmi ZZ , Ahmed R , Alijarad F , Madanur M , Razzaq Z , Majeed M , Bughio M , Cagney D , Aakif M , Mustafa H , Amin A , Khan A , Aftab F , Corrigan M , Redmond HP
Published: April 2021

Introduction

Despite the fact that esophageal food bolus obstruction is a common surgical problem, there are no clear guidelines on its management. Medical treatment with Buscopan and Glucagon is mostly in-effective, requiring a therapeutic Oesophago-Gastro-Duodenoscopy (OGD).

Method

All consecutive cases of food bolus obstructions (FBO) presenting to the Emergency Department (ED) for 18 month period between 01/01/2018 and 30/06/2019 were retrospectively reviewed.

Result

A total of 30 patients were admitted with food bolus obstruction via ED (1.67 per month). Females (67%) constituted most of these patients. Average age was 55 with range of 19-83. 84% of patients presented with Dysphagia, while Odynophagia (10%) and chest pain (6%) were other presenting symptoms. Average duration of symptoms was 17 hours (Range 2 – 48 hours). 44% of patients had OGD done under sedation while others (56%) had under General Anaesthesia (GA). In 70% of cases, food bolus was pushed into stomach, while it was retrieved out in 20%. In 10%, it had already spontaneously passed in stomach on OGD. The etiology of FBO was inflammatory in 60% cases, while an esophageal stricture was seen in 10% only. In 30% cases no cause of FBO was identified. Post-OGD length of stay was on average 1.15 days (range 12 hours – 7 days). 2 patients had aspiration pneumonia prolonging their hospital stay, there was no esophageal perforation or mortality.

Conclusion

Esophageal food bolus obstruction is a common surgical problem, OGD under GA is a safe recommended procedure, which often picks up an underlying pathology.

Take-home message

Esophageal food bolus obstruction is a common surgical problem, OGD under GA is a safe recommended procedure, which often picks up an underlying pathology.
Populism in an Identity Framework: A Feedback Model
Authors: Reveilhac Maud , Morselli Davide
Published: April 2021

Drawing upon the social psychology concept of identity entrepreneurs (Haslam et al., 2010), we develop a feedback model between politicians and the public that strongly emphasizes the circumstances in which public opinion may facilitate populist discursive elements and politics. We thus consider the success of populism as neither inherently driven by political leaders nor primarily driven by increasing populist attitudes in the public and acknowledge the fragmented nature of the populist discourse emphasized by recent studies. We raise the question of whether there is a populist collective identity, which is accountable in terms of populist rhetorical elements, and how it changes over time. To answer this question, we apply the proposed framework to the case of the rise and development of the populist discourse in Switzerland while accounting for its dynamic adaptation to raising public concerns and for the influence of its core rhetorical elements on individual voting behavior.
quemao, a Drosophila Bristle Locus, Encodes Geranylgeranyl Pyrophosphate Synthase
Authors: Lai Chaoqiang , McMahon Robert , Young Chi , Mackay Trudy F C , Langley Charles H
Published: April 2021

The quemao (qm) locus of Drosophila melanogaster is characterized by a P-element-associated mutant lacking most of the large bristles on the thorax and by several EMS-induced recessive lethals. quemao was cloned using a transposon tagging strategy. P-element-mediated transformation demonstrated that the cloned qm DNA sequence (from the 65F cytological region) rescues the mutant phenotype. A 2.3-kb qm transcript was identified by Northern blot analysis by sequencing of the isolated qm cDNA clones and by 5′ rapid amplification cDNA end (RACE). The predicted amino acid sequence (338 residues) of the coding region of the qm transcript shares 42, 31, 13, 20, and 12% identical amino acid sequences with the geranylgeranyl pyrophosphate synthase (GGPPS) of fungi, yeast, plants, archaebacteria, and eubacteria, respectively. It also contains five highly conserved domains common among all known isoprenyl pyrophosphate synthases. The P element associated with the original qm mutant is inserted in the 5′ untranslated region of the transcript. An EMS-induced qm nonsense mutation at the 12th codon leads to recessive lethality at the first larval instar, indicating the essential role of qm in the isoprenoid biosynthesis of insects.
Possible Assortment of a1 and a2 Region Gene Segments in Human MHC Class I Molecules
Authors: Johnson George , Wu Tai T
Published: April 2021

Using pair-wise comparison of aligned nucleotide sequences of distinct and complete human MHC class I molecules, we have constructed triangular tables to study the similarities and differences of various a1 (exon 2) and a2 (exon 3) region sequences. There are two HLA-A (A*6901 and A*6601) and 13 HLA-B (B*4201, B*8101, B*4102, B*4801, B*4007, B*4001, B*4802, Dw53, B*4406, B*4402, B*3901, B*1514 and B*3702) sequences that have identical a1 sequences with other known MHC class I molecules, while their a2 sequences are the same as those of different ones. Of these 15, A*6901, B*4001 and B*4802 have previously been suggested as the results of recombination between A*6801 and A*0201, B*4101 and B*8101, and B*4801 and B*3501, respectively. However, many other sequences can also be used to generate them by recombination. Furthermore, their reciprocal products have never been identified. Thus, gene conversion has subsequently been suggested as an alternative. Another possible genetic mechanism for generating these nucleotide sequence similarities can be assortment, or that some gene segments can be duplicated or multiplicated to be used in different human MHC class I molecules. Interestingly, this genetic mechanism is probably absent for the generation of different mouse MHC class I molecules.
The Maize Regulatory Gene B-Peru Contains a DNA Rearrangement That Specifies Tissue-Specific Expression Through Both Positive and Negative Promoter Elements
Authors: Selinger David A , Lisch Damon , Chandler Vicki L
Published: April 2021

The B-Peru allele of the maize b regulatory gene is unusual relative to most b alleles in that it is expressed in the aleurone layer of the seed. It is also expressed in a subset of plant vegetative tissues. Transgenic maize plants containing the B-Peru gene with the first 710 bases of upstream sequence conferred the same levels of aleurone expression as nontransgenic B-Peru plants, but no pigment was made in vegetative tissues. Transient transformation assays in aleurone tissue localized the aleurone-specific promoter to the first 176 bases of the B-Peru upstream region and identified two critically important regions within this fragment. Mutation of either region alone reduced expression greater than fivefold. Surprisingly, the double mutation actually increased expression to twice the native promoter level. Our results suggest that these two critical sequences, which lie close together in the promoter, may form a negative regulatory element. Several lines of evidence suggest that the B-Peru promoter arose through the translocation of an existing aleurone-specific promoter to the b locus. Immediately upstream of the aleurone-specific promoter elements and in the opposite orientation to the b coding sequence is a pseudogene sequence with strong similarity to a known class of proteins. Our findings that novel aleurone-specific promoter sequences of the B-Peru transcription factor are found adjacent to part of another gene in a small insertion are quite unexpected and have interesting evolutionary implications.
Genetic Analysis of Organ Fusion in Arabidopsis thaliana
Authors: Lolle Susan J , Hsu Wendy , Pruitt Robert E
Published: April 2021

Postgenital organ fusion occurs most commonly during reproductive development and is important in many angiosperms during genesis of the carpel. Although a number of mutants have been described that manifest ectopic organ fusion, little is known about the genes involved in regulating this process. In this article we describe the characterization of a collection of 29 Arabidopsis mutants showing an organ fusion phenotype. Mapping and complementation analyses revealed that the mutant alleles define nine different loci distributed throughout the Arabidopsis genome. Multiple alleles were isolated for the four complementation groups showing the strongest organ fusion phenotype while the remaining five complementation groups, all of which show only weak floral organ fusion, have a single representative allele. In addition to fusion events between aerial parts of the shoot, some mutants also show abnormal ovule morphology with adjacent ovules joined together at maturity. Many of the fusion mutants isolated have detectable differences in the rate at which chlorophyll can be extracted; however, in one case no difference could be detected between mutant and wild-type plants. In three mutant lines pollen remained unresponsive to contact with the mutant epidermis, demonstrating that organ fusion and pollen growth responses can be genetically separated from one another.
Activation of Latent Transgenes in Arabidopsis Using a Hybrid Transcription Factor
Authors: Guyer Dave , Tuttle Ann , Rouse Sabrina , Volrath Sandra , Johnson Marie , Potter Sharon , Görlach Jörn , Goff Steve , Crossland Lyle , Ward Eric
Published: April 2021

A hybrid transcription factor comprising a fusion of the DNA-binding domain of Saccharomyces cerevisiae GAL4 and the transcription activation domain of maize C1 was expressed in stably transformed Arabidopsis. Additional transgenic lines were created containing test genes controlled by a synthetic promoter consisting of concatemeric copies of the cis-acting site recognized by GAL4 (UASG) fused to a minimal promoter. The GAL4/C1 effector line was crossed to two lines containing a synthetic promoter/GUS fusion. Both histochemical staining and GUS activity assays indicate strong activation of GUS expression was achieved only after crossing. The GAL4/C1 effector line was also crossed to 15 lines containing a synthetic promoter/antisense adenylosuccinate synthetase gene. Severely retarded growth, and in some cases lethality, was observed in 40% of the F1 lines. This system of activation by crossing is generally useful for activating expression of test transgenes.
Members of the Arabidopsis Actin Gene Family Are Widely Dispersed in the Genome
Authors: McKinney E C , Meagher R B
Published: April 2021

Plant genomes are subjected to a variety of DNA turnover mechanisms that are thought to result in rapid expansion and presumable contraction of gene copy number. The evolutionary history of the 10 actin genes in Arabidopsis thaliana is well characterized and can be traced to the origin of vascular plant genomes. Knowledge about the genomic position of each actin gene may be the key to tracing landmark genomic duplication events that define plant families or genera and facilitate further mutant isolation. All 10 actin genes were mapped by following the segregation of cleaved amplified polymorphisms between two ecotypes and identifying actin gene locations among yeast artificial chromosomes. The Arabidopsis actin genes are widely dispersed on four different chromosomes (1, 2, 3, and 5). Even the members of three closely related and recently duplicated pairs of actin genes are unlinked. Several other cytoskeletal genes (profilins, tubulins) that might have evolved in concert with actins were also mapped, but showed few patterns consistent with that evoulutionary history. Thus, the events that gave rise to the actin gene family have been obscured either by the duplication of very small genic fragments or by extensive rearrangement of the genome.
Detection of Deleterious Genotypes in Multigenerational Studies. I. Disruptions in Individual Arabidopsis Actin Genes
Authors: Gilliland Laura U , McKinney Elizabeth C , Asmussen Marjorie A , Meagher Richard B
Published: April 2021

Plant actins are involved in numerous cytoskeletal processes effecting plant development, including cell division plane determination, cell elongation, and cell wall deposition. Arabidopsis thaliana has five ancient subclasses of actin with distinct patterns of spatial and temporal expression. To test their functional roles, we identified insertion mutants in three Arabidopsis actin genes, ACT2, ACT4, and ACT7, representing three subclasses. Adult plants homozygous for the act2-1, act4-1, and act7-1 mutant alleles appear to be robust, morphologically normal, and fully fertile. However, when grown as populations descended from a single heterozygous parent, all three mutant alleles were found at extremely low frequencies relative to the wild-type in the F2 generation. Thus, all three mutant alleles appear to be deleterious. The act2-1 mutant allele was found at normal frequencies in the F1, but at significantly lower frequencies than expected in the F2 and F3 generations. These data suggest that the homozygous act2-1/act2-1 mutant adult plants have a reduced fitness in the 2N sporophytic portion of the life cycle, consistent with the vegetative expression of ACT2. These data are interpreted in light of the extreme conservation of plant actin subclasses and genetic redundancy.
The Molecular Basis of Quantitative Genetic Variation in Central and Secondary Metabolism in Arabidopsis
Authors: Mitchell-Olds Thomas , Pedersen Deana
Published: April 2021

To find the genes controlling quantitative variation, we need model systems where functional information on physiology, development, and gene regulation can guide evolutionary inferences. We mapped quantitative trait loci (QTLs) influencing quantitative levels of enzyme activity in primary and secondary metabolism in Arabidopsis. All 10 enzymes showed highly significant quantitative genetic variation. Strong positive genetic correlations were found among activity levels of 5 glycolytic enzymes, PGI, PGM, GPD, FBP, and G6P, suggesting that enzymes with closely related metabolic functions are coregulated. Significant QTLs were found influencing activity of most enzymes. Some enzyme activity QTLs mapped very close to known enzyme-encoding loci (e.g., hexokinase, PGI, and PGM). A hexokinase QTL is attributable to cis-acting regulatory variation at the AtHXK1 locus or a closely linked regulatory locus, rather than polypeptide sequence differences. We also found a QTL on chromosome IV that may be a joint regulator of GPD, PGI, and G6P activity. In addition, a QTL affecting PGM activity maps within 700 kb of the PGM-encoding locus. This QTL is predicted to alter starch biosynthesis by 3.4%, corresponding with theoretical models, suggesting that QTLs reflect pleiotropic effects of mutant alleles.
UV Light Induces IS10 Transposition in Escherichia coli
Authors: Eichenbaum Zehava , Livneh Zvi
Published: April 2021

A new mutagenesis assay system based on the phage 434 cI gene carried on a low-copy number plasmid was used to investigate the effect of UV light on intermolecular transposition of IS10. Inactivation of the target gene by IS10 insertion was detected by the expression of the tet gene from the phage 434 PR promoter, followed by Southern blot analysis of plasmids isolated from TetR colonies. UV irradiation of cells harboring the target plasmid and a donor plasmid carrying an IS10 element led to an increase of up to 28-fold in IS10 transposition. Each UV-induced transposition of IS10 was accompanied by fusion of the donor and acceptor plasmid into a cointegrate structure, due to coupled homologous recombination at the insertion site, similar to the situation in spontaneous IS10 transposition. UV radiation also induced transposition of IS10 from the chromosome to the target plasmid, leading almost exclusively to the integration of the target plasmid into the chromosome. UV induction of IS10 transposition did not depend on the umuC and uvrA gene product, but it was not observed in lexA3 and ΔrecA strains, indicating that the SOS stress response is involved in regulating UV-induced transposition. IS10 transposition, known to increase the fitness of Escherichia coli, may have been recruited under the SOS response to assist in increasing cell survival under hostile environmental conditions. To our knowledge, this is the first report on the induction of transposition by a DNA-damaging agent and the SOS stress response in bacteria.
Distribution of a Limited Sir2 Protein Pool Regulates the Strength of Yeast rDNA Silencing and Is Modulated by Sir4p
Authors: Smith Jeffrey S , Brachmann Carrie Baker , Pillus Lorraine , Boeke Jef D
Published: April 2021

Transcriptional silencing in Saccharomyces cerevisiae occurs at the silent mating-type loci HML and HMR, at telomeres, and at the ribosomal DNA (rDNA) locus RDN1. Silencing in the rDNA occurs by a novel mechanism that depends on a single Silent Information Regulator (SIR) gene, SIR2. SIR4, essential for other silenced loci, paradoxically inhibits rDNA silencing. In this study, we elucidate a regulatory mechanism for rDNA silencing based on the finding that rDNA silencing strength directly correlates with cellular Sir2 protein levels. The endogenous level of Sir2p was shown to be limiting for rDNA silencing. Furthermore, small changes in Sir2p levels altered rDNA silencing strength. In rDNA silencing phenotypes, sir2 mutations were shown to be epistatic to sir4 mutations, indicating that SIR4 inhibition of rDNA silencing is mediated through SIR2. Furthermore, rDNA silencing is insensitive to SIR3 overexpression, but is severely reduced by overexpression of full-length Sir4p or a fragment of Sir4p that interacts with Sir2p. This negative effect of SIR4 overexpression was overridden by co-overexpression of SIR2, suggesting that SIR4 directly inhibits the rDNA silencing function of SIR2. Finally, genetic manipulations of SIR4 previously shown to promote extended life span also resulted in enhanced rDNA silencing. We propose a simple model in which telomeres act as regulators of rDNA silencing by competing for limiting amounts of Sir2 protein.
Female Genotypes Affect Sperm Displacement in Drosophila
Authors: Clark Andrew G , Begun David J
Published: April 2021

Differential success of sperm is likely to be an important component of fitness. Extensive variation among male genotypes in competitive success of sperm in multiply mated females has been documented for Drosophila melanogaster. However, virtually all previous studies considered the female to be a passive vessel. Nevertheless, under certain conditions female fitness could be determined by her role in mediating use of sperm from multiple males. Here we ask whether females differ among genotypes in their tendency to exhibit last-male precedence. Competition of sperm from two tester male genotypes (bwD and B3-09, a third-chromosome isogenic line from Beltsville, MD) was quantified by doubly mating female lines that had been rendered homozygous for X, second, or third chromosomes isolated from natural populations. The composite sperm displacement parameter, P2′, was highly heterogeneous among lines, whether or not viability effects were compensated, implying the presence of polymorphic genes affecting access of sperm to eggs. Genetic variation of this type is completely neutral in the absence of pleiotropy or interaction between variation in the two sexes.
Inference of Population History Using a Likelihood Approach
Authors: Weiss Gunter , von Haeseler Arndt
Published: April 2021

We introduce an approach to revealing the likelihood of different population histories that utilizes an explicit model of sequence evolution for the DNA segment under study. Based on a phylogenetic tree reconstruction method we show that a Tamura-Nei model with heterogeneous mutation rates is a fair description of the evolutionary process of the hypervariable region I of the mitochondrial DNA from humans. Assuming this complex model still allows the estimation of population history parameters, we suggest a likelihood approach to conducting statistical inference within a class of expansion models. More precisely, the likelihood of the data is based on the mean pairwise differences between DNA sequences and the number of variable sites in a sample. The use of likelihood ratios enables comparison of different hypotheses about population history, such as constant population size during the past or an increase or decrease of population size starting at some point back in time. This method was applied to show that the population of the Basques has expanded, whereas that of the Biaka pygmies is most likely decreasing. The Nuu-Chah-Nulth data are consistent with a model of constant population.
A Rank-Based Nonparametric Method for Mapping Quantitative Trait Loci in Outbred Half-Sib Pedigrees: Application to Milk Production in a Granddaughter Design
Authors: Coppieters Wouter , Kvasz Alexandre , Farnir Frédéric , Arranz Juan-Jose , Grisart Bernard , Mackinnon Margaret , Georges Michel
Published: April 2021

We describe the development of a multipoint nonparametric quantitative trait loci mapping method based on the Wilcoxon rank-sum test applicable to outbred half-sib pedigrees. The method has been evaluated on a simulated dataset and its efficiency compared with interval mapping by using regression. It was shown that the rank-based approach is slightly inferior to regression when the residual variance is homoscedastic normal; however, in three out of four other scenarios envisaged, i.e., residual variance heteroscedastic normal, homoscedastic skewed, and homoscedastic positively kurtosed, the latter outperforms the former one. Both methods were applied to a real data set analyzing the effect of bovine chromosome 6 on milk yield and composition by using a 125-cM map comprising 15 microsatellites and a granddaughter design counting 1158 Holstein-Friesian sires.
GIT1, a Gene Encoding a Novel Transporter for Glycerophosphoinositol in Saccharomyces cerevisiae
Authors: Patton-Vogt J L , Henry S A
Published: April 2021

Phosphatidylinositol catabolism in Saccharomyces cerevisiae cells cultured in media containing inositol results in the release of glycerophosphoinositol (GroPIns) into the medium. As the extracellular concentration of inositol decreases with growth, the released GroPIns is transported back into the cell. Exploiting the ability of the inositol auxotroph, ino1, to use exogenous GroPIns as an inositol source, we have isolated mutants (Git−) defective in the uptake and metabolism of GroPIns. One mutant was found to be affected in the gene encoding the transcription factor, SPT7. Mutants of the positive regulatory gene INO2, but not of its partner, INO4, also have the Git− phenotype. Another mutant was complemented by a single open reading frame (ORF) termed GIT1 (glycerophosphoinositol). This ORF consists of 1556 bp predicted to encode a polypeptide of 518 amino acids and 57.3 kD. The predicted Git1p has similarity to a variety of S. cerevisiae transporters, including a phosphate transporter (Pho84p), and both inositol transporters (Itr1p and Itr2p). Furthermore, Git1p contains a sugar transport motif and 12 potential membrane-spanning domains. Transport assays performed on a git1 mutant together with the above evidence indicate that the GIT1 gene encodes a permease involved in the uptake of GroPIns.
The Macromelanophore Locus and the Melanoma Oncogene Xmrk Are Separate Genetic Entities in the Genome of Xiphophorus
Authors: Weis Silke , Schartl Manfred
Published: April 2021

Fish of the genus Xiphophorus are polymorphic for black pigmentation patterns. Certain intra- or interspecific hybrids exhibit enhanced expression of these patterns, leading in many cases to malignant melanoma. Because no recombination was ever observed between the pattern information and the genetic predisposition to develop melanoma after hybridization, a “tumor gene” (Tu) was postulated that encodes both phenotypes. A dominant oncogene, ONC-Xmrk, was then found to be necessary and sufficient for the transforming function of Tu. Here we present molecular evidence that ONC-Xmrk and the pigment pattern information are encoded by separate, although intimately linked loci. No ONC-Xmrk gene was present in the 15 Xiphophorus strains investigated which exhibit no black pigmentation pattern. Five different patterns from Xiphophorus maculatus, X. evelynae, X. milleri, X. cortezi, and X. montezumae were associated with ONC-Xmrk and were melanomagenic, while fish of X. helleri, X. variatus, X. nezahualcoyotl, and X. montezumae with five other patterns had no ONC-Xmrk and consequently did not produce hybrid melanoma. These data provide evidence that ONC-Xmrk is sufficient for tumorigenesis in Xiphophorus hybrids, and that a separate, pigment pattern-encoding locus is closely linked to it.
Complex Structure of Knob DNA on Maize Chromosome 9: Retrotransposon Invasion into Heterochromatin
Authors: Ananiev E V , Phillips R L , Rines H W
Published: April 2021

The recovery of maize (Zea mays L.) chromosome addition lines of oat (Avena sativa L.) from oat × maize crosses enables us to analyze the structure and composition of specific regions, such as knobs, of individual maize chromosomes. A DNA hybridization blot panel of eight individual maize chromosome addition lines revealed that 180-bp repeats found in knobs are present in each of these maize chromosomes, but the copy number varies from ~100 to 25,000. Cosmid clones with knob DNA segments were isolated from a genomic library of an oat-maize chromosome 9 addition line with the help of the 180-bp knob-associated repeated DNA sequence used as a probe. Cloned knob DNA segments revealed a complex organization in which blocks of tandemly arranged 180-bp repeating units are interrupted by insertions of other repeated DNA sequences, mostly represented by individual full size copies of retrotransposable elements. There is an obvious preference for the integration of retrotransposable elements into certain sites (hot spots) of the 180-bp repeat. Sequence microheterogeneity including point mutations and duplications was found in copies of 180-bp repeats. The 180-bp repeats within an array all had the same polarity. Restriction maps constructed for 23 cloned knob DNA fragments revealed the positions of polymorphic sites and sites of integration of insertion elements. Discovery of the interspersion of retrotransposable elements among blocks of tandem repeats in maize and some other organisms suggests that this pattern may be basic to heterochromatin organization for eukaryotes.
Characterization of an Allele-Nonspecific Intragenic Suppressor in the Yeast Plasma Membrane H+-ATPase Gene (PMA1)
Authors: Maldonado Ana M , de la Fuente Natalia , Portillo Francisco
Published: April 2021

We have analyzed the ability of A165V, V169I/D170N, and P536L mutations to suppress pma1 dominant lethal alleles and found that the P536L mutation is able to suppress the dominant lethality of the pma1-R271T, -D378N, -D378E, and -K474R mutant alleles. Genetic and biochemical analyses of site-directed mutants at Pro-536 suggest that this amino acid may not be essential for function but is important for biogenesis of the ATPase. Proteins encoded by dominant lethal pma1 alleles are retained in the endoplasmic reticulum, thus interfering with transport of wild-type Pma1. Immunofluorescence studies of yeast conditionally expressing revertant alleles show that the mutant enzymes are correctly located at the plasma membrane and do not disturb targeting of the wild-type enzyme. We propose that changes in Pro-536 may influence the folding of the protein encoded by a dominant negative allele so that it is no longer recognized and retained as a misfolded protein by the endoplasmic reticulum.
Genetic and Molecular Characterization of the Caenorhabditis elegans Gene, mel-26, a Postmeiotic Negative Regulator of MEI-1, a Meiotic-Specific Spindle Component
Authors: Dow M Rhys , Mains Paul E
Published: April 2021

We have previously described the gene mei-1, which encodes an essential component of the Caenorhabditis elegans meiotic spindle. When ectopically expressed after the completion of meiosis, mei-1 protein disrupts the function of the mitotic cleavage spindles. In this article, we describe the cloning and the further genetic characterization of mel-26, a postmeiotic negative regulator of mei-1. mel-26 was originally identified by a gain-of-function mutation. We have reverted this mutation to a loss-of-function allele, which has recessive phenotypes identical to the dominant defects of its gain-of-function parent. Both the dominant and recessive mutations of mel-26 result in mei-1 protein ectopically localized in mitotic spindles and centrosomes, leading to small and misoriented cleavage spindles. The loss-of-function mutation was used to clone mel-26 by transformation rescue. As suggested by genetic results indicating that mel-26 is required only maternally, mel-26 mRNA was expressed predominantly in the female germline. The gene encodes a protein that includes the BTB motif, which is thought to play a role in protein-protein interactions.
Increased Transmitter Release and Aberrant Synapse Morphology in a Drosophila Calmodulin Mutant
Authors: Arredondo LaChelle , Nelson Heidi B , Beckingham Kathy , Stern Michael
Published: April 2021

The ubiquitous calcium-binding protein calmodulin (CaM) has been implicated in the development and function of the nervous system in a variety of eukaryotic organisms. We have generated mutations in the single Drosophila Calmodulin (Cam) gene and examined the effects of these mutations on behavior, synaptic transmission at the larval neuromuscular junction, and structure of the larval motor nerve terminal. Flies hemizygous for Cam3c1, a mutation in the first Ca2+-binding site, exhibit behavioral, neurophysiological, and neuroanatomical abnormalities. In particular, adults exhibit defects in locomotion, coordination, and flight. Larvae exhibit increased neurotransmitter release from the motor nerve terminal at low [Ca2+] in the presence of the K+ channel-blocking drug quinidine. In addition, synaptic bouton structure at motor nerve terminals is altered. These effects are distinct from those produced by altering the activity of the CaM target enzymes CaM-activated kinase II (CaMKII) and CaM-activated adenylyl cyclase (CaMAC). Furthermore, previous in vitro studies of mutant Cam3c1 demonstrated that although its Ca2+ affinity is decreased, Cam3c1 protein can activate CaMKII, CaMAC, and CaM-activated phosphatase calcineurin in a manner similar to wild-type CaM. Thus, the Cam3c1 mutation might affect Ca2+ buffering or interfere with the activation or inhibition of a CaM target distinct from CaMKII or CaMAC.
The Complete Nucleotide Sequence of a Snake (Dinodon semicarinatus) Mitochondrial Genome With Two Identical Control Regions
Authors: Kumazawa Yoshinori , Ota Hidetoshi , Nishida Mutsumi , Ozawa Tomowo
Published: April 2021

The 17,191-bp mitochondrial DNA (mtDNA) of a Japanese colubrid snake, akamata (Dinodon semicarinatus), was cloned and sequenced. The snake mtDNA has some peculiar features that were found in our previous study using polymerase chain reaction: duplicate control regions that have completely identical sequences over 1 kbp, translocation of tRNALeu(UUR) gene, shortened TψC arm for most tRNA genes, and a pseudogene for tRNAPro. Phylogenetic analysis of amino acid sequences of protein genes suggested an unusually high rate of molecular evolution in the snake compared to other vertebrates. Southern hybridization experiments using mtDNAs purified from multiple akamata individuals showed that the duplicate state of the control region is not a transient or unstable feature found in a particular individual, but that it stably occurs in mitochondrial genomes of the species. This may, therefore, be regarded as an unprecedented example of stable functional redundancy in animal mtDNA. However, some of the examined individuals contain a rather scanty proportion of heteroplasmic mtDNAs with an organization of genes distinct from that of the major mtDNA. The gene organization of the minor mtDNA is in agreement with one of models that we present to account for the concerted evolution of duplicate control regions.
The Complete Nucleotide Sequence of the Mitochondrial DNA of the Dogfish, Scyliorhinus canicula
Authors: Delarbre Christiane , Spruyt Nathalie , Delmarre Cateline , Gallut Cyril , Barriel Véronique , Janvier Philippe , Laudet Vincent , Gachelin Gabriel
Published: April 2021

We have determined the complete nucleotide sequence of the mitochondrial DNA (mtDNA) of the dogfish, Scyliorhinus canicula. The 16,697-bp-long mtDNA possesses a gene organization identical to that of the Osteichthyes, but different from that of the sea lamprey Petromyzon marinus. The main features of the mtDNA of osteichthyans were thus established in the common ancestor to chondrichthyans and osteichthyans. The phylogenetic analysis confirms that the Chondrichthyes are the sister group of the Osteichthyes.
Genealogical Inference From Microsatellite Data
Authors: Wilson Ian J , Balding David J
Published: April 2021

Ease and accuracy of typing, together with high levels of polymorphism and widespread distribution in the genome, make microsatellite (or short tandem repeat) loci an attractive potential source of information about both population histories and evolutionary processes. However, microsatellite data are difficult to interpret, in particular because of the frequency of back-mutations. Stochastic models for the underlying genetic processes can be specified, but in the past they have been too complicated for direct analysis. Recent developments in stochastic simulation methodology now allow direct inference about both historical events, such as genealogical coalescence times, and evolutionary parameters, such as mutation rates. A feature of the Markov chain Monte Carlo (MCMC) algorithm that we propose here is that the likelihood computations are simplified by treating the (unknown) ancestral allelic states as auxiliary parameters. We illustrate the algorithm by analyzing microsatellite samples simulated under the model. Our results suggest that a single microsatellite usually does not provide enough information for useful inferences, but that several completely linked microsatellites can be informative about some aspects of genealogical history and evolutionary processes. We also reanalyze data from a previously published human Y chromosome microsatellite study, finding evidence for an effective population size for human Y chromosomes in the low thousands and a recent time since their most recent common ancestor: the 95% interval runs from ~15,000 to 130,000 years, with most likely values around 30,000 years.
Roles of Prenyl Protein Proteases in Maturation of Saccharomyces cerevisiae a-Factor
Authors: Boyartchuk Victor L , Rine Jasper
Published: April 2021

In eukaryotes small secreted peptides are often proteolytically cleaved from larger precursors. In Saccharomyces cerevisiae multiple proteolytic processing steps are required for production of mature 12-amino-acid a-factor from its 36-amino-acid precursor. This study provides additional genetic data supporting a direct role for Afc1p in cleavage of the carboxyl-terminal tripeptide from the CAAX motif of the prenylated a-factor precursor. In addition, Afc1p had a second role in a-factor processing that was independent of, and in addition to, its role in the carboxyl-terminal processing in vivo. Using ubiquitin-a-factor fusions we confirmed that the pro-region of the a-factor precursor was not required for production of the mature pheromone. However, the pro-region of the a-factor precursor contributed quantitatively to a-factor production.
Genetic Variation and Differentiation at Microsatellite Loci in Drosophila simulans: Evidence for Founder Effects in New World Populations
Authors: Irvin Steven D , Wetterstrand Kris A , Hutter Carolyn M , Aquadro Charles F
Published: April 2021

Drosophila simulans isofemale lines from Africa, South America, and two locations in North America were surveyed for variation at 16 microsatellite loci on the X, second, and third chromosomes, and 18 microsatellites, which are unmapped. D. simulans is thought to have colonized New World habitats only relatively recently (within the last few hundred years). Consistent with a founder effect occurring as colonizers moved into these New World habitats, we find less microsatellite variability in North and South American D. simulans populations than for an African population. Population subdivision as measured at microsatellites is moderate when averaged across all loci (FST = 0.136), but contrasts sharply with previous studies of allozyme variation, which have showed significantly less differentiation in D. simulans than in D. melanogaster. There are substantially fewer private alleles observed in New World populations of D. simulans than seen in a similar survey of D. melanogaster. In addition to possible differences in population size during their evolutionary histories, varying colonization histories or other demographic events may be necessary to explain discrepancies in the patterns of variation observed at various genetic markers between these closely related species.
Molecular Evolution of an Imprinted Gene: Repeatability of Patterns of Evolution Within the Mammalian Insulin-Like Growth Factor Type II Receptor
Authors: Smith Nick G C , Hurst Laurence D
Published: April 2021

The repeatability of patterns of variation in Ka/Ks and Ks is expected if such patterns are the result of deterministic forces. We have contrasted the molecular evolution of the mammalian insulin-like growth factor type II receptor (Igf2r) in the mouse-rat comparison with that in the human-cow comparison. In so doing, we investigate explanations for both the evolution of genomic imprinting and for Ks variation (and hence putatively for mutation rate evolution). Previous analysis of Igf2r, in the mouse-rat comparison, found Ka/Ks patterns that were suggested to be contrary to those expected under the conflict theory of imprinting. We find that Ka/Ks variation is repeatable and hence confirm these patterns. However, we also find that the molecular evolution of Igf2r signal sequences suggests that positive selection, and hence conflict, may be affecting this region. The variation in Ks across Igf2r is also repeatable. To the best of our knowledge this is the first demonstration of such repeatability. We consider three explanations for the variation in Ks across the gene: (1) that it is the result of mutational biases, (2) that it is the result of selection on the mutation rate, and (3) that it is the product of selection on codon usage. Explanations 2 and 3 predict a Ka-Ks correlation, which is not found. Explanation 3 also predicts a negative correlation between codon bias and Ks, which is also not found. However, in support of explanation 1 we do find that in rodents the rate of silent C → T mutations at CpG sites does covary with Ks, suggesting that methylation-induced mutational patterns can explain some of the variation in Ks. We find evidence to suggest that this CpG effect is due to both variation in CpG density, and to variation in the frequency with which CpGs mutate. Interestingly, however, a GC4 analysis shows no covariance with Ks, suggesting that to eliminate methyl-associated effects CpG rates themselves must be analyzed. These results suggest that, in contrast to previous studies of intragenic variation, Ks patterns are not simply caused by the same forces responsible for Ka/Ks correlations.
Different Forces Drive the Evolution of the Acp26Aa and Acp26Ab Accessory Gland Genes in the Drosophila melanogaster Species Complex
Authors: Aguadé Montserrat
Published: April 2021

The Acp26Aa and Acp26Ab genes that code for male accessory gland proteins are tandemly arranged in the species of the Drosophila melanogaster complex. An ∼1.6-kb region encompassing both genes has been sequenced in 10, 24, and 18 lines from Spain, Ivory Coast, and Malawi, respectively; the previously studied 10 lines from North Carolina have also been included in the analyses. A total of 110 nucleotide and 4 length polymorphisms were detected. Silent variation for the whole Acp26A region was slightly higher in African than in non-African populations, while for both genes nonsynonymous variation was similar in all populations studied. Based on Fst estimates no major genetic differentiation was detected between East and West Africa, while in general non-African populations were strongly differentiated from both African populations. Comparison of polymorphism and divergence at synonymous and nonsynonymous sites revealed that directional selection acting on amino acid replacement changes has driven the evolution of the Acp26Aa protein in the last 2.5 myr.