bluuebunny/crossref_metadata_2025_split huggingface dataset:
THE CYTOGENETICS OF A RECESSIVE VISIBLE MUTANT ASSOCIATED WITH A DEFICIENCY ADJACENT TO THE NOTCH LOCUS IN DROSOPHILA MELANOGASTER
Authors: Keppy D O , Welshons W J 
Published: April 2021

ABSTRACT
The recessive visible faswb allele in Drosophila is an interband deletion between salivary band 3C5, 6 and 7. Heterozygosity for the deletion does not suppress recombination between faswb and mutant sites at Notch adjacent to it.—Df(1)w67k30, deficient for salivary bands 3C2 to 6, is to the left of faswb. By crossing over within the homologous bit of interband retained in w67k30 and faswb, the two deficiencies can be linked. Cytologically, 3C7, "fused" to 3C5, 6 in faswb, becomes "fused" to 3C1 when the two are coupled. In the double deletion, the recessive visible phenotype of the faswb "allele" is suppressed. Both w67k30 and faswb can be recovered by uncoupling the two deficiencies.—The data suggest that the mutant faswb does not represent a lesion at Notch; the entire gene or locus seems to be present. The interband deletion in faswb has secondarily moved an intact Notch locus to a foreign environment that interferes with its normal function. When faswb is linked to w67k30, the interference is eliminated and normal Notch functions resume.—The position of Notch on the salivary gland chromosome is reviewed in relation to the information obtained in these experiments.
CONTROL OF GALACTOSYL DIGLYCERIDES IN WHEAT ENDOSPERM BY GROUP 5 CHROMOSOMES
Authors: Hernandez-Lucas C , De Caleya R Fernandez , Carbonero Pilar , Garcia-Olmedo F 
Published: April 2021

ABSTRACT
Lower levels of monogalactosyl diglyceride (MGDG) and digalactosyl diglyceride (DGDG) have been found in tetraploid wheats as compared with those in hexaploid wheats. The same difference has been found between hexaploid cultivars and tetraploid lines derived from them by D genome extraction. A lower level of MGDG and DGDG is also present in Triticum carthlicum (AABB) as compared with Aegilops squarrosa (DD) or with the synthetic T. spelta (AABBDD) obtained from them. Analysis of the appropriate nullitetrasomic and ditelosomic lines indicates that a gene or genes located in the short arm of chromosome 5D are responsible for the observed difference and that group 5 chromosomes can be ranked as to their influence on the MGDG and DGDG levels in the order 5B &gt; 5D &gt; 5A and 5D &gt; 5B &gt; 5A, respectively. These results further support our previous identification of DGDG as the lipid factor responsible for petroleum ether solubility of lipopurothionins. Since DGDG contributes to baking quality by improving the retention of fermentation gases, the present observations imply that the difference in bread-making quality between the two types of wheat is not due only to proteins contributed by the D genome.
EVIDENCE FOR NEWLY INDUCED GENETIC ACTIVITY RESPONSIBLE FOR MALE RECOMBINATION INDUCTION IN DROSOPHILA MELANOGASTER
Authors: Slatko Barton E 
Published: April 2021

ABSTRACT
The T-007 second chromosomal line of Drosophila melanogaster, previously shown to contain a major element, Mr, responsible for male recombination induction, also contains the genetic capability to induce male recombination activity into (nonhomologous) third chromosomes. This newly induced male recombination activity maps to the centromeric region of two third-chromosome lines that were subjected to mapping experiments. The ability of these third chromosome lines to induce male recombination accounts for previous observations concerning the ability of Mr + genotypes (derived from Mr/Mr + heterozygous females) to induce male recombination for only a few generations, when only second chromosomes were selected and backcrossed. The occurrence of this effect, and a similar effect induced in the homologue of T-007, suggests a possible explanation of how natural populations of D. melanogaster have come to contain such high frequencies of these "male recombination" second and third chromosomes, despite their numerous deleterious effects.
GENETICAL AND BIOCHEMICAL CHARACTERIZATION OF QA-3 MUTANTS AND REVERTANTS IN THE QA GENE CLUSTER OF NEUROSPORA CRASSA
Authors: Case Mary E , Pueyo Carmen , Barea J Lopez , Giles Norman H 
Published: April 2021

ABSTRACT
The qa-3 gene, one of the four genes in the qa gene cluster, encodes quinate (shikimate) dehydrogenase (quinate: NAD oxidoreductase, ER 1.1.1.24), the first enzyme in the inducible quinic acid catabolic pathway in Neurospora crassa. Genetic analyses have localized 26 qa-3 mutants at 11 sites on the qa-3 genetic map on the basis of prototroph frequencies. Certain mutants, e.g., 336-3-10 and 336-3-3, are located at opposite ends of the qa-3 gene. Data from four-point crosses (qa-1S mutant 124 x five different qa-3 mutants in triple mutants qa-3, qa-4, qa-2) indicate the following orientation of the qa-3 gene within the qa cluster: qa-1, qa-3 mutant 336-3-10 ("left" end) qa-3 mutant 336-3-3 ("right" end), qa-4, qa-2. Ultraviolet-induced revertants have been obtained from 14 of the qa-3 mutants. The revertable mutants fall into two major classes: those that revert by changes either at the same site or at a second site within the qa-3 gene, and those that revert by unlinked suppressor mutations. The intragenic revertants can be further distinguished by quantative and/or qualitative differences in their quinate dehydrogenase activities. Some revertants with activities either equivalent to or less than wild type produce a thermostable enzyme, and others an enzyme which is thermolabile in vitro at 35°. A concentration of quinic acid or shikimic acid as low as 50 μm protects the enzyme markedly from heat inactivation. The genetic organization and the orientation of the qa-3 gene are discussed with respect to its direction of transcription and to the possible localization of a promoter (initiator) region(s) within the qa gene cluster.
MITOTIC RECOMBINATION IN THE HETEROCHROMATIN OF THE SEX CHROMOSOMES OF DROSOPHILA MELANOGASTER
Authors: Ripoll P , Garcia-Bellido A 
Published: April 2021

ABSTRACT
The frequency of spontaneous and X-ray-induced mitotic recombination involving the Y chromosome has been studied in individuals with a marked Y chromosome arm and different XY compound chromosomes. The genotypes used include X chromosomes with different amounts of X heterochromatin and either or both arms of the Y chromosome attached to either side of the centromere. Individuals with two Y chromosomes have also been studied. The results show that the bulk of mitotic recombination takes place between homologous regions.
CHROMOSOMAL HOMOLOGY OF RABBIT (ORYCTOLAGUS CUNICULUS) LINKAGE GROUP VI WITH RODENT SPECIES
Authors: Fox R R , Van Zutphen L F M 
Published: April 2021

ABSTRACT
Homologous portions of linkage group (LG) VI in the rabbit Oryctolagus cuniculus, chromosome 8 in Mus musculus, and LG V of Rattus norvegicus have been observed. These linkage groups in Oryctolagus and Mus contain the extension locus (e), where recessive alleles are known in many species. Preliminary linkage data have added new loci to linkage group VI of the rabbit, revised the order and map distances on the linkage map, and by comparison with rodent species have strengthened the homology of LG VI in the rabbit with chromosome 8 of the mouse and with LG V of the rat. LG VI now contains five loci with the following order and intervening map distances: Es-1, Es-2 complex—6.3 ± 2.1 cM—Est-1, Est-2 complex—18.5 ± 3.7 cM—e.
MUTATIONAL EVENTS IN THE TRIPLO- AND HAPLO-LETHAL REGION (83DE) OF THE DROSOPHILA MELANOGASTER GENOME
Authors: Roehrdanz Richard L , Lucchesi John C 
Published: April 2021

ABSTRACT
The Drosophila melanogaster genome contains a single region (at 83DE on the polytene chromosome map) for which both heterozygous deficiency and heterozygous duplication are inviable. Seven EMS-induced mutations have been recovered that are viable in combination with a duplication of this region. Two classes of mutations are reported: (1) Mutations that allow survival of flies with either a duplication or a normal third chromosome. These mutations retain Ki, a closely linked marker on the mutagenized chromosome. They fail to complement, and one has been mapped to the vicinity of 83DE. (2) Mutations that allow survival only in heterozygous combination with a duplication and have lost the Ki marker. These mutations represent new deletions of the dose-sensitive information. The possible structural organization of the 83DE region is discussed in light of these two classes of mutations.
CLASSIFICATION OF NORMAL AND MALE-STERILE CYTOPLASMS IN MAIZE. I. ELECTROPHORETIC ANALYSIS OF VARIATION IN MITOCHONDRIALLY SYNTHESIZED PROTEINS
Authors: Forde B G , Oliver R J C , Leaver C J , Gunn R E , Kemble R J 
Published: April 2021

ABSTRACT
Male-sterile cytoplasms of maize have previously been classified into three groups (T, S and C) according to their fertility ratings in various inbred backgrounds. In earlier studies, mitochondria from three male-sterile cytoplasms, representing each of these three groups, have been found to synthesize characteristic variant polypeptides that distinguish them from each other and from those of normal (N) cytoplasm. In order to determine the extent of cytoplasmic variation, we have now analyzed the translation products of mitochondria from 28 additional cytoplasmic sources. The results show that on this basis 18 of the cytoplasms are identical to the USDA (S) cytoplasm, three are identical to the Texas (T) cytoplasm and two are identical to the C cytoplasm. The five remaining cytoplasms are indistinguishable from normal, malefertile (N) cytoplasm. Our classification of the cytoplasms is in general agreement with those based on fertility restoration. However, of three cytoplasms that have previously remained unclassified, two (B and D) have now been assigned to the S group and one (LF) to the N group. No heterogeneity in mitochondrial translation products was detected within the normal or any of the three male-sterile groups. The usefulness of the analysis of mitochondrial translation products as a method for classifying normal and male-sterile cytoplasms is discussed.
GENE FLOW AND THE GEOGRAPHICAL DISTRIBUTION OF A MOLECULAR POLYMORPHISM IN DROSOPHILA PSEUDOOBSCURA
Authors: Jones J S , Bryant S H , Lewontin R C , Moore J A , Prout T 
Published: April 2021

ABSTRACT
This paper discusses the relation between the geographical distribution of an enzyme polymorphism and population structure in Drosophila pseudoobscura. California populations of this species living in very different montane and lowland habitats separated by several kilometers are similar to each other in the frequency of an esterase allele. Previous estimates suggest that gene flow is too limited to account for this homogeneity of genetic structure, so that it must reflect some balancing force of natural selection. We show, however, that dispersal over unfavorable habitats is much greater than earlier supposed. Isolated populations of D. pseudoobscura separated by 15 km from other populations are subject to large amounts of immigration. This is shown by changes in the seasonal abundance of this species and in the annual pattern of lethal alleles in such populations. The genetic structure of an experimentally perturbed isolated population in an oasis returned to normal within a single year, suggesting that such populations are ephemeral and that the oasis is subject to annual recolonization by distant migrants. Direct assessment of marked flies shows that they can move at least 10 km in 24 hours over a desert. Such extensive gene flow may help explain the distribution of the esterase allele, and is relevant to the high level of molecular polymorphism and its general lack of geographic differentiation throughout the range of D. pseudoobscura.
SPONTANEOUS MITOTIC RECOMBINATION AND EVIDENCE FOR AN X-RAY-INDUCIBLE SYSTEM FOR THE REPAIR OF DNA DAMAGE IN DROSOPHILA MELANOGASTER
Authors: Kennison James A , Ripoll Pedro 
Published: April 2021

ABSTRACT
Spontaneous mitotic recombination in the left arm of chromosome 3 was examined in both unirradiated control flies and sibs irradiated early in development by determining the sizes and frequencies of multiple-wing-hair (mwh) clones in the wing blade of heterozygous mwh/+ flies. Approximately 16% of the spontaneous mwh clones arise from events generating cells with normal division rates. The remaining 84% result from events generating cells with an average cell division rate one-third that of the surrounding cells; these are thought to result from events that generate aneuploid cells. Such clones probably arise from a failure correctly to repair spontaneous DNA damage. The frequency of spontaneous events late in development decreases significantly after irradiation as much as 150 hours earlier in development. The suppression of spontaneous events decreases with a longer period of time between irradiation and the final cell divisions in the wing blade. These results suggest the existence of a repair system for DNA damage in Drosophila that is induced by irradiation. The decrease in effect with time following irradiation could result from slow degradation or dilution by subsequent cell growth and division.
Multitechnology characterization of an unusual surface rupturing intraplate earthquake: the ML 5.4 2019 Le Teil event in France
Authors: Vallage A , Bollinger L , Champenois J , Duverger C , Trilla A Guilhem , Hernandez B , Pichon A Le , Listowski C , Mazet-Roux G , Menager M , Pinel-Puysségur B , Vergoz J 
Published: April 2021

SUMMARY
Metropolitan France is a region of slow tectonic deformation with sparse seismicity. On 11 November 2019, the ML 5.4 Le Teil earthquake became the largest seismic event recorded in the last 16 yr. This event was recorded by the national seismic networks and also by a wide variety of other geophysical techniques including infrasound and InSAR measurements. These complementary technologies offer the opportunity to investigate in detail the earthquake source characteristics and the associated ground motion attenuation. Both seismic waveform inversions and InSAR interferogram reveal a shallow rupture on a reverse fault with an associated moment magnitude of 4.8–4.9. Infrasound signals also provide fast evidences pointing towards the area of ground surface displacements, which coincides with La Rouvière fault, in the Cévennes fault system, known as a formerly active normal fault during the Oligocene. The very significant amount of seismic records also helps towards validating the GMPE laws available for the region. This multitechnology characterization documents the kinematics of this rare example of shallow intraplate fault reactivation.
Magnetic hysteresis of magnetite at high temperature: grain size variation
Authors: Dunlop David J 
Published: April 2021

SUMMARY
Thermoremanent magnetization (TRM), the primary magnetic memory of igneous rocks, depends for its stability through geologic time on mineral carriers with high coercivities and high unblocking temperatures. The palaeomagnetic record of past magnetic field directions and intensities is the key to unraveling Earth's tectonic history. Yet we still do not fully understand how the familiar mineral magnetite, in the micrometer grain size range typically responsible for stable TRM, acquires and holds its signal. Direct indicators of magnetite remanence-carrying capacity and coercivity at high temperature T are saturation remanence relative to saturation magnetization Mrs/Ms and coercive force Hc. This study is the first to measure the variation of these hysteresis properties for magnetite, from room temperature to the Curie point, across the entire size range from 25 nm to 135 µm, covering superparamagnetic, single-domain, vortex, pseudo-single-domain and multidomain magnetic behaviour. The paper focuses on: (1) Hc(T) and Mrs(T) observations and their reproducibility; (2) mathematical relationships of Hc(T) and Mrs(T) to Ms(T), used in modelling TRM and for unbiased comparisons of thermal variations; (3) the shapes of magnetite grains and the number of domains they contain, revealed by demagnetizing factors N = Hc/Mrs and (4) the grain size dependences of Hc and Mrs at ordinary and elevated T, delineating domain structure changes and mechanisms of coercivity.
Random Interpolating Sequences in Dirichlet Spaces
Authors: Chalmoukis Nikolaos , Hartmann Andreas , Kellay Karim , Wick Brett Duane 
Published: April 2021

Abstract
We discuss random interpolating sequences in weighted Dirichlet spaces ${{\mathcal{D}}}_\alpha $, $0\leq \alpha \leq 1$, when the radii of the sequence points are fixed a priori and the arguments are uniformly distributed. Although conditions for deterministic interpolation in these spaces depend on capacities, which are very hard to estimate in general, we show that random interpolation is driven by surprisingly simple distribution conditions. As a consequence, we obtain a breakpoint at $\alpha =1/2$ in the behavior of these random interpolating sequences showing more precisely that almost sure interpolating sequences for ${{\mathcal{D}}}_\alpha $ are exactly the almost sure separated sequences when $0\le \alpha &lt;1/2$ (which includes the Hardy space $H^2={{\mathcal{D}}}_0$), and they are exactly the almost sure zero sequences for ${{\mathcal{D}}}_\alpha $ when $1/2 \leq \alpha \le 1$ (which includes the classical Dirichlet space ${{\mathcal{D}}}={{\mathcal{D}}}_1$).
Validation Study for PathogenDx EnviroX-Rv Assay for the Detection of SARS-CoV-2 from Stainless Steel Environmental Surface Swabs Performance Tested MethodSM 122003
Authors: Katchman* Benjamin A , Newland Cory S , Rivas Candy M , O’Brien Kevin , Eggers Rick , Wen Fushi , Hogan Mike 
Published: April 2021

Abstract

Background
The PathogenDx EnviroX-Rv uses endpoint PCR + DNA microarray technology to detect SARS-CoV-2, the causative agent of COVID-19, from stainless-steel environmental sample swabs.

Objective
To validate the PathogenDx EnviroX-Rv assay as part of the Emergency Response Validation (ERV) Performance Tested Method(s)SM (PTM) program.

Method
The PathogenDx EnviroX-Rv assay was evaluated for specificity using in silico analysis of ≥41 000 SARS-CoV-2 sequences and over 50 exclusivity organisms (both near neighbors and background organisms). The candidate method was evaluated in an unpaired study design for one environmental surface (stainless steel) and compared to the US Centers for Disease Control and Prevention (CDC) 2019-Novel Coronavirus (2019-nCoV) Real-Time-Polymerase Chain Reaction (RT-PCR) Diagnostic Panel, Instructions for Use (Revision 4, Effective 6/12/2020).

Results
Results of the in silico analysis demonstrated the high specificity of the method in being able to detect target SARS-CoV-2 sequences and discriminate them from near neighbors and environmental background organisms. In the matrix study, the candidate method demonstrated a statistically significant difference when compared to the results of the CDC method utilized in this study, with the candidate method resulting in more positive replicates as it only requires one target to be present for a positive sample.

Conclusions
The EnviroX-Rv assay rapidly and accurately detected SARS-CoV-2 RNA on environmental swabs from stainless-steel surfaces at a concentration of 2000 genomic copies per 2 × 2” test area.

Highlights
The EnviroX-Rv assay employs dual PCR and hybridization techniques to provide highly accurate results when detecting SARS-CoV-2 from surfaces.
VirtualTaste: a web server for the prediction of organoleptic properties of chemical compounds
Authors: Fritz Franziska , Preissner Robert , Banerjee Priyanka 
Published: April 2021

Abstract
Taste is one of the crucial organoleptic properties involved in the perception of food by humans. Taste of a chemical compound present in food stimulates us to take in food and avoid poisons. Bitter taste of drugs presents compliance problems and early flagging of potential bitterness of a drug candidate may help with its further development. Similarly, the taste of chemicals present in food is important for evaluation of food quality in the industry. In this work, we have implemented machine learning models to predict three different taste endpoints—sweet, bitter and sour. The VirtualTaste models achieved an overall accuracy of 90% and an AUC of 0.98 in 10-fold cross-validation and in an independent test set. The web server takes a two-dimensional chemical structure as input and reports the chemical's taste profile for three tastes—using molecular fingerprints along with confidence scores, including information on similar compounds with known activity from the training set and an overall radar chart. Additionally, insights into 25 bitter receptors are also provided via target prediction for the predicted bitter compounds. VirtualTaste, to the best of our knowledge, is the first freely available web-based platform for the prediction of three different tastes of compounds. It is accessible via http://virtualtaste.charite.de/VirtualTaste/without any login requirements and is free to use.
MutViz 2.0: visual analysis of somatic mutations and the impact of mutational signatures on selected genomic regions
Authors: Gulino Andrea , Stamoulakatou Eirini , Piro Rosario M 
Published: April 2021

Abstract
Patterns of somatic single nucleotide variants observed in human cancers vary widely between different tumor types. They depend not only on the activity of diverse mutational processes, such as exposure to ultraviolet light and the deamination of methylated cytosines, but largely also on the sequence content of different genomic regions on which these processes act. With MutViz (http://gmql.eu/mutviz/), we have presented a user-friendly web tool for the identification of mutation enrichments that offers preloaded mutations from public datasets for a variety of cancer types, well organized within an effective database architecture. Somatic mutation patterns can be visually and statistically analyzed within arbitrary sets of small, user-provided genomic regions, such as promoters or collections of transcription factor binding sites. Here, we present MutViz 2.0, a largely extended and consolidated version of the tool: we took into account the immediate (trinucleotide) sequence context of mutations, improved the representation of clinical annotation of tumor samples and devised a method for signature refitting on limited genomic regions to infer the contribution of individual mutational processes to the mutation patterns observed in these regions. We described both the features of MutViz 2.0, concentrating on the novelties, and the substantial re-engineering of the cloud-based architecture.
BARTweb: a web server for transcriptional regulator association analysis
Authors: Ma Wenjing , Wang Zhenjia , Zhang Yifan , Magee Neal E , Feng Yayi , Shi Ruoyao , Chen Yang , Zang Chongzhi 
Published: April 2021

Abstract
Identifying active transcriptional regulators (TRs) associating with cis-regulatory elements in the genome to regulate gene expression is a key task in gene regulation research. TR binding profiles from numerous public ChIP-seq data can be utilized for association analysis with query data for TR identification, as an alternative to DNA sequence motif analysis. However, integration of the massive ChIP-seq datasets has been a major challenge in such approaches. Here we present BARTweb, an interactive web server for identifying TRs whose genomic binding patterns associate with input genomic features, by leveraging over 13 000 public ChIP-seq datasets for human and mouse. Using an updated binding analysis for regulation of transcription (BART) algorithm, BARTweb can identify functional TRs that regulate a gene set, have a binding profile correlated with a ChIP-seq profile or are enriched in a genomic region set, without a priori information of the cell type. BARTweb can be a useful web server for performing functional analysis of gene regulation. BARTweb is freely available at http://bartweb.org and the source code is available at https://github.com/zanglab/bart2.