bluuebunny/crossref_metadata_2025_split huggingface dataset:
MODIFICATION AND INHERITANCE OF PLEIOTROPIC CROSS RESISTANCE AND COLLATERAL SENSITIVITY IN SACCHAROMYCES CEREVISIAE
Authors: Rank G H , Robertson A J , Phillips K L 
Published: January 2021

ABSTRACT
A meiotic segregant (oliPR1) was isolated with a phenotype of multiple cross resistance and collateral sensitivity. Strain oliPR1 has increased sensitivity to ethidium bromide, dequalinium chloride, acriflavin, paromomycin and neomycin, and increased resistance to oligomycin, rutamycin, venturicidin, triethyltin bromide, antimycin, carbonylcynamide-m-chlorophenylhydrazone, tetra-N-butylammonium bromide, dibenzyldimethylammonium chloride, triphenylmethylphosphonium bromide, chloramphenicol, carbomycin, tetracycline, triton-X-165 and cycloheximide. Single gene inheritance of the cross resistance and collateral sensitivity was shown by 2:2 parental ditype segregation and reversion of the complete phenotype by a spontaneous revertant. The locus conferring the oliPR1 phenotype was mapped 11.7 units from an unspecified centromere. Antibiotic resistance showed incomplete dominance, with the level of hybrid resistance dependent upon the inhibitor tested. Resistant diploids that produced four resistant ascospores were the result of mitotic recombination prior to meiosis. A partial revertant phenotype (sensitive to all inhibitors except oligomycin, antimycin and carbonylcyanide-m-chlorophenylhydrazone) was shown to be due to a single nuclear gene causing partial suppression of oliPR1. Anaerobic pretreatment, 37° and 0.5 M KCl were observed to reduce the growth of oliPR1 when challenged with seven diverse inhibitors (antimycin, carbonylcyanide-m-chlorophenylhydrazone,-chloramphenicol, cycloheximide, oligomycin, triethyltin bromide, and triphenylmethylphosphonium bromide). Resistance to cycloheximide was not altered by the [rho—] state. A revertant of oliPR1 (sensitive to the above inhibitors but resistant to ethidium bromide, paromycin and neomycin) showed anaerobic and temperature sensitization to ethidium bromide, paromomycin and neomycin. Continuous monitoring of oxygen uptake by the revertant after anaerobic pretreatment revealed that anaerobiosis sensitized respiratory adaptation of the revertant to neomycin. It is proposed that oliPR1 is a mutation resulting in the alteration of plasma membrane premeability to many diverse inhibitors.
RIBOSOMAL GENE LOCALIZATION AND DISTRIBUTION (ARRANGEMENT) WITHIN THE NUCLEOLAR ORGANIZER REGION OF ZEA MAYS
Authors: Ramirez Samuel A , Sinclair John H 
Published: January 2021

ABSTRACT
Cytogenetic and molecular hybridization techniques were used to examine the arrangement of rRNA genes at the nucleolar organizer region (NOR) of maize. TB-6a stocks involving a reciprocal translocation between a B chromosome and the NOR of chromosome 6 were used. The amount of rDNA in the different stocks used varied from 1.5 to 4 NOR equivalents depending on the number of B6 choromosomes present. Cytological measurements show that the medial break through the NOR results in an equal partitioning of the heterochromatic knob (the NOR) between chromosome 6 and the B chromosome to which it was translocated. DNA-rRNA hybridization experiments show a linear relationship between the amount of rRNA capable of hybridizing with DNA and the number of NOR equivalents present. The data confirm McClintock's conclusion that the heterochromatic knob, rather than the constricted portion, is the true NOR region. Further, they show that the number of ribosomal genes is correlated with the amount of cytologically visible NOR, suggesting a uniform distribution of genes throughout the locus.
GENETIC LOADS IN HETEROGENEOUS ENVIRONMENTS
Authors: Taylor Charles E 
Published: January 2021

ABSTRACT
A model of population structure in heterogeneous environments is described with attention focused on genetic variation at a single locus. The existence of equilibria at which there is no genetic load is examined.—The absolute fitness of any genotype is regarded as a function of location in the niche space and the population density at that location. It is assumed that each organism chooses to live in that habitat in which it is most fit ("optimal habitat selection").—Equilibria at which there is no segregational load ("loadless equilibria") may exist. Necessary and sufficient conditions for the existence of such equilibria are very weak. If there is a sufficient amount of dominance or area in which the alleles are selectively neutral, then there exist equilibria without segregational loads. In the N, p phase plane defined by population size, N, and gene frequency, p, these equilibria generally consist of a line segment which is parallel to the p axis. These equilibria are frequently stable.
CHROMOSOMAL BASIS OF THE MEROZYGOSITY IN A PARTIALLY DIPLOID MUTANT OF PNEUMOCOCCUS
Authors: Ledbetter Mary Lee S , Hotchkiss Rollin D 
Published: January 2021

ABSTRACT
A sulfonamide-resistant mutant of pneumococcus, sulr-c, displays a genetic instability, regularly segregating to wild type. DNA extracts of derivatives of the strain possess transforming activities for both the mutant and wild-type alleles, establishing that the strain is a partial diploid. The linkage of sulr-c to strr-61, a stable chromosomal marker, was established, thus defining a chromosomal locus for sulr-c. DNA isolated from sulr-c cells transforms two mutant recipient strains at the same low efficiency as it does a wild-type recipient, although the mutant property of these strains makes them capable of integrating classical "low-efficiency" donor markers equally as efficiently as "high efficiency" markers. Hence sulr-c must have a different basis for its low efficiency than do classical low efficiency point mutations. We suggest that the DNA in the region of the sulr-c mutation has a structural abnormality which leads both to its frequent segregation during growth and its difficulty in efficiently mediating genetic transformation.
EFFECTS OF GLUCOSE REPRESSION ON THE TRANSMISSION AND RECOMBINATION OF MITOCHONDRIAL GENES IN YEAST (SACCHAROMYCES CEREVISIAE)
Authors: Birky C William 
Published: January 2021

ABSTRACT
Matings of a number of Saccharomyces cerevisiae stocks give different output ratios of mitochondrial genotypes depending on whether the cells are glucose-repressed or derepressed. The effects of glucose repression are independent of cellular mating type and mitochondrial genotype, and take place at least in part after zygotes are formed. An explanation is proposed in terms of changes in the relative numbers of mitochondrial DNA molecules contributed by the a and α parents, modified by selective replication or destruction of molecules inside the zygote.
PARASEXUAL GENETIC ANALYSIS OF THE CELLULAR SLIME MOLD DICTYOSTELIUM DISCOIDEUM A3
Authors: Rothman Frank G , Alexander Ellen T 
Published: January 2021

ABSTRACT
Haploid strain A3 of the cellular slime mold Dictyostelium discoideum is valuable for biochemical studies because it is capable of axenic growth. Mutants of A3 temperature-sensitive for growth and resistant to the drugs cycloheximide, acriflavin, or methanol were isolated.—Heterozygous diploid recombinants, formed at low frequency by cell and nuclear fusion, were isolated by selecting temperature-resistant progeny of mixed cultures of two nonallelic temperature-sensitive haploids (Loomis 1969). Each drug-resistant mutation was found to be recessive. Two independently isolated methanol-resistant mutants were in one complementation group.—Diploids of A3 heterozygous for drug resistance formed drug-resistant segregants with a frequency of approximately 10-4. Segregants selected for resistance to a single drug were either haploid or diploid; the fraction which was haploid varied from 0.11 to 0.86, depending on the selected marker. Segregants selected for resistance to two or three drugs were almost all haploid.—Using this parasexual cycle of diploid formation and haploidization, linkage of these temperature-sensitive and drug-resistance mutations to each other and to mutations studied by Katz and Sussman (1972) and by Williams, Kessin and Newell (1974b) was analyzed. The methanol-resistant mutants were found to be partially resistant to acriflavin, and unlinked to the mutant selected for acriflavin resistance, which was methanol-sensitive. Of the expected seven linkage groups in D. discoideum, five, and a possible sixth, have been marked.—Linkage analysis of a mutant abnormal in morphogenesis showed that its phenotype results from two unlinked chromosomal mutations
First insight into the whole genome shotgun sequence of the endangered noble pen shell Pinna nobilis: a giant bivalve undergoing a mass mortality event
Authors: Bunet Robert , Prévot Jean-Marc , Vicente Nardo , García-March José Rafa , Martinović Rajko , Tena-Medialdea José , Joksimovic Danijela , Bonnefont Jean-Luc , Coupé Stéphane 
Published: January 2021

ABSTRACT
The noble pen shell Pinna nobilis is a Mediterranean endemic and emblematic giant bivalve. Already considered by the late 20th century to be an endangered species, it is facing a dramatic and rapidly expanding epizooty that has decimated populations since mid-2016. The ecological importance of P. nobilis has prompted important investigations for conservation purposes. Here, we report a first analysis of the whole genome sequencing of this animal. This was performed on an Illumina HiSeq X platform using a single paired-end library of short fragments (2 × 150 bp). The de novo contig assembly had a total size of 584 Mb (96,738 contigs, N50 = 7.6 kb, with 0.4% of ambiguous nucleotides), representing 77.5% of the predicted genome size of 754 Mb. The P. nobilis genome is highly AT-rich, with a GC content of 35.6%. At 1%, heterozygosity was in the range of other bivalves with sequenced genomes. Over one-third (36.2%) of the genome consisted of repeated elements with a surprising larger number of short interspersed nuclear elements compared to other molluscan genomes. We were also able to reconstruct the full mitochondrial genome (c. 19 kb, with 12 protein-coding genes, 2 rRNA and 22 tRNA genes). In the context of the epizootic outbreak affecting P. nobilis, a first insight into the innate immune and stress-related genes found in the sequence is provided.
Cometary records revise Eastern Mediterranean chronology around 1240 CE
Authors: Murata Koji , Ichikawa Kohei , Fujii Yuri I , Hayakawa Hisashi , Cheng Yongchao , Kawamoto Yukiko , Sano Hidetoshi 
Published: January 2021

AbstractEirene Laskarina, Empress of John III Batatzes of the exiled Byzantine Empire of Nicaea (1204–1261 CE), was an important Eastern Mediterranean figure in the first half of the thirteenth century. We reassess the death day of Eirene, which has been variously dated during the years between the end of 1239 and 1241, with the understanding that narrowing the range in which this event occurred contributes much to understanding the political situation in the area around 1240. George Akropolites, a famous official of the Empire, gives an account that connects Eirene's death to a comet that appeared “six months earlier,” thus pointing to two comet candidates that were visible from the Eastern Mediterranean during the years 1239 and 1241, one recorded on “1239 June 3” and the other on “1240 January 31.” Recent historians prefer the former, based on historical circumstances and without a critical assessment of the comet records. We revisit the historical records and reveal that the “1239 June 3” candidate was not a comet. On the other hand, the other candidate was a comet, as supported by multiple historical records in multiple regions, and is also a good fit with Akropolites’ narrative. Therefore, we conclude that Eirene died six months after the comet that was seen on 1240 January 31, which places her death in the summer of 1240. Given that her death day is crucial for determining some other contemporary events across the Eastern Mediterranean, our results offer a solid basis for further research on the thirteenth-century Eastern Mediterranean.
Exploring intentional medication non-adherence in patients with systemic lupus erythematosus: the role of physician–patient interactions
Authors: Leung Jerik , Baker Elizabeth A , Kim Alfred H J 
Published: January 2021

AbstractObjectiveMedication non-adherence contributes to worse health outcomes among SLE patients. The underlying mechanisms that drive medication non-adherence are poorly understood. The purpose of this study was to explore possible mechanisms of medication non-adherence by eliciting patient experiences.MethodsConsented adult patients with ACR- or SLICC-classified SLE were recruited. Ten semi-structured interviews were conducted across six participants. Interviews were audio recorded, transcribed, and analysed using an iterative process. The findings were presented to an interactive public forum with SLE patients, family members and friends of patients, and health-care professionals to assess validity and for elaboration of the concepts developed.ResultsThe following three interrelated themes emerged from the interviews. First, why do rheumatologists not know more about lupus or share what they do know with their patients? Second, why do I have to take so many drugs and why do the drugs not work? Third, if my rheumatologist cannot communicate with me, why should I follow the prescribed medication regimen?ConclusionOur exploratory findings lay out a possible underlying logic by which patients might choose intentionally to engage with medication non-adherence behaviours. Patients suggested that poor communication with their rheumatologists along with a lack of validation of their symptoms contributed to them not valuing the recommendations of physicians. This also contributed to development of a cynical outlook and little belief that medication would improve their condition. Although further work is needed to validate these findings, our preliminary work suggests that interventions focusing on the development of communication skills among both patients and rheumatologists are necessary to reduce medication non-adherence.
Synthesis of libraries and multi-site mutagenesis using a PCR-derived, dU-containing template
Authors: Meinke Gretchen , Dalda Nahide , Brigham Benjamin S , Bohm Andrew 
Published: January 2021

Abstract
Directed DNA libraries are useful because they focus genetic diversity in the most important regions within a sequence. Ideally, all sequences in such libraries should appear with the same frequency and there should be no significant background from the starting sequence. These properties maximize the number of different sequences that can be screened. Described herein is a method termed SLUPT (Synthesis of Libraries via a dU-containing PCR-derived Template) for generating highly targeted DNA libraries and/or multi-site mutations wherein the altered bases may be widely distributed within a target sequence. This method is highly efficient and modular. Moreover, multiple distinct sites, each with one or more base changes, can be altered in a single reaction. There is very low background from the starting sequence, and SLUPT libraries have similar representation of each base at the positions selected for variation. The SLUPT method utilizes a single-stranded dU-containing DNA template that is made by polymerase chain reaction (PCR). Synthesis of the template in this way is significantly easier than has been described earlier. A series of oligonucleotide primers that are homologous to the template and encode the desired genetic diversity are extended and ligated in a single reaction to form the mutated product sequence or library. After selective inactivation of the template, only the product library is amplified. There are no restrictions on the spacing of the mutagenic primers except that they cannot overlap.
An Ebola virus disease model with fear and environmental transmission dynamics
Authors: Juga M.L. , Nyabadza F. , Chirove F. 
Published: January 2021

ABSTRACTRecent Ebola virus disease (EVD) outbreaks have been limited not only to the interactions between humans but also to the complex interplay of the environment, human and socio-economic factors. Changes in human behaviour as a result of fear can also affect disease transmission dynamics. In this paper, a compartmental model is used to study the dynamics of EVD incorporating fear and environmental transmission. We formulate a fear dependent contact rate function to measure the rate of person to person, as well as pathogen to person transmissions. The epidemic threshold and the model equilibria are determined and, their stabilities are analysed. The model is validated by fitting it to data from the 2019 and 2020 EVD outbreaks in the Democratic Republic of Congo. Our results suggest that the fear of death from EVD may reduce the transmission and aid the control of the disease, but it is not sufficient to eradicate the disease. Policymakers need to also implement other control measures such as case finding, media campaigns, Quarantine and increase in the number of beds in the Ebola treatment centers, good laboratory services, safe burials and social mobilisation, to eradicate the disease.HighlightsDue to its high case fatality rate, EVD undoubtedly instills fear in the inhabitants of any affected community.We propose an Ebola model with fear, which considers the pathogens in the environment to quantify the effect of fear and environmental transmission on the EVD disease dynamics.The fear of death from Ebola is proportional to the Ebola disease transmission rate.At high levels of fear, the number of EVD cases decrease.
Distinct mutations and lineages of SARS-CoV-2 virus in the early phase of COVID-19 pandemic and subsequent one-year global expansion
Authors: Chen Yan , Li Shiyong , Wu Wei , Geng Shuaipeng , Mao Mao 
Published: January 2021

AbstractA novel coronavirus, SARS-CoV-2, has caused over 190 million cases and over 4 million deaths worldwide since it occurred in December 2019 in Wuhan, China. Here we conceptualized the temporospatial evolutionary and expansion dynamics of SARS-CoV-2 by taking a series of cross-sectional view of viral genomes from early outbreak in January 2020 in Wuhan to early phase of global ignition in early April, and finally to the subsequent global expansion by late December 2020. Based on the phylogenetic analysis of the early patients in Wuhan, Wuhan/WH04/2020 is supposed to be a more appropriate reference genome of SARS-CoV-2, instead of the first sequenced genome Wuhan-Hu-1. By scrutinizing the cases from the very early outbreak, we found a viral genotype from the Seafood Market in Wuhan featured with two concurrent mutations (i.e. M type) had become the overwhelmingly dominant genotype (95.3%) of the pandemic one year later. By analyzing 4,013 SARS-CoV-2 genomes from different continents by early April, we were able to interrogate the viral genomic composition dynamics of initial phase of global ignition over a timespan of 14-week. 11 major viral genotypes with unique geographic distributions were also identified. WE1 type, a descendant of M and predominantly witnessed in western Europe, consisted a half of all the cases (50.2%) at the time. The mutations of major genotypes at the same hierarchical level were mutually exclusive, which implying that various genotypes bearing the specific mutations were propagated during human-to-human transmission, not by accumulating hot-spot mutations during the replication of individual viral genomes. As the pandemic was unfolding, we also used the same approach to analyze 261,323 SARS-CoV-2 genomes from the world since the outbreak in Wuhan (i.e. including all the publicly available viral genomes) in order to recapitulate our findings over one-year timespan. By 25 December 2020, 95.3% of global cases were M type and 93.0% of M-type cases were WE1. In fact, at present all the four variants of concern (VOC) are the descendants of WE1 type. This study demonstrates the viral genotypes can be utilized as molecular barcodes in combination with epidemiologic data to monitor the spreading routes of the pandemic and evaluate the effectiveness of control measures. Moreover, the dynamics of viral mutational spectrum in the study may help the early identification of new strains in patients to reduce further spread of infection, guide the development of molecular diagnosis and vaccines against COVID-19, and help assess their accuracy and efficacy in real world at real time.
HLA-SPREAD: A Natural Language Processing based resource for curating HLA association from PubMed abstracts
Authors: Dholakia Dhwani , Kalra Ankit , Misir Bishnu Raman , Kanga Uma , Mukerji Mitali 
Published: January 2021

ABSTRACTExtreme complexity in the Human Leukocyte Antigens (HLA) system and its nomenclature makes it difficult to interpret and integrate relevant information for HLA associations with diseases, Adverse Drug Reactions (ADR) and Transplantation. PubMed search displays ∼144,000 studies on HLA reported from multiple diseases in diverse locations. Currently, IPD-IMGT/HLA database houses data on 28,320 HLA alleles. We developed an automated pipeline with a unified graphical user interface HLA-SPREAD that provides a structured information on SNPs, Populations, REsources, ADRs and Diseases information. Information on HLA was extracted from ∼24 million PubMed abstracts extracted using Natural Language Processing (NLP). Python scripts were used to mine and curate information on diseases, filter false positives and categorize to 24 tree hierarchical groups and named Entity Recognition (NER) algorithms followed by semantic analysis to infer HLA association(s). This resource from 112 countries and 32 ethnic groups provides interesting insights on: markers associated with allelic/haplotypic association in autoimmune, cancer, viral and skin diseases, transplantation outcome and ADRs for hypersensitivity. Summary information on clinically relevant biomarkers related to HLA disease associations with mapped susceptible/risk alleles are readily retrievable from HLASPREAD. The resource is available at URLhttp://hla-spread.igib.res.in/. This resource is first of its kind that can help uncover novel patterns in HLA gene-disease associations.