bluuebunny/crossref_metadata_2025 huggingface dataset:
Insertions of Hybrid P Elements in the yellow Gene of Drosophila Cause a Large Variety of Mutant Phenotypes
Authors: Georgiev Pavel , Tikhomirova Tatiana , Yelagin Vjacheslav , Belenkaya Tatiana , Gracheva Elena , Parshikov Alexander , Evgen'ev Mikhail B , Samarina Olga P , Corces Victor G
Published: January 2021

A series of yellow mutations associated with a great variety of tissue-specific phenotypes were obtained from several highly unstable Drosophila melanogaster strains carrying the gypsy-induced y2 allele. These mutations are caused by insertion of additional DNA sequences of variable size 69 bp upstream of the yellow transcription start site. These sequences are flanked by identical copies of a deleted 1.2-kb P element arranged in the same or inverted orientation. The central part of the inserted element consists of genomic sequences originating from different regions of the X chromosome. The mutant phenotype caused by these chimeric elements depends on the nature of the sequences present either in the P element or in the central part of the insertion, suggesting that these sequences are able to affect expression of the yellow gene. In addition, sequences present in the central region of the insertions strongly modify the effects of the gypsy-bound suppressor of Hairy-wing [su(Hw)] and modifier of mdg4 [mod(mdg4)] proteins on yellow transcription. Analyses of these mutations give new insights into the mechanisms by which su(Hw) and mod(mdg4) affect enhancer function.
A General Method for Identifying Recessive Diploid-Specific Mutations in Saccharomyces cerevisiae, Its Application to the Isolation of Mutants Blocked at Intermediate Stages of Meiotic Prophase and Characterization of a New Gene SAE2
Authors: McKee Andrew H Z , Kleckner Nancy
Published: January 2021

We describe a general new approach for identifying recessive mutations that affect diploid strains of yeast Saccharomyces cerevisiae and the application of this method to the identification of mutations that confer an intermediate block in meiotic prophase chromosome metabolism. The method uses a temperature-sensitive conjugation mutation ste7-1 in combination with homothallism. The mutations of interest confer a defect in spore formation that is dependent upon a gene required for initiation of meiotic recombination and development of meiosis-specific chromosome structure (SPO11). Identified in this screen were null mutations of the DMC1 gene, nonnull mutations of RAD50 (rad50S, and mutations in three new genes designated SAE1, SAE2 and SAE3 (Sporulation in the Absence of Spo Eleven). Molecular characterization of the SAE2 gene and characterization of meiotic and mitotic phenotypes of sae2 mutants are also presented. The phenotypes conferred by a sae2 null mutation are virtually indistinguishable from those conferred by the previously identified nonnull mutations of RAD50 (rad50S). Most notably, both mutations confer only weak sensitivity to the radiomimetic agent methyl methane sulfonate (MMS) but completely block resection and turnover of meiosis-specific double-strand breaks. These observations provide further evidence that this constellation of phenotypes identifies a specific molecular function.
Schixophyllum commune Aα Mating-Type Proteins, Y and Z, Form Complexes in All Combinations In Vitro
Authors: Asada Yasuhiko , Yue Changli , Wu Jian , Shen Guang-Ping , Novotny Charles P , Ullrich Robert C
Published: January 2021

The Aα locus of the basidiomycete fungus, Schizophyllum commune, regulates sexual development via proteins Y and Z. Each Aα mating type encodes unique Y and Z isoforms. We used two isoforms of Y (Y4 and Y5) and two isoforms of Z (Z4 and Z5) in affinity assays of protein binding. These assays identified two types of protein interactions. Each full-length Y or Z protein binds to itself and other Y or Z proteins regardless of the Aα mating type from which they are encoded (i.e., mating-type independent binding). A second type of binding, detected with partial-length polypeptides, occurs only between N-terminal regions of Y and Z proteins encoded from different Aα mating types (e.g., Y4Z5 or Y5Z4); we refer to this binding as mating-type dependent binding. Deletion analysis shows that the Y4 specificity domain (an N-terminal region conferring recognition uniqueness to the Y4 isoform) is essential for mating-type dependent binding. Other regions of Y and Z are involved in mating-type independent binding. These results, obtained in vitro, raise the possibility that either of several protein complexes composed of Y and/or Z proteins may occur in vivo.
Divergence of the yellow Gene Between Drosophila melanogaster and D. subobscura: Recombination Rate, Codon Bias and Synonymous Substitutions
Authors: Munté Agustí , Aguadé Montserrat , Segarra Carmen
Published: January 2021

The yellow (y) gene maps near the telomere of the X chromosome in Drosophila melanogaster but not in D. subobscura. Thus the strong reduction in the recombination rate associated with telomeric regions is not expected in D. subobscura. To study the divergence of a gene whose recombination rate differs between two species, the y gene of D. subobscura was sequenced. Sequence comparison between D. melanogaster and D. subobscura revealed several elements conserved in noncoding regions that may correspond to putative cis-acting regulatory sequences. Divergence in the y gene coding region between D. subobscura and D. melanogaster was compared with that found in other genes sequenced in both species. Both, yellow and scute exhibit an unusually high number of synonymous substitutions per site (ps). Also for these genes, the extent of codon bias differs between both species, being much higher in D. subobscura than in D. melanogaster. This pattern of divergence is consistent with the hitchhiking and background selection models that predict an increase in the fixation rate of slightly deleterious mutations and a decrease in the rate of fixation of slightly advantageous mutations in regions with low recombination rates such as in the y-sc gene region of D. melanogaster.
Reproductive Isolation and Morphogenetic Evolution in Drosophila Analyzed by Breakage of Ethological Barriers
Authors: Sánchez Lucas , Santamaria Pedro
Published: January 2021

This article reports the breaking of ethological barriers through the constitution of soma-germ line chimeras between species of the melanogaster subgroup of Drosophila, which are ethologically isolated. Female Drosophila yakuba and D. teissieri germ cells in a D. melanogaster ovary produced functional oocytes that, when fertilized by D. melanogaster sperm, gave rise to sterile yakuba-melanogaster andteissieri-melanogaster male and female hybrids. However, the erecta-melanogaster and orena-melanogaster hybrids were lethal, since female D. erecta and D. orena germ cells in a D. melanogaster ovary failed to form oocytes with the capacity to develop normally. This failure appears to be caused by an altered interaction between the melanogaster soma and the erecta and orena germ lines. Germ cells of D. teissieri and D. orena in a D. melanogaster testis produced motile sperm that was not stored in D. melanogaster females. This might be due to incompatibility between the teissieri and orena sperm and the melanogaster seminal fluid. A morphological analysis of the terminalia of yakuba-melanogaster and teissieri-melanogaster hybrids was performed. The effect on the terminalia of teissieri-melanogaster hybrids of a mutation in doublesex, a regulatory gene that controls the development of the terminalia, was also investigated.
Activation of the lac Repressor in the Transgenic Mouse
Authors: Scrable Heidi , Stambrook Peter J
Published: January 2021

We have introduced sequences encoding the lac repressor of Escherichia coli into the genome of the mouse. One sequence was derived from the bacterial lac operon and the other was created by reencoding the amino acid sequence of lacI with mammalian codons. Both versions are driven by an identical promoter fragment derived from the human β-actin locus and were microinjected into genetically identical pronuclear stage embryos. All transgenes utilizing the bacterial coding sequence were transcriptionally silent in all somatic tissues tested. The sequence re-encoded with mammalian codons was transcriptionally active at all transgene loci and expressed ubiquitously. Using methylation-sensitive enzymes, we have determined the methylation status of lac repressor transgenes encoded by either the bacterial or mammalian sequence. The highly divergent bacterial sequence was hypermethylated at all transgene loci, while the mammalian sequence was only hypermethylated at a high copy number locus. This may reflect a normal process that protects the genome from acquiring new material that has an abnormally divergent sequence or structure.
Characterization of Synthetic-Lethal Mutants Reveals a Role for the Saccharomyces cerevisiae Guanine-Nucleotide Exchange Factor Cdc24p in Vacuole Function and Na+ Tolerance
Authors: White William H , Johnson Douglas I
Published: January 2021

Cdc24p is the guanine-nucleotide exchange factor for the Cdc42p GTPase, which controls cell polarity in Saccharomyces cerevisiae. To identify new genes that may affect cell polarity, we characterized six UV-induced csl (CDC24  synthetic-lethal) mutants that exhibited synthetic-lethality with cdc24-4ts at 23°. Five mutants were not complemented by plasmid-borne CDC42, RSRI, BUD5, BEM1, BEM2, BEM3 or CLA4 genes, which are known to play a role in cell polarity. The csl3 mutant displayed phenotypes similar to those observed with calcium-sensitive, Pet−  vma mutants defective in vacuole function. CSL5 was allelic to VMA5, the vacuolar H+-ATPase subunit C, and one third of cs15 cdc24-4ts cells were elongated or had misshapen buds. A cdc24-4ts Δvma5::LEU2 double mutant did not exhibit synthetic lethality, suggesting that the csl5/vma5 cdc24-4ts synthetic-lethality was not simply due to altered vacuole function. The cdc24-4ts mutant, like Δvma5::LEU2 and cs13 mutants, was sensitive to high levels of Ca2+ as well as Na+ in the growth media, which did not appear to be a result of a fragile cell wall because the phenotypes were not remedied by 1 m sorbitol. Our results indicated that Cdc24p was required in one V-ATPase mutant and another mutant affecting vacuole morphology, and also implicated Cdc24p in Na+ tolerance.
Suppressors of the ndc10-2 Mutation: A Role for the Ubiquitin System in Saccharomyces cerevisiae Kinetochore Function
Authors: Kopski Kristen M , Huffaker Tim C
Published: January 2021

We have isolated a new conditional-lethal mutation, ndc10-2, in the NDC10/CBF2/CTF14 gene that encodes the 110-kD subunit of the Saccharomyces cerevisiae CBF3 kinetochore complex. At the restrictive temperature of 37°, ndc10-2 cells are able to assemble anaphase spindles, but fail to segregate their DNA, consistent with a defect in kinetochore function. To identify other factors that play a role in kinetochore assembly or function, we isolated both dosage and second site suppressors of the ndc10-2 mutation. These screens identified UBC6 as a dosage suppressor, and mutations in UBC6 and UBC7 as second-site suppressors of ndc10-2 heat sensitivity. Both UBC6 and UBC7 encode ubiquitin-conjugating enzymes that function in ubiquitin-mediated protein degradation. Furthermore, overexpression of a mutant ubiquitin suppresses the ndc10-2 mutation. These results implicate the ubiquitin system in the regulation of ndc10-2 function and suggest a role for the ubiquitin system in kinetochore function.
Genealogical Structure Among Alleles Regulating Self-Incompatibility in Natural Populations of Flowering Plants
Authors: Uyenoyama Marcy K
Published: January 2021

A method is proposed for characterizing the structure of genealogies among alleles that regulate self-incompatibility in flowering plants. Expected distributions of ratios of divergence times among alleles, scaled by functions of allele number, were generated by numerical simulation. These distributions appeared relatively insensitive to the particular parameter values assigned in the simulations over a fourfold range in effective population size and a 100-fold range in mutation rate. Generalized least-squares estimates of the scaled indices were obtained from genealogies reconstructed from nucleotide sequences of self-incompatibility alleles from natural populations of two solanaceous species. Comparison of the observed indices to the expected distributions generated by numerical simulation indicated that the allelic genealogy of one species appeared consistent with the symmetric balancing selection generated by self-incompatibility. However, the allelic genealogy of the second species showed unusually long terminal branches, suggesting the operation of additional evolutionary processes.
A Genetic Strategy to Demonstrate the Occurrence of Spontaneous Mutations in Nondividing Cells Within Colonies of Escherichia coli
Authors: Reddy Manjula , Gowrishankar J
Published: January 2021

A genetic strategy was designed to examine the occurrence of mutations in stationary-phase populations. In this strategy, a parental population of cells is able to survive under both permissive and restrictive conditions whereas mutants at a particular target locus exhibit a conditional-lethal phenotype. Thus, by growing the population to stationary phase under restrictive conditions and then shifting it to permissive conditions, mutations that had arisen in stationary phase can be studied without confounding effects caused by the occurrence of similar mutations during growth of the population. In two different applications of this strategy, we have studied the reversion to Lac+ in stationary phase of several Lac– mutations in Escherichia coli. Our results indicate that a variety of spontaneous point mutations and deletions, particularly those that are sensitive to the mechanisms of replication slippage (for their generation) and methyl-directed mismatch repair (for their correction), can arise in nondividing populations of cells within a colony. The frequency of their occurrence was also elevated in mutS strains, which are defective in such mismatch repair. These data have relevance to the ongoing debate on adaptive or directed mutations in bacteria.
Genetic Analysis of the Chlamydomonas reinhadtii I-CreI Mobile Intron Homing System in Escherichia coli
Authors: Seligman Lenny M , Stephens Kathryn M , Savage Jeremiah H , Monnat Raymond J
Published: January 2021

We have developed and used a genetic selection system in Escherichia coli to study functional requirements for homing site recognition and cleavage by a representative eukaryotic mobile intron endonuclease. The homing endonuclease, I-CreI, was originally isolated from the chloroplast of the unicellular green alga Chlamydomonas reinhardtii. I-CreI homing site mutants contained base pair substitutions or single base deletions that altered the rate of homing site cleavage and/or product release. I-CreI endonuclease mutants fell into six phenotypic classes that differed in in vivo activity, toxicity or genetic dominance. Inactivating mutations clustered in the N-terminal 60% of the I-CreI amino acid sequence, and two frameshift mutations were isolated that resulted in premature translation termination though retained partial activity. These mutations indicate that the N-terminal two-thirds of the I-CreI endonuclease is sufficient for homing site recognition and cleavage. Substitution mutations altered in four potential active site residues were examined D20N, Q47H or R70A substitutions inactivated endonuclease activity, whereas S22A did not. The genetic approach we have taken complements phylogenetic and structural studies of mobile intron endonucleases and has provided new information on the mechanistic basis of I-CreI homing site recognition and cleavage.
Estimation of the Amount of DNA Polymorphism When the Neutral Mutation Rate Varies Among Sites
Authors: Misawa Kazuharu , Tajima Fumio
Published: January 2021

Knowing the amount of DNA polymorphism is essential to understand the mechanism of maintaining DNA polymorphism in a natural population. The amount of DNA polymorphism can be measured by the average number of nucleotide differences per site (π), the proportion of segregating (polymorphic) site (s) and the minimum number of mutations per site (s*). Since the latter two quantities depend on the sample size, θ is often used as a measure of the amount of DNA polymorphism, where θ = 4Nμ, N is the effective population size and μ is the neutral mutation rate per site per generation. It is known that θ estimated from π, s and s* under the infinite site model can be biased when the mutation rate varies among sites. We have therefore developed new methods for estimating θ under the finite site model. Using computer simulations, it has been shown that the new methods give almost unbiased estimates even when the mutation rate varies among sites substantially. Furthermore, we have also developed new statistics for testing neutrality by modifying Tajima's D statistic. Computer simulations suggest that the new test statistics can be used even when the mutation rate varies among sites.
Ghost QTL and hotspots in experimental crosses: novel approach for modeling polygenic effects
Authors: Wallin Jonas , Bogdan Małgorzata , Szulc Piotr A , Doerge R W , Siegmund David O
Published: January 2021

Ghost quantitative trait loci (QTL) are the false discoveries in QTL mapping, that arise due to the “accumulation” of the polygenic effects, uniformly distributed over the genome. The locations on the chromosome that are strongly correlated with the total of the polygenic effects depend on a specific sample correlation structure determined by the genotypes at all loci. The problem is particularly severe when the same genotypes are used to study multiple QTL, e.g. using recombinant inbred lines or studying the expression QTL. In this case, the ghost QTL phenomenon can lead to false hotspots, where multiple QTL show apparent linkage to the same locus. We illustrate the problem using the classic backcross design and suggest that it can be solved by the application of the extended mixed effect model, where the random effects are allowed to have a nonzero mean. We provide formulas for estimating the thresholds for the corresponding t-test statistics and use them in the stepwise selection strategy, which allows for a simultaneous detection of several QTL. Extensive simulation studies illustrate that our approach eliminates ghost QTL/false hotspots, while preserving a high power of true QTL detection.
Assessing the performance of qpAdm: a statistical tool for studying population admixture
Authors: Harney Éadaoin , Patterson Nick , Reich David , Wakeley John
Published: January 2021

qpAdm is a statistical tool for studying the ancestry of populations with histories that involve admixture between two or more source populations. Using qpAdm, it is possible to identify plausible models of admixture that fit the population history of a group of interest and to calculate the relative proportion of ancestry that can be ascribed to each source population in the model. Although qpAdm is widely used in studies of population history of human (and nonhuman) groups, relatively little has been done to assess its performance. We performed a simulation study to assess the behavior of qpAdm under various scenarios in order to identify areas of potential weakness and establish recommended best practices for use. We find that qpAdm is a robust tool that yields accurate results in many cases, including when data coverage is low, there are high rates of missing data or ancient DNA damage, or when diploid calls cannot be made. However, we caution against co-analyzing ancient and present-day data, the inclusion of an extremely large number of reference populations in a single model, and analyzing population histories involving extended periods of gene flow. We provide a user guide suggesting best practices for the use of qpAdm.
3. Alternative Dispute Resolution in Family Law
Authors: Hodgson Roiya
Published: January 2021

This chapter first discusses the methods by which a family lawyer may resolve family law disputes, including alternative dispute resolution (ADR). It then reviews the various forms of negotiation that a family lawyer may undertake. These include settlement between clients, negotiation through correspondence, meeting between counsel, and at-court negotiation. Next, the chapter discusses mediation and collaborative law as different forms of ADR used in family law. It outlines MIAMs (mediation information and assessment meetings) and their importance prior to issuing proceedings. It also discusses the various steps of collaborative law. It also briefly considers a recent development in family ADR: arbitration.
4. The Single Family Court
Authors: Hodgson Roiya
Published: January 2021

This chapter is a short but important chapter. It provides an overview of the Single Family Court, which was created in April 2014. This is a huge change from when there used to be two family courts, magistrates’ and county court. It summarizes the effects of the Single Family Court and outlines who is involved in the judicial process within the new structure. It discusses how the allocation of cases within the Single Family Court are done by ‘gatekeepers’ and the new points of entry for cases. It outlines that the rules for allocation can be found in the Family Court (Composition and Distribution of Business) Rules 2014.
14. Procedure for Financial Orders
Authors: Hodgson Roiya
Published: January 2021

This chapter discusses the procedure for financial orders, which includes how to make an application for financial orders, the first appointment, financial dispute resolution hearing, and the final hearing. It covers the drafting required during financial proceedings such as Form E, statement of issues, the chronology, and the questionnaire. It covers funding options available to clients seeking financial orders, the protection of assets forming part of proceedings for financial orders, the pre-action protocol, and the role of consent orders in proceedings for financial orders. It also explains costs orders in relation to financial proceedings, setting aside a financial order and appeals.
16. Protecting Assets and the Family Home in Financial Order Proceedings
Authors: Hodgson Roiya
Published: January 2021

This chapter discusses whether a client can protect assets in financial order proceedings, the provisions of s37 Matrimonial Causes Act 1973, and the availability of ‘home rights’ under the Family Law Act 1996. Section 37 MCA 1973 assists the parties and the courts in preventing the disposition of any assets by either party to the proceedings. An order can be made preventing a party from making a disposition with the intention of defeating the claim for financial relief or an order reviewing a disposition that has already been made. The procedure for this is discussed, along with the fact that the family home is generally the largest asset in financial proceedings.
18. Child Support
Authors: Hodgson Roiya
Published: January 2021

The Child Support Act 1991 introduced a mechanism to recover maintenance from absent parents for their children. It created the Child Support Agency (CSA) as the organization responsible for collecting child support maintenance. This chapter discusses the framework of child support; when a client may be required to pay child support; what a client can do if they do not receive child support; and the future of child support. It examines the CSA scheme, which commenced in 2003, and the Child Maintenance Service, which opened its doors on 29 July 2013. It also looks at the financial provisions under Schedule 1 of the Children Act 1989.
20. Taxation in Family Law
Authors: Hodgson Roiya
Published: January 2021

Family law practitioners must be aware of the tax implications of any financial settlement and make it tax- efficient for the client. This chapter examines the types of tax most relevant to family law. Income tax is a type of tax paid on taxable income and, the basic personal allowance, as well as the higher and further rates, are discussed. Capital gains tax (CGT) arises on disposal of an asset or the receipt of money in respect of an asset if there is a ‘chargeable gain’, and examples of these are listed, as well as the relation of CGT and sponses/civil partners/family assets. Inheritance taxand stamp duty land tax are also discussed.
22. Cohabitation
Authors: Hodgson Roiya
Published: January 2021

Cohabitating relationships are not covered by the same coherent body of law available to married couples or civil partners. Many cohabitants mistakenly believe that they acquire legal rights after a number of years of cohabiting, but this is incorrect. Many clients are shocked to find that they have few legal remedies, and that available are far from straightforward. This chapter begins with a comparison of marriage, civil partnership, and cohabitation. It then goes on to discuss the law on cohabitation contracts, as well as case-law relating to this. The Law Commission Proposals and future developments on cohabitation are then discussed.
24. Introduction to the Children Act 1989
Authors: Hodgson Roiya
Published: January 2021

This chapter examines the Children Act 1989 (CA 1989) and the main principles upon which Children Act proceedings are conducted. It discusses the content of the ‘welfare principle’ and the ‘welfare checklist’ under CA 1989, including the presump-tion of parental involvement. It outlines each part of the welfare checklist, including the wishes and feelings of the child, the likely effect on the child of a change of circumstances, and the child’s age, sex background, and any relevant characteristics. It examines each part in detail, using case-law where relevant. This chapter also explains the principles of ‘no order’ and ‘no delay’.
25. Parental Responsibility
Authors: Hodgson Roiya
Published: January 2021

Parental responsibility (PR) is one of the most important concepts in the Children Act 1989. This chapter provides the definition of PR as taken from Section 3 of the Children Act 1989 and provides examples of what it actually is in relation to decisions and responsibilities that a parent may make on behalf of their child during their childhood. It discusses the nature and scope of PR, and how it is acquired. It covers the law on automatic parental responsibility; how unmarried fathers can acquire PR; and PR for non-natural parents. It also discusses termination of PR orders and agreements. Case-law is used to provide examples.
27. Private Children Law Procedure
Authors: Hodgson Roiya
Published: January 2021

This chapter covers the basic procedure for a s8 Children Act 1989 (CA 1989) order. It discusses who is eligible to apply for an order under s8 CA 1989 and what public funding is still available for proceedings under the CA 1989. It then goes on to explain the procedure for obtaining an order under the CA 1989 in private law proceedings and the Children and Families Act 2014. This includes the procedure for obtaining leave, existing proceedings, other potential applicants, and rules. The hearings which occur are explained, as well as CAFCASS, expert evidence, allegations of harm, and domestic abuse.
33. Protection under the Family Law Act 1996: Non-Molestation Orders
Authors: Hodgson Roiya
Published: January 2021

This chapter discusses the following: the law regarding domestic abuse; practical issues arising from acting for clients facing domestic abuse; and the availability of remedies under the Family Law Act 1996. It also explains when funding may be available under legal aid for orders under the Family Law Act 1996. The concept of ‘associated persons’ is explained and the list of these is provided. Non-molestation orders under the Family Law Act 1996 are explained, as well as the test for a nonmolestation order, evidence, applications by children, and duration of an order. The remedies for clients escaping a forced marriage and criminal law remedies are discussed.
37. Protection from Harassment
Authors: Hodgson Roiya
Published: January 2021

Family lawyers may be consulted by those who are being harassed or stalked by someone who is not an associated person. This chapter examines the law on harassment and the remedies available to clients not protected by the Family Law Act 1996. It explains the relevance of this area in relation to family law and details the Protection from Harassment Act 1997. This was enacted to assist those suffering harassment through stalking, antisocial behaviour, or racial harassment. Criminal liability for harassment, civil remedy for harassment, and restraining orders are also discussed, as well as how these all relate in family practice.
Transethnic analysis of the human leukocyte antigen region for ulcerative colitis reveals not only shared but also ethnicity-specific disease associations
Authors: Degenhardt Frauke , Mayr Gabriele , Wendorff Mareike , Boucher Gabrielle , Ellinghaus Eva , Ellinghaus David , ElAbd Hesham , Rosati Elisa , Hübenthal Matthias , Juzenas Simonas , Abedian Shifteh , Vahedi Homayon , Thelma B K , Yang Suk-Kyun , Ye Byong Duk , Cheon Jae Hee , Datta Lisa Wu , Daryani Naser Ebrahim , Ellul Pierre , Esaki Motohiro , Fuyuno Yuta , McGovern Dermot P B , Haritunians Talin , Hong Myhunghee , Juyal Garima , Jung Eun Suk , Kubo Michiaki , Kugathasan Subra , Lenz Tobias L , Leslie Stephen , Malekzadeh Reza , Midha Vandana , Motyer Allan , Ng Siew C , Okou David T , Raychaudhuri Soumya , Schembri John , Schreiber Stefan , Song Kyuyoung , Sood Ajit , Takahashi Atsushi , Torres Esther A , Umeno Junji , Alizadeh Behrooz Z , Weersma Rinse K , Wong Sunny H , Yamazaki Keiko , Karlsen Tom H , Rioux John D , Brant Steven R ,   for the MAAIS Recruitment Center, Franke Andre ,   for the International IBD Genetics Consortium
Published: January 2021

Inflammatory bowel disease (IBD) is a chronic inflammatory disease of the gut. Genetic association studies have identified the highly variable human leukocyte antigen (HLA) region as the strongest susceptibility locus for IBD and specifically DRB1*01:03 as a determining factor for ulcerative colitis (UC). However, for most of the association signal such as delineation could not be made because of tight structures of linkage disequilibrium within the HLA. The aim of this study was therefore to further characterize the HLA signal using a transethnic approach. We performed a comprehensive fine mapping of single HLA alleles in UC in a cohort of 9272 individuals with African American, East Asian, Puerto Rican, Indian and Iranian descent and 40 691 previously analyzed Caucasians, additionally analyzing whole HLA haplotypes. We computationally characterized the binding of associated HLA alleles to human self-peptides and analyzed the physicochemical properties of the HLA proteins and predicted self-peptidomes. Highlighting alleles of the HLA-DRB1*15 group and their correlated HLA-DQ-DR haplotypes, we not only identified consistent associations (regarding effects directions/magnitudes) across different ethnicities but also identified population-specific signals (regarding differences in allele frequencies). We observed that DRB1*01:03 is mostly present in individuals of Western European descent and hardly present in non-Caucasian individuals. We found peptides predicted to bind to risk HLA alleles to be rich in positively charged amino acids. We conclude that the HLA plays an important role for UC susceptibility across different ethnicities. This research further implicates specific features of peptides that are predicted to bind risk and protective HLA proteins.
Care the epicardial pacemaker wires
Authors: Gonçalves Luísa , Máximo José , Almeida Jorge , Pinho Paulo
Published: January 2021

A patient with previous CABG was hospitalized for fever and Staphylococcus aureus bacteraemia without cardiac involvement. After appropriate antibiotic cycle, the patient recovered and was discharged. Six months later, symptoms and bacteraemia relapsed. A small intriguing ‘cystic’ mass was visualized in the right atrium by echocardiography. Once again, was discharged after successful antibiotic treatment. Four months later, symptoms and Staphylococcus bacteraemia reappeared with increasing mass size and surgery was decided. Intraoperatively, it was perceived that the mass was related to an epicardial pacemaker wire. Retained epicardial wires should be remembered in endocarditis evaluation.
Behavioral Deficits Induced by Somatostatin-Positive GABA Neuron Silencing Are Rescued by Alpha 5 GABA-A Receptor Potentiation
Authors: Fee Corey , Prevot Thomas D , Misquitta Keith , Knutson Daniel E , Li Guanguan , Mondal Prithu , Cook James M , Banasr Mounira , Sibille Etienne
Published: January 2021

Introduction

Deficits in somatostatin-positive gamma-aminobutyric acid interneurons (SST+ GABA cells) are commonly reported in human studies of mood and anxiety disorder patients. A causal link between SST+ cell dysfunction and symptom-related behaviors has been proposed based on rodent studies showing that chronic stress, a major risk factor for mood and anxiety disorders, induces a low SST+ GABA cellular phenotype across corticolimbic brain regions; that lowering Sst, SST+ cell, or GABA functions induces depressive-/anxiety-like behaviors (a rodent behavioral construct collectively defined as “behavioral emotionality”); and that disinhibiting SST+ cells has antidepressant-like effects. Recent studies found that compounds preferentially potentiating receptors mediating SST+ cell functions, α5-GABAA receptor positive allosteric modulators (α5-PAMs), achieved antidepressant-like effects. Together, the evidence suggests that SST+ cells regulate mood and cognitive functions that are disrupted in mood disorders and that rescuing SST+ cell function via α5-PAM may represent a targeted therapeutic strategy.

Methods

We developed a mouse model allowing chemogenetic manipulation of brain-wide SST+ cells and employed behavioral characterization 30 minutes after repeated acute silencing to identify contributions to symptom-related behaviors. We then assessed whether an α5-PAM, GL-II-73, could rescue behavioral deficits.

Results

Brain-wide SST+ cell silencing induced features of stress-related illnesses, including elevated neuronal activity and plasma corticosterone levels, increased anxiety- and anhedonia-like behaviors, and impaired short-term memory. GL-II-73 led to antidepressant- and anxiolytic-like improvements among behavioral deficits induced by brain-wide SST+ cell silencing.

Conclusion

Our data validate SST+ cells as regulators of mood and cognitive functions and demonstrate that bypassing low SST+ cell function via α5-PAM represents a targeted therapeutic strategy.
Complementary and competitive framing of driverless cars: framing effects, attitude volatility, or attitude resistance?
Authors: Ho Shirley S
Published: January 2021

This study answers two research questions regarding framing theory. First, what happens when frames are challenged? Second, how resistant are the opinions that initial frames induce? 1,006 participants completed an online experiment where they were randomly assigned to first view a blog post with either complementary or competitive framing on driverless cars. Participants also viewed a blog post that challenged the stance of the first blog post. Results revealed that complementary frames polarized opinions, while competitive frames neutralized framing effects. Competitive frames induced more resistant opinions than complementary frames did. Attitude and support were susceptible to new, antagonistic information. This study concludes that framing effects are ephemeral and easily challenged by different information.
Development and validation of a machine learning model predicting illness trajectory and hospital utilization of COVID-19 patients: A nationwide study
Authors: Roimi Michael , Gutman Rom , Somer Jonathan , Ben Arie Asaf , Calman Ido , Bar-Lavie Yaron , Gelbshtein Udi , Liverant-Taub Sigal , Ziv Arnona , Eytan Danny , Gorfine Malka , Shalit Uri
Published: January 2021

Objective

The spread of coronavirus disease 2019 (COVID-19) has led to severe strain on hospital capacity in many countries. We aim to develop a model helping planners assess expected COVID-19 hospital resource utilization based on individual patient characteristics.

Materials and Methods

We develop a model of patient clinical course based on an advanced multistate survival model. The model predicts the patient's disease course in terms of clinical states—critical, severe, or moderate. The model also predicts hospital utilization on the level of entire hospitals or healthcare systems. We cross-validated the model using a nationwide registry following the day-by-day clinical status of all hospitalized COVID-19 patients in Israel from March 1 to May 2, 2020 (n = 2703).

Results

Per-day mean absolute errors for predicted total and critical care hospital bed utilization were 4.72 ± 1.07 and 1.68 ± 0.40, respectively, over cohorts of 330 hospitalized patients; areas under the curve for prediction of critical illness and in-hospital mortality were 0.88 ± 0.04 and 0.96 ± 0.04, respectively. We further present the impact of patient influx scenarios on day-by-day healthcare system utilization. We provide an accompanying R software package.

Discussion

The proposed model accurately predicts total and critical care hospital utilization. The model enables evaluating impacts of patient influx scenarios on utilization, accounting for the state of currently hospitalized patients and characteristics of incoming patients. We show that accurate hospital load predictions were possible using only a patient’s age, sex, and day-by-day clinical state (critical, severe, or moderate).

Conclusions

The multistate model we develop is a powerful tool for predicting individual-level patient outcomes and hospital-level utilization.
Analytical Study of the Antifungal Posaconazole in Raw Material: Quantitative Bioassay, Decomposition Chemical Kinetics, and Degradation Impurities by LC-QTOF-MS
Authors: Garcia Cássia V , Bitencourt Andressa S , Oliveira Sendy S , Gobetti Caren , Mendez Andreas S L
Published: January 2021

Background

Posaconazole is a triazole antifungal drug that was approved by the U.S. Food and Drug Administration in 2006. No bioassay of it is available in the literature nor official codes for potency determination in bulk.

Objective

To conduct an analytical study focused on posaconazole in bulk.

Methods

An alternative microbiological assay was validated for drug quantitation, applying agar diffusion technics (3 × 3 design), using Saccharomyces cerevisiae ATCC MYA 1942 as a test microorganism (2% inoculum). An isocratic HPLC–DAD method, with C8 Shim-pack column (250 × 4.6 mm, 5 μm) and methanol–water (75:25 v/v) mobile phase was used for stress stability by photolysis and oxidation, indicating the formation of degradation products, which were investigated by ultra-performance liquid chromatography to quadrupole time-of-flight mass spectrometry.

Results

The established conditions for the bioassay were satisfactory. It was linear in the range evaluated (2.5–10.0 µg/mL), as well as precise, accurate, and robust. Stress tests showed drug susceptibility to the factors evaluated (60% of degradation after 120 min). Kinetics curves for photolytic decomposition followed first-order kinetics. From a photolytic and oxidative degraded matrix, three major degradation products were identified as being derivatives with modifications in the piperazine central ring and in the triazole and triazolone side chains, whose mass spectra results were m/z 683 (DP1), m/z 411 (DP2), and m/z 465 (DP3).

Conclusions

The microbiological method was adequately validated and demonstrated to be equivalent to physico-chemical ones. The impurities found are described for the first time in studies with posaconazole raw material.

Highlights

A microbiological bioassay was developed for posaconazole, first-order kinetics was determined for photolytic degradation, and structures for new degradation products were suggested.
Expression and affinity purification of recombinant mammalian mitochondrial ribosomal small subunit (MRPS) proteins and protein–protein interaction analysis indicate putative role in tumourigenic cellular processes
Authors: Revathi Paramasivam Oviya , Gopisetty Gopal , Subramani Jayavelu , Thangarajan Rajkumar
Published: January 2021

Mitochondrial ribosomal small subunit (MRPS) group of proteins is structural constituents of the small subunit of mitoribosomes involved in translation. Recent studies indicate role in tumourigenic process, however, unlike cytosolic ribosomal proteins, knowledge on the role of MRPS proteins in alternate cellular processes is very limited. Mapping protein–protein interactions (PPIs) onto known cellular processes can be a valuable tool to identify novel protein functions. In this study, to identify PPIs of MRPS proteins, we have constructed 31 glutathione-S-transferase (GST)/MRPS fusion clones. GST/MRPS fusion proteins were confirmed by MALDI-TOF analysis. GST pull-downs were performed using eight GST/MRPS proteins (MRPS9, MRPS10, MRPS11, MRPS18B, MRPS31, MRPS33, MRPS38 and MRPS39), GST alone as pull-down control and HEK293 cell lysate as the source for anchor proteins followed by nLC/MS/MS analysis and probable PPIs of eight MRPS proteins were identified. Three PPIs from GST pull-downs and interaction between six MRPS proteins and p53 previously reported in PPI database were validated. The PPI network analysis revealed putative role in cellular processes with implications for tumourigenesis. Gene expression screening of a cancer cell line panel indicated overexpression of MRPS10 and MRPS31 in breast cancer. Co-expression module identification tool analysis of breast cancer gene expression and MRPS10 and MRPS31 PPIs revealed putative role for PPI with acyl-CoA dehydrogenase in fatty acid oxidation process regulated by brain-derived neurotrophic factor signalling pathway.
Buzz-Pollinated Crops: A Global Review and Meta-analysis of the Effects of Supplemental Bee Pollination in Tomato
Authors: Cooley Hazel , Vallejo-Marín Mario
Published: January 2021

Buzz-pollinated plants require visitation from vibration producing bee species to elicit full pollen release. Several important food crops are buzz-pollinated including tomato, eggplant, kiwi, and blueberry. Although more than half of all bee species can buzz pollinate, the most commonly deployed supplemental pollinator, Apis mellifera L. (Hymenoptera: Apidae; honey bees), cannot produce vibrations to remove pollen. Here, we provide a list of buzz-pollinated food crops and discuss the extent to which they rely on pollination by vibration-producing bees. We then use the most commonly cultivated of these crops, the tomato, Solanum lycopersicum L. (Solanales: Solanaceae), as a case study to investigate the effect of different pollination treatments on aspects of fruit quality. Following a systematic review of the literature, we statistically analyzed 71 experiments from 24 studies across different geopolitical regions and conducted a meta-analysis on a subset of 21 of these experiments. Our results show that both supplemental pollination by buzz-pollinating bees and open pollination by assemblages of bees, which include buzz pollinators, significantly increase tomato fruit weight compared to a no-pollination control. In contrast, auxin treatment, artificial mechanical vibrations, or supplemental pollination by non-buzz-pollinating bees (including Apis spp.), do not significantly increase fruit weight. Finally, we compare strategies for providing bee pollination in tomato cultivation around the globe and highlight how using buzz-pollinating bees might improve tomato yield, particularly in some geographic regions. We conclude that employing native, wild buzz pollinators can deliver important economic benefits with reduced environmental risks and increased advantages for both developed and emerging economies.
Comparative Pathogenesis of Generalist AcMNPV and Specific RanuNPV in Larvae of Rachiplusia nu (Lepidoptera: Noctuidae) Following Single and Mixed Inoculations
Authors: Decker-Franco Cecilia , Taibo Catalina B , Di Rienzo Julio A , Alfonso Victoria , Arneodo Joel D
Published: January 2021

The South American soybean pest, Rachiplusia nu (Guenée), is naturally infected by Autographa californica multiple nucleopolyhedrovirus (AcMNPV) and Rachiplusia nu nucleopolyhedrovirus (RanuNPV). We compared their pathogenicity to fourth-instar R. nu larvae, by evaluating time to death and virus spread throughout the tissues in single and mixed infections. Bioassays showed that generalist AcMNPV had a faster speed of kill than specific RanuNPV, while the mixed-virus treatment did not statistically differ from AcMNPV alone. Histopathology evidenced similar tissue tropism for both viruses, but co-inoculation resulted in mostly AcMNPV-infected cells. In sequential inoculations, however, the first virus administered predominated over the second one. Implications on baculovirus interactions and biocontrol potential are discussed.
Does human germline genome editing violate human dignity? An African perspective
Authors: Shozi Bonginkosi
Published: January 2021

It has been variously claimed that alterations to the human genome for reproductive purposes ought to be prohibited on the basis that doing so is contrary to human dignity. This claim leads to the conclusion that germline genome editing (GGE) ought to be categorically banned in all states committed to upholding human dignity as a right recognized in international human rights documents, and which has been entrenched in the constitutions of many liberal democracies. But is it the case that the right to human dignity is necessarily opposed to GGE? This paper explores this question through critical examination of the concept of human dignity in international human rights, and how it has been interpreted by individual states. Recognizing that the interpretation of human dignity is shaped by cultural context, the paper explores an African perspective on this issue, using South African constitutional jurisprudence on human dignity as an example. It concludes that when viewed through the lens of the African ethic of Ubuntu, there is no justification for a categorical prohibition on GGE, on the grounds that it is contrary to human dignity. This illustrates the need for a global discourse on the regulation on genome editing to be sensitive to varying perspectives—specifically on value-laden questions such as the interpretation of human rights.