bluuebunny/crossref_metadata_2025 huggingface dataset:
ON THE ESTIMATION OF EFFECTIVE NUMBER OF ALLELES FROM ELECTROPHORETIC DATA
Authors: Johnson George B
Published: January 2021

Estimation of the effective number of alleles in natural populations from the frequencies of electrophoretically detected alleles involves significant ambiguity, which should be explicitly considered in the estimate. For large genetic populations the ambiguity importantly affects the value of ne.
GENE-ENZYME RELATIONS OF TRYPTOPHAN MUTANTS IN STREPTOMYCES COELICOLOR A3(2)
Authors: Smithers Charles M , Engel Paulinus P
Published: January 2021

Mutations in twenty-eight tryptophan mutants of S. coelicolor A3(2) were mapped relative to the nearest flanking markers. Mutants lacking single enzymatic activities for phosphoribosyltransferase, phosphoribosylanthranilate isomerase, indodeglycerol phosphate synthase, tryptophan synthase A and tryptophan synthase B were identified.
POSITIVE SELECTION FOR MATING WITH FUNCTIONAL HETEROKARYONS IN TETRAHYMENA PYRIFORMIS
Authors: Bruns Peter J , Brussard Trudy B
Published: January 2021

Allelic assortment of Tetrahymena pyriformis makes possible the isolation of cells which contain both a heterozygous germ line nucleus and a somatic nucleus which expresses phenotypes of only one member of allelic pairs. Cycloheximide-sensitive segregants have been isolated from the vegetative progeny of cells heterozygous for a dominant mutation conferring resistance to cycloheximide; such segregants are called functional heterokaryons. Since progeny from crosses of these cells are cycloheximide-resistant, addition of the drug provides positive selection for successful exconjugants. The timing for expression of the new phenotype during conjugation is presented and used to identify what appear to be immature progeny of round one mating in genomic exclusion. Usefulness of functional heterokaryons in a number of genetic and developmental studies is discussed.
BISEXUAL MATING BEHAVIOR IN A DIPLOID OF SACCHAROMYCES CEREVISIAE: EVIDENCE FOR GENETICALLY CONTROLLED NON-RANDOM CHROMOSOME LOSS DURING VEGETATIVE GROWTH
Authors: Haber James E
Published: January 2021

A diploid strain of Saccharomyces cerevisiae has been isolated which exhabits bisexual mating behavior. The strain mates with either a or α strains with a relative mating efficiency of 1 to 2%. The efficiency of mating is correlated with the frequency with which subclones of this strain revert to a single mating type. Crosses of the bisexual diploid with a/a or α/α diploids yield bisexual segregants with a frequency of approximately 3%. Analysis of the segregation of the mating type alleles and other markers on chromosome III indicates that the primary event which leads to the bisexual phenotype is the loss of one homolog of chromosome III during vegetative growth to produce a monosomic (2n-1) diploid. Evidence is presented that the loss of chromosome I11 and possibly of other chromosomes during vegetative growth is affected by a recessive nuclear gene-her (hermaphrodite)—which is not closely linked to the mating type locus.
AN EMS-SENSITIVITY FACTOR IN MAIZE CONDITIONING ALBINO LEAF STRIPES
Authors: Efron Y
Published: January 2021

A description is given for a recessive EMS-sensitivity factor conditioning albino leaf stripes. In the homozygous condition, there is low frequency of spontaneous leaf stripes. EMS, depending on the concentration, increases markedly the frequency of the stripes in 100% of the treated plants. The effects of EMS, given to the seeds, starts to appear from the 6th to 7th leaf and persists in all the leaves throughout the life cycle of the M1 plants. Only about 20-25% of the M2 plants showed some variegation. These variegated M2 plants were not distributed at random among the different ear-to-row M2 rows.
FURTHER ANALYSIS OF COMPLEX ALLOZYME POLYMORPHISMS IN A BARLEY POPULATION
Authors: Weir B S , Allard R W , Kahler A L
Published: January 2021

New theory has recently been developed for two-locus models. In the light of this theory, an earlier analysis of esterase allozyme data from an experimental barley population has been modified to take proper account of initial gametic phase (linkage) disequilibria. The results show that the directions in which two-locus genotypic frequencies deviated from products of one-locus frequencies in this population followed those predicted by neutral descent theory. The observed departures were, however, much larger in size than predicted by the new descent measure theory, indicating that selection is operating in the population.
ULTRAVIOLET MUTAGENESIS AND ITS REPAIR IN AN ESCHERICHIA COLI STRAIN CONTAINING A NONSENSE CODON
Authors: Person Stanley , McCloskey John Allen , Snipes Wallace , Bockrath Richard C
Published: January 2021

Ultraviolet mutagenesis and its repair were studied mainly in WU36-10-89, a uvr  - strain of Escherichia coli containing a UAG mutation in a gene for leucine biosynthesis. Following ultraviolet (UV) irradiation revertants appearing with or without direct photoreactivation (PR) were classified according to the presence and type of suppressor they contained. We find UV mutation production to be quite specific. An analysis of revertants produced by UV indicates they are formed mainly from GC → AT and that the miscoding is due to a cytosine residue at the site of mutation in a cytosine-thymine (CT) dimer. We propose that the dimer serves as template during some aspects of repair replication and at the time of replication the C in the dimer directs the insertion of A in the complementary strand. We also note that C → A and T →G changes caused by a CT dimer occur much less frequently.
MEIOSIS IN MALE DROSOPHILA MELANOGASTER I. ISOLATION AND CHARACTERIZATION OF MEIOTIC MUTANTS AFFECTING SECOND CHROMOSOME DISJUNCTION
Authors: Gethmann Richard C
Published: January 2021

Two second chromosome, EMS-induced, meiotic mutants which cause an increase in second chromosome nondisjunction are described. The first mutant is recessive and causes an increase in second chromosome nondisjunction in both males and females. It causes no increase in nondisjunction of the sex chromosomes in either sex, nor of the third chromosome in females. No haplo-4-progeny were recovered from either sex. Thus, it appears that this mutant, which is localized to the second chromosome, affects only second chromosome disjunction and acts in both sexes.—The other mutant affects chromosome disjunction in males and has no effect in females. Nondisjunction occurs at the first meiotic division. Sex chromosome disjunction in the presence of this mutant is similar to that of sc4sc8, with an excess of X and nullo-XY sperm relative to Y and XY sperm. In some lines, there is an excess of nullo-2 sperm relative to diplo-2 sperm, which appears to be regulated, in part, by the Y chromosome. A normal Y chromosome causes an increase in nullo-2 sperm, where BsY does not. There is also a high correlation between second and sex chromosome nondisjunction. Nearly half of the second chromosome exceptions are also nondisjunctional for the sex chromosomes. Among the double exceptions, there is an excess of XY nullo-2 and nullo-XY diplo-2 gametes. Meiotic drive, chromosome loss and nonhomologous pairing are considered as possible explanations for the double exceptions.
GENIC VERSUS CHROMOSOMAL VARIATION IN NATURAL POPULATIONS OF DROSOPHILA SUBOBSCURA
Authors: Zouros E , Krimbas C B , Tsakas S , Loukas M
Published: January 2021

Gametic frequencies in one mainland and one island population of D. subobscura were obtained by means of extracting wild chromosomes and subsequently analyzing them for inversions and allozymes. The high degree of cytological heterogeneity which characterizes these populations is not reflected in the genetic data. Two cases of non-random association were observed among eighteen pair-wise comparisons involving gene alleles and inversions to which the locus is linked. In both cases exchange of alleles at the locus is completely suppressed by the inversions. Four cases of linkage disequilibrium were detected among eighteen pairs of loci; two of them could best be explained as transient associations generated by random drift. The results suggest that disequilibria among enzyme loci are not widespread in natural populations—Populations with a lower degree of chromosomal variation are genetically as variable as populations with a higher degree of chromosomal variation. This observation does not support the hypothesis that selection in marginal homokaryotypic populations is for specialized homozygous genotypes.
SEX DETERMINATION IN BEES. II. ADDITIVITY OF MALENESS GENES IN APIS MELLIFERA
Authors: Chaud-Netto José
Published: January 2021

Twenty-two randomly taken morphological characters were used in order to estimate the Mahalanobis generalized distance between diploid males, diploid workers, haploid males and triploid workers. It was found that adult diploid males are metamales and triploid females are slightly masculinized. These facts indicate that the maleness genes are slightly additive.
PLASMON MUTATIONS IN CYTOPLASMIC MALE-STERILE PEARL MILLET, PENNISETUM TYPHOIDES
Authors: Clement William M
Published: January 2021

Spontaneous mutations from sterile to fertile were demonstrated in four different cytoplasmic male-sterile stocks of pearl millet. One stock, ASM-3, was of African origin, and the other three, LMS-1A, ASM-5, and ASM-7, all had the same cyptoplasm of Indian origin, but differed in nuclear make-up. These reversions were shown to be plasmon mutations, rather than genic in nature. ASM-3 mutated at the lowest rate, about 0.03/100 heads. LSM-1A, ASM-5, and ASM-7 all had the same cytoplasm but mutated at the respective rates of 0.15, 0.26, and 1.02/100 heads, indicating that plasmon mutation rate is strongly influenced by the nuclear environment.
HOW MANY GENES ARE SELECTED IN POPULATIONS OF DACUS OLEAE
Authors: Tsakas S , Krimbas C B
Published: January 2021

Three natural populations of Dacus oleae have been sampled for six electrophoretically detected polymorphic genes. The distributions of the allele frequencies in the different populations were analyzed by the method suggested by Lewontin and Krakauer (1973) (the variation in space one) in order to test for selective neutrality. This method, however, which in our case showed that one or more genes are or have been subjected to selection, does not permit estimation of the number of selected loci. An improvement of this method is proposed that permits a minimum estimation of the selected genes. About a third of them seem to be selected in our material. In our case however, where a cytological analysis is not possible, genes are not differentiated from possible inversions including these genes.
Challenges in implementing emergency obstetric care (EmOC) policies: perspectives and behaviours of frontline health workers in Uganda
Authors: Mukuru Moses , Kiwanuka Suzanne N , Gibson Linda , Ssengooba Freddie
Published: January 2021

Uganda is among the sub-Saharan African Countries which continue to experience high preventable maternal mortality due to obstetric emergencies. Several Emergency Obstetric Care (EmOC) policies rolled out have never achieved their intended targets to date. To explore why upstream policy expectations were not achieved at the frontline during the MDG period, we examined the implementation of EmOC policies in Uganda by; exploring the barriers frontline implementers of EmOC policies faced, their coping behaviours and the consequences for maternal health. We conducted a retrospective exploratory qualitative study between March and June 2019 in Luwero, Iganga and Masindi districts selected based on differences in maternal mortality. Data were collected using 8 in-depth interviews with doctors and 17 midwives who provided EmOC services in Uganda’s public health facilities during the MDG period. We reviewed two national maternal health policy documents and interviewed two Ministry of Health Officials on referral by participants. Data analysis was guided by the theory of Street-Level Bureaucracy (SLB). Implementation of EmOC was affected by the incompatibility of policies with implementation systems. Street-level bureaucrats were expected to offer to their continuously increasing clients, sometimes presenting late, ideal EmOC services using an incomplete and unreliable package of inputs, supplies, inadequate workforce size and skills mix. To continue performing their duties and prevent services from total collapse, frontline implementers’ coping behaviours oftentimes involved improvization leading to delivery of incomplete and inconsistent EmOC service packages. This resulted in unresponsive EmOC services with mothers receiving inadequate interventions sometimes after major delays across different levels of care. We suggest that SLB theory can be enriched by reflecting on the consequences of the coping behaviours of street-level bureaucrats. Future reforms should align policies to implementation contexts and resources for optimal results.
Limit Shape of Perfect Matchings on Contracting Bipartite Graphs
Authors: Li Zhongyang
Published: January 2021

We consider random perfect matchings on a general class of contracting bipartite graphs by letting certain edge weights be 0 on the contracting square-hexagon lattice in a periodic way. We obtain a deterministic limit shape in the scaling limit. The results can also be applied to prove the existence of multiple disconnected liquid regions for all the contracting square-hexagon lattices with certain edge weights, extending the results proved in [ 13] for contracting square-hexagon lattices where the number of square rows in each period is either 0 or 1.
Institutional delivery and associated factors among women in Ghana: findings from a 2017–2018 multiple indicator cluster survey
Authors: Kumbeni Maxwell T , Apanga Paschal A
Published: January 2021

Background

Institutional delivery is essential in reducing maternal morbidity and mortality. We investigated the prevalence of institutional delivery and associated factors among women in Ghana.

Methods

National representative data from the 2017–2018 Ghana Multiple Indicator Cluster Survey was used for the analysis. The study included 3466 women, ages 15–49 y, who had a live birth in the last 2 y. Descriptive statistics were used to assess the prevalence of institutional delivery while multivariate logistic regression was used to assess the relationship between our variables of interest and institutional delivery.

Results

The prevalence of institutional delivery among women in Ghana was 77.89% (95% confidence interval [CI] 75.29 to 80.50). High-income households (adjusted odds ratio [aOR] 2.13 [95% CI 1.36 to 3.35]), attending antenatal care at least four times (aOR 2.37 [95% CI 1.54 to 3.65]) and knowing one's human immunodeficiency virus status (aOR 1.41 [95% CI 1.08 to 1.84]) were associated with higher odds of institutional delivery. Living in rural areas (aOR 0.43 [95% CI 0.27 to 0.67]), multiparity (aOR 0.59 [95% CI 0.41 to 0.85]) and no health insurance (aOR 0.57 [95% CI 0.44 to 0.74]) were associated with lower odds of institutional delivery.

Conclusions

The government of Ghana may need to focus on increasing health insurance utilization and antenatal care attendance in order to increase the coverage of institutional delivery.
Cognition, oxidative stress and vitamin B12 levels evaluation on patients under long-term omeprazole use
Authors: Dries Larissa Selbach , Haefliger Rochelli , Seibert Bruna Sherer , de Lima Angélica Gewehr , Cardoso Caroline de Oliveira , Perassolo Magda Susana
Published: January 2021

Objectives

To evaluate the differences concerning cognitive performance, oxidative stress and vitamin B12 levels in omeprazole users under treatment for longer than six months.

Methods

A case-control study was developed with 44 omeprazole users (OU; 81.8 % female, 66 ± 8.7 years old) and 35 nonusers (NOU; 88.6 % female, 62 ± 8.7 years old). The cognitive ability was assessed through tests approaching attention, memory and executive functions. The vitamin B12 was dosage using a chemiluminescent immunoassay and oxidative stress analysis, based on the evaluation of malondialdehyde, enzymatic activity of extracellular superoxide dismutase, glutathione peroxidase, catalase and the ferric reducing antioxidant power in plasma.

Key findings

A significant increase of the ferric reducing antioxidant power [omeprazole users (OU) group = 1690 µM ± 441 and nonusers (NOU) group = 1308 ± 616; P value=0.002] and a decrease on glutathione peroxidase levels [OU group = 0.534 (0.27–10.63) and NOU group = 71.86 (14.36–173.1); P value=0.006] were found on omeprazole users group, as well as differences on cognitive performance, with impairments on executive functions, automatic and attentional processing.

Conclusions

Long-term use of omeprazole is suggested to induce an oxidative stress condition, which causes neurotoxicity and cognitive decline.
Investors’ Attention to Corporate Governance
Authors: Iliev Peter , Kalodimos Jonathan , Lowry Michelle
Published: January 2021

Using unique data on investor views of EDGAR company filings, we document that many investors engage in governance research. However, investors’ monitoring is disproportionately focused on large firms and firms with meetings outside the busy spring proxy season. Using an instrumental variables approach that isolates the drop in governance attention during the busy proxy season, we show that governance research is related to investors’ monitoring of firms, through voice and exit. Moreover, governance research disciplines management, who, as a result, reduce investments and increase payouts. The concentration of attention results in joint monitoring of a relatively small subset of firms.
Cultivar Selection Is an Effective and Economic Strategy for Managing Charcoal Rot of Strawberry in Florida
Authors: Baggio Juliana S. , Cordova Leandro G. , Seijo Teresa E. , Noling Joseph W. , Whitaker Vance M. , Peres Natalia A.
Published: January 2021

Macrophomina phaseolina, the causal agent of charcoal rot, is a soilborne pathogen that affects strawberry crowns leading to plant wilt and collapse. Disease management involves a combination of physical, cultural, and chemical methods. Field trials were conducted for 10 consecutive Florida seasons (2010–11 to 2019–20) to determine the susceptibility of strawberry cultivars to charcoal rot and the effect of cultivar selection on disease and to estimate the economic impact of cultivar selection on disease management. Six cultivars grown commercially in Florida were chosen and grouped as highly susceptible (HS) (‘Strawberry Festival’ and ‘Treasure’), susceptible (S) (‘Florida Radiance’ and ‘Florida Beauty’), and moderately resistant (MR) (Sensation ‘Florida127’ and Winterstar ‘FL05-107’) according to their susceptibility levels. After a primary analysis of the individual trials, a network meta-analysis was conducted to estimate and compare the final disease incidence and the disease progress rate of each susceptibility group. The economic impact of charcoal rot on strawberry production and gross revenue was estimated based on plant production functions, weekly fruit prices, and disease progress over time with parameters obtained via the meta-analytical models. Disease incidence was reduced by 91.5 and 77.3%, respectively, when the MR and S cultivar groups were adopted instead of the HS group. There was a 62.5% reduction in the disease incidence when the MR group was used instead of the S group. Significant differences in disease progress rates were also observed when the MR and S groups were adopted instead of the HS group. Therefore, the adoption of more resistant cultivars is an effective strategy when incorporated into a charcoal rot integrated management program and can significantly impact growers’ revenue by reducing disease incidence, preventing yield loss, and, consequently, minimizing economic losses.
A genetic element in the SARS-CoV-2 genome is shared with multiple insect species
Authors: Tengs Torstein , Delwiche Charles F. , Monceyron Jonassen Christine
Published: January 2021

SARS-CoV-2 is a member of the subgenus Sarbecovirus and thus contains the genetic element s2m. We have extensively mined nucleotide data in GenBank in order to obtain a comprehensive list of s2m sequences both in the four virus families where s2m has previously been described and in other groups of organisms. Surprisingly, there seems to be a xenologue of s2m in a large number of insect species. The function of s2m is unknown, but our data show a very high degree of sequence conservation both in insects and in viruses and that the version of s2m found in SARS-CoV-2 has unique features, not seen in any other virus or insect strains.
Atypical chlamydoconidium-producing Trichophyton tonsurans strains from Ceará State, Northeast Brazil: investigation of taxonomy by phylogenetic analysis and biofilm susceptibility
Authors: Brilhante Raimunda Sâmia Nogueira , Paixão Germana Costa , Pereira Vandbergue Santos , Oliveira Jonathas Sales de , Maciel Juliana Maria , Pereira-Neto Waldemiro de Aquino , Lima-Neto Reginaldo Gonçalves de , Castelo-Branco Débora de Souza Collares Maia , Cordeiro Rossana de Aguiar , Sidrim José Júlio Costa , Rocha Marcos Fábio Gadelha
Published: January 2021

Chlamydoconidium-producing Trichophyton tonsurans strains isolated in Northeastern Brazil have morphological features different from the classic description of this dermatophyte species. This study investigated the phylogenetic relationship of chlamydoconidium-producing T. tonsurans strains isolated in Northeastern Brazil. Also, the effect of terbinafine and farnesol on mature biofilms of T. tonsurans strains was evaluated. The mass spectra of T. tonsurans strains were investigated by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The ITS and LSU loci regions of rDNA and the partial β-tubulin gene were sequenced and the phylogenetic tree was analysed. The effects of terbinafine and farnesol on mature T. tonsurans biofilms were evaluated through the analysis of metabolic activity, quantification of biomass and observation by scanning electron microscopy. MALDI-TOF MS spectra of the chlamydoconidium-producing T. tonsurans strains differed from the spectrum of the control strain (ATCC 28942), presenting an intense ion peak at m/z 4155 Da. Phylogenetic tree analysis showed that the chlamydoconidium-producing strains isolated in Northeastern Brazil are allocated to a single cluster, differing from strains isolated from other countries. As for mature T. tonsurans biofilms, farnesol reduced biomass and metabolic activity by 64.4 and 65.9 %, respectively, while terbinafine reduced the biomass by 66.5 % and the metabolic activity by 69 %. Atypical morphological characteristics presented by chlamydoconidium-producing T. tonsurans strains result from phenotypic plasticity, possibly for adaptation to environmental stressors. Also, farnesol had inhibitory activity against T. tonsurans biofilms, demonstrating this substance can be explored for development of promising anti-biofilm drugs against dermatophytes.
Physically asymmetric division of theC. eleganszygote ensures invariably successful embryogenesis
Authors: Jankele Radek , Jelier Rob , Gönczy Pierre
Published: January 2021

Asymmetric divisions that yield daughter cells of different sizes are frequent during early embryogenesis, but the importance of such a physical difference for successful development remains poorly understood. Here, we investigated this question using the first division ofC. elegansembryos, which yields a large AB cell and a small P1cell. We equalized AB and P1sizes using acute genetic inactivation or optogenetic manipulation of the spindle positioning protein LIN-5. We uncovered that only some embryos tolerated equalization, and that there was a size asymmetry threshold for viability. Cell lineage analysis of equalized embryos revealed an array of defects, including faster cell cycle progression in P1descendants, as well as defects in cell positioning, division orientation and cell fate. Moreover, equalized embryos were more susceptible to external compression. Overall, we conclude that unequal first cleavage is essential for invariably successful embryonic development ofC. elegans.
Complexome profiling on thelpa2mutant reveals insights into PSII biogenesis and new PSII associated proteins
Authors: Spaniol Benjamin , Lang Julia , Venn Benedikt , Schake Lara , Sommer Frederik , Mustas Matthieu , Wollman Francis-André , Choquet Yves , Mühlhaus Timo , Schroda Michael
Published: January 2021

We have identified the homolog of LOW PSII ACCUMULATION 2 (LPA2) inChlamydomonas. AChlamydomonas lpa2mutant grew slower in low light and was hypersensitive to high light. PSII maximum quantum efficiency was reduced by 38%. Synthesis and stability of newly made PSII core subunits D1, D2, CP43, and CP47 were not impaired. Complexome profiling revealed that in the mutant CP43 was reduced to ∼23%, D1, D2, and CP47 to ∼30% of wild-type levels, while small PSII core subunits and components of the oxygen evolving complex were reduced at most by factor two. PSII supercomplexes, dimers, and monomers were reduced to 7%, 26%, and 60% of wild-type levels, while RC47 was increased ∼6-fold. Our data indicate that LPA2 acts at a step during PSII assembly without which PSII monomers and especially further assemblies become intrinsically unstable and prone to degradation. Levels of ATP synthase and LHCII were 29% and 27% higher in the mutant than in the wild type, whereas levels of the cytochromeb6fcomplex were unaltered. While the abundance of PSI core subunits and antennae hardly changed, LHCI antennae were more disconnected in thelpa2mutant, presumably as an adaptive response to reduce excitation of PSI. The disconnection of LHCA2,9 together with PSAH and PSAG was the prime response, but independent and additional disconnection of LHCA1,3-8 along with PSAK occurred as well. Finally, based on co-migration profiles, we identified three novel putative PSII associated proteins with potential roles in regulating PSII complex dynamics, assembly, and chlorophyll breakdown.

One-sentence summary

We provide evidence that theChlamydomonasLPA2 homolog acts at a step in PSII biogenesis without which PSII monomers and further assemblies become unstable and prone to degradation.
Poor adult nutrition impairs learning and memory in a parasitoid wasp
Authors: Farahani Hossein Kishani , Moghadassi Yasaman , Pierre Jean-Sebastien , Kraus Stéphane , Lihoreau Mathieu
Published: January 2021

Animals have evolved cognitive abilities whose impairment can incur dramatic fitness costs. While malnutrition is known to impact brain development and cognitive functions in vertebrates, little is known in insects, whose small brain appears particularly vulnerable to environmental stressors. Here, we investigated the influence of diet quality on learning and memory in the parasitoid waspVenturia canescens. Newly emerged adults were exposed for 24h to either honey, sucrose solution 20%, sucrose solution 10%, or no food, before being conditioned in an olfactory associative learning task in which an odor (orange) was associated to a reward (host larvae). Wasps fed honey showed 3.5 times higher learning performances and 1.5 times longer memory retention times than wasps fed sucrose solutions and starved wasps. Poor diets also reduced longevity and fecundity. Our results demonstrate the importance of early adult nutrition for optimal cognitive function in these parasitoid wasps that must quickly develop olfactory memories for choosing high quality hosts for their progeny.
GENPPI: standalone software for creating protein interaction networks from genomes
Authors: Ferreira William , Lanes Gabriel , Azevedo Vasco , Santos Anderson
Published: January 2021

Motivation

Bacterial genomes are being deposited into online databases at an increasing rate. Genome annotation represents one of the first efforts to understand organisms and their diseases. Some evolutionary relationships that are capable of being annotated only from genomes are conserved gene neighbourhoods (CNs), phylogenetic profiles (PPs), and gene fusions. At present, there is no standalone software that enables networks of interactions among proteins to be created using these three evolutionary characteristics with efficient and effective results.

Results

We developed GENPPI software for theab initioprediction of interaction networks using predicted proteins from a genome. In our case study, we employed 50 genomes of the genusCorynebacterium. Based on the PP relationship, GENPPI differentiated genomes between the ovis and equi biovars of the speciesCorynebacterium pseudotuberculosisand created groups among the other species analysed. If we inspected only the CN relationship, we could not entirely separate biovars, only species. Our software GENPPI was determined to be efficient because, for example, it creates interaction networks from the central genomes of 50 species/lineages with an average size of 2200 genes in less than 40 minutes on a conventional computer. Our software is compelling because the interaction networks that it creates reflect evolutionary relationships among species and were obtained in average nucleotide identity (ANI) analyses. Additionally, this software enables the user to define how he or she intends to explore the PP and CN characteristics through various parameters, enabling the creation of customized interaction networks. For instance, users can set parameters regarding the genus, metagenome, or pangenome. In addition to the parameterization of GENPPI, it is also the user’s choice regarding which set of genomes he or she is going to study.

Availability

The source code in the Common Lisp language, binary files for different operating systems, and GENPPI software tutorials are available at {{github.com/santosardr/genppi}}.

Contact

santosardr@ufu.br

Supplementary information

Supplementary data are available atBioinformaticsonline.
A generalization of t-SNE and UMAP to single-cell multimodal omics
Authors: Do Van Hoan , Canzar Stefan
Published: January 2021

Emerging single-cell technologies profile multiple types of molecules within individual cells. A fundamental step in the analysis of the produced high-dimensional data is their visualization using dimensionality reduction techniques such as t-SNE and UMAP. We introduce j-SNE and j-UMAP as their natural generalizations to the joint visualization of multimodal omics data. Our approach automatically learns the relative contribution of each modality to a concise representation of cellular identity that promotes discriminative features but suppresses noise. On eight datasets, j-SNE and j-UMAP produce unified embeddings that better agree with known cell types and that harmonize RNA and protein velocity landscapes. j-SNE and j-UMAP are available in the JVis Python package.
Global transcriptome analysis ofStenotrophomonas maltophiliain response to growth at human body temperature
Authors: Patil Prashant P. , Kumar Sanjeet , Kaur Amandeep , Midha Samriti , Bansal Kanika , Patil Prabhu B.
Published: January 2021

Stenotrophomonas maltophilia(Smal) is a typical example of an environmental originated opportunistic human pathogen, which can thrive at different habitats including the human body and can cause a wide range of infections. It must cope with heat stress during transition from the environment to the human body as the physiological temperature of the human body (37 ◻) is higher than environmental niches (22-30 ◻). Interestingly,S. rhizophilaa phylogenetic neighbour of Smal within genusStenotrophomonasis unable to grow at 37 ◻. Thus, it is crucial to understand how Smal is adapted to human body temperature, which could suggest its evolution as an opportunistic human pathogen. In this study, we have performed comparative transcriptome analysis ofS. maltophiliagrown at 28 ◻ and 37 ◻ as temperature representative for environmental niches and human body respectively. RNA-Seq analysis revealed several interesting findings showing alterations in gene expression levels at 28 ◻ and 37 ◻, which can play an important role during infection. We have observed downregulation of genes involved in cellular motility, energy production and metabolism, replication and repair whereas upregulation of VirB/D4 Type IV secretion system, aerotaxis, cation diffusion facilitator family transporter and LacI family transcriptional regulators at 37 ◻. Microscopy and plate assays corroborated altered expression of genes involved in motility. The results obtained enhance our understanding of the strategies employed byS. maltophiliaduring adaptation towards the human body.

Impact statement

Stenotrophomonas maltophilia(Smal) is a WHO listed multidrug resistant nosocomial pathogen. Interestingly,S. maltophiliaspecies can grow both at 28 ◻ and 37 ◻ unlike its closest taxonomic relative, i.e.,S. rhizophilaand also majority species belonging this genus. Hence this ability to grow at 37 ◻, i.e., human body temperature might have played key role in the unique success and emergence of this species as opportunistic human pathogen. Using transcriptome sequencing, we have identified set of genes which are differentially regulated at 37 ◻ and investigated their evolutionary history. This study has revealed regulation of genes involved in motility, metabolism, energy, replication, transcription, aerotaxis and a type IV secretion system might have a role in successful adaption to a distinct lifestyle. The findings will be helpful in further systematic studies on understanding and management of an emerging human pathogen such as Smal.
KDM1A maintains genome-wide homeostasis of transcriptional enhancers
Authors: Agarwal Saurabh , Bonefas Katherine M. , Garay Patricia M. , Brookes Emily , Murata-Nakamura Yumie , Porter Robert S. , Macfarlan Todd S. , Ren Bing , Iwase Shigeki
Published: January 2021

Transcriptional enhancers enable exquisite spatiotemporal control of gene expression in metazoans. Enrichment of monomethylation of histone H3 lysine 4 (H3K4me1) is a major chromatin signature of transcriptional enhancers. Lysine (K)-specific demethylase 1A (KDM1A, also known as LSD1), an H3K4me2/me1 demethylase, inactivates stem-cell enhancers during the differentiation of mouse embryonic stem cells (mESCs). However, its role in undifferentiated mESCs remains obscure. Here, we show that KDM1A actively maintains the optimal enhancer status in both undifferentiated and lineage-committed cells. KDM1A occupies a majority of enhancers in undifferentiated mESCs. KDM1A levels at enhancers exhibit clear positive correlations with its substrate H3K4me2, H3K27ac, and transcription at enhancers. In Kdm1a-deficient mESCs, a large fraction of these enhancers gains additional H3K4 methylation, which is accompanied by increases in H3K27 acetylation and increased expression of both enhancer RNAs (eRNAs) and target genes. In postmitotic neurons, loss of KDM1A leads to premature activation of neuronal activity-dependent enhancers and genes. Taken together, these results suggest that KDM1A is a versatile regulator of enhancers and acts as a rheostat to maintain optimal enhancer activity by counterbalancing H3K4 methylation at enhancers.
7,8-Dimethyl-11H-indeno[1,2-b]quinoxalin-11-one
Authors: Chen Lin , Hu Jin , Sun Hong-Shun
Published: January 2021

In the title compound, C17H12N2O, the mean planes of the indene ring and quinoxaline system (r.m.s. deviations = 0.0131 and 0.0082 Å) are approximately parallel to one another, making a dihedral angle of 1.2 (5)°. This means that the indeno[1,2-b]quinoxaline ring is almost in the same plane (r.m.s. deviation = 0.0181 Å).
Cultural information needs of long-settled immigrants, their descendants and family members: use of collective and personal information sources about the home country
Authors: Krtalic Maja
Published: January 2021

Purpose

This paper presents findings from a study that explored why and how long-settled immigrants, their descendants and family members seek and use information about their country of origin and how they manage personal information about their cultural heritage legacy.

Design/methodology/approach

15 semi-structured interviews were conducted with participants from the Croatian community in New Zealand.

Findings

The main findings reveal two categories of information needs related to a home country: internally motivated and externally motivated. Information is accessed through a network of family and friends, cultural societies and embassies. These information sources are perceived as reliable and trustworthy, and able to offer an interpretation of information along with access to information. The findings highlight the value of personal collections as information sources and the impact of personal information management practices on preserving and sharing information about one's cultural heritage.

Originality/value

This article contributes to the discussion about information needs and practices of immigrant communities by offering arguments that focus on (1) long-settled immigrants, their descendants and family members, and (2) seeking information about home country culture and heritage, and (3) the role of personal collections and personal information management in maintaining personal cultural heritage. The results of this study may be of use to libraries, archives and museums in designing and offering their services to expatriates of their country and immigrants in their country, and to the wider information management sector developing services in personal information management.
Labour supply responses to financial wealth shocks: evidence from Italy
Authors: Bottazzi Renata , Trucchi Serena , Wakefield Matthew
Published: January 2021

We look at how strongly shocks to wealth affect labour supply, using Italian data. We use asset price shocks to provide a measure of wealth changes that is exogenous to the household's saving and labour supply. Results point to significant effects of wealth on hours of work, whether agents leave their jobs and labour earnings. The magnitude of these effects can be substantial – for example, for individuals who suffered larger wealth losses during the financial crisis. Responses are similar for men and women on average, but older working‐age individuals have relatively strong responses that drive the population results. Short‐run effects are somewhat persistent.
An Evaluation of Remotely Sensed and In Situ Data Sufficiency for SGMA‐Scale Groundwater Studies in the Central Valley, California
Authors: Kim Kyra H. , Liu Zhen , Rodell Matthew , Beaudoing Hiroko , Massoud Elias , Kitchens James , Dudek Marissa , Saylor Patrick , Corcoran Forrest , Reager John T.
Published: January 2021

California’s Central Valley aquifer is a critical freshwater resource for the state, providing drinking water to 6.5 million residents and irrigation water for more than half of the nation’s produce. Increasing demands have led to a steady decline of aquifer water levels, leading to irreversible compaction and land subsidence. The Sustainable Groundwater Management Act of California (SGMA), instituted in 2014, requires high‐priority regions to establish sustainability plans by 2020–2022 that mitigate groundwater depletion and land subsidence. Many regions within the Central Valley lack groundwater monitoring wells or continuous well data, rendering in situ monitoring challenging. When combined with other data, National Aeronautics and Space Administration’s Gravity Recovery and Climate Experiment (GRACE) and GRACE Follow‐On missions provide valuable information about groundwater storage changes at a subbasin scale. Interferometric Synthetic Aperture Radar measurements can map land subsidence, and Global Positioning System can be used to estimate crustal uplift. Yet, all of these measurements have differences in resolution, coverage, discretization, and record length. Here we assess the various datasets that are potentially useful for Central Valley subbasin groundwater monitoring and provide an analysis of gaps and other issues in regard to their suitability for SGMA‐related analysis. Finally, we offer the next steps and recommendations on data treatment and integration.
Comparative analysis of the Memorial Sloan Kettering Bowel Function Instrument and the Low Anterior Resection Syndrome Questionnaire for assessment of bowel dysfunction in rectal cancer patients after low anterior resection
Authors: Quezada‐Diaz Felipe F. , Elfeki Hossam , Emmertsen Katrine J. , Pappou Emmanouil P. , Jimenez‐Rodriguez Rosa , Patil Sujata , Laurberg Søren , Garcia‐Aguilar Julio
Published: January 2021

Aim

Neoadjuvant therapy and total mesorectal excision (TME) for rectal cancer are associated with bowel dysfunction symptoms known as low anterior resection syndrome (LARS). Our study compared the only two validated instruments—the LARS Questionnaire (LARS‐Q) and the Memorial Sloan Kettering Bowel Function Instrument (MSK‐BFI)—in rectal cancer patients undergoing sphincter‐preserving TME.

Methods

One hundred and ninety patients undergoing sphincter‐preserving TME for Stage I–III rectal cancer completed the MSK‐BFI and LARS‐Q simultaneously at a median time of 12 (range 1–43) months after restoration of bowel continuity. Associations between the MSK‐BFI total/subscale scores and the LARS‐Q score were investigated using Spearman rank correlation (r s). Discriminant validity for the two questionnaires was assessed, and the questionnaires were compared with the European Quality of Life Instrument.

Results

Major LARS was identified in 62% of patients. The median MSK‐BFI scores for no LARS, minor LARS and major LARS were 76.5, 70 and 57, respectively. We found a strong association between MSK‐BFI and LARS‐Q (r s −0.79). The urgency/soilage subscale (r s −0.7) and the frequency subscale (rs −0.68) of MSK‐BFI strongly correlated with LARS‐Q. Low correlation was observed between the MSK‐BFI diet subscale and LARS‐Q (r s −0.39). On multivariate analysis, both questionnaires showed worse bowel function in patients with distal tumours. A low to moderate correlation with the European Quality of Life Instrument was observed for both questionnaires.

Conclusions

The MSK‐BFI and LARS‐Q showed good correlation and similar discriminant validity. As the LARS‐Q is easier to complete, it may be considered the preferred tool to screen for bowel dysfunction.
In children and young people with type 1 diabetes using Pump therapy, an additional 40% of the insulin dose for a high‐fat, high‐protein breakfast improves postprandial glycaemic excursions: A cross‐over trial
Authors: Smith Tenele A. , Smart Carmel E. , Fuery Michelle E. J. , Howley Peter P. , Knight Brigid A. , Harris Mark , King Bruce R.
Published: January 2021

Aim

To determine the insulin requirement for a high‐fat, high‐protein breakfast to optimise postprandial glycaemic excursions in children and young people with type 1 diabetes using insulin pumps.

Methods

In all, 27 participants aged 10–23 years, BMI <95th percentile (2–18 years) or BMI <30 kg/m2 (19–25 years) and HbA1c ≤64 mmol/mol (≤8.0%) consumed a high‐fat, high‐protein breakfast (carbohydrate: 30 g, fat: 40 g and protein: 50 g) for 4 days. In this cross‐over trial, insulin was administered, based on the insulin‐to‐carbohydrate ratio (ICR) of 100% (control), 120%, 140% and 160%, in an order defined by a randomisation sequence and delivered in a combination bolus, 60% ¼ hr pre‐meal and 40% over 3 hr. Postprandial sensor glucose was assessed for 6 hr.

Results

Comparing 100% ICR, 140% ICR and 160% ICR resulted in significantly lower 6‐hr areas under the glucose curves: mean (95%CI) (822 mmol/L.min [605,1039] and 567 [350,784] vs 1249 [1042,1457], p ≤ 0.001) and peak glucose excursions (4.0 mmol/L [3.0,4.9] and 2.7 [1.7,3.6] vs 6.0 [5.0,6.9],p < 0.001). Rates of hypoglycaemia for 100%‐160% ICR were 7.7%, 7.7%, 12% and 19% respectively (p ≥ 0.139). With increasing insulin dose, a step‐wise reduction in mean glucose excursion was observed from 1 to 6 hr (p = 0.008).

Conclusions

Incrementally increasing the insulin dose for a high‐fat, high‐protein breakfast resulted in a predictable, dose‐dependent reduction in postprandial glycaemia: 140% ICR improved postprandial glycaemic excursions without a statistically significant increase in hypoglycaemia. These findings support a safe, practical method for insulin adjustment for high‐fat, high‐protein meals that can be readily implemented in practice to improve postprandial glycaemia.
Green Flags and headache: A concept study using the Delphi method
Authors: Pohl Heiko , Do Thien Phu , García‐Azorín David , Hansen Jakob Møller , Kristoffersen Espen Saxhaug , Nelson Sarah E. , Obermann Mark , Sandor Peter S. , Schankin Christoph J. , Schytz Henrik Winther , Sinclair Alexandra , Schoonman Guus G. , Gantenbein Andreas R.
Published: January 2021

Objective

The aim of this study was to collect and rate Green Flags, that is, symptoms or pieces of information indicating that a patient is more likely to suffer from a primary than from a secondary headache.

Background

When assessing headaches, a central question to be answered is whether the pain is primary or secondary to another disorder. To maximize the likelihood of a correct diagnosis, relevant signs and symptoms must be sought, identified, and weighed against each other.

Methods

The project was designed as a Delphi study. In the first round, an expert panel proposed green flags that were rated anonymously in two subsequent rounds. Proposals with an average rating of 4.0 and higher on a scale from 0 to 5 reached consensus.

Results

Five Green Flags reached consensus: (i) “The current headache has already been present during childhood”; (ii) “The headache occurs in temporal relationship with the menstrual cycle”; (iii) “The patient has headache‐free days“; (iv) “Close family members have the same headache phenotype”; and (v) “Headache occurred or stopped more than one week ago.”

Conclusions

We propose five Green Flags for primary headache disorders. None being a pathognomonic sign, we recommend searching for both Green Flags and Red Flags. If both are present, a secondary headache should be suspected. Overall, the application of the Green Flag concept in clinical practice is likely to increase diagnostic accuracy and improve diagnostic resource allocation. Prospective studies in clinical populations should be conducted to validate these Green Flags.
Formononetin ameliorates muscle atrophy by regulating myostatin‐mediated PI3K/Akt/FoxO3a pathway and satellite cell function in chronic kidney disease
Authors: Liu Lingyu , Hu Rong , You Haiyan , Li Jingjing , Liu Yangyang , Li Qiang , Wu Xiaohui , Huang Jiawen , Cai Xiangsheng , Wang Mingqing , Wei Lianbo
Published: January 2021

Muscle atrophy is a common complication in chronic kidney disease (CKD). Inflammation and myostatin play important roles in CKD muscle atrophy. Formononetin (FMN), which is a major bioactive isoflavone compound in Astragalus membranaceus, exerts anti‐inflammatory effects and the promotion of myogenic differentiation. Our study is based on myostatin to explore the effects and mechanisms of FMN in relation to CKD muscle atrophy. In this study, CKD rats and tumour necrosis factor α (TNF‐α)‐induced C2C12 myotubes were used for in vivo and in vitro models of muscle atrophy. The results showed that FMN significantly improved the renal function, nutritional status and inflammatory markers in CKD rats. Values for bodyweight, weight of tibialis anterior and gastrocnemius muscles, and cross‐sectional area (CSA) of skeletal muscles were significantly larger in the FMN treatment rats. Furthermore, FMN significantly suppressed the expressions of MuRF‐1, MAFbx and myostatin in the muscles of CKD rats and the TNF‐α‐induced C2C12 myotubes. Importantly, FMN significantly increased the phosphorylation of PI3K, Akt, and FoxO3a and the expressions of the myogenic proliferation and differentiation markers, myogenic differentiation factor D (MyoD) and myogenin in muscles of CKD rats and the C2C12 myotubes. Similar results were observed in TNF‐α‐induced C2C12 myotubes transfected with myostatin‐small interfering RNA (si‐myostatin). Notably, myostatin overexpression plasmid (myostatin OE) abolished the effect of FMN on the phosphorylation of the PI3K/Akt/FoxO3a pathway and the expressions of MyoD and myogenin. Our findings suggest that FMN ameliorates muscle atrophy related to myostatin‐mediated PI3K/Akt/FoxO3a pathway and satellite cell function.