bluuebunny/crossref_metadata_2025 huggingface dataset:
Y chromosome loops in Drosophila melanogaster.
Authors: Bonaccorsi S , Pisano C , Puoti F , Gatti M
Published: January 2021

Primary spermatocyte nuclei of fixed testes of Drosophila melanogaster exhibit three large clusters of thread-like structures, each consisting of two long, continuous, loop-shaped filaments. No comparable intranuclear structures are observed in spermatogonia, secondary spermatocytes or spermatids. The threads begin to form in young spermatocytes, grow throughout spermatocyte development, reach their maximum size in mature spermatocytes and disintegrate prior to meiotic metaphase I. The presence of each cluster of threads depends upon the presence of a specific region of the Y chromosome; when this region is deleted the cluster is absent, and when it is duplicated the cluster is also duplicated. Together these observations strongly suggest that these structures represent giant Y chromosome lampbrush-like loops analogous to those described in Drosophila hydei. Two antibodies, one polyclonal and one monoclonal, differentially react with the three loops of D. melanogaster. Moreover, two of these loops are specifically stained by Giemsa at pH 10. By indirect immunofluorescence with these antibodies followed by Giemsa staining, each loop can be unambiguously identified and its presence and normality readily assessed. This enabled us to perform fine mapping experiments to determine the relationships between the Y chromosome fertility factors and the loops. The loop-forming sites map within the kl-5, kl-3 and ks-1 fertility factors. Regions h3 and h21 of the Y chromosome correspond to the loop-forming sites of kl-5 and ks-1, respectively. Each of these regions contains about 1300 kb of DNA and spans about one-third of its locus. The loop-forming site of the kl-3 locus is coextensive with region h7-h9 which contains about 4300 kb of DNA and corresponds to the minimum physical size of this locus. These data suggest that each loop is an integral part of a different fertility factor, representing the cytological manifestation of its activity in primary spermatocytes. The kl-2, kl-1 and ks-2 fertility regions do not produce any visible intranuclear structure and do not affect the kl-5, kl-3 and ks-1 loops. Thus, these loci may either not form loops at all or produce loop-like structures that we are unable to see because they are physically minute, destroyed by our fixation procedure, or both.
RFLP Maps Based on a Common Set of Clones Reveal Modes of Chromosomal Evolution in Potato and Tomato.
Authors: Bonierbale M W , Plaisted R L , Tanksley S D
Published: January 2021

Potato (Solanum tuberosum L.) and tomato (Lycopersicon esculentum) are members of the Solanaceae (nightshade family) and have the same basic chromosome number (x = 12). However, they cannot be cross-hybridized and, until now, it was unknown how conserved the gene order might be between these two species. We report herein the construction of a genetic linkage map of potato chromosomes based on genomic and cDNA clones from tomato. The potato map was drawn from segregation data derived from the interspecific cross S. phureja X (S. tuberosum X S. chacoense) (2n = 2x = 24), and consists of 135 markers defining 12 distinct linkage groups. Nearly all of the tomato probes tested hybridized to potato DNA, and in most cases, the copy number of the employed clones was the same in both species. Furthermore, all clones mapped to the same linkage group in both species. For nine chromosomes, the order of loci appears to be identical in the two species, while for the other three, intrachromosomal rearrangements are apparent, all of which appear to be paracentric inversions with one breakpoint at or near the centromere. These results are consistent with cytogenetic theory, previously untested in plants, which predicts that paracentric inversions will have the least negative effect on fitness and thus be the most likely form of chromosomal rearrangements to survive through evolutionary time. Linkage maps based on a common set of restriction fragment length polymorphism markers provide a basis for uniting the previously separate disciplines of tomato and potato genetics. Using these maps, it may now be possible to test theories about homologies or orthologies of other genes, including those coding for disease resistance and stress tolerances.
Ribosomal gene structure, variation and inheritance in maize and its ancestors.
Authors: Zimmer E A , Jupe E R , Walbot V
Published: January 2021

We have examined the structure of nuclear genes coding for ribosomal RNAs in maize and its wild relatives, the teosintes and Tripsacum. Digestion of the rDNA (genes coding for 18S, 5.8S and 26S RNAs) with 15 restriction endonucleases (with six base pair recognition sites) yields essentially a single map for the approximately 10,000 repeat units within an individual plant or species. Both length and site variation were detected among species and were concentrated in the intergenic spacer region of the rDNA repeat unit. This result is in agreement with patterns of rDNA change observed among wheat and its relatives (Triticeae), and among vertebrate species. Digestion of these nuclear DNAs with BamHI and subsequent hybridization with a 5S RNA gene-specific probe allowed determination of the size of the 5S gene repeat unit in maize, teosintes, and Tripsacum. Groupings in the genus Zea were characterized by distinct repeat unit types five Tripsacum species examined shared a 260 base pair major repeat unit type. Additionally, several other restriction endonuclease cleavage patterns differentiated among the 5S DNAs within the genus Zea. The rDNA and 5S DNA restriction site variation among the species can be interpreted phylogenetically and agrees with biochemical, karyotypic, and morphological evidence that places maize closest to the Mexican teosintes. For both gene arrays, contributions from each parental genome can be detected by restriction enzyme analysis of progeny from crosses between maize and two distantly related teosintes, Zea luxurians or Zea diploperennis, but certain teosinte arrays were underrepresented in some of the hybrids.
Comparison of non-mutant and mutant waxy genes in rice and maize.
Authors: Okagaki R J , Wessler S R
Published: January 2021

The waxy gene, which is responsible for the synthesis of amylose in endosperm and pollen, is genetically well characterized in many grasses including maize and rice. Homology between the previously cloned maize waxy gene and the rice gene has facilitated our cloning of a 15-kb HindIII fragment that contains the entire rice gene. A comparison of the restriction maps of the maize and rice genes indicates that many restriction sites within translated exons are conserved. In addition, the rice gene encodes a 2.4-kb transcript that programs the in vitro synthesis of a 64-kD pre-protein which is efficiently precipitated with maize waxy antisera. We demonstrate that these gene products are altered in rice strains containing mutant waxy genes. Southern blot analysis of 16 rice strains, ten containing waxy mutations, reveals that the waxy gene and flanking restriction fragments are virtually identical. These results contrast dramatically with the high level of insertions and deletions associated with restriction fragment length polymorphism and spontaneous mutations among the waxy alleles of maize.
A cladistic analysis of phenotype associations with haplotypes inferred from restriction endonuclease mapping. II. The analysis of natural populations.
Authors: Templeton A R , Sing C F , Kessling A , Humphries S
Published: January 2021

Genes that code for products involved in the physiology of a phenotype are logical candidates for explaining interindividual variation in that phenotype. We present a methodology for discovering associations between genetic variation at such candidate loci (assayed through restriction endonuclease mapping) with phenotypic variation at the population level. We confine our analyses to DNA regions in which recombination is very rare. In this case, the genetic variation at the candidate locus can be organized into a cladogram that represents the evolutionary relationships between the observed haplotypes. Any mutation causing a significant phenotypic effect should be imbedded within the same historical structure defined by the cladogram. We showed, in the first paper of this series, how to use the cladogram to define a nested analysis of variance (NANOVA) that was very efficient at detecting and localizing phenotypically important mutations. However, the NANOVA of haplotype effects could only be applied to populations of homozygous genotypes. In this paper, we apply the quantitative genetic concept of average excess to evaluate the phenotypic effect of a haplotype or group of haplotypes stratified and contrasted according to the nested design defined by the cladogram. We also show how a permutational procedure can be used to make statistical inferences about the nested average excess values in populations containing heterozygous as well as homozygous genotypes. We provide two worked examples that investigate associations between genetic variation at or near the Alcohol dehydrogenase (Adh) locus and Adh activity in Drosophila melanogaster, and associations between genetic variation at or near some apolipoprotein loci and various lipid phenotypes in a human population.
Activation of silent genes by transposons Tn5 and Tn10.
Authors: Wang A , Roth J R
Published: January 2021

The presence of transposons Tn10 or Tn5 in the genome increases the frequency with which a silent (promoter-less) gene (hisD) is mutationally activated. The activation frequency is increased 5-25-fold by Tn10 and 30-90-fold by Tn5. Activation of the hisD gene is achieved by transposition of the entire transposon or one of its flanking insertion sequences to a region just upstream of the silent gene, between a Rho-dependent termination site in the adjacent hisG gene and the hisD gene. For both Tn5 and Tn10 the component insertion sequences were found to transpose much more frequently than the entire composite element. Transposons Tn5 and Tn10 have previously been shown to carry promoters which direct transcripts into sequences adjacent to their insertion sites.
Genetic analysis of the fungus, Bremia lactucae, using restriction fragment length polymorphisms.
Authors: Hulbert S H , Ilott T W , Legg E J , Lincoln S E , Lander E S , Michelmore R W
Published: January 2021

Restriction fragment length polymorphisms (RFLPs) were developed as genetic markers for Bremia lactucae, the biotrophic Oomycete fungus which causes lettuce downy mildew. By using 55 genomic and cDNA probes, a total of 61 RFLP loci were identified among three heterothallic isolates of B. lactucae. Of these 61 RFLP loci, 53 were heterozygous in at least one of the three strains and thus were informative for linkage analysis in at least one of two F1 crosses that were performed. Analysis of the cosegregation of these 53 RFLPs, eight avirulence loci and the mating type locus allowed the construction of a preliminary genetic linkage map consisting of 13 small linkage groups. Based on the extent of linkage detected among probes, the genome of B. lactucae can be estimated to be approximately 2000 cM. Linkage was detected between a RFLP locus and an avirulence gene, providing a potential starting point for chromosome walking to clone an avirulence gene. The high frequency of DNA polymorphism in naturally occurring isolates and the proper Mendelian segregation of loci detected by low copy number probes indicates that it will be possible to construct a detailed genetic map of B. lactucae using RFLPs as markers. The method of analysis employed here should be applicable to many other outbreeding, heterozygous species for which defined inbred lines are not available.
GENE TRANSFER IN CAULOBACTER CRESCENTUS: POLARIZED INHERITANCE OF GENETIC MARKERS
Authors: Newton Austin , Allebach Eileen
Published: January 2021

Recombination frequencies were determined for 15 independently isolated auxotrophs of C. crescentus crossed pairwise in all possible combinations. The results indicate that the mutants may be grouped into at least two types: "fertile" strains, which recombine with all other mutants at frequencies ranging from less than 10-6 to 3 × 10-2, and "nonfertile" strains which recombine with fertile strains at high frequencies and with other nonfertile strains at low or negligible frequencies. Several lines of evidence indicate a polarized inheritance of markers. Two of these are (1) the preferential inheritance of unselected markers from the nonfertile parent in fertile × nonfertile crosses, and (2) the consistent ordering of markers based on the frequency at which the mutants recombine with each of the three fertile strains. Although the evidence is not conclusive at this point, the results are most consistent with conjugation as the mechanism of gene transfer in these bacteria.
HETEROKARYON INCOMPATIBILITY GENES IN NEUROSPORA CRASSA DETECTED USING DUPLICATION-PRODUCING CHROMOSOME REARRANGEMENTS
Authors: Mylyk Orest M
Published: January 2021

Evidence is presented for five or six previously undetected heterokaryon incompatibility (het) loci, bringing to about ten the number of such genes known in Neurospora crassa. The genes were detected using chromosome duplications (partial diploids), on the basis of properties previously known for het genes in duplications. Duplications homozygous for het genes are usually normal in growth and morphology, whereas those heterozygous are strikingly different. The heterozygotes are inhibited in their initial growth, produce brown pigment on appropriate medium, and later "escape" from their inhibition, as a result of somatic events, to produce wild-type growth.—Five normal-sequence strains were crossed to 14 duplication-producing chromosome rearrangements, and the duplication progeny were examined for properties characteristic of duplications heterozygous for known het genes. Each cross produced duplications for a specific region of the genome, depending on the rearrangement. Normal-sequence strains were wild types from nature, chosen from diverse geographic locations to serve as sources of genetic variation.—The duplication method was very effective. Most of the longer duplications uncovered het genes. The genes are: het-5 (on linkage group IR, in the region covered by duplications produced using rearrangement T(IR→VIR)NM103), het-6 (on IIL, covered by T(IIL→VI)P2869 and T(IIL→IIIR)AR18 duplications), het-7 (tentatively assigned to IIIR, T(IIIR→VIL)D305), het-8 (VIL, T(VIL→IR)T39M777), het-9 (VIR, T(VIR→IVR)AR209), and het-10 (VIIR, T(VIIR→IL)5936).
MUTATION OF A HETEROTHALLIC STRAIN TO HOMOTHALLISM
Authors: Hopper Anita K , Hall Benjamin D
Published: January 2021

Upon mutagenesis, a heterothallic αα diploid strain mutated to homothallism. The gene confering homothallism is nuclear, recessive, and unlinked to mating type. This gene is not allelic to the HO gene, which is responsible for previously described instances of homothallism in yeast. We have designated this new gene for homothallism as cmt (change of mating type).
MACRONUCLEAR GENETICS OF TETRAHYMENA. II. MACRONUCLEAR LOCATION OF SOMATIC MUTATIONS TO CYCLOHEXIMIDE RESISTANCE
Authors: Orias Eduardo , Newby Candace J
Published: January 2021

Somatic cycloheximide-resistant mutants of syngen 1 of Tetrahymena pyriformis were isolated and genetically characterized. Two properties of the mutants were independently examined: (a) The transmission of the mutant phenotype during conjugation and (b) the kinetics of phenotypic assortment during vegetative propagation. The results of both studies strongly support the idea that these somatic mutations have a macronuclear location. The kinetics of assortment are consistent with the idea that the syngen 1 macronucleus contains about 45 assorting genetic units. The sib-selection method employed here, used in conjunction with the analysis of assortment kinetics and a previously described test for randomness of distribution, provides a probe of macronuclear genetics applicable to many ciliates, including those in which conjugation is not known to occur or is not under experimental control.
PATERNAL LOSS (PAL): A MEIOTIC MUTANT IN DROSOPHILA MELANOGASTER CAUSING LOSS OF PATERNAL CHROMOSOMES
Authors: Baker Bruce S
Published: January 2021

The effects of a male-specific meiotic mutant, paternal loss (pal), in D. melanogaster have been examined genetically. The results indicate the following. (1) When homozygous in males, pal can cause loss, but not nondisjunction, of any chromosome pair. The pal-induced chromosome loss produces exceptional progeny that apparently failed to receive one, or more, paternal chromosomes and, in addition, mosaic progeny during whose early mitotic divisions one or more paternal chromosomes were lost. (2) Only paternally derived chromosomes are lost. (3) Mitotic chromosome loss can occur in homozygous pal  + progeny of pal males. (4) Chromosomes differ in their susceptibility to pal-induced loss. The site responsible for the insensitivity vs. sensitivity of the X chromosome to pal mapped to the basal region of the X chromosome at, or near, the centromere. From these results, it is suggested that pal  + acts in male gonia to specify a product that is a component of, or interacts with, the centromeric region of chromosomes and is necessary for the normal segregation of paternal chromosomes. In the presence of pal, defective chromosomes are produced and these chromosomes tend to get lost during the early cleavage divisions of the zygote. (5) The loss of heterologous chromosome pairs is not independent; there are more cases of simultaneous loss of two chromosomes than expected from independence. Moreover, an examination of cases of simultaneous somatic loss of two heterologs reveals an asymmetry in the early mitotic divisions of the zygote such that when two heterologs are lost at a somatic cleavage division, almost invariably one daughter nucleus fails to get either, and the other daughter nucleus receives its normal chromosome complement. It is suggested that this asymmetry is not a property of pal but is rather a normal process that is being revealed by the mutant. (6) The somatic loss of chromosomes in the progeny of pal males allows the construction of fate maps of the blastoderm. Similar fate maps are obtained using data from gynandromorphs and from marked Y chromosome (nonsexually dimorphic) mosaics.
TEMPERATURE-SENSITIVE CELL-LETHAL MUTANTS OF DROSOPHILA: ISOLATION AND CHARACTERIZATION
Authors: Arking Robert
Published: January 2021

One hundred and twenty-one temperature-sensitive (ts) sex-linked lethals were screened by means of X-ray-induced somatic crossing over to determine if any were ts cell-lethal mutants. Cell-lethal mutations were identified by their ability to block the development of homozygous clones when raised under restrictive conditions (29°). Twenty-two ts cell-lethal mutants were isolated and categorized into three classes, depending upon the patterns of damage observed in larval and imaginal tissues. The phenotypes produced by these mutations ranged from those which affected only a limited set of structures (i.e., genital discs only) to those which affected diverse tissues at all stages of the life cycle. Each mutation has its own characteristic time-dependent pattern, frequency, and type of damage. All the mutations affect imaginal tissue, but only one-third of the mutations affect both larval and imaginal tissue. The fastest-acting lethals need 15 hours at the restrictive temperature to kill the cells and the slowest-acting lethals require at least 48 hours. By choosing the appropriate mutant and by manipulating the times of exposure to the restrictive temperature, it has proven possible to produce duplications and deficiencies in specific structures of the adult. A mechanism by which lethality might yield such structures is suggested. In addition, 15 of the mutants are ts female sterile mutants. Only one of these 15 mutants can recover its fertility when shifted back down to the permissive temperature (22°).
GENETIC DISSECTION OF SEGREGATION DISTORTION II. MECHANISM OF SUPPRESSION OF DISTORTION BY CERTAIN INVERSIONS
Authors: Hartl Daniel L
Published: January 2021

In(2L+2R)Cy and In(2LR)Pm2 are inversion-bearing chromosomes, the former carrying a paracentric inversion in each arm and the latter carrying a long pericentric. Both chromosomes produce normal segregation ratios when present in heterozygous males with certain segregation distorter chromosomes. The apparent suppression of distortion by these chromosomes was long attributed to a failure of synapsis, but this hypothesis has fallen out of favor recently because a large number of chromosome aberrations, particularly translocations and inversions, suppress distortion even though their breakpoints fall into no recognizable pattern. Although failure of synapsis does not appear to be the mechanism of suppression of distortion, what is responsible for the suppression remains unknown. In this paper it is shown that In(2L+2R)Cy and In(2LR)Pm2 suppress segregation distortion because they carry Rsp, a component of the segregation distorter system that renders a chromosome insensitive to distortion. Both chromosomes induce "suicide" of chromosomes carrying Sd Rsp+.
Democracy and sovereignty: Afterword to the Foreword by Neil Walker
Authors: Rubinelli Lucia
Published: January 2021

Neil Walker’s analysis in his Foreword article of the centrality of sovereignty to contemporary politics is compelling, in that it reveals the extent to which this concept underpins current theorizing about the state and its legal structure. In this Afterword, I explore two questions that arise from Walker’s analysis: why has sovereignty remained so central to our legal and political thinking? And is the centrality of sovereignty desirable? I suggest that the answer to both questions may have to do with the connection tying modern understandings of sovereignty with the democratic principle of popular power.
Leveraging data visualization and a statewide health information exchange to support COVID-19 surveillance and response: Application of public health informatics
Authors: Dixon Brian E , Grannis Shaun J , McAndrews Connor , Broyles Andrea A , Mikels-Carrasco Waldo , Wiensch Ashley , Williams Jennifer L , Tachinardi Umberto , Embi Peter J
Published: January 2021

Objective

We sought to support public health surveillance and response to coronavirus disease 2019 (COVID-19) through rapid development and implementation of novel visualization applications for data amalgamated across sectors.

Materials and Methods

We developed and implemented population-level dashboards that collate information on individuals tested for and infected with COVID-19, in partnership with state and local public health agencies as well as health systems. The dashboards are deployed on top of a statewide health information exchange. One dashboard enables authorized users working in public health agencies to surveil populations in detail, and a public version provides higher-level situational awareness to inform ongoing pandemic response efforts in communities.

Results

Both dashboards have proved useful informatics resources. For example, the private dashboard enabled detection of a local community outbreak associated with a meat packing plant. The public dashboard provides recent trend analysis to track disease spread and community-level hospitalizations. Combined, the tools were utilized 133 637 times by 74 317 distinct users between June 21 and August 22, 2020. The tools are frequently cited by journalists and featured on social media.

Discussion

Capitalizing on a statewide health information exchange, in partnership with health system and public health leaders, Regenstrief biomedical informatics experts rapidly developed and deployed informatics tools to support surveillance and response to COVID-19.

Conclusions

The application of public health informatics methods and tools in Indiana holds promise for other states and nations. Yet, development of infrastructure and partnerships will require effort and investment after the current pandemic in preparation for the next public health emergency.
Determination of Seven Antidepressants in Pericardial Fluid by Means of Dispersive Liquid–Liquid Microextraction and Gas Chromatography–Mass Spectrometry
Authors: Cabarcos-Fernández P , Tabernero-Duque M J , Álvarez-Freire I , Bermejo-Barrera A M
Published: January 2021

Although blood is often used to detect and quantify the presence of drugs, there are some instances where samples obtained from other biological matrices, like pericardial fluid (PF), are necessary since adequate blood samples may not be available. PF is an epicardial transudate, which contains plasma components that include toxicological substances making this sample useful when blood samples are not available. This fluid is a well-preserved postmortem sample and can easily be collected in larger amounts without significant contamination, compared with other body fluids. Although studies involving PF began around the 1980s, the adequacy of such fluid as a biological matrix has been poorly investigated. Antidepressants are frequently detected in postmortem samples from forensic cases. Nowadays, they constitute some of the most commonly prescribed drugs worldwide. A total of seven antidepressants (venlafaxine, mirtazapine, olanzapine, paroxetine, sertraline, fluoxetine and citalopram) were evaluated in this study. A new extraction method involving dispersive liquid–liquid microextraction (DLLME) is presented in which chloroform and acetonitrile are determined to be the best extraction and dispersing solvents. The experimental design was achieved using StatGraphics 18. The response surface methodology enabled us to know the optimal volume for the two solvents used in the DLLME. The detection technique used was gas chromatography–mass spectrometry with electron impact ionization as ionization source. A temperature gradient has been used and the total chromatographic separation time was 19.43 min. Validation results met the international validation guidance (Food and Drug Administration (FDA)). Under the optimal condition, the method offered good validation parameters showing a new efficient, simple, rapid and sensitive method. The analytical method was applied to 31 PF samples. Twenty-one samples were positive with concentrations between 0.19 and 8.48 µg/mL. Venlafaxine and olanzapine were the antidepressants most frequently found.
The mechanoreceptors of the trilobite larva ofLimulus polyphemus(Linnaeus, 1758) (Merostomata: Xiphosurida: Limulidae)
Authors: Fornshell John A
Published: January 2021

Three types of mechanoreceptors were found on the cuticle of the first post-hatching instar of the trilobite larva of Limulus polyphemus (Linnaeus, 1758) examined by scanning electron microscopy: 1) tactile sensilla on the margin of the carapace of the prosoma; 2) sensilla, adapted to detect near-field sound energy in the form of particle motions and water currents, on the dorsal surface of the carapace covering the prosoma; 3) sensilla, having a helical structure of unknown function and not seen before, on the walking legs and pusher. The morphology of the mechanoreceptors of L. polyphemus, specifically the sensilla capable of sensing particle motions, may shed some light on the mechanisms of near-field sound or particle motion detection of these Jurassic “living fossils.”
Beware the respiratory epithelial adenomatoid hamartoma—a malignant masquerador
Authors: Kumar Shivani Angelique , O’Meara Connor , Fredericks Sue , Havas Thomas
Published: January 2021

Respiratory epithelial adenomatoid hamartoma (REAH) is a rare benign tumour, which can masquerade as a sinonasal malignancy. Commonly arising from the posterior nasal septum, we present the second described case of a lateral nasal cavity wall REAH in a 68-year-old male with a 2-year history of progressive left nasal obstruction. Clinical and radiological assessment predicted malignancy; however, histopathology identified a benign pathology. He was subsequently treated with narrow local excision under general anaesthetic with no evidence of recurrence at post-operative intervals.
Consensual Unions, Property Rights, and Patrimonial Violence against Women in Latin America
Authors: Deere Carmen Diana , León Magdalena
Published: January 2021

Consensual unions in Latin America are becoming more common than marriages. We analyze the evolution of the laws recognizing consensual unions as well as those proscribing domestic violence, including patrimonial violence, for nineteen countries. While the formal property rights of married women and those in consensual unions are now similar, we show that the latter are in a more precarious position, experiencing higher incidences of intimate partner violence. In Colombia and Ecuador, the women in consensual unions also experience higher rates of economic and patrimonial violence. Drawing on qualitative research, we also explore the barriers to women in consensual unions exercising their property rights.
Predictability of leaf traits with climate and elevation: a case study in Gongga Mountain, China
Authors: Xu Huiying , Wang Han , Prentice I Colin , Harrison Sandy P , Wang Genxu , Sun Xiangyang
Published: January 2021

Leaf mass per area (Ma), nitrogen content per unit leaf area (Narea), maximum carboxylation capacity (Vcmax) and the ratio of leaf-internal to ambient CO2 partial pressure (χ) are important traits related to photosynthetic function, and they show systematic variation along climatic and elevational gradients. Separating the effects of air pressure and climate along elevational gradients is challenging due to the covariation of elevation, pressure and climate. However, recently developed models based on optimality theory offer an independent way to predict leaf traits and thus to separate the contributions of different controls. We apply optimality theory to predict variation in leaf traits across 18 sites in the Gongga Mountain region. We show that the models explain 59% of trait variability on average, without site- or region-specific calibration. Temperature, photosynthetically active radiation, vapor pressure deficit, soil moisture and growing season length are all necessary to explain the observed patterns. The direct effect of air pressure is shown to have a relatively minor impact. These findings contribute to a growing body of research indicating that leaf-level traits vary with the physical environment in predictable ways, suggesting a promising direction for the improvement of terrestrial ecosystem models.
Screening of plant growth-promoting rhizobacterial strains for the degradation and utilization of exogenous pectin as a soul carbon source
Authors: Hassan Mohammad K.
Published: January 2021

Universal primers forgyrBwere used to screen 79 strains ofBacillusspecies. The genomic DNA from each strain was extracted, and the PCR product ofgyrBwas amplified and purified for gene sequencing. Gene sequences were edited, and aligned, andBacillus amyloliquefacienssubsp.plantarum(Bap) strains identified based on thegyrBphylogenetic tree. Two primers (exuTanduxuB) were designed to detect pectin-associated transporter geneexuTand D-mannonate oxidoreductase geneuxuB. The Bap strains were then screened for the presence of theexuTanduxuBgenes. These two pectin-utilizing genes were confirmed in 57 and 54 Bap strains by PCR amplification. Second, anin vitrotests were conducted to screen 59 Bap strains using pectin as a sole carbon source to confirm the pectate lyase and utilizing activity. Pectate Agar (PA) and Tris-Spizizen Salts (TSS) medium were used for thein vitropectate lyase and degradation assays.
A simple method of suspending implant wear particles for more physiological modelling of cell-particle interactionsin vitro
Authors: Poon Christine
Published: January 2021

Arthroplasty implants e.g. hip, knee, spinal disc sustain relatively high compressive loading and friction wear, which lead to the formation of wear particles or debris between articulating surfaces. Despite advances in orthopaedic materials and surface treatments, the production of wear debris from any part of a joint arthroplasty implant is currently unavoidable. Implant wear debris induces host immune responses and inflammation, which causes patient pain and ultimately implant failure through progressive inflammation-mediated osteolysis and implant loosening, where the severity and rate of periprosthetic osteolysis depends on the material and physicochemical characteristics of the wear particles. Evaluating the cytotoxicity of implant wear particles is important for regulatory approved clinical application of arthroplasty implants, as is the study of cell-particle response pathways. However, the wear particles of polymeric materials commonly used for arthroplasty implants tend to float when placed in culture media, which limits their contact with cell cultures. This study reports a simple means of suspending wear particles in liquid medium using sodium carboxymethyl cellulose (NaCMC) to provide a more realistic proxy of the interaction between cells and tissues to wear particlesin vivo, which are free-floating in synovial fluid within the joint cavity. Low concentrations of NaCMC dissolved in culture medium were found to be effective for suspending polymeric wear particles. Such suspensions may be used as more physiologically-relevant means for testing cellular responses to implant wear debris, as well as studying the combinative effects of shear and wear particle abrasion on cells in a dynamic culture environments such as perfused tissue-on-chip devices.
Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma
Authors: Risom Tyler , Glass David R , Liu Candace C , Rivero-Gutiérrez Belén , Baranski Alex , McCaffrey Erin F , Greenwald Noah F , Kagel Adam , Strand Siri H , Varma Sushama , Kong Alex , Keren Leeat , Srivastava Sucheta , Zhu Chunfang , Khair Zumana , Veis Deborah J , Deschryver Katherine , Vennam Sujay , Maley Carlo , Hwang E Shelley , Marks Jefferey R , Bendall Sean C , Colditz Graham A , West Robert B , Angelo Michael
Published: January 2021

Ductal carcinomain situ(DCIS) is a pre-invasive lesion that is thought to be a precursor to invasive breast cancer (IBC). To understand how the tumor microenvironment (TME) changes with transition to IBC, we used Multiplexed Ion Beam Imaging by time of flight (MIBI-TOF) and a 37-plex antibody staining panel to analyze 140 clinically annotated surgical resections covering the full spectrum of breast cancer progression. We compared normal, DCIS, and IBC tissues using machine learning tools for multiplexed cell segmentation, pixel-based clustering, and object morphometrics. Transition from DCIS to IBC was found to occur along a trajectory marked by coordinated shifts in location and function of myoepithelium, fibroblasts, and infiltrating immune cells in the surrounding stroma. Taken together, this comprehensive study within the HTAN Breast PreCancer Atlas offers insight into the etiologies of DCIS, its transition to IBC, and emphasizes the importance of the TME stroma in promoting these processes.
Timing and localization of myasthenia gravis-related gene expression
Authors: Vergoossen Dana L.E. , Keo Arlin , Mahfouz Ahmed , Huijbers Maartje G.
Published: January 2021

Myasthenia gravis (MG) is an acquired autoimmune disorder caused by autoantibodies binding acetylcholine receptors (AChR), muscle-specific kinase (MuSK), agrin or low-density lipoprotein receptor-related protein 4 (Lrp4). These autoantibodies inhibit neuromuscular transmission by blocking the function of these proteins, and thereby cause fluctuating skeletal muscle weakness. Several reports suggest that these autoantibodies might also affect the central nervous system (CNS) in MG patients. A comprehensive overview of the timing and localization of the expression of MG-related antigens in other organs is currently lacking. To investigate the spatio-temporal expression of MG-related genes outside skeletal muscle, we usedin silicotools to assess public expression databases. Acetylcholine esterase, nicotinic AChR α1 subunit, agrin, collagen Q, Dok7, Lrp4, MuSK and rapsyn were included as MG-related genes because of their well-known involvement in either congenital or autoimmune MG. We investigated expression of MG-related genes in 1) all human tissues using GTEx data, 2) specific brain regions, 3) neurodevelopmental stages, and 4) cell types using datasets from the Allen Institute for Brain Sciences. MG-related genes show heterogenous spatio-temporal expression patterns in the human body as well as in the CNS. For each of these genes several (new) tissues, brain areas and cortical cell types with (relatively) high expression were identified suggesting a potential role for these genes outside skeletal muscle. The possible presence of MG-related antigens outside skeletal muscle suggests that autoimmune MG, congenital MG or treatments targeting the same proteins may affect MG-related protein function in other organs.
Sugar feeding enhances gut immunity and protects against arboviral infection in the mosquito vectorAedes aegypti
Authors: Almire Floriane , Terry Sandra , McFarlane Melanie , Sziemel Agnieszka M. , Terhzaz Selim , Varjak Margus , McDonald Alma , Kohl Alain , Pondeville Emilie
Published: January 2021

As mosquito females require a blood meal to reproduce, they can act as vectors of numerous pathogens, such as arboviruses (e.g.Zika, dengue and chikungunya viruses), which constitute a substantial worldwide public health burden. In addition to blood meals, mosquito females can also take sugar meals to get carbohydrates for their energy reserves. It is now recognised that diet is a key regulator of health and disease outcome through interactions with the immune system. However, it has been mostly studied in humans and model organisms. So far, the impact of sugar feeding on mosquito immunity and in turn, how this could affect vector competence for arboviruses has not been analysed. Here, we show that sugar feeding increases and maintains antiviral immunity in the digestive tract of the main arbovirus vectorAedes aegypti. Our data demonstrate that the gut microbiota does not mediate the sugar-induced immunity but partly inhibits it. Importantly, sugar intake prior to an arbovirus-infected blood meal further protects females against infection with arboviruses from different families, highlighting a broad antiviral action of sugar. Sugar feeding blocks arbovirus initial infection and dissemination from the gut, lowers infection prevalence and intensity, thereby decreasing transmission potential of female mosquitoes. Overall, our findings uncover a crucial role of sugar feeding in mosquito antiviral immunity and vector competence for arboviruses. SinceAe. aegyptialmost exclusively feed on blood in some natural settings, our findings suggest that this could increase the spread of mosquito-borne arboviral diseases.
The AFB1 auxin receptor controls rapid auxin signaling and root growth through membrane depolarization inArabidopsis thaliana
Authors: Serre Nelson BC , Kralík Dominik , Yun Ping , Shabala Sergey , Slouka Zdeněk , Fendrych Matyáš
Published: January 2021

The existence of an electric gradient across membranes is essential for a cell operation. In plants, application of the growth regulator auxin (IAA) causes almost instantaneous membrane depolarization in various cell types, making membrane depolarization a hallmark of the rapid non-transcriptional responses to IAA. Auxin triggers rapid root growth inhibition; a process that underlies gravitropic bending. The growth and depolarization responses to auxin show remarkable similarities in dynamics, requirement of auxin influx and the involvement of the TIR1/AFB auxin coreceptors, but whether auxin-induced depolarization participates in root growth inhibition remains unanswered. Here, we established a toolbox to dynamically visualize membrane potentialin vivoinArabidopsis thalianaroots by combining the DISBAC2(3) fluorescent probe with microfluidics and vertical stage microscopy. This way we show that auxin-induced membrane depolarization tightly correlates with rapid root growth inhibition and that the cells of the transition zone/early elongation zone are the most responsive to auxin. Further, we demonstrate that auxin cycling in and out of the cells through AUX1 influx and PIN2 efflux is not essential for membrane depolarization and rapid root growth inhibition but acts as a facilitator of these responses. The rapid membrane depolarization by auxin instead strictly depends on the AFB1 auxin receptor, while the other TIR1/AFB paralogues contribute to this response. The lack of membrane depolarization in the afb1 mutant explains the lack of the immediate root growth inhibition. Finally, we show that AFB1 is required for the rapid depolarization and rapid growth inhibition of cells at the lower side of the gravistimulated root. These results are instrumental in understanding the physiological significance of membrane depolarization for the gravitropic response of the root and clarify the role of AFB1 as the receptor central for rapid auxin responses, adding another piece to the puzzle in understanding the biology of the phytohormone auxin.
Protist and Fungal Metaxin-like Proteins: Relationship to Vertebrate Metaxins that Function in Protein Import into Mitochondria
Authors: Adolph Kenneth W.
Published: January 2021

Metaxin-like proteins are shown to be encoded in the genomes of a wide range of protists and fungi. The metaxin proteins were originally described in humans and mice, and were experimentally demonstrated to have a role in the import of nascent proteins into mitochondria. In this study, metaxin-like proteins of protists and fungi predicted from genome sequences were identified by criteria including their sequence homology with vertebrate metaxin proteins and the existence of distinctive metaxin protein domains. Protists of diverse taxa, including amoebae, protozoa, phytoplankton, downy mildews, water molds, and algae, were found to possess genes for metaxin-like proteins. With fungi, the important taxonomic divisions (phyla) of Ascomycota, Basidiomycota, Chytridiomycota, Mucoromycota, and Zoopagomycota had species with metaxin-like protein genes. The presence of distinctive GST_N_Metaxin, GST_C_Metaxin, and Tom37 domains in the predicted proteins indicates that the protist and fungal proteins are related to the vertebrate metaxins. However, the metaxin-like proteins are not direct homologs of vertebrate metaxins 1, 2, or 3, but have similarity to each of the three. The alignment of the metaxin-like proteins of a variety of protists with vertebrate metaxins 1 and 2 showed about 26% and 19% amino acid identities, respectively, while for fungal metaxin-like proteins, the identities were about 29% and 23%. The different percentages with the two vertebrate metaxins indicates that the metaxin-like proteins are both metaxin 1-like and, to a lesser degree, metaxin 2-like. The secondary structures of protist and fungal metaxin-like proteins both consist of nine α-helical segments, the same as for the vertebrate metaxins, with a negligible contribution from β-strand. Phylogenetic analysis demonstrated that the protist and fungal metaxin-like proteins and the vertebrate metaxins form distinct and separate groups, but that the groups are derived from a common ancestral protein sequence.
Taxonomy-aware, sequence similarity ranking reliably predicts phage-host relationships
Authors: Zielezinski Andrzej , Barylski Jakub , Karlowski Wojciech M.
Published: January 2021

Background

Similar regions in virus and host genomes provide strong evidence for phage-host interaction, and BLAST is one of the leading tools to predict prokaryotic hosts from phage sequences. However, BLAST-based host prediction has three major limitations: (i) top-scoring sequences do not always point to the actual host, (ii) mosaic phage genomes may match to many, typically related, bacteria, and (iii) phage and host sequences may diverge beyond the point where their relationship can be detected by a BLAST alignment.

Results

We created an extension to BLAST, named Phirbo, that improves host prediction quality beyond what is obtainable from standard BLAST searches. The tool harnesses information concerning sequence similarity and bacteria relatedness to predict phage-host interactions. Phirbo was evaluated on three benchmark sets of known phage-host pairs, and it improved precision and recall by 11-40 percentage points over currently available, state-of-the-art, alignment-based, alignment-free, and machine learning host prediction tools. Moreover, the discriminatory power of Phirbo for the recognition of phage-host relationships surpassed the results of other tools by at least 10 percentage points (Area Under the Curve = 0.95), yielding a mean host prediction accuracy of 57% and 68% at the genus and family levels respectively, and drops by 12 percentage points when using only a fraction of phage genome sequences (3 kb). Finally, we provide insights into a repertoire of protein and ncRNA genes that are shared between phages and hosts and may be prone to horizontal transfer during infection.

Conclusions

Our results suggest that Phirbo is a simple and effective tool for predicting phage host relationships.
Reducing disease and producing food: Effects of 13 agrochemicals on snail biomass and human schistosomes
Authors: Haggerty Christopher J E , Halstead Neal , Civitello David J. , Rohr Jason R
Published: January 2021

Agrochemical use is predicted to increase 2-5 fold by 2050 to meet food demand. Evidence suggests that agrochemical pollution could increase snails that transmit the disease schistosomiasis to 250 million people, but most agrochemicals remain unexamined. Here we quantify the relative effects of fertilizer, six insecticides, and six herbicides on snail genera responsible for 90% of global schistosomiasis cases. We identified fertilizers and 4 of 6 insecticides as high risk for increasing snail biomass by increasing snail resources (vegetative habitat and periphytic food) and reducing snail predators, respectively. Herbicides generally had negative effects on snails by reducing vegetative habitat, with two herbicides increasing snails in the absence of aquatic vegetation. Parasite production, which reflects human infection risk, scaled positively to snail biomass. Our findings suggest that fertilizers and insecticides are more likely to increase human schistosomiasis than herbicides and revealed several low risk agrochemicals that might increase crop production without increasing schistosomiasis.
Source identity shapes spatial preference in primary auditory cortex during active navigation
Authors: Amaro Diana , Ferreiro Dardo N. , Grothe Benedikt , Pecka Michael
Published: January 2021

Localizing and identifying sensory objects while navigating the environment are fundamental brain functions. However, how individual objects are neuronally represented during unrestricted self-motion is mostly unexplored. We trained gerbils on a behavioral foraging paradigm that required localization and identification of sound-sources during free navigation. Chronic multi-electrode recordings in primary auditory cortex during task performance revealed previously unreported sensory object representations. Strikingly, the egocentric angle preference of the majority of spatially sensitive neurons changed significantly depending on the task-specific identity (outcome association) of the sound-source. Spatial tuning also exhibited larger temporal complexity. Moreover, we encountered egocentrically untuned neurons whose response magnitude differed between source identities. Using a neural network decoder we show that together, these neuronal response ensembles provide spatio-temporally co-existent information about both the egocentric location and the identity of individual sensory objects during self-motion, revealing a novel cortical computation principle for naturalistic sensing.

Highlights

Localization task during free navigation prompts diverse spatial tuning in gerbil A1

Spatial preference of individual neurons changes with sound-source identity

Ego- and allocentric information are spatio-temporally coexistent in A1 ensembles

Active sensing reveals new cortical representations for sensory object identification