1,720,976 research outputs found
Are the heterogeneous nuclear ribonucleoproteins SQUID and Hrb87F involved in the regulation of circadian rhythmicity in Drosophila melanogaster?
Full text linkThe search for new genes involved in circadian rhythmicity in Drosophila melanogaster led to the identification of the RNA binding proteins Hrb87F and SQUID, as partners of Cryptochrome, the photoreceptor responsible for light-synchronization of the circadian clock. In the clock machinery, different post-transcriptional mechanisms have evolved to adjust and consolidate the oscillation of clock genes and proteins in interlocked negative feedback loops. The aim of my PhD project was to study the possible involvement of Hrb87F and SQUID in the post-transcriptional control of the circadian clock in Drosophila.
These preliminary data were confirmed by Co-Immunoprecipitation and western-blot experiments using transgenic flies expressing a tagged version of Cry (HACRY) under the control of the driver timGAL4, for SQUID, while for Hrb87F the interaction was validated by yeast two-hybrid assay, in which dCRY was challenged to Hrb87F as prey.
To achieve more information about a possible role of the clock in the expression of Squid and Hrb87F in Drosophila head, the analysis of the expression profile of the two hnRNPs (mRNAs and proteins) was performed during the 24 hours in wild type (wt) and clock mutant per0 flies. As for Hrb87F, mRNA levels showed an oscillatory trend in LD (Light-Dark) and DD (Dark-Dark) either in wt and per0 flies; the protein levels oscillate in LD and DD in wt flies, but not in per0, suggesting a potential role for the circadian clock in the translational/posttranslational control of the protein. As for Squid, neither the mRNA nor the protein showed rhythmic expression in LD and DD.
Subsequently, the involvement of SQUID and Hrb87F in the generation of the circadian rhythmicity was studied analyzing the locomotor activity pattern of flies’ mutant for each of the two genes. Mutants for both genes showed an impairment of the daily rhythmicity, with a loss of the morning anticipation in LD and low levels of rhythmicity in DD at 29°C, 23°C, 18°C and 15°C, suggesting that Squid and Hrb87F could play a role either in the generation and in the light-synchronization of the circadian behaviour. However, the analysis of locomotor activity in constant light, performed in order to further dissect the possible role of Squid in the light synchronization of the clock, revealed that the light-synchronization of the clock is not impaired in these flies.
The expression of period and timeless and the alternative splicing variants in relation to the temperature were also analyzed in wt and Squid mutant brains by using multiplex real time PCR. The results suggest that the expression of period and timeless mRNA is altered in Squid mutant compared to wt both in LD and DD at each temperature. Moreover, the quantities of per unspliced at high temperature and tim unspliced at low temperature are lower both in LD and DD in the
mutant. This suggests an increase of the splicing events and thus an involvement of SQUID in the post-transcriptional control of clock genes.
In collaboration with Dr Milena Damulewicz (Jagiellonian University of Krakow - Poland), the expression of PERIOD was analyzed in the clock neurons by immunocytochemistry in flies reared at both 18°C and 23°C in LD and DD. At 23°C and 18°C the oscillation of PER in l-LNvs clock neurons is lost, while, in s-LNvs, the accumulation of protein is delayed by 3 hours with a broader peak that reflects a low kinetic of degradation. The analysis of PDF projections from clock neurons shows a profound disorganization of PDF release, suggesting that it can, at least partially, account for the locomotor activity defect observed in the Squid mutant.
Taken together, these results highlight the possible involvement of the hnRNPs Hrb87F and SQUID in the generation and maintenance of circadian rhythmicity in Drosophila melanogaster
Genomic insights into shank and eggshell color in Italian local chickens
Full text linkEggshell and shank color in poultry is an intriguing topic of research due to the roles in selection, breed recognition, and environmental adaptation. This study delves into the genomics foundations of shank and eggshell pigmentation in Italian local chickens through genome-wide association studies analysis to uncover the mechanisms governing these phenotypes. To this purpose, 483 animals from 20 local breeds (n = 466) and 2 commercial lines (n = 17) were considered and evaluated for shank and eggshell color. All animals were genotyped using the Affymetrix Axiom 600 K Chicken Genotyping Array. As regards shank color, the most interesting locus was detected on chromosome Z, close to the TYRP1 gene, known to play a key role in avian pigmentation. Additionally, several novel loci and genes associated with shank pigmentation, skin pigmentation, UV protection, and melanocyte regulation were identified (e.g., MTAP, CDKN2A, CDKN2B). In eggshell, fewer significant loci were identified, including SLC7A11 and MITF on chromosomes 4 and 12, respectively, associated with melanocyte processes and pigment synthesis. This comprehensive study shed light on the genetic architecture underlying shank and eggshell color in Italian native chicken breeds, contributing to a better understanding of this phenomenon which plays a role in breed identification and conservation, and has ecological and economic implications
Characterizing the fecal bacteria and archaea community of heifers and lactating cows through 16S rRNA next-generation sequencing
Full text linkThe aim of this study was to describe the fecal bacteria and archaea composition of Holstein-Friesian and Simmental heifers and lactating cows, using 16S rRNA gene sequencing. Bacteria and archaea communities were characterized and compared between heifers and cows of the same breed. Two breeds from different farms were considered, just to speculate about the conservation of the microbiome differences between cows and heifers that undergo different management conditions. The two breeds were from two different herds. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were the most abundant phyla in all experimental groups. Alpha- and beta-diversity metrics showed significant differences between heifers and cows within the same breed, supported by principal coordinate analysis. The analysis of Holstein-Friesian fecal microbiome composition revealed 3 different bacteria families, 2 genera, and 2 species that differed between heifers and cows; on the other hand, Simmental heifers and cows differed only for one bacteria family, one archaeal genus, and one bacteria species. Results of the present study suggest that fecal communities of heifers and cows are different, and that fecal microbiome is maintained across experimental groups
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Genome-wide analyses identifies known and new markers responsible of chicken plumage color
Full text linkThrough the development of the high-throughput genotyping arrays, molecular markers and genes related to phenotypic traits have been identified in livestock species. In poultry, plumage color is an important qualitative trait that can be used as phenotypic marker for breed identification. In order to assess sources of genetic variation related to the Polverara chicken breed plumage colour (black vs. white), we carried out a genome-wide association study (GWAS) and a genome-wide fixation index (FST) scan to uncover the genomic regions involved. A total of 37 animals (17 white and 20 black) were genotyped with the Affymetrix 600 K Chicken single nucleotide polymorphism (SNP) Array. The combination of results from GWAS and FST revealed a total of 40 significant markers distributed on GGA 01, 03, 08, 12 and 21, and located within or near known genes. In addition to the well-known TYR, other candidate genes have been identified in this study, such as GRM5, RAB38 and NOTCH2. All these genes could explain the difference between the two Polverara breeds. Therefore, this study provides the basis for further investigation of the genetic mechanisms involved in plumage color in chicken
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
Genome-wide association study for morphological and hunting-behavior traits in Braque Français Type Pyrénées dogs: A preliminary study
No full textHigh-throughput genotyping offers great potential to increase our understanding of the genomic basis of canid variation. Braque Français Type Pyrénées (BRA) are smart, agile, and friendly dogs originally developed for tracking, hunting, and retrieving feathered game. On a population of 44 unrelated BRA dogs, single nucleotide polymorphism (SNP) genotype data from the CanineHD Whole-Genome Genotyping BeadChip and evaluation scores for 12 traits related to morphology and hunting performance were available. After quality filtering, 95,859 SNPs on the 38 dog autosomes (CFA) were retained. Phenotypic scores were expressed on a scale from 1 (worst) to 6 (best) and were mostly poorly to moderately correlated except for some morphological traits (e.g. r = 0.81 between the conformation of the head and that of the eye). From GWAS, a total of 378 SNP-phenotype associations with posterior odds of association > 1 have been detected. The strongest associations were found for the eye conformation, for the skull/muzzle ratio, and for connection to the hunter. These included both new and previously identified markers and genes potentially involved with type and behavior traits in BRA. Six of the significant markers mapped within SETDB2, a gene known to be related to pointing behavior in dogs. These results advance our understanding of the genetic basis for morphology and hunting behavior in dogs and identify new variants which are potential targets for further research
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