Miracle-dz/UniFAR-FTUs huggingface dataset:
Distinguishing the Role of the c-myb Proto-Oncogene in Mouse Models of Cardiovascular Disease

Despite considerable advances in our understanding of disease processes, cardiovascular diseases remain the top cause of mortality and morbidity in society today. Investigating the molecular and cellular mechanisms involved in the pathogenesis of these diseases to discover new therapeutic targets is of utmost importance. While much is known about the specific roles of transcription factor c-myb in leukocytes, comparatively little is known about c-myb in the context of cardiovascular disease. c-myb regulates vascular smooth muscle cell (VSMC) differentiation from embryonic stem cells, as well as the proliferation of mature VSMCs. The literature points toward several areas of opportunity to examine the role of c-myb in cardiovascular biology: first, to examine the role of c-myb in the regulation of adult vessel-resident VSMC progenitor cell proliferation and differentiation in response to vessel injury and the molecular mechanisms involved in c-myb-mediated VSMC differentiation. Second, while transgenic models manipulating c-myb have yielded significant insight in regards to homeostasis of the immune system, little is known about a role for c-myb in the regulation of baseline function of the cardiovascular system. While c-myb regulates VSMC differentiation and pathological VSMC
Faberia pinnatifida (Asteraceae; Cichorieae), a New Species from Sichuan, China

Abstract Faberia pinnatifida (Asteraceae; Cichorieae), a species occurring at high altitudes in Muli and Yanyuan Xian, Sichuan, China, is described as new based on morphological, palynological, andmolecular phylogenetic data. The ITS data indicate that F. pinnatifida is closely related to F. glaucescens and F. thibetica, but it is easily distinguished from F. glaucescens by its scapigerous stem with only one or two leaves, and from F. thibetica in its much taller stature and elliptic to oblanceolate leaf blade. Faberia pinnatifida somewhat resembles F. ceterach in the scapigerous stem and pinnatifid leaves, but readily differs in its corymbiform synflorescence and nodding capitula bearing ca. 30 florets.
Contribuição para o estudo imunológico da blastomicose de Lutz (blastomicose sul-americana)

Numerosos pesquisadores têm dedicado seus esforços ao estudoimunológico das mícoses profundas. Procuraremos fazer revisãolimitada da literatura pertinente ao assunto, para justificarmosnossos estudos na blastomicose de Lutz.
Inactivation of chromosomal genes of the choline bacterial microcompartment through transformation of Escherichia coli 536

• BMCs allow a controlled space for enzymatic activity such as the breakdown of choline forming TMA and acetaldehyde reducing the toxicity of the aldehyde (1,3,6) • Higher concentrations of TMA in plasma which is produced by bacteria in the human gut is correlated with a higher risk of cardiovascular disease (Fig 2) (4) • Understanding how TMA is produced can lead to development of therapies for cardiovascular disease Tiffany Nicole Harris, Department of Microbiology, Iowa State University, Ames, IA Dr. Thomas Bobik, Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA
Dichotomius (Luederwaldtinia) schiffleri (Coleoptera: Scarabaeidae) mitochondrial genome and phylogenetic relationships within the superfamily Scarabaeoidea

Abstract The mitochondrial DNA of Dichotomius (Luederwaldtinia) schiffleri was characterized and its phylogenetic position was reconstructed in Scarabaeoidea. This mitogenome presented 14,802 bp-long, richness in AT of 77.4% and 37 genes, including 13 protein-coding, 22 transfer RNAs, and two ribosomal RNAs. In addition, it was observed intergenic spacers and reading frame overlaps. The phylogenetic trees reconstructed from protein sequences provided best resolution, indicating Scarabaeinae and Aphodiinae as a sister groups, as previously reported in other molecular phylogenies.
Effects of Micron Fish Bone with Different Particle Size on the Properties of Silver Carp (Hypophthalmichthys molitrix) Surimi Gels

Qualities of silver carp surimi (SCS) gels incorporated with micron fish bone of different particle size (22 to 0.12 μm) were evaluated. Textural values, whiteness, and water holding capacity of the SCS gels with setting significantly increased ( ) as the micron fish bone particle size decreased. As the particle size decreased, more calcium ion was apparently released from the fish bone ( ). Consequently the released calcium ion increased the activity of endogenous transglutaminase (TGase) and resulted in the formation of more myosin heavy chain (MHC) cross-links in the SCS gel with setting. Fish bone with particle size below 0.48 μm was steadily trapped in the three-dimensional SCS gel network without disrupting the matrices. Results indicated that size reduction of the incorporated micron fish bone improved qualities of the SCS gel with setting by the means of releasing more calcium ion and maintaining better gel matrices.
The mitogenome of the southern Brook Lamprey, Ichthyomyzon gagei (Cyclostomata: Petromyzontidae)

Abstract The southern brook lamprey (Ichthyomyzon gagei) is a non-parasitic lamprey endemic to the southeastern US. Here, we report the complete mitogenome of this basal vertebrate and found its genomic organization to be similar to that of other reported lamprey mitogenomes. Nucleotide sequence identities for individual proteins range from 90% to 94% when compared with the congeneric species I. fossor and I. unicuspis. Finally, phylogenetic analysis revealed I. gagei to be sister to these other species of Ichthyomyzon. These genomic data provide a baseline for future investigations regarding the molecular evolution of basal vertebrates.
Customizing material into embodied cap by sponge crab

Getting camouflaged with environmental material can improve survivability of animals. How animals select and customize the material to fit it to their body design remains unclear. To address the question, we examined the cap making behavior of the sponge crab, Lauridromia dehaani that carries sponge as a cap. We tested their preference to size of original material, the whole area size of cap that the crabs cut off, and its hole size of the caps that the crabs customize to make it suitable for their body. Three different sizes of artificial sponge were given to the crabs experimentally so that they could choose one sponge among them. We video recorded the process of cap making behavior, and measured the size of caps. Although a certain fixed behavioral pattern was observed in the cap making behavior, choice and size of cap hole considerably varied even in a single individual. To fully consider the individuality, we incorporated it into hierarchical statistical models. Estimating the parameters in the models by a Bayesian approach revealed that large individuals tended to choose large sponges with the variability specific to each individual. Furthermore, the individual-specific tendency was also observed in the relationship of the carapace width and the cap hole size. These results imply that the crabs update the cap making behavior by recalibration, given that they have to molt to become large. These findings might give a new insight into body extending capability of crustaceans.
Studien der Genexpressionsänderung während der Entwicklung von Drosophila melanogaster mittels DNA-Microarrays

Die Fruchtfliege Drosophila melanogaster ist einer der am besten untersuchten Modellorganismen in der Entwicklungsbiologie. Die Kenntnis des Genoms und die Zahl der annotierten protein-kodierenden Gene von Drosophila sind jedoch Schwankungen unterworfen, da sie meist auf Computerberechnungen bereits bekannter Gene und nur teilweise auf experimentellen Nachweisen beruhen. Um das Transkriptom von Drosophila im Verlauf der Entwicklung zu untersuchen und neue potentielle Gene zu identifizieren wurde im Rahmen dieser Arbeit ein DNA-Microarray entwickelt, mit dem Veranderungen in der mRNA-Expression analysiert wurden. Auf der Grundlage einer neuentwickelten ab initio Genvorhersage im Rahmen einer Koorporation wurden spezifische Primer generiert, die eine Amplifikation der potentiellen Gene ermoglichten. Mit einem zweistufigen PCR-Protokoll konnten 20.948 (98%) PCR-Fragmente von 21.396 vorhergesagten Genen amplifiziert werden. Diese wurden als Basis fur die Herstellung des Microarrays verwendet. So war es moglich die Vorteile computergestutzter in silico- Berechnungen der moglichen Gene mit experimentellen Analysen zu kombinieren, um die Expression von Genen zu detektieren. Durch Optimierung der Protokolle und Methoden in der DNA-Chip-Konstruktion wurde ein hochdichter Microarray hergestellt, der nahezu das gesamte Transkriptom von Drosophila reprasentiert. Die Analyse differentiell exprimierter Gene erfolgte jeweils mit zwei RNA-Populationen die wahrend der reversen Transkription mit unterschiedlichen Fluoreszenzfarbstoffen markiert und anschliesend auf einem Microarray co-hybridisiert wurden. Es wurden Hybridisierungen mit der RNA aus 9 unterschiedlichen Entwicklungsstadien von Drosophila melanogaster durchgefuhrt, die den gesamten Lebenszyklus der Fliege umfassten. Nach der Quantifizierung der detektierten Signalintensitaten erfolgte die bioinformatische Datenanalyse mit unterschiedlichen Softwareprogrammen. Die Genexpressionsanalysen ergaben das 13.812 Gene im Verlauf der Entwicklung von Drosophila exprimiert werden, wovon ungefahr 2.500 bisher unbekannten Genen entsprechen. Es konnte auserdem gezeigt werden, das die Entwicklungsstadien spezifische Regulationen von Genaktivitaten aufweisen, die mit morphologischen Veranderungen wahrend der Entwicklung korrelieren und das Gengruppen ahnlicher biochemischer oder physiologischer Funktion gemeinsam reguliert werden.
Diversity, distribution and preliminary conservation status of the flora of Burkina Faso

West Africa is a floristically understudied region that is facing severe environmental changes in the 21 st century. Basic distribution data and information on the conservation status for most plant species of the region are scarce, and good information only exists for small areas of interest or for key species. This lack of knowledge seriously hampers urgently needed regional conservation efforts. Here we present comprehensive distribution information and preliminary, automated species conservation assessments for the flora of Burkina Faso, a country in tropical West Africa with a flora and vegetation typical for the savanna belt of the region. We documented and analysed the distribution of 1,568 species or 80% of the flora of Burkina Faso based on an expert curated dataset comprising ca. 150,000 occurrence records from herbarium specimens and vegetation surveys. We used this dataset and environmental niche models to calculate three indicator variables for a preliminary, automated conservation assessment. We classified 350 species (18% of the flora, excluding introduced species) as potentially "Critically Endangered", "Endangered", "Vulnerable" or "Near-Threatened" on the national level. The analyses confirmed species-rich areas in the south-west and south-east of the country, and showed a particular concentration of potentially Endangered species in the south. Furthermore, the proportion of potentially Endangered species differed between plant families, growth forms and habitats. Our results set the base for further plant geographical and ecological studies and are a data-driven baseline for further conservation assessments and large scale conservation strategies of the West African flora.
Genetic differentiation of Turkish Althaea L. and Alcea L. species

Random amplified polymorphic DNA (RAPD) analysis and SDS-PAGE analysis of total seed proteins were used to estimate genetic differences between/within four Althaea (Malvaceae) and eighteen Alcea species. The 4 Althaea and 18 Alcea species were found to have species-specific protein profiles. The total of 223 different RAPD bands for Althaea species were generated by the 11 primers and total of 116 different RAPD bands by the 8 random primers for Alcea species. The results of the POPGENE cluster analysis were in broad agreement with previous morphological classifications of these four species. Statistical significance within Alcea and Althaea population was tested using of molecular variance (AMOVA) approach used in Arlequin. According to the results, there is a large genetic differentiation between species A. hirsuta with A. armeniaca, A. officinalis with A. hirsuta, FST 0.24 and FST 0.21, respectively. There is also wide differentiation between Alcea species. FST statistics range from 0,126 (A. guestii between A. striata ssp. striata) to 0,685 (A. biennis between A. acaulis). The results suggest that RAPD and SDS-PAGE markers can be used to reveal genetic differentiation between species and genus.
COMPARATIVE STUDY OF THE ANTIOXIDANT ACTIVITIES OF METHANOLIC EXTRACT AND SIMULATED GASTROINTESTINAL ENZYME DIGEST OF BAMBARA NUT (Vigna subterranean)

The present investigation seeks to compare the antioxidant activities of solvent extracted (methanol) and in vitro enzyme digested Bambara nut. Bambara nut was extracted with methanol and another portion was subjected to an in vitro human digestion model that stimulated the composition of the gastrointestinal tract. The HPLC-DAD phenolic analysis revealed the presence of some phenolic acids and flavonoids, with reduced levels of most of the identified compounds after cooking process. The result of the antioxidant indices (total phenol, total flavonoid, ferric reducing antioxidant power, ABTS and DPPH radical scavenging activities) of the methanolic extract revealed a higher potency for the raw methanolic extract compared with the cooked methanolic extract. The assessment of the in vitro enzyme digested Bambara nut for antioxidant action revealed a high activity for the enzyme digested Bambara nut compared with the methanolic extract. Conversely, the cooking process improved the antioxidant activity after in vitro enzyme digestion. The result of this study indicates that the selected legume has some phyto-constituents with some measure of antioxidant action and that the phyto-constituents will be better released after passing through the gastrointestinal tract, and therefore could be harnessed as a functional food with potential health benefits.
Prevalence of Salmonella species from poultry eggs of local stores in Duhok

Background: Salmonellosis is one of the foodborne illness acquired by consumption of infected raw or undercooked eggs and causes major public health problem. The aim of this study was isolation and identification of Salmonella spp . from the eggshells and the egg contents samples. Methods: In this study, a total 350 eggs were randomly collected from five local stores in Duhok and Zakho city over a period of 6 months in summer of 2016. Eggs from each local store were collected and transferred to the microbiology laboratory. The conventional culture method used for detection of Salmonella spp . Results: Out of the 350 eggs, seventeen (4.85%) samples of eggshells contaminated with Salmonella spp. and none of the egg content samples were contaminated with Salmonella genus. Out of 17 positive eggs, three different Salmonella serotypes were identified including; Salmonella enteritidis (10 strains), Salmonella typhimurium (5 strains), Salmonella typhi (2 strains). Conclusions: The results of the present study provide the recent dataset of the prevalence of Salmonella spp. in eggs sold at local stores in the city. All isolates showed resistant to tetracycline, oxacillin and sulphadimethoxazole due to the indiscriminate use of these antibiotics in chicken at sub-therapeutic level or prophylactic doses which promotes selection of antimicrobial resistant strains and also increases the human health risks associated with consumption of contaminated quail eggs. To the best of our knowledge, this is the first study in Zakho- Duhok city, investigating the occurrence of Salmonella spp . in eggshell and content egg sold at local stores.
Alternative translation initiation unraveled by N-terminomics and ribosome profiling

A single eukaryotic gene can give rise to a variety of protein forms (proteoforms) as a result of genetic variation and multi-level regulation of gene expression. In addition to alternative splicing, an increasing line of evidence shows that alternative translation contributes to the overall complexity of proteomes. Identifying the repertoire of proteins and micropeptides expressed by alternative selection of (near-)cognate translation initiation sites and different reading frames however remains challenging with contemporary proteomics. Mass spectrometry enabled identification of proteoforms is expected to benefit from transcriptome and translatome data by the creation of customised and sample-specific protein sequence databases. Here, we focus on contemporary integrative omics approaches that complement proteomics with DNA and/or RNA oriented technologies to elucidate the mechanisms of translational control. Together, these technologies enable to map the translation (initiation) landscape and more comprehensively define the inventory of proteoforms raised upon alternative translation, thus assisting in the (re-)annotation of genomes.
Two new species of the genus Euphthiracarus (Acari: Oribatida: Euphthiracaridae) from Hainan Island, China

ABSTRACT Euphthiracarus is the most speciose genus of the oribatid family Euphthiracaridae. In this study, two new species of Euphthiracarus (Oribatida: Euphthiracaridae) from Hainan Island, China, Euphthiracarus paraoblongus sp. nov. and Euphthiracarus singularis sp. nov., are described and illustrated. An updated key to all known species of Euphthiracarus in China is provided. http://zoobank.org/urn:lsid:zoobank.org:pub:C1A23769-58A1-4FA8-8CB3-EF58D297D092
Heterogeneous timing of asexual cycles in Plasmodium falciparum quantified by extended time-lapse microscopy

Malarial fever arises from the synchronous bursting of human red blood cells by the Plasmodium parasite. The released parasites re-infect neighboring red blood cells and undergo another asexual cycle of differentiation and proliferation for 48 hours, before again bursting synchronously. The synchrony of bursting is lost during in vitro culturing of the parasite outside the human body, presumably because the asexual cycle is no longer entrained by host-specific circadian cues. Therefore, most in vitro malaria studies have relied on the artificial synchronization of the parasite population. However, much remains unknown about the degree of timing heterogeneity of asexual cycles and how artificial synchronization may affect this timing. Here, we combined time-lapse fluorescence microscopy, long-term culturing and follow single cells to directly observe and measure the heterogeneous timing of in vitro asexual cycles. We first demonstrate that unsynchronized laboratory cultures are not fully asynchronous and the parasites exhibit a bimodal distribution in their first burst times. We then show that synchronized and unsynchronized cultures had similar asexual cycle periods, which indicates that artificial synchronization does not fundamentally perturb asexual cycle dynamics. Last, we demonstrate that sibling parasites descended from the same schizont exhibited significant variation in asexual cycle period, although smaller than the variation between non-siblings. The additional variance between non-siblings likely arises from the variable environments and/or developmental programs experienced in different host cells.
Biological modeling as a mechanical study of aldehydes oxidation by xantine oxidase enzyme

In the mechanism for purine metabolism the xanthenes oxidase enzyme has physiological importance. According to this hypothesis the xanthenes oxidase enzyme catalyzes the oxidation of xanthine to uric acid which plays a crucial role in gout, facilitate the reduction of oxidizing substrate and important for drug oxidation. Our calculation results indicate that in the catalysis stage the transition state is predicted in well tetrahedral complex formation with the strong bond formation ofOeq-CCRH and SMo-HRH, and the cleavage of OCRH-HRH and Mo-Oeq. This transition state is more reactant like, one imaginary negative frequency is performed and, high activation barriers are often obtained due to the absence of factors that stabilize the accumulation of charge on the substrate at the transition state. In this case the protonated aldehyde substrates more favored for the oxidation reaction with xanthine oxidase in comparison with the corresponding deprotenated aldehydes. And a step wise mechanism is found to be more favored for the oxidation of protonated formaldehyde with a proton coupled electron transfer and intermediate formation in the product bound. The result indicates that the enzyme xanthine oxidase is responsible for the oxidation of aldehydes based on the environment of the active site located. Our mechanistic study of the protonated formaldehyde oxidation provides an understanding in how the reaction path takes place and provides the way to study the catalytic mechanism on different oxidation substrates by xanthine oxidase enzyme.
DNA double-strand break formation and signalling in response to transcription-blocking topoisomerase I complexes

La topoisomerase I (Top1) elimine les surenroulements de l'ADN generes lors de la transcription en produisant transitoirement des complexes de clivage Top1-ADN (Top1cc). Ces Top1cc transitoires peuvent etre stabilises par les camptothecines, dont sont derives des agents anticancereux, et par les frequentes alterations de l'ADN. Bien que les Top1cc stabilises soient des lesions qui bloquent efficacement la transcription, la comprehension des processus moleculaires qui resultent du blocage des complexes transcriptionnels par les Top1cc est encore limitee. Des travaux precedents ont montre que les Top1cc stabilises produisent des cassures double-brin (DSBs) de l'ADN dependantes de la transcription qui activent ATM. Dans ce projet, nous avons utilise des cellules quiescentes traitees avec la camptothecine pour induire des Top1cc bloquant la transcription et nous avons etudie les mecanismes de la production et de la signalisation des DSBs. Nous montrons que les DSBs sont produites preferentiellement dans les regions sub-telomeriques lors de la reparation des Top1cc bloquant la transcription par les cassures simple-brin de l'ADN generees apres la proteolyse de la Top1 et avant l'action de Tdp1. L'analyse de la signalisation de ces DSBs revele une nouvelle fonction de DNA-PK dans la promotion de l'ubiquitinylation conduisant (i) a l'activite complete d'ATM aux sites des DSBs en favorisant l'ubiquitination d'H2AX et H2A, et (ii) a l'augmentation de la reparation des Top1cc en favorisant la proteolyse de la Top1. Enfin, nous montrons que les DSBs co-transcriptionnelles induisent la mort des cellules quiescentes. L'ensemble de ces resultats apportent un nouvel apercu des reponses cellulaires aux camptothecines, et suggerent que les DSBs qui resultent des Top1cc bloquant la transcription puissent contribuer a la pathogenese du syndrome neurodegeneratif SCAN1, qui est cause par une deficience en Tdp1.