Miracle-dz/UniFAR-FTUs huggingface dataset:
Giantin knockout models reveal the capacity of the 1 Golgi to regulate its biochemistry 2 by controlling glycosyltransferase expression 3

The Golgi is the cellular hub for glycosylation, controlling accurate processing of complex proteoglycans 20 and glycolipids. Its structure and organisation is dependent on golgins which tether cisternal membranes 21 and incoming transport vesicles. Here we show that knockout of the largest golgin, giantin, leads to 22 substantial changes in gene expression despite only limited effects on Golgi structure. Notably, 22 Golgi- 23 resident glycosyltransferases, but not glycan processing enzymes or the ER glycosylation machinery, are 24 differentially expressed following giantin ablation. Most of these glycosyltransferases are highly 25 downregulated following genetic knockout of giantin, including a near-complete loss of expression of 26 GALNT3 in both mammalian cell and zebrafish models. Furthermore, knockout zebrafish exhibit 27 increased bone mass density, hyperostosis, and ectopic calcium deposits recapitulating phenotypes of 28 hyperphosphatemic familial tumoral calcinosis, a disease caused by mutations in GALNT3. Our data 29 reveal a new feature of Golgi homeostasis, the ability to regulate glycosyltransferase expression to 30 generate a functional proteoglycome. 31 In the absence of a clearly defined role for giantin at the Golgi, we sought to study its function in an 99 engineered KO cell line. In this system, as well as a zebrafish model, we show for the first time that 100 giantin regulates the expression of Golgi-resident glycosyltransferases.
A prize-collecting Steiner tree application for signature selection to stratify diffuse large B-cell lymphoma subtypes

Background: With the explosion of high-throughput data available in biology, the bottleneck is shifted to effective data interpretation. By taking advantage of the available data, it is possible to identify the biomarkers and signatures to distinguish subtypes of a specific cancer in the context of clinical trials. This requires sophisticated methods to retrieve the information out of the data, and various algorithms have been recently devised. Results: Here, we applied the prize-collecting Steiner tree (PCST) approach to obtain a gene expression signature for the classification of diffuse large B-cell lymphoma (DLBCL). The PCST is a network-based approach to capture new insights about genomic data by incorporating an interaction network landscape. Moreover, we adopted the ElasticNet incorporating PCA as a classification method. We used seven public gene expression profiling datasets (three for training, and four for testing) available in the literature, and obtained 10 genes as signature. We tested these genes by employing ElasticNet, and compared the performance with the DAC algorithm as current golden standard. The performance of the PCST signature with ElasticNet outperformed the DAC in distinguishing the subtypes. In addition, the gene expression signature was able to accurately stratify DLBCL patients on survival data. Conclusions: We developed a network-based optimization technique that performs unbiased signature selection by integrating genomic data with biological networks. Our classifier trained with the obtained signature outperformed the state-of-the-art method in subtype distinction and survival data stratification in DLBCL. The proposed method is a general approach that can be applied on other classification problems.
Detection of tox A gene in Pseudomonas aeruginosa that isolates from different clinical cases by using PCR.

Current study obtained (75) isolate of Pseudomonas aeruginosa collected from different cases included : 28 isolates from otitis media, 23 isolates from burn infections, 10 isolates from wound infections, 8 isolates from urinary tract infections and 6 isolates from blood, during the period between 1/9/2014 to 1/11/2014 The result revealed that the tox A gene was present in 54 isolates (72%) of Pseudomonas aeruginosa. The gel electrophoresis showed that the molecular weight of tox A gene was 352 bp. The result shows 17 isolates (60.71%) from otitis media has tox A gene, 18 isolates (78.26%) from burn followed by 8 isolate (80%) from wound infection and 5 isolates (62.5%) from urinary tract infection , finally 6 isolates (100%) from blood have this gene.
Description and characterization of the digestive gland microbiome in the freshwater mussel Villosa nebulosa (Bivalvia: Unionidae)

Here we characterize the digestive gland microbiome from wild and cultured (hatchery-reared) Alabama rainbows (Villosa nebulosa) using 16 S rRNA gene pyrosequencing in order to understand the effects of propagation on microbial community structure in freshwater mussels. Digestive glands from nine Alabama rainbows were analysed, five from the wild and four from a hatchery. Pyrosequencing yielded a total of 32,962 bacterial sequences and 387 operational taxonomic units (OTUs). Tenericutes was the dominant phylum in all samples (>87%), followed by Proteobacteria (4.6%), Fusobacteria (4.5%) and Bacteroidetes (1.4%). Digestive gland microbiomes were overwhelmingly dominated by OTUs related to the genus Mycoplasma. These Mycoplasma-like sequences could not be ascribed unequivocally to the genus Mycoplasma (less than 90% sequence identity) and probably represent new lineages within the class Mollicutes. We identified a core microbiome in the digestive gland of V. nebulosa, with all individual mussels sharing 9 OTUs. However, the microbiome from mussels collected from the wild was significantly different from that of hatchery-reared mussels. Our results show that novel microbial communities exist within the digestive gland of freshwater mussels.
Regulação do metabolismo de glicose e ácido graxo no músculo esquelético durante exercício físico

The glucose-fatty acid cycle explains the preference for fatty acid during moderate and long duration physical exercise. In contrast, there is a high glucose availability and oxidation rate in response to intense physical exercise. The reactive oxygen species (ROS) production during physical exercise suggests that the redox balance is important to regulate of lipids/carbohydrate metabolism. ROS reduces the activity of the Krebs cycle, and increases the activity of mitochondrial uncoupling proteins. The opposite effects happen during moderate physical activity. Thus, some issues is highlighted in the present review: Why does skeletal muscle prefer lipids in the basal and during moderate physical activity? Why does glucose-fatty acid fail to carry out their effects during intense physical exercise? How skeletal muscles regulate the lipids and carbohydrate metabolism during the contraction-relaxation cycle?
Effect of Mycobacterium avium subsp. paratuberculosis serostatus on carcass weight and conformation and fat cover scores

The paper was designed to assess the influence of Mycobacterium avium subsp. paratuberculosis (MAP) infection status of cows at culling (antibody positive vs negative) on carcass traits: weight and conformation and fat cover scores. A generalized least squares linear model was used to assess the influence of MAP on weight. Subsequently, a random effects logistic regression was completed in order to model the relation between MAP and conformation score (fair vs poor carcasses). A random effects ordered logistic model was used to estimate the influence on fat cover. The results indicated that seropositives had carcass weights 58.45 (34.65-83.35) kg lower than seronegatives. Regarding conformation score, the odds of having poor conformation instead of fair was 3.85 (1.35-11.85) times higher in seropositives. The odds of seropositives achieving a higher fat cover was approximately 5 (1.41-9.09) times lower than the odds for seronegatives. The estimated effects could be useful when assessing the economic benefits of a paratuberculosis control program.
Prevalence of heart disease in a population of domestic cats in Poland: A retrospective study

The survey included 514 cats brought to the Department of Small Animals within 5 years. The cats were examined cardiologically (clinical examination, echocardiography and electrocardiographic examination) and then divided into cats with cardiac changes and cats with problems other than heart disease. The study was designed to show the most common cardiac disease in cats and the breeds represented. The study found that the most prevalent cardiac diseases in cats were cardiomyopathies, which were found in 16% of all cats examined, while congenital malformations were found in 8% of the cats. Cats of 19 different breeds were represented, most of which were European Shorthair cats and Maine Coons. The European Shorthair breed had the largest number of healthy cats (40.9% of all healthy cats) as well as the largest number of cats with congenital heart disease (35.9% of all cats with congenital heart disease) and the largest number of cats with cardiomyopathies (50.6% of all cats with cardiomyopathies).
Geographic distribution modeling of the margay (Leopardus wiedii) and jaguarundi (Puma yagouaroundi): a comparative assessment

The Neotropical region currently harbors 8 recognized species of small cats, including the margay (Leopardus wiedii) and jaguarundi (Puma yagouaroundi). These similar-sized species have broad geographic distributions and commonly occur in sympatry. We constructed species occurrence databases and used the maximum entropy (Maxent) modeling approach to develop models of habitat suitability for each of these species. We identified the environmental predictors with the highest importance for species occurrence and evaluated how they influence habitat suitability for both wild cats. Variables related to temperature and precipitation were good predictors of species occurrence, with both cats responding similarly to them. However, margay showed higher variation in habitat suitability depending on local climatic predictors. The estimated models indicated high niche similarity (> 76%) between these cats, but despite this we identified different areas with the most favorable conditions for each species' occurrence. Approximately 50% and 72% of the entire suitable area were estimated as being moderately to highly suitable for margay and jaguarundi, respectively, with the margay model comprising a higher proportion of forest environments in comparison to that of the jaguarundi. These findings will be relevant in the context of conservation planning when indicating the priority areas for their long-term preservation.
Length–weight relationships for 22 crustaceans and cephalopods from the Gulf of Cadiz (SW Spain)

Life history traits are available for many fish species in different regions, but less so for invertebrates such as cephalopods and crustaceans, though, they are increasingly needed for implementing an ecosystem-based approach. Recent food web modelling in the Gulf of Cadiz has identified invertebrates as keystone groups. However, information on life history traits of such groups remains incomplete in this region. To fill this knowledge gap, we report length–weight relationships for 12 cephalopods and 10 crustaceans collected in the Gulf of Cadiz from 2009 to 2013. This study reports, for the first time, life history traits of nine species in the area (Chlorotocus crassicornis , Pasiphaea sivado , Plesionika heterocarpus , Plesionika martia , Processa canaliculata , Solenocera membranacea , Allotheutis media , Sepia orbignyana and Sepietta oweniana ). For each species, length–weight relationships, minimum and maximum lengths, mean weights, and depth ranges are presented. Overall, the results revealed that all species showed negative allometric growth (hypoallometry), except P. sivado , the only species showing an isometric growth pattern. We expect that this study will contribute to link sustainable fisheries with biodiversity conservation goals enabling the implementation of operational ecosystem-based management in the Gulf of Cadiz.
Developing novel transgenic reporters to study Lowe syndrome in zebrafish

12 Declaration . 13 Copyright . 14 Acknowledgements. 15 Abbreviations . 16 Chapter 1: Introduction . 19 1.1 Lowe Syndrome and Dent’s Disease . 20 1.1.1 The structure of OCRL1 . 20 1.1.2 OCRL1 cellular localisation . 22 1.1.3 OCRL1 functions in phosphoinositide homeostasis. 23 1.1.4 OCRL1 is required for membrane trafficking and endocytosis. 25 1.1.5 Other cellular functions of OCRL1 . 26 1.1.5.1 Actin dynamics . 26 1.1.5.2 Ciliogenesis . 27 1.1.5.3 Cell polarity . 28 1.1.5.4 Cell migration . 28 1.1.5.5 Cytokinesis . 28 1.1. 6 Genetic conservation and homologous genes . 29 1.2 The vertebrate kidney . 30 1.2.1 Gross structure of the kidney . 30 2 1.2.2.1 The glomerulus . 32 1.2.2. 2 The proximal tubule . 33 1.2.2.3 The loop of Henle . 34 1.2.2.4 Distal tubule and collecting duct . 34 1.3 Megalin mediated endocytosis in the renal tubule . 35 1.3.1 Megalin and cubulin structure . 35 1.3.2 Trafficking in the proximal tubule . 38 1.3.3 Diseases associated with megalin . 38 1.4 Zebrafish as a model organism . 39 1.4. 1 The zebrafish kidney . 39 1.4. 2 Zebrafish kidney models . 41 1.4. 3 Assessment of renal function in zebrafish . 42 1.4. 4 Phenotypic screening in zebrafish . 43 1.4. 5 Zebrafish as a model of Lowe syndrome . 43 1.5 Transgenic methods in zebrafish . 45 Chapter 2: Aims . 47 2.1 Aims of the project . 48 Chapter 3: Materials and Methods . 52 3.1 List of reagents. 53 3.2 List of antibodies . 55 3.3 Molecular cloning methods . 56 3.3.1 Genomic DNA extraction . 56 3.3.2 RNA Extraction . 56 3 3.3.3 cDNA synthesis . 57 3.3.4 Polymerase chain reaction . 57 3.3.5 DNA and RNA visualisation . 58 3.3.6 Restriction enzyme digestion . 58 3.3. 7 Vector/Insert ligation . 59 3.3. 8 Bacterial transformation . 59 3.3. 9 Culture Media . 59 3.3.10 Screening for ligation inserts. 59 3.3.11 Miniprep of plasmid DNA . 60 3.3.12 Maxiprep of plasmid DNA . 60 3.3.12 DNA sequencing . 60 3.3.13 Gateway Cloning . 60 3.3.14 Cloning for fusion proteins . 61 3.3.15 Plasmid generation . 61 3.4 Bacterial protein expression . 63 3.4. 3 Optimization of expression . 63 3.4. 4 Large scale protein purification . 64 3.5 Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis (SDS-PAGE) . 65 3.5.1 Gel Preparation . 65 3.5.2 Coomassie Staining . 66 3.6 Cell culture . 66 3.6. 1 Maintenance of cells . 66
Formação de biofilme em aço inoxidável por Aeromonas hydrophila e Staphylococcus aureus usando leite e diferentes condições de cultivo Biofilm formation by Aeromonas hydrophila and Staphylococcus aureus on stainless steel using milk and different conditions of cultivation

The aim of this research was to verify the capability of biofilm formation on stainless steel by Aeromonas hydrophila and Staphylococcus aureus using milk and different conditions of cultivation. The variables consisted in mono and multi-species cultivation of these microorganisms and in the temperatures of 4, 7 and 18 °C. Containers containing 1000 mL of milk, population density of 10 5 CFU.mL –1 of each microorganism, and ten suspended chips of stainless steel AISI 304 (10 × 20 mm) were used to seal up and storage, under 60 rpm of agitation for 10 days. The analyses were conducted every 48 hours. Sessile cells of A. hydrophila and S. aureus and were enumerated by plating in m-Aeromonas selective agar and Baird-Parker agar. Complementary studies included the generation time calculation, enumeration of planktonic cells, and visualization of chips by scanning electron microscopy. S. aureus, in mono-cultivation, formed biofilm at 18 °C and at 7 °C. At 4 °C was observed attachment. The presence of A. hydrophila reduced the performance of S. aureus. In this condition, S. aureus formed biofilm at 18 °C. A. hydrophila formed biofilm under all conditions.
Two commercial formulations of natural compounds for Varroa destructor (Acari: Varroidae) control on Africanized bees under tropical climatic conditions

It is not uncommon for natural pesticide products to perform inconsistently under different test conditions. Because patented treatments based on natural products have not been tested for the control of Varroa destructor on Africanized hybrid bees under tropical climates in field conditions, an experiment comparing the efficacy of two such natural products was performed. Apilife Var® is a product based on thymol, menthol, eucalyptus and camphor, mixed in a matrix of vermiculite. Hive Clean® contains oxalic acid, sucrose, citric acid, formic acid and propolis. Eighteen Jumbo type hives with Africanized hybrid bees of Apis mellifera from the central region of Veracruz, Mexico, were used. A hive was considered as an experimental unit. Hive Clean® and Apilife Var® treatments consisted of 6 hives each, and the control consisted of 3 hives at an apiary at Tejería, Veracruz, Mexico. The experiment took place from October to December 2013, with an average temperature of 28° C. A Mann-Whitney Rank Sum test was used to separate the corrected percentage of fallen varroa. Apilife Var® was significantly more effective (p = 0.002) with a median number of fallen varroa of 95.8% (mean = 95.5%). The results show that Apilife Var® is a product with a considerable acaricide action on varroa infestations, with an even emission of volatiles under a tropical subhumid climate, with no harm to the bee population on the hive. On the other hand, Hive Clean® showed a median percentage of fallen varroa of 19.7% (mean = 16.7%), indicating lower efficacy levels than those reported by European laboratories under temperate climates and with European bees (A. mellifera carnica). Thus, this product may need to be reformulated and re-tested under tropical climate conditions with Africanized bees.
Phosphoproteomic profiling of microsomal fractions in leaves of Cogon grass ('Imperata cylindrica')

Cogon grass ['Imperata cylindrica' (L.) Beauv. var. 'major'] is one of the top-ten weeds. It is a distributed C4 plant. In particular, one ecotype (Chuwei) is salt and flooding tolerant. Imperata leaves harvested from Chuwei and Sarlun control site were subjected to microsomal fractionation followed by membrane shaving using trypsin. The resulting peptides were further enriched by columns and mass spectrometry analyses for phosphopeptide identification. The phosphoproteomic analysis identified 20 phosphorylation sites from 16 unique phosphorylated peptides in the microsomal fractions isolated from leaves of 'Imperata', of which 5 are specific to Chuwei ecotype. Out of these 5 phosphopeptides, 2 belong to sugar transporters, including a sucrose transporter SUT1 which appears to be a novel and C4-specific phosphorylation site. Whereas the other 3 belong to photosynthesis proteins of which 2 are C4 enzymes. Interestingly, two independent phosphopeptides of tonoplast monosaccharide transporter 2 (TMT2) were identified in Chuwei ecotype and the other salt-intolerant Sarlun population individually. Our phosphoproteomic study identified differentially phosphorylated peptides of membrane proteins which may play an important role in the salt stress response of 'Imperata'.
The Incidence of Hepatitis E Virus in Domestic Pigs

Abstract Hepatitis E virus (HEV) is the causative agent of hepatitis E — an emerging zoonotic disease distributed worldwide. The aim of this study was to determine the prevalence of HEV in Slovakian domestic pigs, as this has not been studied yet. Clinical samples (n = 269) from fourteen randomly selected domestic pig farms for three different age categories of pigs were analysed and the subsequently detected isolates were genetically characterized. The reverse transcriptase polymerase chain reaction (RT-PCR) analysis revealed that 32 pigs (11.9 %) of all age categories were HEV RNA positive. The highest occurrence was detected in fattening pigs (14.8 %) and the lowest in weaning pigs (12.5 %). The HEV RNA was not observed at all in the youngest category (the suckling piglets). The phylogenetic analysis revealed that all Slovak HEV isolates clustered into two genetic groups of the genotype HEV-3.
Chlamydia muridarum Alters the Immune Environment of the Murine Genital Tract to be More Permissive for Infection with Neisseria gonorrhoeae in a Novel Coinfection Model

Abstract : Coinfection with Neisseria gonorrhoeae and Chlamydia trachomatis occurs frequently, yet studies of the interaction between these two pathogens within the host have been hindered by the lack of an experimental model. Here we describe development and characterization of a female mouse model of gonococcal and chlamydial coinfection. BALB/c mice were first infected with C. muridarum, the mouse chlamydiae, and then inoculated with N. gonorrhoeae following estradiol treatment to promote long-term gonococcal colonization. Viable gonococci and chlamydiae were recovered by vaginal swab and organisms were visible in the tissue by immunohistochemical staining. Coinfected mice had a higher percentage of vaginal neutrophils compared to mice infected with either pathogen alone and significantly more gonococci were recovered from coinfected mice compared to mice infected with N. gonorrhoeae alone.
The Future of Urban Brown Bear Management in Sapporo, Hokkaido, Japan: a Review

Abstract. Recently, brown bears have moved deeper inside urban areas in Sapporo, the fifth-largest city with a population of 1.9 million in Japan. Here, I review urban large carnivore management and its human dimension and discuss how to create a model of harmonious coexistence that includes both management of human—brown bear conflict (HBC) and conservation of the lush, green environment of Sapporo. Although large carnivores that use urban landscapes can temporarily obtain an abundance of high-energy foods, they are also subject to high rates of human-derived mortality. Brown bear invasions of the city center of Sapporo are still rare and are likely caused by bear population increase and distribution expansion within the last decade. It is important to manage urban borders to reduce their attractiveness. A verdant environment and biodiversity conservation are considered to be important to urban residents in Sapporo. Urban HBC, however, is an unavoidable consequence of this style of living. Because a variety of stakeholders affected by HBC and its management live in the city, their various values should be reflected in wildlife management policy through a more collaborative, community-based decision-making model.