Miracle-dz/UniFAR-FTUs huggingface dataset:
High incidence of otolith abnormality in juvenile European flounder Platichthys flesus from a tidal freshwater area

ABSTRACT Otolith abnormality has been reported for a wide range of freshwater and marine fish species. In this study, the sagittal otolith morphology and mineralogy of juvenile European flounder, Platichthys flesus, were examined to describe the incidence and types of structural deformities in this species. Juvenile flounder were collected over the years 2013–2015 in the tidal freshwater section of an estuarine nursery (Minho estuary, NW Portugal). Otolith abnormality was found in 43% of the individuals and, in most cases, occurred in both otoliths. Despite an abnormal mineralogy confirmed by scanning electron microscopy, the morphometry and the mineral polymorph composition of abnormal otoliths did not differ from normal ones (i.e. aragonite). This contrasts with other studies where vaterite and/or calcite were found to replace aragonite in abnormal otoliths. Further studies are needed to elucidate whether abrupt salinity changes associated with habitat transitions may have played a role in the abnormal otolith biomineralization in this species.
The effect of bacterial colonization of the embryo transfer catheter on Outcome of In vitro Fertilization–Embryo transfer treatment

Background: In vitro fertilization–embryo transfer (IVF − ET) has become a core treatment method for managing infertility. Bacterial contamination of the ET catheter may affect outcome, but there is still no consensus of evidence. Objectives: This study aims to assess the effect of bacterial colonization of the ET catheter tip on the clinical pregnancy rate in an IVF–ET treatment. Methods: An analytical cross-sectional study among women undergoing IVF–ET treatment was undertaken. The patients selected had both cervical swab and the tip of the ET catheter cultured. The patients were grouped into positive (bacterial isolated) and negative (no bacterial isolated) based on the culture result. The clinical pregnancy rate (primary outcome) between the two groups was compared. Results: A total of 80 patients were selected. In 34 patients (42.25%), the cervical culture was positive, while 46 patients (57.50%) had negative cervical culture. Catheter tip culture was positive in 27 patients (33.75%) and negative in 53 patients (66.25%). The predominant microorganisms isolated were Escherichia coli (23.75%), Staphylococcus spp. (18.75%), and Streptococcus spp. (15.00%). The clinical pregnancy rate was 26.25%. The significant factors affecting clinical pregnancy were the age of the patient (P = 0.044), duration of infertility (P = 0.01), and culture result (P = 0.03). Conclusion: Bacterial colonization of the ET catheter tip is associated with a reduction in the clinical pregnancy rate. Utility of routine cervical swab; microscopy, culture, and sensitivity at recruitment of patients for IVF–ET treatment is highlighted.
The Histone H3, Lysine 79 Methyltransferase Activity of DOT1L is Necessary for Murine Yolk Sac Erythro-Myeloid Progenitor Self-Renewal and Erythroblast Survival

Disruptor of Telomere silencing 1-Like (DOT1L), is a histone 3, lysine 79 (H3K79) methyltransferase that has been implicated in multiple processes, including activation of transcription, regulation of the cell cycle, leukemogenesis, and mouse embryonic development. Previous studies found that Dot1L deficiency results in an erythropoietic defect, leading to lethal anemia at around mid-gestation (Feng et al., 2010, Blood). The precise molecular mechanism(s) by which DOT1L regulates embryonic hematopoiesis has not yet been elucidated, however. DOT1L is a large protein (1540aa), and it is involved in several, diverse processes. However, its only documented activity has been as an intrinsic, histone methyltransferase. Additional functional domains of the protein might be responsible for its diverse activities, including murine hematopoiesis. This study sought to determine whether the methyltransferase activity of DOT1L is essential for hematopoiesis. To test this hypothesis, a Dot1L methyltransferase mutant (Dot1L MM) mouse line was created. Using the Cas9/CRISPR system, a Dot1L point mutation was induced in cultured murine embryonic stem cells (mESC). These mESCs contained a wildtype allele, and the second had a single amino acid change in the methyltransferase domain of Dot1L, thereby eliminating its methyltransferase activity, but preserving the rest of the protein. These mutant mESCs were injected into blastocysts to produce chimeric mice. The chimeras possessing the methyltransferase mutation were back crossed onto the C57/BL6 background, producing male and female offspring heterozygous for the mutation. Through intercrosses of the F1 generation, it was found that the Dot1L MM mice display an embryonic lethality between embryonic days 10.5 and 13.5, similar to the Dot1L knockout mice, as reported in our previous studies. Additionally, ex vivo blood differentiation assays and extensively self-renewing erythroblast (ESRE) cultures were performed using E10.5 yolk sacs from Dot1L MM and knockout mice. The data showed that the Dot1L MM and knockout yolk sacs display similar phenotypes. In blood differentiation cultures, Dot1L knockout and MM yolk sac cells form the same types of hematopoietic colonies as in wildtype (erythroid, myeloid, and mixed), but there is a decrease in colony size and number compared to the wildtype. In the ESRE cultures, Dot1L knockout and MM yolk sac cells form significantly fewer ESREs and have increased cell death compared to wildtype. Strikingly, the cells in these cultures also exhibit a profound genomic instability, implicating DOT1L methyltransferase activity in maintenance of the genome as well as the viability of hematopoietic progenitors. These results suggest that the methyltransferase activity of DOT1L plays a predominant role in the activity of the protein as a whole, and is responsible for its function in facilitating early murine hematopoiesis.
Metabolic Abnormalities and Adipose Tissue Leukocyte Dynamics in a Murine Model of Obesity, Weight Loss, and Weight Regain

x Chapter 1 – Introduction . 1 Defining Obesity . 1 Epidemiology of Obesity . 3 Comorbidities Associated with Obesity . 4 Murine Models of Obesity . 6 Molecular Drivers of Obesity-Associated Insulin Resistance and Inflammation 9 Leukocyte Mediators of Obesity-Associated Inflammation . 13 Scope of the Dissertation. 19 Chapter 2 – Adipose Tissue Dendritic Cells are Independent Contributors to Obesity-Induced Inflammation and Insulin Resistance . 24 Abstract . 24. 24 Introduction . 25 Materials and Methods . 27 Results . 32 Discussion . 45 Chapter 3 – Macrophage Proliferation Sustains Adipose Tissue Inflammation in Formerly Obese Mice . 51 Abstract . 51. 51
CCR5 antagonists used as topical microbicides modulate CCR5 expression and may potentially compound HIV infection

CCR5 antagonists, such as Maraviroc (MVC) and 5P12-RANTES, are being evaluated as HIV preventatives. The advantage of these drugs is that they restrict HIV entry via CCR5 receptor. However, sub-clinical concentrations could paradoxically increase HIV risk by increasing CCR5 expression. Peripheral blood mononuclear cells (PBMCs) and cervical tissues were cultured with one HIV antiretrovirals (ARVs), Maraviroc (MVC), 5P12-RANTES, dapivirine (DPV), or griffithsin (GRFT). Immune cells isolated from PBMCs/cervical tissue were stained with live/dead stain and monoclonal antibodies. Samples were analyzed using a BD LSRII flow cytometer and FlowJo v. 10.1 software. To determine if suboptimal concentrations of antiretrovirals (ARVs) influence HIV susceptibility, PBMCs/cervical tissue were treated with MVC, 5P12-RANTES, DPV, or GRFT and challenged with HIV-1BaL. Supernatant was collected on days 3, 7, and 11 and then tested for viral p24 by the AlphaLISA. In PBMCs, 10 nM and 1nM MVC induced significant enhancement of CCR5+ expression levels when compared to DPV or GRFT treated cells, respectively. There were no significant changes in CCR5 MFI or percent positive cells found in the cervical tissue. HIV replication, via p24 production, did not increase for any drug concentration in PBMCs, but 975nM MVC significantly increased p24 expression in cervical tissue. MVC is an effective therapeutic for HIV-infected persons, but may be problematic for HIV prevention due to its dose and time dependent qualities. Likewise, 5P12-RANTES showed similar trends in CCR5 expression. Topical application of CCR5 antagonists may be effective for only a short period in the genital tract. Conversely, DPV and GRFT did not affect CCR5 expression. The use of CCR5 antagonists for HIV prevention should be reconsidered as other options become available. The public health impact of improving topical HIV drugs could potentially reduce global HIV prevalence and shift toward an HIV-free world.
Genetic regulation of growth and nutrient content under phosphorus deficiency in the wild barley introgression library S42IL

Phosphorus (P) is an important macronutrient required for plant growth and yield formation. Since decades, breeders aim to optimize P efficiency in crops. We studied a set of 47 wild barley (Hordeum vulgare ssp. spontaneum, Hsp) introgression lines (ILs) in hydroponic culture to identify quantitative trait loci (QTLs) improving growth and nutrient content under P deficiency. Applying a mixed model analysis, a total of 91 independent QTLs were located among 39 ILs, of which 64 QTLs displayed trait-improving Hsp effects. For example, an unknown Hsp allele on barley chromosome 4H increased shoot dry weight under P deficiency in three overlapping ILs by 25.9%. Likewise, an Hsp allele on barley chromosome 6H increased root dry weight under P deficiency in two overlapping ILs by 27.6%. In total, 31 QTLs confirmed Hsp effects already identified in previous field and glasshouse experiments with the same ILs. We conclude that wild barley contains numerous trait-improving QTL alleles, which are active under P deficiency. In future, the underlying genes can be subjected to cloning and, simultaneously, used in elite barley breeding.
Diversity and Efficiency of Rhizobia Communities from Iron Mining Areas Using Cowpea as a Trap Plant

ABSTRACT Mining is an important economic activity. However, its impact on environment must be accessed, mainly on relevant processes for their sustainability. The objective of this study was to evaluate the diversity and efficiency of symbiotic nitrogen fixing bacterial communities in soils under different types of vegetation in the Quadrilatero Ferrifero: ironstone outcrops, Atlantic Forest, neotropical savanna, and a rehabilitated area revegetated with grass. Suspensions of soil samples collected under each type of vegetation were made in a saline solution [. ]
Modulation Of Transcription In The Murine Gut Epithelium In Development, Differentiation, And Disease

The intestinal epithelium is a continuously self-renewing tissue that must balance its function as the site of nutrient absorption with its role as a barrier between the body and the external environment. With its high cellular turnover and continual exposure to lumenal antigens, the intestinal epithelium is highly susceptible to developing diseases, such as inflammatory bowel disease (IBD) and cancer. Understanding the factors that control intestinal epithelial development are key to discovering disease etiology and to engineering new treatments. In mammals, studies have pointed to dysregulation of RNA Polymerase III as playing a role in oncogenic transformation. A deletion in the gene encoding Polr3b, a Pol III subunit, impairs development of the intestinal epithelial progenitor cells in zebrafish. Thus, I hypothesized that POLR3B also has an important role in the mammalian intestinal epithelium. I characterized mice expressing an intestinal epithelium-specific hypomorphic Polr3b mutation. Neonatal Polr3b mutants have severely reduced survival and growth, reduced intestinal epithelial proliferation, and lack normal crypt development. Thus, Pol III is essential for the establishment of the intestinal epithelium in mice. Given that normal Pol III is required for adequate protein production in order to sustain the high rate of proliferation in mammalian gut, this enzyme is a questionable target for cancer drugs. It was reported that Mucin2 (Muc2), the main component of intestinal mucus, is a direct transcriptional target of FOXA1 and FOXA2 in the mouse intestinal epithelium. I hypothesized that in addition to Muc2, the FOXA factors transcriptionally regulate other genes that are required for the maintenance of the intestinal mucosa. The Foxa1/a2-deficient colonic epithelium in mice of advanced age (>7 months) displays increased susceptibility to spontaneous colitis. I performed FOXA1 and FOXA2 chromatin immunoprecipitation assays followed by ultra-high throughput sequencing (ChIP-Seq) analysis on wild type mouse colonic crypts, as well as RNA-seq on Foxa1/a2-deficient and control aged colon. Of the FOXA1/ A2-bound, differentially expressed genes, glycosyltransferases were overrepresented, including the IBD risk gene Fut2, which was downregulated in mutant colon. Degree Type Dissertation Degree Name Doctor of Philosophy (PhD) Graduate Group Cell & Molecular Biology First Advisor Klaus H. Kaestner Second Advisor Jonathan P. Katz This dissertation is available at ScholarlyCommons: https://repository.upenn. edu/edissertations/2388
Assessment and Potential Application of the Probiotic Strain, Bacillus amyloliquefaciens JFP2, Isolated from Fermented Seafood-Jeotgal in Flounder Paralichthys olivaceus Juveniles

The strain Bacillus amyloliquefaciens JFP2 was isolated from Jeotgal, traditional fermented seafood from Jeju Island, South Korea to assess its probiotic and antibacterial effect against fish pathogens. The isolate JFP2 was identified using scanning electron microscopic analysis and 16S rRNA gene sequence analysis. The isolated strain, B. amyloliquefaciens JFP2 showed a broad spectrum of antibacterial activity against both Gram-positive and Gramnegative fish pathogenic bacteria namely Aeromonas hydrophila, Edwardsiella tarda, Photobacterium damselase sup-sps, Photobacterium phosphoreum, Streptococcous parauberis, S. iniae and Vibrio anguillaram. The bacteriocin JFP2 with a molecular mass of 37 kDa that was purified by ammonium sulphate precipitation followed by carboxymethyl-Sephadex column chromatography, showed antibacterial activity at a range of temperatures, from 4o-45oC and at a range of pH values from 2-12. However, loss of antibacterial activity was observed after treating the bacteriocin with proteolytic enzymes such as pepsin, proteinase K, and trypsin. The mode of antibacterial action shown by the bacteriocin JFP2 was bacteriolytic in nature, resulting in cell wall degradation of A. hydrophila. Dietary inclusion of the isolated JFP2 strain showed improved growth performance in juvenile flounder along with increased disease resistance against Streptococcus iniae. These results indicate that the bacteriocin JFP2 belongs to class IIIa bacteriocin that could be used as a potential alternative antibacterial agent to control pathogenic diseases in aquaculture and seafood industries. The IJA appears exclusively as a peer-reviewed on-line open-access journal at http://www.siamb. org.il. To read papers free of charge, please register online at registration form. Sale of IJA papers is strictly forbidden.
Morphology, phylogeny, growth rate and nodularin production of Nodularia spumigena from Brazil

ABSTRACT Blooms of the toxic cyanobacterium Nodularia spumigena occur in various locations worldwide, but have not been observed in Brazil until recently. Three Nodularia strains were isolated from summer blooms in experimental shrimp production ponds of Penaeus vannamei in Rio Grande, in southern Brazil; these strains were characterized by morphology, phylogeny, growth rate and toxicity. The strains were identified as N. spumigena based on the size of vegetative cells, heterocytes and akinetes under a light microscope and based on the number of gas vesicles per μm2 under a transmission electron microscope. The 16S rRNA gene sequences of the three strains showed high identity (> 99%) with N. spumigena sequences available on the NCBI database but were grouped closer in the phylogenetic tree with N. spumigena strains from Australia and USA than those from the Baltic Sea. The growth rate in batch culture varied between 0.2 and 0.6 μ d−1 based on cell density, optical density and chlorophyll-a content. The three strains produced the hepatotoxin nodularin (ELISA plate kit) with similar toxicity values (4.8–4.9 µg l−1). We conclude that the three isolated strains are N. spumigena with similar rates of growth and nodularin production. The presence of N. spumigena now represents a potential problem in aquaculture and estuarine environments in Brazil.
Comparative study of the inhibitory efficacy of some medicinal plant oils on the growth of pure isolates from a group of pathogenic microorganisms in vitro

The present in vitro study was undertaken to evaluate the antimicrobial efficacy of essential oils of four medicinal plants including: Eugenia caryophyllus, Sesamum indicum, Linum usitatissimum, and Mentha piperita against the growth of seven pathogenic microorganisms: two gram-positive bacteria; Staphylococcus cohnii cohnii, Micrococcus spp. , and five gram-negative bacteria; Pseudomonas aeroginosa, Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, and Enterobacter cloacae. The method employed to test the antimicrobial efficacy was the Agar Well Diffusion test. The antimicrobial activity of Eugenia caryophyllus oil against the growth of all the test microorganisms except Proteus mirabilis was statically superior to the rest of the test oils with mean diameter of zone of inhibition; 28.5±0.87 mm, 12.25±0.25 mm, 22.25±0.66 mm, 23.08±1.16 mm, 27.83±1.39 mm, and 10.91±0.39 mm against the growth of Staphylococcus cohnii cohnii, Micrococcus spp. , Pseudomonas aeroginosa, Escherichia coli, Klebsiella pneumoniae, and Enterobacter cloacae respectively. Sesamum indicum oil produce significant effect against Pseudomonas aeroginosa and Proteus mirabilis with mean diameter of zone of inhibition; 21.75±1.29 mm and 14.25±1.03 mm respectively. Linum usitatissimum revealed positive results against Micrococcus spp. Only with mean diameter of zone of inhibition; 30.41±0.46 mm. while the oil of Mentha piperita did not show any inhibitory activity against each of the test microorganisms.
The Phylogeny of the Prasinophyceae and Pleurastrophyceae (Chlorophyta) Inferred From Ribosomal RNA Genes and Morphology.

The phylogeny of the problematic green algal classes Prasinophyceae and Pleurastrophyceae (Chlorophyta) sensu Mattox and Stewart (1984) was inferred from ultrastructural and biochemical data, and from ribosomal RNA gene sequence data. Analysis of a data set of ultrastructural and biochemical characters (with a predominance of flagellar and cell covering features) revealed a monophyletic Pleurastrophyceae and a monophyletic Prasinophyceae. Rerooting experiments indicated that the ancestral flagellate was likely Pedinomonas-like or Mamiellales-1ike. The cladograms generated from the ribosomal RNA gene sequence data show that the Pleurastrophyceae is not monophyletic; however, pleurastrophycean taxa are more closely related to the Chlorophyceae than to any other class. The Ulvophyceae is the sister group to the Chlorophyceae plus Pleurastrophyceae clade. The Charophyceae and land plants represent a basal divergence relative to the Chlorophyceae plus
Effect of Irrigation Dose Based on Vegetation Indices Calculation Using Multispectral Sensor

The agricultural sector is vital for the Greek economy, the Greek producers and consumers. The new era in agriculture leads scientists to find new more effective ways to estimate plant growth and biomass production and to increase water use efficiency. Given the above, a research project was organized at the Laboratory of Agricultural Hydraulics, University of Thessaly. For the first time in the climatic conditions of Central Greece, the project aims to assess another method to estimate the growth and biomass production of corn, based on multispectral photos and vegetation indices using a low cost multispectral camera and drone. Three surface drip irrigation treatments in three replications were organized and a randomized complete block design was used. The crop water needs were calculated according to the daily evapotranspiration using the Penman-Monteith procedure as it was presented by the Food Agricultural Organisation. The amount of water in each treatment was equal to A) 100% of the daily evapotranspiration (ETo), B) 75% of the ETo, and C) 50% of the ETo. Vegetation indices were calculated based on multispectral photos taken from a drone and the Simple and Multiple Regression analysis were used to estimate the maize growth and biomass production in Greek conditions. Different equations were formed to estimate the maize growth and biomass production and vegetation indices were used as independent variables. The results showed that vegetation indices can be used in the agriculture process to estimate maize growth and biomass production. In this paper the results of two consecutive years, 2018 and 2019 are presented.
Studies on the process optimization for preparation of Chhana Kheer by using artificial sweetener aspartame

Kheer is a cereal based traditional dairy dessert. Chhana is a heat-acid coagulated product of milk. Chhana Kheer which is a conventional dessert containing chhana and sugar. Dietetic Chhana Kheer was developed with artificial sweetener aspartame so that it would serve as a dietetic food for consumer and offer the same delicacy as a traditional conventional dairy product.Four treatment samples were studied viz., T0 (Chhana Kheer Control) prepared from cow milk with sugar (@ 7%), T1, T2 and T3containing artificial sweetener aspartame at the rate of 0.010%, 0.015% and 0.020% respectively. Highest moisture percentage was recorded in the treatment T0 (52.72) followed by T1 (52.02), T2 (51.92) and T3 (51.56). All the treatments were sensorily acceptable but Treatment T1 received highest score (8.35) on 9 point Hedonic scale. The SPC count, Yeast and Mould count were within the limits of microbiological standards. The coliform count was obtained nil among all the samples. The cost of production observed a reducing trend from T0 to T3 which further added to the significance of experimental replacement of sugar with aspartame. Thus an acceptable quality of Chhana Kheer can be prepared using aspartame.
Magnetite (Fe3O4) Nanoparticles Alleviate Growth Inhibition and Oxidative Stress Caused by Heavy Metals in Young Seedlings of Cucumber (Cucumis Sativus L)

Accumulation of heavy metals in the ecosystem and their toxic effects through food chain can cause serious ecological and health problems. In the present study, experiments were performed to understand how the addition of magnetite (Fe3 O4 ) nanoparticles reduces the toxicity caused by Cd, Pb, Cu, and Zn in cucumber plants. Plant growth parameters, lipid peroxidation, and antioxidant enzymes were measured in seedling samples treated with either metals or metals supplemented with Fe3 O4 to demonstrate the reduction in metal-induced oxidative stress conferred by Fe3 O4 . Results showed that the toxic effect of metals on seedling growth parameters can be arranged in the rank order of inhibition as follows: Cu > Cd > Zn > Pb. Exposure to metals significantly decreased the seedlings growth, the activities of superoxide dismutase (SOD) and peroxidases (POD), while the malondialdehyde (MDA) content significantly increased in cucumber seedlings. The reducing activity of nano-Fe3 O4 against heavy metals stresses was confirmed in this study by the decrease in MDA content. The correlation between the decrease of MDA concentration and the increase in SOD and POD activities in the presence of nano-Fe3 O4 suggest that the MDA reduction in the tested seedlings can result from the increased enzyme activity.