Miracle-dz/UniFAR-FTUs huggingface dataset:
Mammary Epithelial Cell Subtype-Specific Analysis of Ras Pathway Activation

Breast cancers can be divided into subtypes based in part on how closely the tumor cells resemble mammary epithelial cell (MEC) subtypes resident in normal breast tissue. Though breast cancer subtypes differ in their aggressiveness and their response to treatment, the mechanisms by which distinct subtypes arise remain unknown. Traditionally, attempts to explain the varied clinical behavior of breast cancers rely on defining the genetic lesions harbored within individual tumors. However, recent evidence suggests that distinct breast cancer subtypes may arise from distinct MEC lineages, suggesting that some biological features of a given breast cancer subtype may be attributable to its antecedent “cell of origin”. Elucidating whether MEC lineage impacts the biology of descendant breast cancers presents a formidable challenge. By the time a tumor is clinically detectable, breast cancers have undergone clonal evolution that precludes a reliable retrospective determination of the cell of origin. As such, prospective analyses may be required to determine whether distinct MEC subtypes yield distinct cancer subtypes. We hypothesized that distinct MEC compartments yield different phenotypes in response to an identical oncogenic stimulus. To test this possibility, we generated mouse models that permit doxycycline-dependent expression of transgenes in an MEC compartment-restricted manner and developed strategies to monitor transgene-mediated phenotypes in real-time. As a first step toward studying malignant transformation of distinct MEC subtypes in mice, we tested experimental strategies designed to permit restriction of transgene expression to distinct MEC compartments in vitro. Transgenic mammary epithelium was partially disaggregated and propagated in 3D culture as mammary organoids, preserving the bilayered arrangement of the basal and luminal MEC compartments. Pairing a tet operator-driven H2BeGFP reporter transgene with either a basal or luminal MEC transactivator enabled MEC compartment-restricted reporter gene expression. Notably, nuclear fluorescence resulting from H2B-eGFP expression enabled visualization of cellular dynamics within discrete MEC compartments. Through extended, multiparameter live cell imaging of organoids, time-lapse movies were generated that enabled visualization of MEC migration as well as tracking and quantitation of mitotic and apoptotic events.
Biochemical Characterization of a Recombinant Xylanase from Thermus brockianus, Suitable for Biofuel Production

To discover new industrially relevant, thermoactive xylanases a gene library from Thermus brockianus was constructed. Function-based screening revealed a novel xylanaseencoding gene (xyn10) which was successfully expressed in E. coli BL21 (DE3). The resulting protein (38.7 kDa), a member of glycoside hydrolase family 10 was purified to homogeneity and biochemically characterized. Catalytic activity was detected up to 115 °C and highest activity was measured at 95 °C and pH 6.0. The protein was extremely thermostable and showed 80 % remaining activity after incubation at 50-70 °C for 24 h. HPLC analysis showed that Xyn10 hydrolyzes insoluble and soluble substrates, such as oat spelt xylan, xylan from beech- and birchwood forming xylobiose and xylose. Specific activity of the enzyme was 1119.5 U/mg for oat spelt xylan and 994.0 U/mg for beechwood xylan, respectively. The xylanase exhibited remarkable stability in the presence of various detergents and chaotropic agents, such as CHAPS, guanidine hydrochloride and urea.
Protonation-Dependent Diphosphate Cleavage in FPP Cyclases and Synthases

The cleavage of the magnesium-assisted diphosphate group (the PPi group) is one significant and prevalent rate-limiting step triggering the enzyme catalysis synthesis of terpenoid natural products. However, the PPi cleavage procedure has been rarely studied in most theoretical research of the terpenoid biosynthetic mechanism. In this work, QM(DFT)/MM MD simulations were employed to illuminate the detailed PPi cleavage mechanism in three different enzyme systems (ATAS, TEAS, and FPPS). We found that the most rational protonation state of the PPi group is highly dependent on the Mg2+ coordination modes and the enzyme classes. The deprotonation of PPi is favorable for triggering the catalysis reaction in ATAS, while monoprotonation in FPPS and biprotonation in TEAS are advantageous. As a result, similar PPi cleavage occurs by means of nucleophilic substitution reactions in TEAS/FPPS/ATAS but presents an SN1, SN2, and borderline mechanism, respectively. Finally, the alternative functions of PPi protonation an.
The Role of Mannitol and Mannitol Dehydrogenase in Plant-Pathogen Interactions

JENNINGS, DIANNE BROOKS. The Role of Mannitol and Mannitol Dehydrogenase in Plant-Pathogen Interactions. (under the direction of John David Williamson and David Mason Pharr.) Reactive oxygen species (ROS) are known to act as both signaling molecules and direct antimicrobial agents in plant defense against pathogens. Many plant pathogens have the ability to synthesize mannitol, a potent ROS quencher, and there is growing evidence that at least some phytopathogenic fungi use mannitol to suppress ROS mediated defenses. Here we show that mannitol production and secretion in the phytopathogenic fungus, Alternaria alternata is induced in the presence of host plant extracts. Additionally we demonstrate that the catabolic enzyme mannitol dehydrogenase (MTD) is induced in a non-mannitol-producing plant in response to both fungal elicitor and specific inducers of plant defense responses. This indicates a mechanism whereby the plant can counteract fungal suppression of ROS-mediated defenses by catabolizing mannitol of fungal origin. To further clarify this interaction, tobacco plants were transformed with celery Mtd cDNA under a constitutive promoter, resulting in production of an enzymatically active MTD protein. This constitutive MTD expression conferred enhanced resistance to A. alternata, and this resistance did not correlate with expression of PR1a, a protein often used as an indicator of systemic acquired resistance. Constitutive Mtd expression did not enhance tolerance to two non-mannitol secreting pathogens, the fungal pathogen Cercospora nicotianae and the bacterial pathogen Pseudomonas syringae pv. tabaci. These results are consistent with the hypothesis that MTD plays a role in plant resistance to mannitol secreting fungal pathogens by catabolizing mannitol of fungal origin. The Role of Mannitol and Mannitol Dehydrogenase in Plant-Pathogen Interactions by Dianne Brooks Jennings A dissertation submitted to the Graduate Faculty of North Carolina State University in partial fulfillment of the requirements for the Degree of Doctor of Philosophy Department of Horticultural Science and Plant Physiology Program
Synthesis and α-chymotrypsinolysis of regular poly(ester amides) based on phenylalanine, diols, and terephthalic acid

Regular poly(ester amides) containing rigid p-phenylene fragments in the backbone were synthesized by three different methods including (A) polycondensation of activated terephthalates with bis(L-plenylalanine)-α,ω-alkylene diester di-p-toluenesulfonates, (B) interaction of bisazlactones with aliphatic diols, and (C) polycondensation of N,N'-terephthaloyl-bis-L-phenylalanine potassium salts with 1,2-dibromoethane, Specific α-chymotrypsin-induced hydrolysis of the synthesized poly(ester amide)s and some low-molecular-mass substrates modeling the elementary unit of poly(ester amides) was studied by the method of potentiometric titration under nearly physiological conditions. Introduction of the rigid p-phenylene fragments instead of flexible poly(methylene) units markedly decreases the susceptibility of both low-molecular-mass substances and the corresponding macromolecules to the specific hydrolysis.
Long-term assessment of temporal variability in spatial patterns of early life stages of fishes to facilitate estuarine conservation

ABSTRACT Estuaries are among the most productive coastal ecosystems, supporting a wide variety of marine fishes and their early stages. High spatial and temporal variability in estuaries implies that management strategies must incorporate dynamic features to be efficient. In our study, we analysed 13 years of data on ichthyoplankton from the Patos Lagoon estuary (Brazil) to assess whether temporal variability can show distinct spatial patterns of fish eggs and larval distribution and to discuss how these results can be helpful to conservation planning. Spatial patterns of fish egg and larval assemblages were evaluated using cluster analysis. Indicator taxa for each group were also calculated as a product of the relative frequency and relative average abundance in each group. In addition, we used generalized linear models to analyse fish egg and larval abundance in relation to environmental variables. Results showed that fish eggs and larvae exhibit high variability among months, years and sampling stations in the time series. Temporal occurrence and spatial distribution were mainly associated with salinity. We found distinct spatial patterns for fish eggs and larvae in the Patos Lagoon estuary. Groups identified were different among years and indicated by a distinct genus. Our results can be considered as a first exploratory step to help managers to decide which species and temporal scale should be studied in detail and incorporated in management plans. Spatial conservation planning incorporating fluctuations in abundance and assemblage structure over time may help to ensure conservation for biodiversity persistence in highly dynamic ecosystems such as the Patos Lagoon estuary.
Shelf life improvement of sorghum beer (pito) through the addition of Moringa oleifera and pasteurization

Pito is a traditional alcoholic beverage that is mostly brewed in the three northern regions of Ghana. Although widely consumed and used in many festivities, poor storability limits its economic potential as an income-generating venture for most women. This study was carried out to improve the shelf-life of pito through the addition of Moringa oleifera leaf extract and pasteurization (75 to 80°C). Microbial enumeration, physico-chemical parameters (pH, extract (%) and alcohol) and consumer preference scores were used as quality indices of each pito treatment carried out. There was a general decline in coliform and fungi growth and in the physico-chemical (pH, extract (%) and alcohol) properties during the 56 days of storage. Microbial load, extract (%), alcohol content and pH were significantly different (P<0.05) among treatments. Pasteurized moringa pito had the least microbial load. The treated pito samples had higher values in pH, extract (%) and alcohol content than the untreated pito during storage. There was high consumer acceptability of pasteurized pito from the 0 day to the 28 days of storage, with a mean score of 4.27 ± 0.75 to 3.61 ± 1.36. However, the moringa treated pito (pasteurized moringa pito and moringa pito) was less preferred (with a mean score of 2.86 ± 1.19 to 1.87 ± 0.92) from the 0 day to the 28 days of storage. The untreated pito was also acceptable for a period of seven days. Based on the findings of this research, it can be concluded that pasteurization and/or the addition of M. oleifera leaf extract can improve the shelf-life of pito for four weeks, but addition of moringa extract in pito reduced consumer preference for it. Further research using other antimicrobial plants is recommended as consumers did not like pito with the M. oleifera leaf extract. Keywords: Moringa , pasteurization, pito, shelf-life, storage
Engagement of biotechnology in the protection of threatened plant species in Poland

The paper summarizes the contribution of various biotechnological techniques to the protection of the Polish flora. Polish national programmes of wild plant conservation follow the international conventions on the conservation of nature and wildlife. Among the 2750 plant species of the Polish flora, only 296 are listed in the Polish Red Book, but the list of threatened and protected plants includes about 500 species. Biotechnology could serve as a tool for plant protection in various aspects, but the most important among them are: (i) vegetative propagation in vitro; and (ii) protection of the morphogenetic potential of cultured cells, tissues and organs. Extended subcultures and cryopreservation in particular ensure a high level of competence in long-term cultures. For dicotyledons, monocotyledons and ferns, some examples of various biotechnological methods used are presented and discussed.
Allosteric dynamics of SAMHD1 studied by molecular dynamics simulations

SAMHD1 is a human cellular enzyme that blocks HIV-1 infection in myeloid cells and non-cycling CD4+T cells. The enzyme is an allosterically regulated triphosphohydrolase that modulates the level of cellular dNTP. The virus restriction is attributed to the lowering of the pool of dNTP in the cell to a point where reverse-transcription is impaired. Mutations in SAMHD1 are also implicated in Aicardi-Goutieres syndrome. A mechanistic understanding of the allosteric activation of the enzyme is still elusive. We have performed molecular dynamics simulations to examine the allosteric site dynamics of the protein and to examine the connection between the stability of the tetrameric complex and the Allosite occupancy.
Description of the larval stages of the Stromateoid fish Ariomma melanum, and its abundance and distribution in the Gulf of Mexico

The larval stages of Ariomma melanum are described from a series of specimens 2.0 mm to 24 mm SL. Specimens were collected primarily during annual spring ichthyoplankton surveys in the Gulf of Mexico from 1983 to 1987. A. melanum larvae may be identified as small as 2.0 mm based upon characters such as body shape, a bulbous occiput, and distinctive pigmentation patterns. Larvae were found primarily in the northeastern Gulf of Mexico. Adults are also concentrated in this area, occurring at bottom depths that ranged from 225 m to 480 m. Larvae were present at low levels throughout the year with peak abundance occurring in the spring and summer. Variation in abundance was also considerable between years. Larval A. melanum was most abundant in 1983, decreasing to a low in 1986, and was present in large numbers again in 1987. Substantial populations of A. melanum may exist along the deep shelf in the northeastern Gulf of Mexico. Sampling has been sporadic over the depth range of this species so real abundance is not known. However, even if the stocks are considerable, the potential for commercial exploitation is questionable at this time.
A 3D Culture System of Human Immortalized Myometrial Cells

[Abstract] Myometrium forms the middle layer of the uterus and is mainly composed of the smooth muscle cells. The cells in vitro are usually grown in a single layer (2-dimensional; 2D) format, whereas in vivo cells are structured in an extracellular matrix scaffolding that allows the cells to communicate and respond to environmental cues. We have developed human myometrium and leiomyoma 3-dimensional (3D) culture, wherein the cells retain their molecular characteristics and respond to environmental cues (Malik and Catherino, 2012; Malik et al. , 2014). [Background] using the artificial 2D format of cell culture into cell culture model system, where the cells are grown in a matrix that allows them to attach and more physiologic configuration. the cells with a more natural state of differentiation and the cultured cells develop an in vivo tissue-like environment. detailed protocol for 3D cell culture growth
Enzymatic Synthesis of Gallic Acid from Tannic Acid

The principle and method for enzymatic synthesis of gallic acid,isolation and selection of the Aspergillus niger strains, characteristics of this biotechnology, products quality of gallic acid and the uses in domestic food and pharmaceutical industries are briefly introduced. The process exhibits advantages of easily available raw materials, high tannin enzyme activity, stable production, low cost, easy operation and excellent product quality.
Increased Proliferating Activity and Bcl-2 Protein Expression in Eutopic Endometrium with Endometriosis

Objective: To evaluate the expression of proliferating activity and Bcl-2 protein property in eutopic endometrium with endometriosis. Methods: Endometrial tissues were obtained for endometrial biopsy from 2 groups of women. The study groups were 10 samples, which consisted of eutopic endometrial tissue with endometriosis. The remaining 10 samples were control group, which consisted of eutopic endometrial tissue without endometriosis. Expressions of Ki-67 and Bcl-2 protein were immunohistochemically investigated by polyclonal antibody. The computer program (Image pro (+), USA) was used to analysis the staining intensity of tissue samples objectively. Endometrial cells were cultured for 72 hours and the MTT colorimetric assay was used to detect cell proliferation. Results: In the group of eutopic endometrium with endometriosis, the activity of cell proliferation was significantly increased. The expression of Ki-67 protein and MTT assay were significantly higher than those in the control group. And expression of Bcl-2 protein was significantly higher than those in the control group (P
Expression of the dspA/E gene of Erwinia amylovora in non-host plant Arabidopsis thaliana

ABSTRACT In the Erwinia amylovora genome, the hrp gene cluster containing the dspA/E/EB/F operon plays a crucial role in mediating the pathogenicity and the hypersensitive response (HR) in the host plant. The role of the dspA/E gene derived from E. amylovora was investigated by monitoring the expression of the β-glucuronidase (GUS) reporter system in transgenic Arabidopsis thaliana cv. Pri-Gus seedlings. A mutant ΔdspA/E strain of E. amylovora was generated to contain a deletion of the dspA/E gene for the purpose of this study. Two-week-old seedlings of GUS transgenic Arabidopsis were vacuum-infiltrated with the wild-type and the mutant (ΔdspA/E) E. amylovora strains. The Arabidopsis seedlings were fixed and stained for GUS activity after 3–5 days following infiltration. The appearance of dense spots with blue staining on the Arabidopsis leaves indicated the typical characteristic of GUS activity. This observation indicated that the wild-type E. amylovora strain had induced a successful and efficient infection on the A. thaliana Pri-Gus leaves. In contrast, there was no visible GUS expression on leaf tissues which were inoculated with the ΔdspA/E mutant E. amylovora strain. These results indicate that the dspA/E gene is required by the bacterial cells to induce HR in non-host plants.
New contribution to the aphid fauna of Turkey

Au cours des 50 dernieres annees, l'inventaire de la faune aphidienne de la Turquie a remarquablement progresse : 35 especes reconnues en 1956, 90 en 1957, 219 en 1964, 258 en 1975 puis 410 a ce jour. La liste commentee de ces especes est suivie d'une importante bibliographie. Quelques especes peu connues telles que Macrosiphoniella aktashica (Nevsky, 1928) nouvelle combinaison, Mariaella lambersi Szelegiewicz, 1961 et Swirskiaphis polychaeta Hille Ris Lambers, 1966 sont l'objet d'une redescription couvrant non seulement les formes deja publiees mais aussi des formes inconnues auparavant comme l'aile et les sexues de la premiere espece, les sexues de la deuxieme et l'aile de la troisieme. Les 39 especes nouvellement signalees dans le present article, les 19 especes et sous-especes decrites de Turquie entre 1963 et 2005 et quelques autres especes sont generalement accompagnees d'un commentaire sur leur distribution geographique, leurs hotes et leurs particularites morphologiques.
Adaptation of a Single-Stage Chemostat System to Model Functional Aspects of the Human Distal Gut Microbiota

ADAPTATION OF A SINGLE-STAGE CHEMOSTAT SYSTEM TO MODEL FUNCTIONAL ASPECTS OF THE HUMAN DISTAL GUT MICROBIOTA Kathleen F.B. Schroeter Advisors: University of Guelph, 2014 Dr. Emma Allen-Vercoe and Dr. Cezar Khursigara The human gastrointestinal (GI) microbiota plays an important role in health and disease; in particular, commensal colonic biofilms have become a key focus of modern research efforts. However, in vitro models of the distal gut that also investigate colonic biofilm formation are still in their infancy. In this study we modified an in vitro single-stage chemostat model to successfully capture and sample the early colonizer biofilm communities associated with the healthy human distal gut. Mucin and sIgA, host-derived macromolecules used by the gut microbiota as binding sites for biofilm formation, were used to condition biofilm sampling sections. Fecal communities and defined microbial populations were used to validate the biofilm capture model and were analyzed with 16S-DGGE (a molecular fingerprinting technique) and community 16S rRNA gene sequencing. More diverse biofilm growth was captured on biologically relevant substrata compared to controls for all tested communities. We also identified members of the Enterobacteriaceae, Gammaproteobacteria incertae sedis, and to a lesser extent, the Streptococcaceae, Bifidobacteriaceae and Lactobacillaceae families as contributing to early biofilm formation. In addition, defined microbial communities were able to successfully simplify the fecal community from which they were isolated while still retaining considerable complexity in the planktonic (steady state) and biofilm forms. We were also able to create reproducible, defined microbial communities derived from feces that achieved the same ecological and functional steady state as one another in the chemostat model, despite the inclusion of isolate inocula with different starting biomass proportions. Overall, the research presented in this thesis has helped to advance our current understanding of the structure of healthy biofilm communities in the distal colon. This information may help to guide researchers and clinicians who aim to modulate the microbiota of patients with acute or chronic GI diseases, including the use of, for example, microbial ecosystem therapeutics to treat and cure Clostridium difficile infections. In the future, our experimental approach could also be applied to the investigation of different types of distal gut communities in a state of health and disease, in addition to other niches of the human microbiome, including vaginal, oral, skin and nasopharyngeal microbiotas.
Digestibility of Leaf Proteins of Gnetum spp Vegetables in Rats and Effects of Some Certain Antinutrients

Aims: Study digestibility of leaf proteins of Gnetum africanum and Gnetum buchholzianum and effects of some antinutritional factors on young male rats Wistar albinos . Study Design: Nutritional enhancement of use of Gnetum spp leafy vegetables. Methodology: Proteins and antinutritional factors were determined using standard analytical methods. Standard diet AIN-93 was used as reference for preparation of experimental diets used for in vivo digestibility of these leafy vegetables. Rats were fed with diets containing the corresponding 5% (GA5P and GB5P for G. africanum and G. buchholzianum respectively) or 10% (GA10P and GB10P) of leaf proteins. Results: Results showed that mean proteins contents was 16.70 mg/100g. Average contents of crude fibers, Neutral Detergent Fibers, Acid Detergent Fibers, crude phenolic compounds, tannins and phytates were respectively 36.17, 41.97, 37.80 g/100 g and 478.80, 244.94, 215.64 mg/100. Rats’ growth was more promoted by diets containing 5% proteins. Protein Efficiency Ratio and Net Protein Efficiency Ratio were low. Digestibility Coefficient, Biological Value and Net Protein Utilization were high for 5% proteins diets. Principal Component Analyses revealed that fibers and antinutrients reduced growth and nitrogen retention from diet containing 10% proteins. Conclusion: Gnetum spp. leafy vegetables have high contents of fiber, phenolic compounds and phytates which contribute to reduction of digestibility of theirs proteins.