Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of neural stem cells in tumourigenesis of the central nervous system

To develop targeted brain tumour therapies that carry fewer side effects it is essential to understand brain tumour histogeneiss and identify the cell of origin. It has been suggested that neoplastic transformation of neural stem/progenitor cells in the adult brain can result in the development of intrinsic brain tumours. Using the Cre-LoxP system we have developed a model that allows us to inactivate tumour suppressor genes Rb, p53 and PTEN in neural stem/progenitor cells both in vivo and in vitro. In vivo recombination of these tumour suppressor genes in neural stem/progenitor cells resulted in the formation of intrinsic brain tumours, with the phenotype depending on the combination of recombined genes. Intracerebral engraftment of in vitro recombined neural stem/progenitor cells produced a similar tumour phenotype pattern. However, while in vivo recombination of Rb and p53 frequently caused brain tumours, in vitro recombined and engrafted Rb-/-; p53-/- neurospheres rarely generated tumours. The converse was true following in vivo recombination of Rb and PTEN. These results suggest that microenvironment influences tumour formation. An increased number of tumourigenic neural stem/progenitor cells expressed the cancer stem cell marker CD133 when compared to control cells. In vivo engraftment of purified CD133+ Rb-/-; p53-/-; PTEN-/- neural stem/progenitor cells resulted in the preferential development of gliomas. We also showed that astrocytes are not capable of forming tumours following either orthotopic recombination or in vitro recombination and engraftment. In conclusion, we found that (i) certain phenotypes of brain tumours develop from neural stem/progenitor cells in the subventricular zone, (ii) the combination of inactivated tumour suppressor genes is the most significant but not sole determinant of in vitro functional profile and behaviour in vivo, (iii) the cellular microenvironment of neural stem/progenitor cells influences their tumourigenic profile, and (iv) terminally differentiated astrocytes do not contribute to tumour development in this model.
Effect of different agricultural practices on population dynamics of Azotobacter chroococcum and on its nitrogen fixing potentiality in Trans-Ganga and Trans-Yamuna plains of India

A study was conducted for two consecutive years 2003-04 and 2004-05 at Allahabad, one of the most fertile regions of Indo-Gangetic plane on wheat crop. The aim was to assess the effect of different agricultural practices on the population dynamics and nitrogen fixing potentiality of free living aerobic nitrogen fixing bacteria Azotobacter chroococcum. Heavy input of fertilizers, mechanical tillage, frequent irrigation, monocropping have resulted in decrease in population of Azotobacter chroococcum and its nitrogen fixing potentiality. The fields in which there was judicious use of chemical fertilizers along with crop rotation, use of FYM, low tillage practice shows better population of the Azotobacter chroococcum as well as nitrogen fixing potentiality. Crop rotation and use of the FYM have exerted better effect on the growth and development of Azotobacter chroococcum as well as its nitrogen fixing potentiality.
Functional and quantitative proteomics using SILAC in cancer research

In recent years, mass spectrometry-based proteomics has emerged as a powerful tool in cancer research and the importance of quantitation strategies has become appreciated. Several methods based on stable isotope coding and MS have been established and have become increasingly popular as alternatives to 2D-PAGE-based methods (Gorg et al., 2005). Among these methods, stable-isotope labeling by amino acids in cell culture (SILAC) has shown great promise for the simultaneous identifi cation and quantitation of complex protein mixtures (Mann, 2006). Here we present two applications of functional and quantitative proteomics in cancer research. In the fi rst approach, the discovery of novel FGFR3-related effectors and signaling mechanisms is being addressed. FGFR3 is one of the four receptor-tyrosine kinases that respond to fi broblast growth factor (FGF) and its overexpression has been related to bladder cancer, cervical carcinomas and multiple myeloma. In our experiments a bladder cancer cell line (RT112) and the HEK293 cell line stably transfected with FGFR3 are being used together with the SILAC strategy to compare protein expression levels in pY IPs from cells stimulated or unstimulated with Functional and quantitative proteomics using SILAC in cancer research
A Study of Nuclear Medicine Contrast Retention in Vascular Access Ports

Vascular access ports were investigated to determine the retention rate of injected radiotracers during PET scan acquisition. A total of 30 ports were tested, including 3 different port models from a single manufacturer. Both 18F-fluorodeoxyglucose (FDG) and 18F-Sodium Fluoride (Na18F) contrast agents were used. Radioactivity counts and images acquired by PET was the primary means used to identify retention of radioactivity in those ports. In repeatable experiments, AngioDynamicsTM port lines including Smart PortTM CT, BioFloTM Port, and BioFloTM Dual Port exhibited radioactive contrast retention ranged from 0.86 ± 0.12 to 1.38 ± 0.23%, following an injection of 10 mL saline. These port models tested satisfy the interest to be identified procedurally for potential use in clinical Nuclear Medicine PET contrast studies.
Estimation of Potential Evapotranspiration by Multiple Linear Regression Method

Prediction of evapotranspiration is important for study, design and management of irrigation systems. In this study, the potential of Multiple Linear Regression model using least squares is investigated in modeling of mean monthly evapotranspiration (PET) obtained using the standard FAO-56 Penman-Monteith equation. Various combinations of daily climatic data, namely solar radiation, air temperature, relative humidity and wind speed, are used as inputs to the model, so as to evaluate the degree of effect of each of these variables on PM estimated PET. Residual Analysis, Co-efficient of Determination and Residual Error is used as comparison criteria for evaluation of the model performance. The Multiple Linear Regression model gave Residual errors of 0.83mm/day and Co-efficient of Determination of 0.995 for the meteorological station considered. Based on the residual analysis results it was found that the Multiple Linear Regression model followed a linear trend. The input variables of the model were adequate and this model could be successfully employed in estimating the monthly Potential Evapotranspiration in the study area.
A computational approach to identify predictive gene signatures in Triple Negative Breast Cancer

Microarray technology has been extensively used to detect patterns in gene expression that stem from regulatory interactions. Seminal studies demonstrated that the synergistic use of microarray-based techniques and bioinformatics analysis of genomic data might not only further the understanding of pathological phenotypes, but also provide lists of genes to dissect a disease into distinct groups, with different diagnostic or prognostic characteristics. Nonetheless, optimism for microarray-based technologies as clinical tools has suffered of both perceptual and real setbacks. Criticism is largely on the ground of general non-reproducibility of gene signatures and the inability to replicate results. The research activity illustrated in this thesis aimed at fulfilling methodological gaps still hampering the identification of gene signatures with proved prognostic and predictive value and, finally, affecting their reliability, reproducibility, and applicability. Specifically, we developed computational methods to efficiently merge gene expression profiles of tumors from multiple, independent, retrospective studies and to construct meta-datasets storing high throughput gene expression profiles and clinical information from thousands cancer patients. Moreover, we expanded on the concept of gene signature and derived consensus signatures, i.e. linear weighted combinations of gene signatures that, singularly, recapitulate independent signaling pathways or specific molecular mechanisms, while intertwined together render a more comprehensive molecular model of tumor progression or chemo-resistance. This approach has been applied to breast cancer, in general, and to triple negative breast cancer (TNBC), in particular, and resulted in the identification of gene signature combinations with increased robustness and power to predict cancer progression or response to therapy over the use of single signatures.
Chemical cytometry : ultrasensitive analysis of single cells

Preface ORIGIN, CURRENT STATUS, AND FUTURE PERSPECTIVES OF CHEMICAL CYTOMETRY The Cell and Cytometry Flow and Image Cytometry Chemical Cytometry Chemical Cytometry of DNA and mRNA Metabolic Cytometry Future Perspectives on Instrumentation for Chemical Cytometry METABOLIC CYTOMETRY - THE STUDY OF GLYCOSPHINGOLIPID METABOLISM IN SINGLE PRIMARY CELLS OF THE DORSAL ROOT GANGLIA Introduction Material and Methods Results and Discussion Conclusions CELL SIGNALING STUDIES AT THE SINGLE-CELL LEVEL Introduction Analytes Examined and Reporters Used Cell Preparation and Reporter Loading Cell Lysis and Sampling Techniques Electrophoresis Separation Conditions Detection Automation and Throughput ULTRASENSITIVE DETECTION OF LOW-COPY-NUMBER MOLECULES FROM SINGLE CELLS Introduction Microchip Designs for Single-Cell Analysis and/or Cell Manipulation Ultrasensitive Detection Methods for Single-Cell Analysis Single-Cell Analysis with Single-Molecule Sensitivity on Integrated Microfluidic Chip Conclusions CAPILLARY ELECTROPHORESIS OF NUCLEIC ACIDS AT THE SINGLE-CELL LEVEL Introduction On-Line Cell Analysis Direct Gene and Gene Expression Analysis Without Amplification Potential Alternative Techniques for Single-Cell Gene and Gene Expression Analysis Conclusions MICROFLUIDIC TECHNOLOGY FOR SINGLE-CELL ANALYSIS Introduction Biological Significance of Single-Cell Analysis Microfluidic Devices in Our Laboratories Materials, Methods, and Protocols Conclusions ON-CHIP ELECTROPORATION AND ELECTROFUSION FOR SINGLE-CELL ENGINEERING Introduction Single-Cell Electroporation in Microfluidic Devices Single-Cell Electrofusion in Microfluidic Devices Conclusions ELECTROPORATIVE FLOW CYTOMETRY FOR SINGLE-CELL ANALYSIS Introduction Flow-Through Electroporation under Constant Voltage Electroporative Flow Cytometry for Detecting Protein Translocation Electroporative Flow Cytometry for Measuring Single-Cell Biomechanics Electroporative Flow Cytometry for Selectively Releasing and Analyzing Specific Intracellular Molecules Conclusion ULTRASENSITIVE ANALYSIS OF INDIVIDUAL CELLS VIA DROPLET MICROFLUIDICS Introduction Droplet Properties Droplet Generation Cell Encapsulation Droplet Manipulation Droplet Concentration Control Temperature Control of Droplets Detection in Droplets Conclusions PROBING EXOCYTOSIS AT SINGLE CELLS USING ELECTROCHEMISTRY Introduction Measurement Requirements Electrode Fabrication Measurements at Single Cells Fusion Pore Dynamics Conclusions ELECTROCHEMICAL DETERMINATION OF ENZYME ACTIVITY IN SINGLE CELLS Introduction Electrochemical Detection Coupled with Capillary Electrophoresis Voltammetry Scanning Electrochemical Microscopy (SECM) High-Throughput ECD Perspective SINGLE-CELL MASS SPECTROMETRY Introduction Mass Spectrometry Overall Outlook for Single-Cell MS OPTICAL SENSING ARRAYS FOR SINGLE-CELL ANALYSIS Introduction to Fiber-Optic Single-Cell Arrays Advantages of Fiber-Optic Single-Cell Arrays Fiber-Optic Arrays Singe-Cell Arrays for Bacteria Single-Cell Arrays for Yeast Single-Cell Arrays for Mammalian Cells Image and Data Analysis for Single-Cell Arrays Summary
Handbook of maize : genetics and genomics

Maize and the Origins of Plant Genetics. - East, Emerson, and the Birth of Maize Genetics. - Barbara McClintock. - The Birth of Maize Molecular Genetics. - Mutagenesis - the Key to Genetic Analysis. - Maize Improvement. - Development of Hybrid Corn and the Seed Corn Industry. - Maize and the Biotech Industry. - Modern Maize Breeding. - The Maize Genome. - Cytogenetics and Chromosomal Structural Diversity. - Maize Genome Structure and Evolution. - Genetic Diversity, Linkage Disequilibrium and Association Mapping. - The Polyploid Origin of Maize. - Maize Centromeres and Knobs (neocentromeres). - Transposons Ac/Ds, En/Spmand their Relatives in Maize. - Mutator and MULE transposons. - The LTR-Retrotransposons of Maize. - Helitrons: Their Impact on Maize Genome Evolution and Diversity. - Maize GEvo: A Comparative DNA Sequence Alignment Visualization and Research Tool. - Meiotic Genes and Meiosis in Maize. - Homologous Recombination in Maize. - Paramutation: Heritable in TransEffects. - Imprinting in Maize. - Chromatin, DNA Methylation, RNAi and Epigenetic Regulation. - The B Chromosome of Maize. - Mitochondria and Chloroplasts. - Maize Genetic and Genomic Technologies. - Genetic Mapping and Maps. - Genetic Analyses with Oat-Maize Addition and Radiation Hybrid Lines. - Maize Chromosome Tools: Quantitative Changes in Chromatin. - Transposon Resources for Forward and Reverse Genetics in Maize. - TILLING and Point Mutation Detection. - Gene Expression Analysis. - Maize Transformation. - Doubled Haploids. - Databases and Data Mining. - Sequencing Genes and Gene Islands by Gene Enrichment. - Genes and Gene Families. - Maize Transcription Factors. - The Genetics and Biochemistry of Maize Zein Storage Proteins. - The Cytochrome P450 Superfamily of Monooxygenases. - Cell wall Biosynthetic Genes of Maize and their Potential for Bioenergy Production. - Future Prospects. - The Future of Maize.
Identification and characterization of proteins expressed in the nectar of ornamental tobacco

A small set of proteins, termed Nectarins, are secreted into the nectar of ornamental tobacco (Mcofwz/%% fongf a Mcofwrna fowferog). The most highly expressed protein, Nectarin I (29 kD monomer), was originally identified as a germin-like protein (GLP) of unknown function. This remarkably stable protein was later shown to possess manganese dependent superoxide dismutase activity. Hydrogen peroxide, the product of SOD activity, was found to accumulate in nectar at levels up to 4 mM. The promoter (1.2 kb) of the Nectarin I gene was fused to the reporter gene chloramphenicol acetyl transferase (CAT) and shown to be expressed in mature nectary tissues only at times when nectar is actively being secreted. Nectarin n (35 kD) was identified as a dioscorin-like protein and found to be a degradation product of Nectarin m (40 kD). These proteins were shown to posses monodehydroascorbate reductase and carbonic anhydrase activity. Nectarin V (-65 kD) was identified as a berberine bridge enzyme-like protein and found to contain a covalently bound molecule of FAD. Both Nectarin m and Nectarin V shared very similar expression patterns with those of Nectarin I. The hypothesis of this work is that nectar proteins are secreted into nectar to maintain an axenic state and to protect the developing gynoecium from microbial attack and oxidative damage. Specifically, the proposed functions of these nectar proteins include: the production of hydrogen peroxide for floral defense, maintenance of nectar pH, and maintenance of ascorbate levels in nectar.
Fate-mapping neural stem cells in the mouse ventral neural tube by Cre-lox transgenesis

Neurons and glia (astrocytes and oligodendrocytes) are the two major cell types that make up the central nervous system (CNS). They are generated from precursor domains within the neuroepithelial germinal zone (ventricular zone, VZ) that surrounds the ventricles of the brain and the central canal of the spinal cord (the embryonic neural tube). In general, neurons are generated before glia. The intra-spinal circuits that control movement and locomotion are made up of different neuronal and glial elements that develop separately but come together to form interconnected functional units. To understand the logic of circuit development and ultimately circuit-driven behaviour, it is necessary to understand where and when each type of cell originates. To identify the products of the most ventral progenitor domain in the developing spinal cord, known as (Nkx2.2-expressing p3 domain), I made use of Cre-loxP technology. I generated a transgenic mouse line that expresses an inducible form of Cre recombinase (CreERT2) under Nkx2.2 transcriptional control and crossed this with a Cre-dependant reporter mouse to visualize p3-derived progeny. I confirmed that the p3 domain generates Sim1-expressing V3 interneurons, serotonergic interneurons as well as visceral motor neurons of the hindbrain. p3 progenitors also produce two spatially restricted subtypes of astrocytes, a few oligodendrocytes and ventrallypositioned ependymal cells. Unexpectedly, my studies also revealed that pre-ganglionic motor neurons of the sympathetic nervous system (SPNs, visceral motor neurons of the thoracic spinal cord), as well as a population of dorsally-located Sim1-expressing interneurons, are produced from Nkx2.2-expressing precursors. SPNs have been generally believed to originate from the same progenitor pool as HB9-positive somatic motor neurons (sMNs), defined by expression of Olig2 (pMN domain, immediately dorsal to p3). Supporting this idea, no spinal sMNs or SPNs are formed in Olig2-null mice. However, I found that Nkx2.2-expressing p3 precursors do not generate any HB9-positive sMNs, implying that sMNs and SPNs derive from distinct precursors - the latter from the most ventral part of the pMN domain that transiently co-expresses Nkx2.2 and Olig2. Thus, segregation of SPNs and sMNs occurs already in the neuroepithelium before their post-mitotic progenitors migrate away from the VZ into the ventral horns. This is how visceral and somatic MNs are known to develop in the brainstem, so my results provide a unifying theme to MN development at different levels of the neuraxis.
ACELLULAR AORTIC MATRIX FOR THE REPAIR OF LARGE VENTRAL HERNIA IN A BUCK

IntroductionVentral hernia is the protrusion of abdominal content(s)through the defect in the abdominal wall with an intact lining of thesac (Engelsman et al ., 2007). The only effective treatment is surgeryto restore integrity of the abdominal wall and prevent incarcerationand strangulation of herniated abdominal contents. Tense sutureapplication to approximate and close the defect led to wounddehiscence and recurrent hernia. The use of mesh allows a tensionfree repair of abdominal hernias. The prosthetic materials suchas polypropylene mesh leads to complications like mesh extrusion,fistula formation, wound infection, seroma and adhesions (Molloyet al., 1991). The synthetic degradable materials do not providegood strength during degradation process (Tyrell et al., 1989). Gulati and Cole (1994) observed less immunogenicity and bettertolerance of acellular grafts in rats and rabbits. Acellular dermalgrafts have been used successfully for the reconstruction ofabdominal wall defects in rats (Chung et al., 2003) and rabbits(Gangwar et al., 2006). Kumar et al. (2004) used glutaraldehydepreserved diaphragm of porcine origin for the repair of largeumbilical hernia in dog with excellent recovery. Carbon fibres andcarbon fibres mesh has been used for the repair of umbilicalhernias in bovines (Gangwar et al., 2008a and b). Decellularizedswine aorta has been used for repair of abdominal wall herniadefects in rat model with excellent results (Bellows et al., 2008). Invivo biocompatibility evaluation of acellular aortic matrix (AAM) ofbuffalo origin in Guinea pig model revealed that AAM isbiocompatible (Devarathnam, 2010), with these results, presentstudy was undertaken to evaluate the efficacy of acellular aorticmatrix of buffalo (Bubalus bubalis) origin for reconstruction ofventral hernia in a buck.Materials and MethodsPresent study was conducted in the Biomaterial andBioengineering Laboratory, Division of Surgery and in the ReferalVeterinary Polyclinic, Indian V eterinary Research Institute, Izatnagar-243122, Uttar Pradesh, India. This communication deals with thesurgical management of ventral hernia in a buck. A Jamunaparibreed buck aged 3 years having body weight of 35 kg was presentedwith the history of swelling in the right ventral abdomen. Clinicalexamination revealed large ventral hernia of abdominal wall. Thesize of hernial ring was 10-12 cm in diameter (Fig. 1). Since thehernia ring was large so it was decided to perform hernioplasty.Preparation of acellular aortic graftFresh posterior aorta of buffalo origin was collected fromlocal abattoir and immediately preserved in ice-cold sterilephosphate buffered saline solution (pH 7.4) containing 0.1%amikacin and 0.02% EDTA. The tissue was rinsed with normalsaline before the start of protocol. The maximum time periodbetween retrieval and the initiation of protocol was less than 4 h.The tissue was cut into desired sizes and made acellular using
Marine conservation planning in practice: lessons learned from the Gulf of California

1. Overfishing, pollution, coastal development and climate change threaten marine biodiversity globally and compromise the services that marine ecosystems provide. Systematic conservation planning (SCP) provides a framework to identify areas where actions can be effective in addressing these threats, while minimizing the costs of interventions. This study investigated the application of SCP in the Gulf of California, a marine hotspot where seven prioritization exercises have been undertaken. 2. The review of planning exercises showed that the use of SCP methods has progressed slowly (gaps include planning for land-sea connections and ecosystem services) and highlighted benefits and difficulties of applying SCP principles and tools. 3. Despite some convergence, important spatial differences were found in priorities between plans. Convergence was evident in well-studied shallow and benthic marine ecosystems. There were also important differences related to the planning approach, methods and extent. Divergence between methodological and spatial similarities between plans suggests that additional factors (e.g. manually delineating priority areas, incorporating updated datasets, random error), in addition to data and objectives, play an important role in defining the distribution of conservation priorities. 4. According to expert opinion, the implementation of new marine protected areas (MPAs) in the region has been influenced by some of the planning exercises. However, uptake of planning outputs has progressed slowly for many reasons (e.g. conflicting mandates and interests between organizations, limited technical capacities and resources, insufficient political commitment). Other benefits of planning included: developing institutional skills and knowledge; improving collaboration and coordination between organizations (including agencies, and local, regional and national NGOs); converging on the need to assess priorities for marine conservation in regional context; and building trust among organizations. 5. The existence of multiple marine conservation plans in the Gulf of California also highlighted some of the complexities and benefits of having multiple sets of priorities.
Differentiation and identification of grapevine accessions of Ukraine by means of molecular markers.

A molecular-genetic analysis of polymorphism in grapevine varieties, clones and new selections from the collection of the Tairov National Research Centre for Viticulture and Winemaking was conducted by using 9 microsatellite loci. Th e data were N-coded and analysed with the application of the MEGA 4 programme in order to build a dendrogram of the genetic relationships. Th e bootstrap test was used to examine fi delity of the phylogenetic trees. Th e molecular-genetic polymorphism was investigated using chloroplast DNA markers. Th ree diff erent haplotypes were identifi ed by cpSSR locus ccmp10.