cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Investigation of a novel role for the histone chaperone Asf1 in ploidy-control
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: In this proposal, we describe preliminary data that indicate a hitherto undetected role for the evolutionary conserved histone chaperone Asf1 in ploidy-control. The research proposed here has been designed to explore the mechanism and underlying genetics of this novel Asf1 function using yeast genetics, recombinant DNA technology, and fluorescence microscopy. Biochemical evidence indicated that Asf1 plays an important role in replication-coupled nucleosome assembly. Unexpectedly, we found evidence that loss of ASF1 in diploid baker's yeast promotes the random duplication of either one of the two homologs of chromosome II, but not of other chromosomes. This phenomenon may represent a novel route to aneuploidy. Chromosome II is the only chromosome in baker's yeast that bears a complete set of histone genes, suggesting that defects in replication-coupled nucleosome assembly can be suppressed by increasing the number of histone genes. The experiments of this proposal serve to address two specific aims. Specific Aim 1: Determine the extent of gene duplication in asf1? cells and its relationship to histone dosage and replication-coupled nucleosome assembly. The experiments of this Aim will address whether all genes of chromosome II are duplicated, and whether duplication encompasses genes of other chromosomes, too, whether gene duplication can be suppressed by increasing the number of histone genes only, and whether deletion of other genes involved in replication-dependent nucleosome assembly will likewise promote the duplication of chromosome II genes. Specific Aim 2: Analysis of the mechanism of gene duplication in asf1 mutant cells. The experiments of this Aim will determine whether gene duplication occurs by mitotic nondisjunction or endoreplication and whether either one of these mechanisms is directed at chromosome II or generally applies to all chromosomes with subsequent selection for chromosome II gene duplication events.
Economic impact of Hurricane Sandy: Potential economic activity lost and gained in New Jersey and New York
Creators: name: No Name Supplied
Publisher: name: No Publisher Supplied
Year: 2013

description: This report examines potential long-term economic effects of Hurricane Sandy in terms of losses and gains in economic activity.  This impact analysis is for all the counties in New Jersey and the 13 counties in lower New York that that were declared as disaster areas by the Federal Emergency Management Agency (FEMA).
Additional file 3: of Integrative microRNA and mRNA deep-sequencing expression profiling in endemic Burkitt lymphoma
Creators: name: Oduor, Cliff
name: Kaymaz, Yasin
name: Kiprotich Chelimo
name: Otieno, Juliana
name: Ong’echa, John
name: Moormann, Ann
name: Bailey, Jeffrey
Publisher: name: Figshare
Year: 2017
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: 60506 Virology
subject: Computational Biology

description: Differentially expressed Genes between eBL tumor cells and GC B cells (logFC > 2, p-value
Infrastructure investments necessary for economic success
Creators: name: No Name Supplied
Publisher: name: No Publisher Supplied
Year: 2013

description: In this report, Facing Our Future concludes that New Jersey has failed to adequately maintain and invest in the infrastructure necessary to spur long-term economic competitiveness. This report  presents the long-term needs and required infrastructure investments in each of three areas: electric power, transportation and water systems. The report provides a fact-based, analysis-driven opportunity to understand and explore realistic ways in which New Jersey can spur economic development – and economic success – through infrastructure investments.
Physical versus verbal spousal control efforts
Creators: name: Abbamonte, John Michael
Publisher: name: No Publisher Supplied
Year: 2014

description: Alongside the growing obesity epidemic is the average American's risk of developing type 2 diabetes. In order to manage type 2 diabetes, a patient must maintain a strict diet, exercise, and medication regimen. Adherence to these lifestyle changes is notoriously difficult, and when patients cannot successfully self manage their own diabetes-related health behaviors, their social networks sometimes become involved. Spouses often are the most proximal network member involved in diabetes management by regulating their partners' behavior, yet little is known about the implications of such involvement. Although the current literature addresses how individuals with type 2 diabetes are affected by their network members' involvement in disease management through engaging in health-related social control, the implications for individuals who engage in such attempts remain largely unexplored. Given the worry and uncertainty about short-term and long-term consequences of uncontrolled diabetes, this study seeks to examine one unexplored component of spouses' well-being related to social control, anxious feelings. Little is known about which social control tactics aimed at different adherence behaviors are particularly likely to be associated with anxious feelings; thus, this study further seeks to compare the levels of anxious feelings between individuals who exert control by physical means and those who exert control by verbal means. While no form of social control was found to be related to anxious or depressive feelings, patients' behavioral response and self-rated health did emerge as unique predictors of anxious feelings, and could indicate a more intricate picture of how social dynamics relate to mental health.
A screen for inhibitors of oncogenic miRNA processing
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: This project aims to apply the fragment-based ligand discovery method called Tethering to identify small molecules that bind biosynthetic precursors of the oncogenic miRNA miR-21. MiR-21 is the target for development of anti cancer agents given its role as an oncogenic miRNA. While Tethering has been shown to be effective for discovering molecular fragments that are useful as starting points for protein-binding drugs, this method has not been applied to RNA. Molecules that bind to precursors of miR-21 are expected to block the RNA processing steps required to generate the mature miRNA. We propose here to synthesize RNA targets for Tethering that bear thiol functional groups near sites known to be important for miR-21 precursor processing. These RNAs will be screened against a disulfide fragment library available from the Small Molecule Discovery Center at UCSF. Hits will be identified as new peaks in the mass spectra of reaction mixtures and will be rank ordered based on their conjugation strength. High scoring hits will be candidates for further development as inhibitors of miR-21 processing.
Defining the mechanistic link between AR-dependent gene regulation and cell proliferation
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: Prostate cancers are dependent on the activity of the androgen receptor (AR), but the mechanism by which the AR controls cell cycle is poorly understood. Androgen ablation therapies targeting the AR are initially successful, but eventually castrate resistant prostate cancers (CRPCs), which continue to rely on the AR, emerge. CRPCs employ various mechanisms to circumvent the requirement for androgens including the expression of low molecular weight (LMW)-AR isoforms that are missing the ligand binding domain. Castrate resistant 22Rv1 cells express high levels of the LMW-AR isoforms. Studies indicate that ablation of these isoforms inhibits proliferation, confirming their importance for cell cycle transversal. Studies conducted by our colleague Dr. Hsing-Jien Kung found that LMW-AR isoforms were able convert the androgen dependent LNCaP cells to castrate resistant cells. Therefore, in two distinct cell lines, the LMW-AR isoforms drive cell proliferation in the absence of androgen. Our chromatin immunoprecipitation (ChIP)/ promoter array studies of 22Rv1 cells found that the LMW-AR binding sites are a subpopulation (~5%) of sites that bind full length AR. The analysis of LMW-AR binding in LNCaP cells using ChiP/tiling array also identified LMW-AR binding sites. However, in both studies the majority of AR binding sites in the gemone would not have been identified using these methodologies. Our hypothesis is that the LMW-AR isoforms control transcripts that are critical for proliferation in both cell lines. The goal of Specific Aim 1 is to use ChIP-seq to conduct a global analysis of LMW-AR binding sites in 22Rv1 and LNCaP cells in steroid-depleted media. The complementary analysis will utilize RNA-sequence (seq) to define the RNA transcripts that are regulated by the LMW-AR isoforms in steroid depleted media. Combining ChIP-seq and RNA-seq using two distinct cell lines will identify putative AR-dependent genes that are required for proliferation in the absence of androgen. In Specific Aim 2 the importance of candidate genes that are LMW-AR regulated will be analyzed using siRNA-mediated knockdown of the putative transcripts. Defining the mechanistic link between AR and cell cycle progression will allow for the development of novel therapeutics that target critical AR-regulated proteins.
Bouquet of bees
Creators: name: Bernstein, Laura
Publisher: name: No Publisher Supplied
Year: 2014

description: This poetry collection questions a person’s role within two family units: one given as a child, and one chosen as an adult. Speakers reflect on some familial experiences and learn how to reclaim their own voices and bodies as these two worlds collide. The majority of these poems are written in ordinary speech; this doesn’t mean the poems aren’t challenging. Newborns swaddle their parents, an esteemed cello steals human voices, and skirts turn into jellyfish. No matter what circumstance is unveiled, the speakers try to remember to handle their situations in a similar fashion: with risk, a sense of play, and compassion.
An examiniation of ovulatory shifts in extra-pair attractions among sexual minority women
Creators: name: Bowler, Gianna M.
Publisher: name: No Publisher Supplied
Year: 2014

description: There is a growing body of research suggesting that women’s preferences and behaviors differ during different phases of their menstrual cycle. However, the vast majority of past research focuses solely on heterosexual women. The present study furthers prior research by examining sexual minority women when they are most likely to be fertile (versus during other points in their menstrual cycles), and their attraction to potential partners outside their current relationships. Participants were &3 women (38 heterosexual; Mage = 19.&8, 35 sexual minority women; Mage = 29.69) in exclusive romantic relationships. Women’s fertility status, sexual orientation, and sexual attraction to partners outside of their romantic relationships were assessed during two separate times in their menstrual cycle in the form of an online survey. Findings reveal that consistency of sexual attraction to men versus women among sexual minority women predicts the target of their extra pair attractions during their most fertile phase of the menstrual cycle. These findings suggest the importance of examining evolutionary adaptations promoting reproductive fitness among women of diverse sexual orientations.
The glypican Dally shapes follicle cell patterning by regulating the epidermal growth factor receptor ligand Gurken
Creators: name: Brownstein, Steven Harris
Publisher: name: No Publisher Supplied
Year: 2014

description: Heparan sulfate proteoglycans (HSPGs) have been shown to interact with morphogens of many signaling pathway.  During Drosophila oogenesis, the major contributors to tissue patterning are the bone morphogenic protein (BMP) and epidermal growth factor receptor (EGFR) signaling pathways.  It was previously shown that BMP signaling is regulated by the HSPG, dally (division abnormally delayed), in the wing, and also in patterning of the follicle cells (FCs).  The EGFR pathway is responsible for axis determination as well as follicle cell pattering.  Using genetic perturbation, we demonstrate that Dally regulates the distribution of EGFR signaling through the restriction of the TGFα-like ligand Gurken (GRK).  When dally is perturbed by uniform overexpression or depletion in the FCs, the GRK gradient is either narrowed, or widened, respectively.  In these backgrounds, changes in EGFR activation, measured by dpERK, are consistent with the shapes of GRK patterning.  These effects on EGFR activation lead to corresponding results on follicle cell pattering where a decrease in midline clearing of BR in overexpression of dally, corresponding to a reduced gap between the dorsal appendages (DAs).  Expressing a mutant form of Dally, lacking an anchor to the membrane, perturbed the GRK gradient, leading to tissue patterning and eggshell morphology defects.  Based upon these results, we propose that Dally is required for the formation of the GRK gradient for optimal EGFR signaling activation.
Additional file 21: of Comprehensive genomic analysis of the CNGC gene family in Brassica oleracea: novel insights into synteny, structures, and transcript profiles
Creators: name: Kaleem Kakar
name: Zarqa Nawaz
name: Kakar, Khadija
name: Essa Ali
name: Abdulwareth Almoneafy
name: Raqeeb Ullah
name: Ren, Xue-Liang
name: Qing-Yao Shu
Publisher: name: Figshare
Year: 2017
Subjects: subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology
subject: 60506 Virology
subject: Computational Biology

description: Cumulative values of expression for Arabidopsis CNGC genes in different developmental samples. The expression data for 21Â days old of wild type and mutant plants was obtained from Schmid et al. [48]. The information about different genotype mutants is given below the figures. (PDF 225Â kb)
Self-amplifying microRNAs for oncogene targeting
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: MicroRNA; Gene regulation; Ribozymes; Self-cleavage; Replicon, RNA replication; RNA-dependent-RNA-polymerase; Subgenomic RNA; Prostate cancer; Oncogenes
Optimized gene modification of hematopoietic stem cells for lymphoma immunotherapy
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: Non-Hodgkin lymphoma; Immunotherapy; Gene therapy; Hematopoietic stem cells; Cellular therapy; Chimeric antigen receptor; Graft-versus-lymphoma effect; Hematopoietic stem cell transplantation; Lentiviral vector; Cetuximab
"Eating death"
Creators: name: Boyles, Kerry L
Publisher: name: No Publisher Supplied
Year: 2014

description: This thesis examines the overarching narrative of sinful female appetite that conflates eating with immorality, sexuality, and perversity. I begin by tracing nineteenth-century depictions of Eve, Lilith and the lamia as antecedents of the female vampires of the fin de siècle. I use these mythic women as an entrée into Victorian cultural associations with food and eating and analyze the ways that female vampires in Sheridan Le Fanu’s Carmilla (18&2), George MacDonald’s Lilith (1895), and Bram Stoker’s Dracula (189&) evoke nineteenth-century anxieties about food, fat, and female appetite. Female vampires reflect moral uneasiness over gustatory indulgence and their unrestrained appetites represent a plethora of perverse desires. The vampires of Carmilla, Lilith, and Dracula seem to embody divided femininity, changing from the “angel” to the “whore.” However, they personify (at all times) all of the complexities and contradictions of femininity. These women are “desiring-machines,” and variously embody singular qualities that are just part of their complex, ever-shifting subjectivities. They are light and dark, feminine and masculine, virginal and sexual, pure and corrupt, vaginal and phallic, weak and powerful, dead and alive, animal and human, victim and victimizer, mother and    abortionist. By combining these extremes, they are the “abject” – concomitantly both alluring and repulsive – and their destruction suggests an inability for the patriarchal figures to permit female complexity and their desires to crush female subversion. Vampirism acts as a liberating “fall” for the constrained women featured in Lilith, Carmilla and Dracula, even as the texts validate and valorize their destruction.
Injectable cell delivery vehicle for bone repair
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: Bone defects resulting from trauma, disease, or congenital malformation represent a significant clinical challenge. Cell-based therapies, commonly using mesenchymal stem cells (MSCs), are an exciting strategy to stimulate bone healing. The implantation of MSCs into bone defects is a promising alternative to bone grafts, but many defects still do not heal properly. Numerous studies have demonstrated the necessity of transplanting MSCs with a biomaterial to localize cells at the defect, limit migration away from the site, and potentially include signals to instruct cellular behavior. Performance and companion animals also suffer from bone fractures and bone defects, frequently causing a dramatic shift in the animal’s quality of life and potentially resulting in death. Compared to applications for human patients, the regulatory burden for new cell- and materials-based therapies used in veterinary medicine is markedly reduced, thus representing a tremendous commercial opportunity to develop and provide improved strategies for tissue repair and healing. Recently, my laboratory derived a novel composite injectable hydrogel from natural polymers for cell delivery into the defect under ultrasound guidance. Unlike hydrogels derived from a single polymer, the composite hydrogel capitalizes on the benefits of several polymers to achieve faster gelation and resorption than individual constituents, while increasing hydrogel osteoconductivity. The implantation of autologous MSCs into bone defects of thoroughbred racehorses using our novel injectable hydrogel has consistently promoted near complete repair of bone deficits. However, the mechanism of action is completely unknown and requires further exploration. We will rigorously examine the contribution of each constituent of the hydrogel system to promote bone formation and capillary vessel formation using a battery of in vitro assays, coupled with a sheep model of bone repair. Specifically, MSCs will be suspended in hydrogels containing cues that simultaneously promote differentiation toward osteoblasts and upregulate secretion of vessel-stimulating proteins. We will also examine various strategies for sterilization of this material without impairing its efficacy. These studies will provide the foundation of knowledge necessary to advance this technology toward a viable commercial product for use in treating defects in large and small animals.
“I like going places"
Creators: name: Dar, Anandini
Publisher: name: No Publisher Supplied
Year: 2014

description: This dissertation examines how ethnic youth centers and other sites between the home and the school inform the everyday and political geographies of working class South Asian immigrant youth growing up in a post 9/11 New York. Caught between no longer being young children and not yet adults, the teens of this study spend much of their time in liminal spaces of youth centers, streets, malls, which I refer to as third spaces. Based on a multi-sited ethnography at one youth center for South Asian youth in Queens, New York between 2010 and 2012, I accompanied teens attending this center to other places where they hang out, such as, rallies and social justice and political workshops in NYC and other neighboring northeastern cities, malls, parks, subways, and online sites. Additionally, I analyze discourses of the mission, philosophy and ideologies of the youth center programs.  After the 9/11 attacks on the world trade center in New York, ethnic and religious identities, that is, being South Asian and Muslim, have become racialized and politicized categories wrongfully associated with terrorism, resulting in racial bullying and hate crimes affecting South Asian youth and families. Unlike literature on youth centers, this research highlights how, in this era, ethnically-based youth centers address these socio-political and cultural difficulties youth face everyday and help them connect with and negotiate their socio-political realities without insulating or “islanding” young people.   I argue that it is in third spaces that youth’s political identities and engagement with politics begin to take shape as they attend social justice workshops and rallies to fight against racial crimes, and aspire to “go places,” socially and politically. Further, I argue that youth’s political agency manifests in their cultural and performative practices, offering new ways through which to understand young people’s political lives. This dissertation highlights the connections between context, young people, representations, and politics, as it situates the constructions of racial and ethnic identity as intersecting dynamics to understanding youth’s political geographies. This multi-disciplinary study contributes to South Asian studies, political geographies, ethnic studies and children and youth studies scholarship.
Point of Care Blood Analysis Device for TB Diagnosis
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: IFN-gamma is an important cytokine that possesses antiviral, antiproliferative, differentiation inducing, and immunoregulatory properties. This cytokine is mainly produced by T-helper (CD4) cells and cytotoxic T-cells. Interferon-gamma–release assays (IGRAs) are alternatives to the tuberculin skin test (TST) for TB diagnosis. An in vitro whole blood test that detects M. tuberculosis infection by measuring IFN-gamma responses to TB antigens was approved in the United States. However, IGRAs are expensive, relatively complex and labor intensive to perform. Our goal is to develop an alternative device for detection of TB infections based on IFN-gamma release. This device is based on a combination of microfluidics and novel molecular recognition technology developed in the Revzin lab. This technology has been shown to work in an academic lab and has been protected by a provisional patent. In addition, we have begun exploring commercial potential, have participated in and made the finals of Big Bang business competition at UC Davis in 2011 and have received partners for innovation (PFI) commercialization award from the UC Davis School of Medicine. What is lacking at the moment is 1) a field deployable prototype device and 2) evidence that our device is suited for TB detection and is comparable to current FDA approved technologies. Thus, we are requesting funding for prototype development and feasibility testing of the device.
Barreropsylla excelsa Jordan 1953
Creators: name: Lareschi, Marcela
name: Sanchez, Juliana
name: Autino, Analía
Publisher: name: Zenodo
Year: 2016
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Siphonaptera
Stephanocircidae
Barreropsylla
Barreropsylla excelsa

description: Barreropsylla excelsa Jordan, 1953
NHM. Argentina—Río Negro: San Carlos de Bariloche. Mammalia—Rodentia—Cricetidae— Akodon sp. Chile; Argentina—Neuquén. Río Negro: San Carlos de Bariloche, San Pedro. Mammalia—Rodentia—Cricetidae— Abrothrix hirta, Abrothrix olivacea, Akodon dolores, Akodon iniscatus, Akodon sp., Euneomys chinchilloides, Geoxus valdivianus, Irenomys tarsalis, Loxodontomys micropus, Oligoryzomys longicaudatus. Probably the type host is Abrothrix sp., common in the area (Patton et al. 2015).
description: Published as part of Lareschi, Marcela, Sanchez, Juliana & Autino, Analía, 2016, A review of the fleas (Insecta: Siphonaptera) from Argentina, pp. 239-258 in Zootaxa 4103 (3) on page 244, DOI: 10.11646/zootaxa.4103.3.3, http://zenodo.org/record/262230
Antibodies for Fibroinflammatory Lung Disease Detection
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: Fibroinflammatory lung diseases are a group of chronic human disorders that are difficult to detect, treat and classify, including COPD, chronic treatment-refractory asthma and pulmonary fibrosis. A major activator of the profibrotic cytokine TGF-beta is the cell surface integrin molecule avb8, which is increased in expression in fibroinflammatory disorders of the lung. Since TGF-beta is a central molecular mediator of fibroinflammatory processes, we hypothesized that inhibiting the activation of TGF-beta via avb8 neutralization could be used to treat fibroinflammatory disease. We have developed a panel of antibodies that react with avb8. One of them named 37E1B5 has been engineered and fully humanized with state-of-the-art antibody engineering technology. 37E1B5 shows profound activity in preventing fibroinflammatory disease in humanized avb8 transgenic mice in chronic asthma and COPD lung disease models. Other antibodies to avb8 are potential useful diagnostic reagents for fibroinflammatory diseases, since these antibodies can quantitatively detect the expression differences of avb8 in tissue sections from different lines of humanized transgenic mice harboring varied bacterial artificial chromosome (BAC) DNA copy numbers. Our animal test data suggest that these antibodies will be effective in identifying patients at risk of fibroinflammatory diseases in the lung and other organs expressing avb8. In fact, these are the first monoclonal antibody reagents that can specifically detect avb8 in intact human paraffin embedded tissues. We now propose to use the same antibody engineering strategies that we have successfully employed to generate the out-licensed 37E1B5 to develop more and better antibodies suitable for clinical diagnostic kits, and for injectable in vivo imaging reagents. These novel reagents will be created based on existing avb8 antibody leads, using yeast display technology and mammalian cell expression systems together with other molecular engineering techniques. This work will be expedited by the synergistic collaboration of a lung integrin biologist (Nishimura) and world-class antibody engineers (Marks, Lou). The utility of engineered antibodies to detect increased fibroblast cell mass and increased avb8 expression will be tested in BAC integrin avb8 transgenic mice in biologically relevant fibroinflammatory disease models. The best antibodies will be fully humanized and optimized for use in humans.
Selection of the most appropriate depopulation method for the welfare of poultry
Creators: name: EURCAW-Poultry-SFA
Publisher: name: Zenodo
Year: 2025
Subjects: depopulation
Avian Influenza
decision tree
housing system
poultry characteristics
welfare
stunning and killing methods

description: This document provides a structured set of decision trees to guide the selection of the most appropriate depopulation method for poultry during Avian Influenza and similar outbreaks, with the main focus on prioritizing animal welfare. Each method is assessed based on the human, technical, and environmental resources required to ensure compliance with welfare standards, assuming all these necessary resources are available. Methods that minimize pain, distress, and suffering are ranked higher, regardless of resource feasibility in specific contexts. The top 3 methods in terms of welfare are: captive bolt stunning, lethal injections, and whole-house gassing. The decision trees are dynamic, designed as a "live" document to be updated as scientific knowledge and commercial technologies evolve. They are primarily aimed at the competent authorities of the EU Member states.
Development Of New DNA Isolation Method
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: The objective of this proposal is to establish a prototype of a new DNA extraction method to extract trace amounts of DNA from various types of samples not only with improved selectivity and purity but also with minimum loss. Advantages of the proposed method (the Mtase method) include the high efficiency and selectivity for DNA and the capture mechanism that allows for a broader range of sample treatment steps to obtain the final sample with higher purity and yields. We believe that the Mtase method will provide a better alternative to the currently available commercial methods, which suffer from suboptimal yields (filtration-based methods) or limited sample sizes (paramagnetic particle-based methods). Through our previous efforts, we have established the protocol and evaluated the proof-of-concept of the Mtase method. These efforts have generated preliminary data demonstrating its sensitivity as high as sub-femtogram range of DNA, compared to the current method with sensitivity of approximately nanogram level. Another advantage of the Mtase method is that it is highly flexible; it can be developed for use in versatile formats and volumes including planar surfaces, magnetic beads, and microfluidic devices. Therefore, we aim to further improve current status of the method and to build a prototype to demonstrate and evaluate its commercial potential. First, we will: (1) introduce cleavable linkers to release the purified DNA from the surface for further analyses; (2) optimize the Mtase method with a series of sample types including complex biological and environmental samples; (3) develop the method using a series of different surface matrices, such as magnetic beads, microplates, microfluidic devices, strips of plastic tubes and planar glass, to explore the most effective choices for commercialization. DNA extraction plays pivotal roles in many versatile research areas. Once adapted to the desired format for commercialization, this novel, efficient, and highly sensitive DNA isolation method will find myriad of applications.
Additional file 3: of Comprehensive genomic analysis of the CNGC gene family in Brassica oleracea: novel insights into synteny, structures, and transcript profiles
Creators: name: Kaleem Kakar
name: Zarqa Nawaz
name: Kakar, Khadija
name: Essa Ali
name: Abdulwareth Almoneafy
name: Raqeeb Ullah
name: Ren, Xue-Liang
name: Qing-Yao Shu
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Microbiology
subject: FOS: Biological sciences
subject: Genetics
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Phylogenetic tree of CNGC proteins from B. oleracea (encoded by BoCNGCs). A multiple sequence alignment was performed using ClustalX 2.0 program with default settings. Maximum likelihood (ML) tree was create with MEGA 6.0, under the Jones-Taylor-Thornton (JTT) model. The bootstrap values from 1000 resampling are given at each node. (PDF 201Â kb)
Graphene Oxide and Sulfur Nanocomposite Cathode
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: Elemental sulfur (S) is very attractive as a cathode material for high-specific-energy rechargeable lithium batteries, because a battery based on the lithium/sulfur (Li/S) couple would yield a theoretical specific energy of 2600Wh/kg, compared to ~500 Wh/kg for Li Ion cells. In addition, S is also inexpensive, abundant and nontoxic. However, the loss of sulfur cathode material as a result of polysulfide dissolution causes significant capacity fading in rechargeable lithium/sulfur cells. Here, we use a chemical approach to immobilize sulfur and lithium polysulfides via the reactive functional groups on graphene oxide (GO). This approach enabled us to obtain a uniform and thin (~ tens of nanometers) sulfur coating on GO sheets by a simple chemical reaction-deposition strategy and a subsequent low temperature thermal treatment process. The unique structure of the GO-S nanocomposite can improve the overall electrochemical performance when it is used as a cathode material for Li/S batteries. Firstly, it can accommodate the significant volume changes of the S as it is converted to Li2S on discharge, and back to elemental S on recharge. Secondly, the low-temperature heat treatment process can partially remove and/or chemically modify some of the functional groups on the GO surface and improve the electronic conductivity; the partially reduced GO with its large surface area along with ubiquitous cavities can establish more intimate electronic contact with the S and avoid particle aggregation and loss of electrical contact with the current collector. Thirdly, the low-temperature heat-treated GO still contains various kinds of functional groups. These functional groups have strong adsorbing ability to anchor S atoms and to effectively prevent the subsequently formed Li polysulfides from dissolving in the electrolyte during cycling. We evaluated the electrochemical Li storage capability of these heat-treated GO-S nanocomposites as cathode materials for Li/S cells in an ionic liquid-based electrolyte. We have demonstrated Li/GO-S cells with a high reversible capacity of 950 – 1400 mAh/g, stable cycling for more than 50 deep cycles at 0.1C, and rate capability of up to 2C (Note that the theoretical capacity for S is 1645 mAh g-1). With our proposed improvements using a new heat-treatment process, an elstomer binder, and a ion-selective membrane, we expect to extend our cell’s cycle life to 1000 cycles, which should be very competitive for commercialization.
Additional file 8: of Integrative microRNA and mRNA deep-sequencing expression profiling in endemic Burkitt lymphoma
Creators: name: Oduor, Cliff
name: Kaymaz, Yasin
name: Kiprotich Chelimo
name: Otieno, Juliana
name: OngâEcha, John
name: Moormann, Ann
name: Bailey, Jeffrey
Publisher: name: Figshare
Year: 2017
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Hematology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Computational Biology

description: miRNA-mRNA pairs permutation test results. (PDF 302 kb)
Glucosamine analogs for the treatment of Multiple Sclerosis.
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: Multiple sclerosis (MS) is an autoimmune disorder of the central nervous system and is the most common cause of neurological disability in young adults. Current treatment strategies for MS are predominated by injectable therapies that do not target an underlying cause of the disease, have modest efficacy, high cost and/or side effects that limit tolerability and compliance. Our published data in both mice and humans indicates that genetic and environmental dysregulation of the addition of sugars to proteins drives autoimmune T cell mediated demyelination in MS. Virtually all cell surface and secreted proteins in animal cells are modified by the addition of complex sugars, imparting critical structural information not directly defined by the genetic code. In mice, defective attachment of specific sugars to proteins results in T cell hyper-activity and a spontaneous MS-like autoimmune disease. In humans, multiple genetic and environmental MS risk factors converge to dysregulate the addition of sugars to proteins in T cells. Therapeutically correcting the addition of sugars to proteins in MS patients may provide the first therapy directly targeting an underlying cause of the disease. Indeed, our lab and others have shown that the simple sugar N-acetylglucosamine inhibits autoimmune T cell responses, prevents and treats mouse models of MS and autoimmune diabetes and improved disease in 8 of 12 human children with treatment-resistant inflammatory bowel disease. While these findings are significant, N-acetylglucosamine is a dietary supplement with both biological and drug development limitations. Biological activity is limited by membrane permeability and high concentrations required to achieve desired effects. As a glucosamine-related dietary supplement currently available over the counter in the USA, further development of N-acetylglucosamine via clinical trials in MS is challenging. To address these issues, we have developed novel analogs of N-acetylglucosamine with chemical alterations to increase cellular permeability. Indeed, one analog increases sugar attachment to proteins at a 1000 fold lower concentration. In addition to efficacy at much lower concentrations, these novel compounds provide stronger intellectual property protection and thereby should promote further development as a pharmaceutical.
Acronirmus Eichler 1953
Creators: name: Gustafsson, Daniel R.
name: Bush, Sarah E.
name: Palma, Ricardo L.
Publisher: name: Zenodo
Year: 2019
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Phthiraptera
Philopteridae
Acronirmus

description: Availability of Acronirmus Eichler, 1953
Mey (2017: 91) argues that the name Acronirmus Eichler, 1953 is not taxonomically available, claiming that the correct name for that genus-group is Hirundiniella Carriker, 1963. His argument is based on the lack of a type species designation in the original description of Acronirmus by Eichler (1953), as required by Article 13.3 of the Code (1999).
There is no doubt that Acronirmus Kéler, 1939 is unavailable because, although a type species is designated by monotypy (Article 68.3 of the Code 1999), Kéler (1939) did not include a description of the genus. As a result, Hopkins & Clay (1952: 20) regarded Acronirmus as a nomen nudum. However, Eichler (1953) published the name Acronirmus again, but in an independent publication; thus, Eichler, 1953 became the author and publication date for Acronirmus. Eichler (1953) included a description of the genus and listed a single species under it, i.e. Acronirmus buettikeri Eichler, 1953, which he described including the designation of a holotype, thus making the name available. In a comparative section of his paper, Eichler (1953) also indicated that he considered Acronirmus gracilis (Burmeister, 1838) a member of this genus. However, only Ac. buettikeri was described and illustrated by Eichler (1953).
Carriker (1963) also correctly regarded “ Acronirmus Kéler, 1939 ” as a nomen nudum, but failed to notice that Eichler’s (1953) publication of Acronirmus is independent and described the new genus Hirundiniella for the lice that are now placed in Acronirmus Eichler, 1953.
Price et al. (2003) considered Ac. buettikeri to be the type species of Acronirmus by monotypy. Gustafsson & Bush (2017) agreed with this assessment, but erroneously stated that the type species of Acronirmus was Ac. buettikeri by original designation. Considering that Eichler (1953) only listed a single species explicitly, described and illustrated it by referring to examined specimens, we agree with Price et al. (2003) in considering Acronirmus to be validly described by Eichler (1953). Eichler’s (1953) inclusion of Ac. gracilis in the short comparative section, without mentioning characters of this species, does not, in our opinion, invalidate the designation of Ac. buettikeri as the type species by monotypy.
description: Published as part of Gustafsson, Daniel R., Bush, Sarah E. & Palma, Ricardo L., 2019, The genera and species of the Brueelia - complex (Phthiraptera: Philopteridae) described by Mey (2017), pp. 252-284 in Zootaxa 4615 (2) on page 254, DOI: 10.11646/zootaxa.4615.2.2, http://zenodo.org/record/3244680
Additional file 4: of Comprehensive genomic analysis of the CNGC gene family in Brassica oleracea: novel insights into synteny, structures, and transcript profiles
Creators: name: Kaleem Kakar
name: Zarqa Nawaz
name: Kakar, Khadija
name: Essa Ali
name: Abdulwareth Almoneafy
name: Raqeeb Ullah
name: Ren, Xue-Liang
name: Qing-Yao Shu
Publisher: name: Figshare
Year: 2017
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Evolutionary Biology
subject: Ecology
subject: 69999 Biological Sciences not elsewhere classified
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Developmental Biology
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Phylogenetic tree of CNGC genes from Arabidopsis (AtCNGCs). A multiple sequence alignment was performed using ClustalX 2.0 program with default settings. Maximum likelihood (ML) tree was create with MEGA 6.0, under the Jones-Taylor-Thornton (JTT) model. The bootstrap values from 1000 resampling are given at each node. (PDF 180Â kb)
Development of Targeted Anti-Cancer Platinum Analogs
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: Neuroblastoma (NB) is the most common solid tumor in children. Cisplatin, a first generation platinum analog, is first-line therapy in the treatment of NB and together with other drugs can result in cures of the disease in about 50% of children. Unfortunately, cisplatin is highly toxic and causes irreversible kidney damage and hearing loss. Cisplatin induced hearing loss is especially devastating in children because it results in lifelong learning difficulties. Moreover, the toxicities are dose-limiting. That is, high dose cisplatin, which may be curative, cannot be administered. Neuroblastoma has a high level of expression of the norepinephrine transporter (NET), an influx transporter responsible for accumulating norepinephrine in neuroendocrine cells. Designing therapeutic agents to be transported by NET therefore confers a promising approach to achieve targeted delivery of cytotoxic agents in tumor cells, which could result in higher activity and reduced toxicity. In preliminary studies we designed, synthesized and tested platinum analogs to target NET. We identified two analogs, which have similar potencies as cisplatin in NB cell lines. Importantly, preliminary in vivo studies suggest that both analogs exhibit substantially less ototoxicity and nephrotoxicity in mice. The overall goal of our studies is to perform bridging-the-commercialization gap studies with our lead and back-up anti-cancer platinum analogs. In particular, we will determine the toxicities of the lead and back-up analog in mice at various doses. From these studies we will identify a maximum tolerate dose (MTD), the highest dose that does not cause any measurable toxicity in the mice. By administering both compounds at the MTD, we will determine their effectiveness in treating mice harboring neuroblastoma tumors. The proposed studies will confer high commercialization potential for the two lead compounds since both analogs would be poised for critical Investigational New Drug (IND) enabling studies.
Post-transcriptional regulation of gene expression by ELAVL1
Creators: name: University Of California Office Of The President
Publisher: name: University of California Office of the President
publisherIdentifier: https://ror.org/00dmfq477
publisherIdentifierScheme: ROR
Year: 2024

description: The role of post-transcriptional regulators of gene expression in cancer-relevant molecular processes is increasingly recognized. The mRNA-binding protein HuR (ELAVL1) is overexpressed in a variety of cancers and affects tumor growth and malignancy; studies in various systems have connected HuR to the stress response, cell proliferation, survival and senescence, muscle differentiation, and T cell activation. Reacting to signals in the above processes, HuR carries out its cellular function by binding to hundreds of mRNAs, leading to changes in their translation and stability by poorly understood mechanisms. Genetic knockouts of HuR in a cancer T cell line generated in our lab demonstrate a clear function for HuR in control of the apoptotic program and cytokine production upon activation. In robust agreement with the phenotypes, RNA-seq data in KO cells indicates that HuR controls the levels of hundreds of mRNAs in functionally relevant categories, including apoptotic factors, as well as most cytokines. Furthermore, the data leads us to hypothesize that HuR controls the major transcription factors NFATC1 and NFKB2 that drive activation and proliferation programs. Using this experimental system, we propose to investigate the regulatory mechanisms that link HuR with NFATC1 and NFKB2 and upstream activation, and to determine and validate additional functionally important downstream targets of HuR. Overall, the study will shed light on the mechanisms of post-transcriptional control that enable HuR to mis-regulate the expression programs in cancer cells.