cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Microgonium
Creators: name: Ahamada H. Saïd
name: Sabine Hennequin
name: Germinal Rouhan
name: Jean-Yves Dubuisson
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Polypodiopsida
Hymenophyllales
Hymenophyllaceae
Microgonium

description: Subgenus Microgonium
Subgenus Microgonium is represented by four species. All Comorian species have glabrous lamina margins, submarginal false veins and sori more or less immerged in the laminae with tubular base and lips more or less developed, sometimes dilated as a collar but never bilabiate, and with undifferentiated margins. The widespread D. cuspidatum was cited for the archipelago in literature (Roux 2009) but represented in collection by only four specimens. This contradicts its supposed abundance in the region, as well observed in Mascarenes (pers. obs.; Grangaud 2010). In addition the species is usually distributed from sea level up to 1350–1400 m, and more frequently below 1000 m. All the supposedly Comorian specimens (including recent collects firstly identified as D. cuspidatum) were collected at high elevations, above 1000 m. A precise investigation of these specimens reveals in fact that they are not D. cuspidatum but rather the distinct D. erosum (Willd.) J.P.Roux. Didymoglossum cuspidatum would be absent in Comoros but confusion with D. erosum as detailed here-after remains easy. This explains why we, however, chose to maintain D. cuspidatum in the Xper database, in order to allow its potential identification in future collects.
description: Published as part of Ahamada H. Saïd, Sabine Hennequin, Germinal Rouhan & Jean-Yves Dubuisson, 2017, Disentangling the diversity and taxonomy of Hymenophyllaceae (Hymenophyllales, Polypodiidae) in the Comoros, pp. 1-53 in European Journal of Taxonomy 313 on page 16, DOI: 10.5852/ejt.2017.313, http://zenodo.org/record/896401
Mechanism and inhibition of the human de novo DNA methyltransferase DNMT3A
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 aberrant silencing of tumor suppressor genes by de novo DNA methylation is a reversible, epigenetic pathway leading to all forms of cancer. A key enzyme in this process is the de novo DNA methyltransferase, DNMT3A. DNMT3A interacts with itself to form multimeric structures, as well as with partner proteins like DNMT3L and Myc, which regulate DNMT3a. The structure of a truncated murine DNMT3A suggests that the enzyme forms homo-tetrameric structures with itself, and hetero-tetrameric structures with DNMT3L. We shall determine if DNMT3A forms monomers, dimers and tetramers in a concentration-dependent fashion, and if these different forms are functionally distinct. We shall determine if the different forms of DNMT3A are altered in their processive methylation of biologically relevant DNA sequences. We shall probe the structural basis of the multimeric forms of DNMT3A through protein engineering, and introduce mutant DNMT3A enzymes into human cells to determine if they impact cellular methylation. We and others have demonstrated that RNA molecules potently inhibit DNMT3A and we will determine if this occurs through changes in the enzyme’s processivity. Finally, we shall identify small molecules that disrupt the DNMT3L:DNMT3A complex. Such molecules are likely to be less toxic than currently used DNMT-targeting drugs which are quite cytotoxic. Methods Purified, recombinant human DNMT3A and DNMT3L will be used with various substrates and assays. Mutant DNMT3A enzymes will be generated by protein engineering methods. Fluorescence-based screening of small molecules will be carried out to identify those that disrupt the DNMT3L-mediated activation of DNMT3A activity.
Dissecting chromatin modifications that interact to regulate cell growth and response to DNA damage
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: Chromatin modification is linked to diverse cancers and to normal function of key oncogenes such as Myc and p53. This proposal builds on our discovery of critical connections between two modifying activities with chemically opposing roles: the Esa1 acetyltransferase and the Rpd3 deacetylase. Both enzymes are broadly conserved with human homologs that have been directly tied to specific cancers as well as regulated processes that are disrupted in cancers, such as apoptosis and repair of DNA damage. The proposed studies will deepen basic mechanistic understanding of chromatin modification and growth control and may establish novel targets for genetic or pharmacological intervention for cancers. The objectives and methods for this project are focused to answer four questions: 1) What is the molecular basis for the functional interaction between RPD3 and ESA1? We found that deletion of RPD3 suppresses loss of transcriptional silencing and viability in esa1 mutants. Rpd3 exists in two biochemically distinct complexes whose specific functions are not yet understood. We will genetically dissect the complexes to determine the specificity of suppression. 2) What is the chromatin basis of rpd3?-mediated suppression? To test the hypothesis that suppression is mediated at the level of histone acetylation, we will evaluate effects of rpd3? strains through biochemical and genetic assays of acetylation. 3) What are the critical genomic targets of rpd3?-mediated suppression? Building on rich data sets, we will analyze both candidate genes and genomic locations to define relevant targets of suppression through both expression and binding assays. 4) Does a specific HDAC oppose Esa1 activity in repair of DNA damage? The rpd3 suppression is potent for transcription and silencing defects, yet powerless for rescuing repair defects. We will test all other known Class I-III HDAC mutants to determine if there is a parallel molecular mechanism for damage suppression. The project proposed is based on significant preliminary results. We expect that progress made with CRCC funding will provide the foundation for a strong application for extramural funding in 2010.
Defining the molecular mechanisms underlying cancer initiation
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: Background: While a great deal is known about the accumulation of genetics hits that contribute to cancer, the identity of cells targeted by tumorigenesis remains unknown. It has been proposed that stem cells of the epidermis represent the most likely target of tumorigenesis given their longevity in the tissue, and their unique ability to self-renew and differentiate down multiple lineages. This hypothesis has not been directed tested previously because of a lack of appropriate genetic tools. Previous efforts to identify cancer cells of origin relied on descriptions of cell identity in existing tumors. Transgenic models of tumor initiation by overexpression of oncogenes suggest that almost any cell in the epidermis can serve as a cancer cell of origin as long as the stimulus is strong enough. To accurately identify cancer cells of origin in the epidermis, each cell type must be prospectively assayed on an equal basis. Only by generating equivalent genetic hits in each cell type, can the relative ability of various cells to initiate tumors be determined. Objective/hypothesis: Our central hypothesis is that epidermal stem cells possess unique molecular and functional characteristics that make them more sensitive to tumor initiation than their progeny. Our unique model system allows tumor initiating cells to be generated and isolated in a temporal fashion. We will use this system to isolate and molecularly profile cancer cells of origin to determine the molecular underpinnings of cancer initiation. Study Design: Our preliminary data shows that a conditional allele of a common oncogene driven by its endogenous promoter with inducible Cre recombinase driven by cell type specific promoters allows oncogene expression in stem cells or their progeny. The development of these in vivo systems allows us to manipulate temporal and cell-type specificity of oncogenesis and directly compare the tumor initiating potential of two cell types for the first time in the epidermis. We will ablate tumor suppressor genes in concert with oncogene induction. We are now quantifying the tumors formed to compare the results obtained with a single genetic hit in each cell type. By isolating cells as they are transformed during tumor initiation, a complete gene expression profile can be compiled. For this project we aim to compare the molecular profile of cancer initiating cells with those that receive the same stimulus, but are unable to initiate tumorigenesis, to understand the molecular basis for increased sensitivity to tumorigene
Polymer conjugated peptide mediated immunotherapeutic agents
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: We propose to synthesize a new immunotherapeutic agent based on polymer-conjugated tumortargeting peptides that also contain a protected immunogen – a wholly synthetic, bispecific immunotherapeutic agent. Unlike other immunotherapeutic approaches, our approach does not use proteins or cells. Proteins and cell therapies are expensive to produce, difficult to store, have limited shelf-lives and may be patient-specific. Our proposed synthetic immunological therapeutics are tumor specific but patient-independent and designed to elicit an immune response only when activated at the tumor site. Once localized to the tumor, the immunogen is deprotected, effectively marking the cancerous cells for destruction by the patient’s own immune system. We propose to protect the immunogen using photolytically cleavable protecting groups. Specifically, we will conjugate previously identified peptides YCDGFYACYMDV and KCCYSL that target the HER2 receptor overexpressed in certain breast cancers to poly(ethylene glycol) (PEG) chain that will also be bound to a protected immunogenic structure. The immunogen will consist of a protected mannose dendrimer, which should bind to mannose binding lectin to initiate complement upon deprotection. Unlike other approaches, the conjugation allows for more stable and potentially effective peptide-based therapeutics without interference of amino acid sequences found in proteins, and enables the presentation of many different immunogens and/or antigens. We also expect a longer blood clearance times compared to short peptides and small molecules, and expect the photocleavable moieties and PEG chains to protect the immunogen from immune recognition. By enlisting a patient’s own immune system to fight cancer, we hope for a more effective treatment with fewer side effects, whether alone or in combination with other therapies such as surgery, chemotherapy and radiation. Specific Aims a) Synthesize protected bispecific immunotherapeutic agent using peptides that target the HER2 receptor b) Measure the binding constants to HER2 receptors, investigate non-specific binding and determine whether or not the conjugates are endocytosed or remain on the surface of the targeted cells c) Measure the in vitro immunotherapeutic activity of these conjugates when localized to cancerous cells
Evaluating stucturally different pectic oligosaccharides in inhibiting adhesion of e. coli 015&:H& to human gut epithelial cells in vitro
Creators: name: Vakkalanka, Malathi Srilakshmi
Publisher: name: No Publisher Supplied
Year: 2013

description: Bacterial adhesion to glycosylated cellular surfaces is a major concern in human health and disease. Inhibition of bacterial adhesion by suitable carbohydrates may lead to an anti-adhesion therapy as a novel prophylactic approach against bacterial infections and a potential alternative to the use of antibiotics. Selections of six pectic oligosaccharides derived from citrus peel albedo, which were different in terms of their monosaccharide composition and physical properties, were evaluated for their ability to interfere with the adhesion of Escherichia coli O15&:H& to HT29 cells in vitro. Attachment was determined in the human HT29 cell line by viable count of adherent bacteria. Most of the pectic oligosaccharides in buffer at pH &.2 were anti-adhesive at a dose of 0.001 - 0.05 mg/ml, reducing adhesion of E.coli by 50 - 90% and concentrations of 0.5 - 5 mg/ml resulted in less than 50% reduction of adhesion to no effect. Based on the results, lower concentrations were more effective in reducing adhesion when compared to the higher concentrations. The pectic oligosaccharides with a homogalacturonan structure, low molecular weight and lower degree of esterification were the most effective in reducing the adhesion when compared to the oligosaccharides with an arabinose rich rhamnogalacturonan structure with higher molecular weight and higher degree of esterification. These results show that the pectic oligosaccharides with different monosaccharide composition and physical properties can display a wide range of anti-adhesive activity.
Tetramorium robustior Forel, stat. n.
Creators: name: Bolton, B.
Publisher: name: Zenodo
Year: 1979
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Tetramorium
Tetramorium robustior

description: Tetramorium robustior Forel stat. n.
(Fig. 16)
Tetramorium (Xiphomyrmex) andrei st. robustior Forel, 1892: 521. Syntype workers, Madagascar: Foret d'Andrangoloaka (Sikora) (MHN, Geneva) [examined].
Worker. TL 4.6 - 4.9, HL 1.00 - 1.04, HW 0.98 - 1.02, CI 98 - 100, SL 0.80 - 0.82, SI 78 - 80, PW 0.74 - 0.78, AL 1.30 - 1.32 (3 measured).
Mandibles striate; median clypeal carina distinct. Frontal carinae strongly developed and sinuate, diverging to the level of the eyes, converging behind the eyes and then diverging again posteriorly, each carina directed towards the occipital corner but merging with the sculpture before reaching it. Antennal scrobe a well-defined groove capable of accommodating the scape. Posteromedian portion of head in front of the occipital margin transversely shallowly concave. Pronotum and mesonotum bluntly marginate laterally. Propodeal spines long and strong, metapleural lobes elongate triangular, dentiform and acute. Petiole node in profile roughly rectangular, slightly broader above than below due to the weak concavity of both the anterior and posterior faces; a second result of this concavity is that the antero- and posterodorsal angles of the node slightly overhang the faces below them. In dorsal view the node longer than broad. Head regularly longitudinally rugose with a fine but conspicuous punctulation between the rugae. Dorsal surfaces of alitrunk and pedicel more coarsely longitudinally rugose. Gaster unsculptured. All dorsal surfaces of head and body with numerous fine, erect to suberect hairs. Leading edges of antennal scapes with short, suberect curved hairs, which are shorter than the maximum width of the scape.
T. robustior is close to andrei but is a more stockily built species with a slightly differently shaped petiole node, relatively broader head and shorter antennal scapes. In view of these differences it is my opinion that robustior is best treated as a good species, at least until more material is available and the variation of the two forms is known in more detail.
Material examined
Madagascar: no loc. (Sikora); Parc Nat. Mont. d'Ambre (W. L. & D. E. Brown); Bemanevika, Souspref.
Bealanana (A. Peyrieras).
description: Published as part of Bolton, B., 1979, The ant tribe Tetramoriini (Hymenoptera: Formicidae). The genus Tetramorium Mayr in the Malagasy region and in the New World., pp. 129-181 in Bulletin of the British Museum (Natural History) Entomology 38 on page 147
Systems analysis of oral cancer
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: Oral cancer, predominantly oral squamous cell carcinoma (OSCC), is the 6th most common human cancer. Approximately 35,000 people in the US will be newly diagnosed with oral cancer in 2008. Worldwide the problem is far greater, with new cases annually exceeding 480,000. Despite the high morbidity rate of oral cancer, the molecular events leading to the progression of oral precancer to cancer are still elusive. Currently there are no molecular and clinical parameters that can predict the malignant progression of oral precancer. In this proposal, we aim to determine key target genes and signal pathways activated during the progression of oral precancer to cancer using a systems biology approach. First we will conduct both quantitative proteome analysis (stable isotope labeling and 2-D LC-MS/MS) and expression microarray analysis of oral precancer/cancer. Next, the weighted gene co-expression network analysis (WGCNA) method will be used to analyze the microarray data and determine highly significant and connected genes. Finally these genes will be correlated with the quantitative proteomics data to identify key target genes concordantly changed at both mRNA and protein levels. Gene Ontology and pathway analysis will be performed to reveal biological processes and signaling networks based on the identified genes. Our proposed studies will also investigate the correlation between the two-dimensional expression data. The hypothesis is that a cluster of genes are concordantly altered at mRNA/protein expression levels and they have a synergistic role in oral carcinogenesis. Our long-term goal is to understand the cellular function and signaling pathways of the identified key target genes. The outcome of this project may lead to clinical tools for early detection and novel targets for therapeutic intervention in oral cancer.
Gymnotus maculosus Albert & Miller 1995
Creators: name: Angulo, Arturo
name: Betts, Joel T.
name: González-Alemán, Néstor J.
name: Castañeda, Edgar
name: Berghe, Eric Van Den
name: Elías, Diego J.
name: Mcmahan, Caleb D.
name: Matamoros, Wilfredo A.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Gymnotiformes
Gymnotidae
Gymnotus
Gymnotus maculosus

description: Gymnotus maculosus Albert & Miller 1995 (Fig. 7D). Spotted Knifefish; Pez Cuchillo, Pez Cuchillo Manchado, Pez Navaja, Pez Machete, Anguila, Anguila Falsa, Madre de Barbudo, Guabina
Vouchers: UCR 0457-011 (2) and 0460-006 (4). Distribution: North and Central America; from southern Mexico to central Costa Rica, Atlantic and Pacific drainages; (Nicaragua) Pr, GM, KP, Es, BF, IM, To, Sa, SJ, RF and LN (Atlantic); 2–210 masl; Pri, Pot. Occurrence and conservation status: Nat; LC (2019), population trend unknown.
Literature: Bussing (1998: 132; brief description, including illustrations and an identification key, and information on distribution, with a map, and ecology) and Angulo (2021: 29; listed, including information on distribution).
description: Published as part of Angulo, Arturo, Betts, Joel T., González-Alemán, Néstor J., Castañeda, Edgar, Berghe, Eric Van Den, Elías, Diego J., Mcmahan, Caleb D. & Matamoros, Wilfredo A., 2023, Continental fishes of Nicaragua: diversity, distribution and conservation status; with an annotated and illustrated checklist of species and an identification guide to families, pp. 1-89 in Zootaxa 5376 (1) on page 26, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Didymoglossum kirkii (Hook.) Ebihara & Dubuisson
Creators: name: Ahamada H. Saïd
name: Sabine Hennequin
name: Germinal Rouhan
name: Jean-Yves Dubuisson
Publisher: name: Zenodo
Year: 2017
Subjects: Biodiversity
Taxonomy
Plantae
Tracheophyta
Polypodiopsida
Hymenophyllales
Hymenophyllaceae
Didymoglossum
Didymoglossum kirkii

description: Didymoglossum kirkii (Hook.) Ebihara & Dubuisson
Didymoglossum kirkii (Hook.) Ebihara & Dubuisson in Ebihara et al., Blumea 51: 236 (2006). –
Trichomanes kirkii Hook. in Hooker & Baker, Synopsis filicum 3: 78 (1867). – Type: ‘Comoro Isl., Johanna Isl.’, J. Kirk s.n. (holo-: K000435666!).
Crepidomanes seu Microgonium kirkii (Hook.) Copel., The Philippine Journal of Science 67: 104 (1938), nom. nud. Note: these combinations were never validly published but just suggested in a synonym list by Copeland, and were nevertheless cited by Tardieu-Blot (1951).
Short description
Lithophytic or epiphytic; long-creeping filiform rhizomes, rootless and densely covered by dense black trichomes, bearing widely separated pending fronds; fronds well stipitate, up to 9 cm long, lanceolate to obovate, entire with undulate margins to mostly pinnate, less often pinnate-pinnatifid or bipinnate, with pinnate venation, and false veins parallel to true veins in addition to a submarginal false vein; few sori at the apex of pinnae, epitactic, cylindrical with a slightly dilated mouth.
Global distribution
Comoros.
Distribution in Comoros
Anjouan, Grande Comore, Mayotte, Mohéli.
Additional specimens examined
COMOROS: [ANJOUAN?], s. loc., 1886, L.Humblot 1552 (P00139630, P00139631, P00139632, P00312476). ANJOUAN, s. loc., May 1850, LH.Boivin s.n. (P00301470, P00301471); s. loc., 1905?, M.Lavanchie s.n. (P00301469). GRANDE COMORE, Base du Massif du Karthala, 10 Jun. 2006, J.­N.Labat et al. 3807 (P00527430); Versant ouest du volcan Karthala, bois proche de Convalescence, 24 Oct. 2008, M.Pignal et al. 3401 (P02439792); Massif forestier à l’ouest de la route régional 125 (départ de la piste à 2–3 km au sud de Tsinimouapanga), 10 Nov. 2008, G.Rouhan et al. 925 (P00684886). MAYOTTE, Qualey, Aug. 1847, L.H.Boivin 2883 (P00312471); Combani, Le long du Mroni Mouala, 17 Apr. 1999, M.Pignal et al. 1209 (P00139596); Rivière Camboni, 12 Nov. 2002, F.Rakotondrainibe et al. 6673 (P00311387). MOHÉLI, Piste entre Miringoni et le Chalet St Antoine, 4 Nov. 2008, G.Rouhan et al. 879 (P02439804); Chalet St Antoine, 5 Nov. 2008, M.Pignal et al. 3485 (P02439795).
Note
Didymoglossum kirkii, the only Hymenophyllaceae endemic to the Comoros, is the largest Comorian Didymoglossum species with fertile stipitate fronds up to 9 cm long which are entire or most often pinnatifid, or pinnate to bipinnate (Fig. 3A). In addition, rachises are often clearly distinct in D. kirkii compared to other Didymoglossum species.
description: Published as part of Ahamada H. Saïd, Sabine Hennequin, Germinal Rouhan & Jean-Yves Dubuisson, 2017, Disentangling the diversity and taxonomy of Hymenophyllaceae (Hymenophyllales, Polypodiidae) in the Comoros, pp. 1-53 in European Journal of Taxonomy 313 on page 18, DOI: 10.5852/ejt.2017.313, http://zenodo.org/record/896401
Development of high band gap materials for tandem solar cells and simulation studies on mechanical tandem solar cells
Creators: name: Vijayakumar, Vishnuvardhanan
Publisher: name: No Publisher Supplied
Year: 2013

description: Development of low cost, high efficiency tandem solar cells is essential for large scale adoption of solar energy especially in densely populated regions of the world. In this thesis four-terminal mechanical (stack like) tandem solar cells were evaluated using detailed simulation models and design criteria for selecting candidate materials were established. Since silicon solar cells are low cost and have a multi-giga watt global manufacturing and supply chain capacity already in place then only tandem stacks incorporating silicon as one of the layers in the device was investigated. Two candidate materials which have high band gaps that could be used as top cells in the mechanical tandem device were explored as part of the thesis.   Dye-sensitized solar cells (DSSC) sensitized with N&19 dye (one of the candidates for the top cell) were fabricated with the goal of enabling a flexible processing path to lower cost. Stainless steel (SS) mesh substrates were used to fabricate anodes for flexible DSSC in order to evaluate them as replacements for more expensive Transparent Conducting Oxides (TCO's). Loss mechanisms in DSSC's due to SS mesh oxidation were quantified and protective coatings to prevent oxidation of SS mesh were developed. The second material which was evaluated for use as the top cell was copper zinc tin sulfide (CZTS). CZTS was deposited through a solution deposition route. Detailed investigations were done on the deposited films to understand the chemistry, crystal structure and its opto-electronic properties. Deposited CZTS films were found to be highly crystalline in <112> direction. The films had a direct band gap of 1.5 eV with absorption coefficient greater than 104 cm-1 in agreement with published values.  In the second part of the thesis detailed electrical and optical simulation models of the mechanical tandem solar cells were developed based on the most up-to-date materials physical constants available for each layer. The modeling was used to quantify the various theoretical and practical loss mechanisms in tandem devices. Two configurations were evaluated, first was silicon / germanium tandem cell and the second was gallium arsenide / silicon tandem cell. The simulation models were validated by their close match to the performance of experimental standalone solar cells devices reported in the literature.   Finally the efficiency limits of the present generation of high band gap solar cells were discussed. Voltage and current loss of the high band gap solar cells were compared with present generation silicon solar cells and challenges in improving their efficiencies were described.
Induction of cell death in T-cell acute lymphoblastic leukemia by modulation of calcium signalling
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: Ca2+ signalling though the CRAC (Ca2+-release-activated Ca2+) channel is a key step for proliferation and cell death of immune cells. In the past two years, the PI identified and named Orai1 as a long-sought component of the CRAC channel. We have shown that severe combined immune deficiency (SCID) patients have a missense mutation within the Orai1 gene, further emphasizing the predominant role of Orai1 in immune cells. The preliminary data using T cells from the Orai1-/- mice we recently generated showed the minimum requirement of the intracellular Ca2+ level to induce programmed cell death exists at approximately 200 nM. Deletion of Orai1 gene; thereby lowering the intracellular Ca2+ levels resulted in strong resistance to apoptosis and hyper-proliferation of Orai1- T cells. In addition, increase of the intracellular Ca2+ levels induced cell death in a leukemic T cell-line, strongly indicating Ca2+ signalling as a major pathway leading to programmed cell death of T cells. Our long term goal is to test the possibility to develop a small molecule that boosts the Ca2+ signalling; thereby potentiates cell death of leukemic T cells. The specificity of the drug can be justified by strong predominance of Orai1 in immune cells. As a short term goal, we will test the hypothesis that modulation of Ca2+ signalling influences the process of Notch1-induced lymphoblastic leukemia using a murine bone marrow transplant model. Gain-of-function Notch1 mutations are found in 50%-70% of human T cell acute lymphoblastic leukemia cases. Bone marrow cells from the Orai1- mice, or transduced with viral vectors containing the hyperactive form of Orai1 along with activated Notch1, will be transplanted. The influence of Ca2+ modulation in the pathological process of leukemia will be determined.
Control of connective tissue remodeling by the conserved DNA repair factor XAB2
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 nucleotide excision repair (NER) pathway removes particular DNA lesions from the genome and protects against cancer. Mutations in 8 genes encoding components of the NER machinery each cause xeroderma pigmentosum (XP), an inherited disease characterized by a 1000-fold increase in the risk of UV-induced skin cancers. Although intrinsic cellular phenotypes contribute to the predisposition to cancer, the functions of many NER factors are not fully understood. This proposal focuses on XAB2, a protein that physically interacts with the XPA protein and participates in transcription and transcriptioncoupled NER. My laboratory isolated the C. elegans ortholog of XAB2 in a genetic screen for mutants that molt excessively, a process that involves complete remodeling of the collagen-rich external skeleton and stem-cell like divisions in the epidermis. The dysfunction of related processes in vertebrates contributes to the growth and metastasis of skin tumors. We propose to study the mechanism by which xab-2 prevents the pathologic remodeling of connective tissue in C. elegans. We hypothesize that XAB-2 regulates the conserved tumor suppressor microRNA let-7 and/or the conserved cell cycle and circadian clock gene lin-42/Period, established regulators of cell fate in the epidermal lineage. Genetic analysis will order xab-2 relative to let-7 and lin-42/per in the heterochronic pathway. We will go on to test the model that XAB-2 promotes let-7 expression, leading to down-regulation of lin- 42. We expect our findings to apply to the deregulation of let-7 and/or Per characteristic of many human cancers. An alternative model is that XAB-2 arrests cell division in response to DNA damage or age, thereby repressing the molting cycle. We will ask if local UVdamage causes a systemic delay in molting that depends on xab-2, using fluorescent reporter proteins. Considering that XPA and Per participate in the S-phase cell cycle checkpoint, we will also look for physical interactions among XAB-2, LIN-42/Per, and RAD-3/XPA. We anticipate the discovery of a systemic checkpoint controlling cell division and ECM turnover in a manner dependent on NER factors. The dysfunction of related checkpoints may accelerate skin cancers associated with NER disorders.
Additional file 1: of Single cell transcriptomics suggest that human adipocyte progenitor cells constitute a homogeneous cell population
Creators: name: Acosta, Juan
name: Joost, Simon
name: Karlsson, Kasper
name: Ehrlund, Anna
name: Xidan Li
name: Aouadi, Myriam
name: Kasper, Maria
name: Arner, Peter
name: RydĂŠn, Mikael
name: Laurencikiene, Jurga
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: 69999 Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Hematology
subject: Computational Biology

description: Supplemental methods. (DOCX 32 kb)
Additional file 1: Figure S1. of Modelling stunting in LiST: the effect of applying smoothing to linear growth data
Creators: name: Cousens, Simon
name: Perin, Jamie
name: Christian, Parul
name: Wu, Lee
name: Soofi, Sajid
name: Bhutta, Zulfiqar
name: Lanata, Claudio
name: Guerrant, Richard
name: Lima, Aldo
name: KĂĽre MĂ¸Lbak
name: Valentiner-Branth, Palle
name: Checkley, William
name: Gilman, Robert
name: R. Sack
name: Black, Robert
name: Humphrey, Jean
name: Neff Walker
Publisher: name: Figshare
Year: 2017
Subjects: subject: Biochemistry
subject: Medicine
subject: Genetics
subject: FOS: Biological sciences
subject: Biotechnology
subject: 39999 Chemical Sciences not elsewhere classified
subject: FOS: Chemical sciences
subject: 69999 Biological Sciences not elsewhere classified
subject: 80699 Information Systems not elsewhere classified
subject: FOS: Computer and information sciences
subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: Inorganic Chemistry
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: Plant Biology

description: Distribution of measured lengths/heights against transformed age for 21786 children. (DOCX 1363 kb)
Loricariidae Rafinesque 1815
Creators: name: Angulo, Arturo
name: Betts, Joel T.
name: González-Alemán, Néstor J.
name: Castañeda, Edgar
name: Berghe, Eric Van Den
name: Elías, Diego J.
name: Mcmahan, Caleb D.
name: Matamoros, Wilfredo A.
Publisher: name: Zenodo
Year: 2023
Subjects: Biodiversity
Taxonomy
Animalia
Chordata
Siluriformes
Loricariidae

description: Family Loricariidae Rafinesque 1815 (Fig. 3D). Suckermouth Armored Catfishes; Peces Diablo, Plecos, Peces Gato Acorazados
Description: Body generally elongate, robust, caudally depressed, covered by bony plates; usually less than 70 cm in length; mouth ventral, with papillose lips; pectoral, pelvic and dorsal fins usually with strong spines; adipose fin usually present, with a spine at the anterior border (Angulo et al. 2021, Nelson et al. 2016). Distribution: Freshwater; naturally from Costa Rica, Panama and South America, introduced elsewhere (Nelson et al. 2016). One genus and one species in Nicaraguan freshwaters.
description: Published as part of Angulo, Arturo, Betts, Joel T., González-Alemán, Néstor J., Castañeda, Edgar, Berghe, Eric Van Den, Elías, Diego J., Mcmahan, Caleb D. & Matamoros, Wilfredo A., 2023, Continental fishes of Nicaragua: diversity, distribution and conservation status; with an annotated and illustrated checklist of species and an identification guide to families, pp. 1-89 in Zootaxa 5376 (1) on page 26, DOI: 10.11646/zootaxa.5376.1.1, http://zenodo.org/record/10208788
Studies in viral population genetics and bioinformatics
Creators: name: Wagh, Kshitij
Publisher: name: No Publisher Supplied
Year: 2013

description: This thesis consists of two studies pertaining to the evolution and genomic signatures of viruses. Viruses are obligate intracellular parasites that have a great impact on human, animal and plant health. The first study involves the human infecting Influenza A H5N1 viruses. H5N1 is an avian virus which occasionally infects humans, with a 50-60% mortality rate.  Human-to-human transmission is limited, and most H5N1 infections are transmitted to humans from birds. Under such a transmission scheme, there can be a possibility of a biased transmission of H5N1 strains from birds to humans. Such a biased transmission could arise due to higher efficiency of some avian strains in infecting humans, an enhanced ability of the human immune response to clear some of the human-infecting avian strains, etc. We developed a novel strategy to identify such signatures and analyzed publicly available H5N1 hemagglutinin sequences from China, Egypt, and Indonesia. In each geographic region, it was found that human infecting strains arose from a subset of the avian viral pool characterized by geography specific mutations. These mutations lie in functionally important regions of hemagglutinin proteins involved in viral attachment to cells, immune response etc. After correcting for this transmission bias, an absence of further widespread bias was observed. This research also showed that vaccine evasion mutant viruses are unlikely to infect humans, a finding with significant implications for rational vaccine design.    As a separate project, we developed a new method to detect novel capsid sequences. It is expected that a large part of the virosphere still remains uncharacterized. Viruses show remarkably high levels of sequence diversity. Hence, sequence similarity based methods have limited success in detection of novel viral sequences in metagenomic studies. However, in contrast to high sequence diversity, the capsid proteins from diverse families of icosahedral viruses show a conserved eight stranded beta barrel known as the ``Jelly-roll'' fold. Motivated by this structural conservation, we sought to classify such capsid protein sequences using a machine learning approach on alignment free features. The nature of the alignment free features suitable for the problem are first discussed. Using these alignment free features, a high-accuracy Support Vector Machine (SVM-Caps) was developed for classifying jelly-roll capsid proteins against other proteins. The predictive power of this classifier was compared to that of BLAST, a popular tool based on sequence similarity. SVM-Caps was found to have comparable but lower power to detect capsid sequences of known viral families, but significantly higher power in detection of capsid sequences from novel families. As an application of this method, the viral metagenomic data from the French Lake Bourget study were analyzed and many potential novel capsid sequences were found.
Additional file 1: of Psychological symptoms among hospital nurses in Taiwan: a cross sectional study
Creators: name: Chen, Mei-Ju
name: Shiue-Shan Weng
Publisher: name: Figshare
Year: 2017
Subjects: subject: Medicine
subject: Sociology
subject: FOS: Sociology
subject: 69999 Biological Sciences not elsewhere classified
subject: FOS: Biological sciences
subject: Developmental Biology
subject: Science Policy

description: Self-administered questionnaire. This is the self-administered questionnaire used in the study. (DOCX 15Â kb)
Tetramorium ranarum
Creators: name: Bolton, B.
Publisher: name: Zenodo
Year: 1979
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Tetramorium
Tetramorium ranarum

description: The ranarum -group
Antennae with 11 segments; sting appendage spatulate. Mandibles sculptured, usually striate, more rarely otherwise. Petiole strongly nodiform, many species in the group with postpetiole unsculptured but the petiole is usually sculptured to some extent. Small species with HW usually <0.80. Dorsal (outer) surfaces of hind tibiae with pubescence which is usually decumbent or appressed, only very rarely otherwise.
This small group of seven species is restricted to the Malagasy region. Their closest relatives appear to be the members of the African angulinode-group, but in them the mandibles are always smooth and unsculptured.
description: Published as part of Bolton, B., 1979, The ant tribe Tetramoriini (Hymenoptera: Formicidae). The genus Tetramorium Mayr in the Malagasy region and in the New World., pp. 129-181 in Bulletin of the British Museum (Natural History) Entomology 38 on page 147
Tetramorium coillum Bolton, 1979, sp. n.
Creators: name: Bolton, B.
Publisher: name: Zenodo
Year: 1979
Subjects: Biodiversity
Taxonomy
Animalia
Arthropoda
Insecta
Hymenoptera
Formicidae
Tetramorium
Tetramorium coillum

description: Tetramorium coillum sp. n.
(Fig. 21)
Holotype worker. TL 2.8, HL 0.72, HW 0.67, CI 93, SL 0.46, SI 69, PW 0.48, AL 0.78.
Mandibles coarsely longitudinally striate, anterior clypeal margin with a distinct notch or impression. Maximum diameter of eye 0.12, about 0.18 x HW. Frontal carinae strong to behind level of eyes, but fading out before they reach the occipital area and becoming confused with the remaining sculpture. Antennal scrobes very feeble, all of the scrobal area sculptured. Propodeal spines strong, feebly upcurved along their length, metapleural lobes triangular and acute. Petiole in profile strongly nodiform, with a sharp anterodorsal angle and with a minute peak at the angle due to the presence of a transverse dorsal carina. Posterodorsal angle of petiole rounded. Node of petiole in dorsal view as broad as long. Dorsum of head finely and irregularly longitudinally rugulose, with a conspicuous punctulate ground-sculpture between them, the rugulae forming a weak reticulum occipitally. Dorsal alitrunk reticulate-rugulose, the sculpture more strongly developed than on the head, the individual rugulae low and rounded, with a beaded appearance dorsally due to the presence of fine aligned punctulation. Spaces between reticular meshes mostly smooth. Petiole dorsum finely and densely rugulose, the postpetiolar dorsum with extensive shining areas but with some rugulae present, especially posterolaterally. Gaster unsculptured. Short, fine acute hairs present on all dorsal surfaces of head and body. Colour dark brown.
Paratype workers. As holotype, TL 2.7 - 2.8, HL 0.66 - 0.72, HW 0.62 - 0.66, CI 91 - 94, SL 0.44 - 0.47, SI 69 - 72, PW 0.45 - 0.47, AL 0.72 - 0.78. Maximum diameter of eye 0.11 - 0.12, about 0.17 - 0.19 x HW.
Holotype worker, Madagascar: Bemanevika, Souspref. de Bealanana, 20. x. 1975, forest humus and litter, AB 46 (A. Peyrieras) (MCZ, Cambridge). Paratypes. 12 workers and 2 dealate females with same data as holotype (MCZ, Cambridge; BMNH).
This small species is closest related to ranarum and quasirum but differs from both of these by retaining rugular sculpture on the postpetiole and by having the anterodorsal angle of the petiole node sharp.
description: Published as part of Bolton, B., 1979, The ant tribe Tetramoriini (Hymenoptera: Formicidae). The genus Tetramorium Mayr in the Malagasy region and in the New World., pp. 129-181 in Bulletin of the British Museum (Natural History) Entomology 38 on pages 147-148
Regulated expression of the Sall2 transcription factor in human colon cancer
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: Despite important advances in treatment and diagnosis human colorectal cancer is one of the most deadly neoplasms in the world. Colon cancer is the second most common cause of cancer death in the United States. A major challenge for research is to identify genetic changes associated with the development and particularly the spread of colon cancer, as it is metastases rather than the primary cancers that kill. We have identified the Sall2 transcription factor as a protein that is virtually undetectable in normal colon mucosa but highly expressed in colon cancer metastases resected from patients. Furthermore, in the metastases a significant fraction of Sall2 is localized to the nucleus, and therefore functional. We hypothesize that Sall2 is an oncogene that promotes the growth and spread of colon cancer. We propose to define the mechanism through which Sall2 expression is elevated in cancer. Preliminary data suggest that p53 by acting through Siah ubiquitin ligases suppresses Sall2 expression. We will use wild-type (wt) and p53 mouse embryo fibroblasts (MEFs) and colon cancer cells, and MEFs from wt and Siah deficient mice to define the roles of p53 and Siah proteins in regulation of Sall2 expression. This will involve use of immunohistochemistry, Western blotting and quantitative RT-PCR. We will also assay p53, Siah and Sall2 mRNA and protein expression in normal colonic mucosa and colon cancer metastases to and genotype these tissues for p53 and/or Siah mutations. These experiments will determine whether inappropriately low expression or mutation of p53 and/or Siah proteins account for elevated Sall2 in colon cancer metastases. Finally we will determine whether Sall2 promotes the growth of tumors from colon cancer cells in which its expression has been modulated in nude mice. These studies will identify Sall2 as an important mediator of colon cancer and determine why its expression is deregulated.
Determining the role of Pygopus 2 protein in Wnt-induced tumorigenesis and stem cell expansion
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 Wnt/ß-catenin signaling pathway plays a central role in regulating normal and malignant mammary stem/progenitor cells. Deregulation of this pathway results in the aberrant formation of ß-catenin/TCF transcriptional complexes and leads to mammary tumors accompanied by an expanded stem/progenitor cell population. Our laboratory cloned mouse Pygopus 2 (Pygo2), a coactivator of ß-catenin/TCF-dependent transcription, and found it to be expressed in stem and progenitor cells of the developing mammary gland and up-regulated in breast cancers. Functional studies of Pygo2 may yield insights into the molecular mechanism of Wnt-induced tumorigenesis and the involvement of stem/progenitor cells, as well as uncover Wnt-independent roles for Pygo2 in breast tumorigenesis. Objective/Hypothesis: To study the in vivo function of Pygo2, we generated and analyzed skin/mammary epithelia-specific Pygo2 knockout mice. These mice display a reduced number of mammary stem/progenitor cells, a phenotype opposite of that caused by aberrantly activated Wnt/ß- catenin signaling. Based on these findings, we hypothesize that loss of Pygo2 will rescue Wnt signaling-induced mammary stem/progenitor cell expansion and tumorigenesis. Methods: We propose two complimentary approaches to study the role of Pygo2 in Wntmediated tumorigenesis: an in vivo mouse genetic approach and an in vitro cell-based approach. We will generate Pygo2-deficient mice that carry either a K14-?N-ß-catenin or a MMTV-Wnt1 transgene, which are known to mimic over-activated Wnt signaling. We will compare the extent of mammary stem/progenitor cell expansion and tumorigenesis in these compound mutants with that in K14-?N-ß-catenin or MMTV-Wnt1 single transgenic mice. We will generate stable mouse mammary epithelial cell lines that overexpress Wnt1 but are deficient in Pygo2 expression, and compare the tumorigenic potential of these cells with their Pygo2-expressing counterparts using in vitro (proliferation, apoptosis, anchorage-independent growth, clonogenic potential, matrix invasion) and in vivo (subcutaneous transplantation onto nude mice) assays.