Miracle-dz/UniFAR-FTUs huggingface dataset:
Regulation of gene expression in the immune system and in virally-transformed cells

The correct development and functioning of the immune system is critical for the defence of the host organism against pathogens and cancers. V(D)J recombination generates diversity of immunoglobulin (Ig) and T cell receptor (TCR) genes by the regulated joining of variable (V), diversity (D) and joining (J) gene segments. Tissue-specific enhancers in the DNA genome activate these genes to undergo recombina-tion by triggering non-coding transcription through the recombining gene segments, following interaction with the respective promoters. How this is achieved is un-known. The specificity of enhancer/promoter interactions was examined using the murine Igλ chain locus. The transcription factors that bind to the three main promoters were identified by DNase I footprinting. Of these, a factor termed E47 was shown to interact with IRF4 by co-immunoprecipitation experiments. The importance of these interactions was confirmed by mutagenesis where it was shown that mutations of any of the binding sites in DNA for the transcription factors or mutations in the amino acids involved in protein-protein interactions decreased the rate of transcrip-tion. Together, these studies suggest that IRF4/E47 interactions may play a key role in triggering locus activation. RNA-Seq data from HPV-positive samples and cell lines were analysed to identify putative biomarkers for cervical cancer. Infection with HPVs is the main cause for cervical cancer accounting for 10-15% of cancer-related deaths in women world-wide. It is established that HPVs escape the immune response over decades to es-tablish tumorigenesis but the specific mechanism is unknown. Virus integration into the host genome and deregulation of several genes may play a key role in promot-ing cancer; of particular interest are those transcripts that form the “surfacesome”. Among these, particular interest was given to connexin 26 (Cx26), which is classified as cancer-predisposition gene and was found to be commonly down regulated in all samples analysed. Recombinant adenoviruses expressing the two HPV16 oncogenes were generated and employed to transduce HaCaT cells to analyse Cx26 mRNA and protein levels coupled with dye transfer assays to study the structural behaviour of connexins. The data presented showed that E6 and E7 alter Cx26 protein expression by relocating Cx26 within the cytoplasm from the membrane-bound form. This was confirmed in the dye transfer assay where cell-cell communications were lost
The Role of Pre-H2 Domains of α- and δ-Epithelial Na+ Channels in Ion Permeation, Conductance, and Amiloride Sensitivity*

Epithelial Na+ channels (ENaC) regulate salt and water re-absorption across the apical membrane of absorptive epithelia such as the kidney, colon, and lung. Structure-function studies have suggested that the second transmembrane domain (M2) and the adjacent pre- and post-M2 regions are involved in channel pore formation, cation selectivity, and amiloride sensitivity. Because Na+ selectivity, unitary Na+ conductance (γNa), and amiloride sensitivity of δ-ENaC are strikingly different from those of α-ENaC, the hypothesis that the pre-H2 domain may contribute to these characterizations has been examined by swapping the pre-H2, H2, and both (pre-H2+H2) domains of δ- and α-ENaCs. Whole-cell and single channel results showed that the permeation ratio of Li+ and Na+ (PLi/PNa) for the swap α chimeras co-expressed with βγ-ENaC in Xenopus oocytes decreased significantly. In contrast, the ratio of PLi/PNa for the swap δ constructs was not significantly altered. Single channel studies confirmed that swapping of the H2 and the pre-H2+H2 domains increased the γNa of α-ENaC but decreased the γNa of δ-ENaC. A significant increment in the apparent inhibitory dissociation constant for amiloride (\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(K_{i}^{\mathrm{amil}}\) \end{document}) was observed in the α chimeras by swapping the pre-H2, H2, and pre-H2+H2 domains. In contrast, a striking decline of \batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(K_{i}^{\mathrm{amil}}\) \end{document} was obtained in the chimeric δ constructs with substitution of the H2 and pre-H2+H2 domains. Our results demonstrate that the pre-H2 domain, combined with the H2 domain, contributes to the PLi/PNa ratio, single channel Na+ conductance, and amiloride sensitivity of α- and δ-ENaCs.
Plant Growth and Development: Hormones and Environment

CHAPTER 1 Special Features of Plant Development CHAPTER 2 Cell Wall, Cell Division, and Cell Growth CHAPTER 3 Embryogenesis CHAPTER 4 Determination, Differentiation, and Dedifferentiation in Plants CHAPTER 5 General Features of Plant Hormones, Their Analysis, and Quantitation CHAPTER 6 Auxins CHAPTER 7 Gibberellins CHAPTER 8 Cytokinins CHAPTER 9 Brassinosteroids CHAPTER 10 Abscisic Acid CHAPTER 11 Ethylene CHAPTER 12 Jasmonates and Other Defense-Related Compounds CHAPTER 13 Uptake and Transport of Hormones CHAPTER 14 Apical Dominance and Some Other Phenomena Illustrating Correlative Effects of Hormones CHAPTER 15 Hormonal Regulation of Cell Division and Cell Growth CHAPTER 16 Abscisic Acid and Stress Tolerance in Plants CHAPTER 17 Fruit Development and Ripening CHAPTER 18 Seed Development and Maturation CHAPTER 19 Seed Germination, Mobilization of Food Reserves, and Seed Dormancy CHAPTER 20 Vegetative Storage Proteins, Tuberization, Senescence, and Abscission CHAPTER 21 Ethylene Signal Perception And Transduction CHAPTER 22 Auxin Signal Perception and Transduction CHAPTER 23 Abscisic Acid Signal Perception and Transduction CHAPTER 24 Molecular Biology o f Action of Gibberellins, Cytokinins, Brassinosteroids, and Jasmonates CHAPTER 25 Signal Transduction in Plants CHAPTER 26 Photoperception and Signaling CHAPTER 27 Tropic and Nontropic Responses to Environmental Signals
REPAIR OF BIPYRIMIDINE PHOTOPRODUCTS AT TELOMERES OF ULTRAVIOLET LIGHT IRRADIATED MAMMALIAN CELLS

Telomeres at chromosome ends promote genome stability, survival, and proliferation in cells, and prevent degenerative diseases and cancer in humans. Human telomeres are 10-15 kilobases long and consist of about 1500 tandem TTAGGG repeats. Six telomeric proteins form a shelterin complex that protects the telomeres from being recognized as a chromosome break, thereby preventing inappropriate repair and chromosome fusions. Telomeric DNA sequences are vulnerable to ultraviolet light (UV)-induced damage. UV creates primarily two types of photoproducts within DNA: cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4 PPs). Unrepaired photoproducts can stall or block DNA replication and transcription, or if tolerated and bypassed, can introduce mutations that cause genomic instability which can drive carcinogenesis. In genomic DNA, these potentially harmful cellular effects are avoided through a specialized nucleotide excision repair (NER) pathway that removes photoproducts and restores normal DNA. This dissertation investigated if photoproducts also form at chromosome ends and if they are repaired over time by NER. We exposed skin fibroblasts BJ-hTERT (NER proficient) and XP-A (NER deficient) to 10 J/m2 UVC which induces CPD and 6-4 PP lesions. We then extracted genomic and telomeric DNA from these fibroblasts and measured the rate of lesion disappearance. Post UVC exposure, BJ-hTERT cells repaired all detectable telomeric 6-4 PPs by six hours and telomeric CPDs by two days. However, XP-A cells did not repair telomeric 6-4 PPs. We observed that unrepaired photoproducts inhibit telomere TRF1 protein binding to telomeric DNA in vitro, and that cellular UVC irradiation of NER deficient cells causes telomere aberrations. Our novel findings have uncovered the presence and importance of a major DNA repair pathway at telomeres and increase our understanding of how unrepaired bulky adducts at telomeres may impact telomere structure and function. Telomere maintenance is essential in protection against age-related diseases and cancer in humans. The public health relevance of our study thus, relates to its potential usefulness in developing biomarkers of toxicology for aging and cancer.
Forcing mechanisms of the Bay of Bengal circulation

A state-of-the-art ocean general circulation model, set up for the North Indian Ocean and driven by climatological wind stress simulates most of the observed features of the near-surface circulation of the Bay of Bengal. The prominent features of the annual cycle are an anticyclonic gyre with a poleward East India Coastal Current (EICC) during February-May, and an equatorward EICC during October-December, During the summer monsoon, the coastal current flows poleward in the south and equatorward in the north, To identify the principal mechanisms governing this cycle, we carried out experiments with modified winds, When spatially uniform wind stress was applied only over the Bay, the circulation is similar to, but weaker than the observed, and can be linked to two coastal Kelvin wave pulses which originate along the eastern boundary of the Bay during the summer and winter monsoons, When the Bay is forced with observed winds, the wind stress curl strengthens the poleward EICC during February-May and the equatorward EICC during October-December. The principal contribution of equatorial winds is to generate the equatorward coastal current during the summer monsoon off the east coast of India.
Floristic and Taxonomic Accounts of the Genus Euglena (Euglenophyceae) from Korean Fresh Waters

This paper contains descriptions, illustrations and key to identify 22 taxa of the genus Euglena collected from 58 sites of Korean fresh waters. Of these, 12 taxa are recorded for the first time in the euglenoid flora of Korea: E. archaeoplastidiata, E. caudata, E. granulata, E. oblonga, E. obtusa, E. deses var deses, E. deses var. intermedia, E. ehrenbergii var. baculifera, E. limnophila, E. texta, E. truncata, and E. variabilis. Most of the members are cosmopolitan, whereas E. archaeoplastidiata, E, ehrenbergii var. baculifera, E. truncata, and E. variabilis are the rare taxa in the world flora of euglenoids.
Germinação e crescimento de plântulas de Enterolobium contortisiliquum (Vell.) Morong em função da localização da semente no fruto e regimes de temperatura = Germination and seedling growth of Enterolobium contortisiliquum (Vell.) Morong as a funtion ...

O conhecimento dos aspectos que envolvem todo o mecanismo do processo de germinacao de sementes em especies florestais ainda se encontra muito aquem em comparacao com as especies cultivadas. Objetivou-se estudar a influencia da localizacao da semente no fruto sobre a germinacao e crescimento de plântulas de tamboril (Enterolobium contortisiliquum) sob dois regimes de temperatura. Foram separadas as sementes das regioes proximal, central e distal do fruto. As sementes de cada regiao foram submetidas aos testes de primeira contagem, porcentagem final e indice de velocidade de germinacao, em dois regimes de temperatura (25 °C constante e 20–30 °C alternados), alem do envelhecimento acerado. As plântulas provenientes desses testes foram analisadas pelas determinacoes do comprimento e massa seca da parte aerea, raiz e total. O experimento foi conduzido em delineamento inteiramente casualizado, seguindo um esquema fatorial 3x2 (tres regioes e duas temperaturas) com quatro repeticoes. Os dados com distribuicao normal foram submetidos a analise de variância e as medias comparadas pelo teste de Tukey (5%); quando nao normal utilizou-se o teste nao parametrico de Mann-Whitney (5%). Houve interacao dos fatores para o indice de velocidade de germinacao, comprimento total, massa seca total e massa seca da parte aerea das plântulas. Nao se observou diferencas entre as localizacoes para as variaveis de avaliacao das plântulas. Quanto a germinacao, sob 25 °C as sementes da regiao distal do fruto germinaram mais rapidamente. Independente dos tratamentos a porcentagem de germinacao foi sempre superior a 95%, mesmo quando envelhecidas. Conclui-se que nao ha diferenca entre as temperaturas de 25 e 20-30 °C para a germinacao de tamboril; que a localizacao das sementes no fruto nao influencia na formacao das plântulas; e que a velocidade de germinacao e o crescimento das plântulas provenientes de sementes das regioes proximal e distal sao mais sensiveis as mudancas de temperatura.
Caracterización morfológica y evaluación de la colección nacional de germoplasma de camu camu Myrciaria dubia (H.B.K) Mc Vaugh, del INIA Loreto-Perú

The aim of this study was to characterize and evaluate morphologically the national collection of germplasm INIA camu camu made up of 43 accessions collected in the Loreto region, for conservation and use. The results show that the germplasm of camu camu has high variability and three types of plant architecture (column, intermediate and branched). The flowers are hermaphrodite or androgynous and have herkogamy empowering the outcrossing or cross-pollination. The color of the fruit depends on the state of maturation of the same, varies from green to red-violet, the number of seeds per fruit varies from 1 to 4, the number of fruits per kg is 90 to 148. Twenty one accessions were found with yields greater than 15 kg per plant and 16 accessions of over 2000 mg of ascorbic acid /100 g of pulp. In addition, we identified 10 promising accessions by fruit yield and ascorbic acid contents. Through Principal Component Analysis was determined that the variables are positively associated with the fruit yield, plant height and stem diameter. The dendrogram derived from cluster analysis allowed the identification of three groups based on fruit yield, the first group consists of 22 accessions whose fruit yields are between 2.29 and 11.97 kg / plant, the second group 16 accessions that have yields 16.97 to 30.35 kg of / plant, and the third group consists of 5 accessions from 36.52 to 39.24 yields kg/plant.
Study of Heterosis in Interspecific Hybrids of Cotton (Gossypium hirsutum L. x Gossypium barbadense L.)

A line x tester analysis was undertaken to estimates the magnitude of heterosis in interspecific hybrids of cotton (Gossypium hirsutum L. x Gossypium barbadense L.) for yield and its components characters in 56 entries including (42 hybrids along with 13 parents and 1 standard check hybrid). Analysis of variance indicated the significant difference among the parents and hybrids for all thirteen characters studied which revealed existence of variability among the genotypes. Studies revealed that for seed cotton yield per plant out of 42 cross combinations, 10 hybrids had registered significant positive estimates of heterobeltiosis. The hybrids, GJC 101 x TCB 27 (31.64%) followed by SI 13-31 x ARBB 1302 (29.35%) and GN Cot. 22 x ARBB 1302 (28.83%) had significant value with maximum estimates of heterobeltiosis. Six hybrids had registered significant positive standard heterosis over G. Cot. HB 102, of which, GN Cot. 22 x ARBB 1302 (24.61%) followed by GJC 101 x TCB 27 (22.71%) and AC 738 x ARBB 1302 (20.71%) had significant value with maximum estimates and its attributing characters like total number of bolls per plant, average boll weight, lint yield per plant, seed index and lint index.
Natural selection on hatchling body size and mass in two environments in the common lizard (Lacerta vivipara)

Differences in life-history traits among populations living in different environments can arise as adaptations to different selective regimes present in these environments. In this study, we investigated patterns of natural selection on body size (snout-vent length and tail length) and mass in hatchlings of the common lizard (Lacerta vivipara) raised in two different environments, where the local populations of L. vivipara have different life-history traits. To investigate patterns of natural selection, we raised hatchlings from one high-altitude population in outdoor enclosures located at high and low altitude and we recaptured them before they entered hibernation. We found significant directional selection for higher hatchling body mass and tail length at both sites, whereas hatchling snout-vent length was not correlated with survival. Stabilizing selection gradients were not significant for any of the traits considered at both sites. Differential hatchling mortality may directly affect maternal investment in litter size. In this case, the proper focus of selection might be on mothers. We checked this issue by estimating: (1) the trade-off between litter size and hatchling size and mass; and (2) the correlation between litter size and the proportion of living offspring per litter. Although litter size was negatively associated with hatchling size and mass, we did not find any correlation between fecundity and offspring survival. In conclusion, we found no differences in the patterns of selection between the two environments. These findings are in agreement with previous results showing that differences in life-history traits between these highand low-altitude populations may arise from plastic responses to proximate cues, rather than genetic adaptation to different selection
Principles of Gene Manipulation

1. Gene Manipulation: An All-Embracing Technique 2. Basic Techniques 3. Cutting And Joining DNA Molecules 4. Basic Biology Of Plasmid And Phage Vectors 5. Cosmids, Phasmids And Other Advanced Vectors 6. Cloning Strategies 7. Sequencing And Mutagenesis 8. Cloning In Bacteria Other Than E. Coli 9. Cloning In Saccharomyces Cerevisiae And Other Fungi 10. Gene Transfer To Animal Cells 11. Genetic Manipulation Of Animals 12. Gene Transfer To Plants 13. Advances In Transgenic Technology 14. Applications Of Recombinant DNA Technology.
Detection and functional analysis of Ca2+ microdomains and BK channels in olfactory receptor neurons of larval Xenopus laevis

Olfactory receptor neurons (ORNs) sense odors through the interaction of odorants with their receptors, accomplishing the first step of olfactory signaling via the generation of action potentials (APs). It is well known that BK channels and voltage-gated Ca2+ channels (VGCCs) are involved in the fine tuning of APs in many neurons, however, due to the low expression levels of both channels in ORNs, it is still unknown whether they remain functioning. In the current study, a co-localization of BK channels and voltage-dependent Ca2+ microdomains is observed on the surface of ORNs of Xenopus laevis, and the functional Ca2+ microdomains may comprise mainly the VGCC clusters rather than single Ca2+ channels. Moreover, the distance between BK channels and VGCCs is also estimated by using various Ca2+ buffers, and the estimate is around 50 to 200 nm but no less than 30 nm. Besides, blocking BK channels with Iberiotoxin (IbTx) or chelating Ca2+ ions by BAPTA results in a significant increase in the decay time of AP falling phases, and IbTx also decreases the firing rates of ORNs in response to odorant stimuli. Taken together, the current findings demonstrate that despite the low expression level, by forming functional Ca2+ microdomains, BK channels and VGCCs achieve a key function in olfactory signaling, shaping the APs and facilitating the firing rates.
Evaluation of passive integrated transponders for identification of Kakapo, Strigops habroptilus

Abstract We assessed the reliability and safety of subcutaneously inserted passive integrated transponders (PITs or microchips) for individually identifying Kakapo, Strigops habroptilus. The viability and location of the PITs inserted into 57 adult birds were assessed and the birds’ health evaluated after an average 16 months after implantation. Also, the growth rates of 21 chicks implanted at five weeks of age were monitored before and after implantation and their PITs assessed four months later. All transponders in both adults and juveniles were found to be working and located in the general area of implantation. No complications, health effects or growth rate changes were detected in either adult or juvenile birds. Kakapo are excellent candidates for this tagging system as their large body size allows the PIT to be deposited far from the insertion hole, and this combined with their flightlessness, possibly contributes to minimising transponder migration and loss. Although PITs have now been evaluated in several bird species, we suggest caution in generalising the results from this study to smaller, flighted species.
Pertumbuhan dan Biomassa Spirulina sp dalam Skala Laboratoris

Spirulina is unicelular algae used as a natural food of brawn shrimp and fish larval that has high nutritional valve. The aims of this research is to asses growth and biomass of spirulina sp at laboratorium scale. Method was carried out by culturing Spirulina sp using walne culture media. The density of Spirulina sp was conuted for 9 days . The result of this research shows that optimal density cuhich was 11.698. 103 unit/ml occurred on the day 7th with wet weight was o,042 gr/l and dry weight was 0,0375 gr/l. Spirulina biomass an increased as a responsive of their growth at a certain level
Frequency of Powdery Mildew Resistances in Spring Barley Cultivars in Czech Variety Trials

Dreiseitl A. (2012): Frequency of powdery mildew resistances in spring barley cultivars in Czech variety trials. Plant Protect. Sci., 48: 17–20. In 2006–2010, resistance to the powdery mildew pathogen was studied in 277 spring barley cultivars. They were represented by 54 cultivars in Czech official variety trials, of which 42 were foreign, and 223 cultivars in variety trials conducted by domestic breeding companies in that period. Sixty-eight domestic cultivars (28.8%) exhib ited heterogeneity in the examined trait, i.e. they were composed of lines with different resistances to powdery mildew. Thirteen known resistances were identified (Ab, Ar, HH, La, Ly, Mlo, Ri, Ro, Ru, Sp, St, Tu2 and We). The most frequent resistance was Mlo detected in 160 homogeneous cultivars (= 76.6%). The newly described resistance Ro was found in 13 cultivars. Frequency of other resistances was low (maximally 2.4%). Unknown resistances were found in 16 cultivars, in five of which they were effective to all used pathotypes of the patho gen. Research on cultivars possessing unknown resistances and registered heterogeneous cultivars continues.
Tracking Underreported Financial Flows: China’s Development Finance and the Aid–Conflict Nexus Revisited

China’s provision of development finance to other countries is sizable but reliable information is scarce. We introduce a new open-source methodology for collecting project-level development finance information and create a database of Chinese official finance (OF) to Africa from 2000 to 2011. We find that China’s commitments amounted to approximately US$73 billion, of which US$15 billion are comparable to Official Development Assistance following Organization for Economic Cooperation and Development definitions. We provide details on 1,511 projects to fifty African countries. We use this database to extend previous research on aid and conflict, which suffers from omitted-variable bias due to the exclusion of Chinese development finance. Our results show that sudden withdrawals of “traditional” aid no longer induce conflict in the presence of sufficient alternative funding from China. Our findings highlight the importance of gathering more complete data on the development activities of “nontraditional donors” to better understand the link between aid and conflict.