Miracle-dz/UniFAR-FTUs huggingface dataset:
Leaf phenology and insect grazing of Japanese white birch saplings grown under free-air ozone exposure

Ground-level ozone (O3) increases yearly and negatively affects the growth of birches via leaf dynamics. Leaf area is directly related to plant production and is usually reduced by elevated O3 (eO3) and insect herbivores. The objective of this study was to explore factors affecting change in leaf number of white birch saplings and insects grazing under eO3. In order to accomplish this objective, we observed seasonal changes in leaf phenology and determined foliar defense chemicals in saplings grown under ambient air and free-air O3 enrichment (60 nmol molfor daytime). The leaf phenology showed the total number of emerged leaves was about 10 per shoot in the control and eO3 plots. However, the number of attached leaves per shoot at ambient air decreased after mid-July, probably due to grazing by larvae of the leaf beetle. In addition, the concentration of condensed tannin in early leaves was higher in the eO3 plot than that in the control plot. Such leaves with decreased nutritional value under eO3 may prevent feeding of leaf beetles. These findings lead to the plausible understanding of an indirect effect of eO3 on leaf phenology via foliar defense of white birch against insect herbivores.
The Tissue Distribution of White Spot Syndrome Virus (WSSV) in Experimentally Infected Kuruma Shrimp (Marsupenaeus Japonicus) as Assessed by Quantitative Real-Time PCR

White spot syndrome virus (WSSV) is a highly lethal, stress dependent virus belonging to the genus Whispovirus and the family Nimaviridae. Among the various crustaceans, shrimp species are the most susceptible to WSSV infection. In the current study, a quantitative real-time PCR method was established in order to quantify the levels of WSSV in various tissues of shrimp that had been experimentally infected using the immersion bioassay. Two different concentrations of viral inoculums (high and low concentration) were used in the infection procedure. Following infection, we detected WSSV in hemolymph and other tissues including the lymphoid organ, heart, stomach and gills. Although the tissue distribution between the groups exposed to either high or low concentrations of WSSV were found to be similar, the final viral load of the tissues correlated to the concentration of WSSV used in the initial exposure. An increased viral load was confirmed in the lymphoid organ, heart, stomach and gills 10 days following infection. In contrast, an increased concentration of WSSV-DNA in hemolymph was confirmed at only 4 days post-infection.
RAR beta trans-repression of AP-1 transcription factor in HeLa cervical cancer cells : consequences on transcription of viral and cellular AP-1 controlled genes

In many types of cancer, including cervical cancer, the nuclear retinoic receptor s2 (RARs2) gene is epigenetically modified and unable to be significantly induced. RARs2 can act as a tumor suppressor, since loss of its expression is associated with human tumor progression. One mechanism of RARs2-mediated growth inhibition is based on its ability to constitutively repress the AP-1 transcription factor, but this mechanism has never been demonstrated in cervical cancer cells. In this thesis the biological consequences of reconstitute RARs2 receptor expression in cervical cancer cells was investigated. For this purpose, human papillomavirus HPV-18 positive HeLa cells were stably transfected with RARs2 cDNA under the control of the s-actin promoter. The characterization of the RARs2 tranfectants revealed a strongly reduced AP-1 binding to the corresponding specific oligonucleotides, even in the absence of atRA treatment. In HeLa cells, the AP-1 reduction correlates with diminished HPV-18 oncogene transcription and slower cellular growth. Western blot analysis demonstrated that the only member of the AP-1 family consistently reduced in HeLa RARs2 clones was c-Jun, despite ongoing gene expression. In order to understand by which mechanism c-Jun is reduced, and since the phosphorylation of c-Jun is important for protein stabilization, HeLa RARs2 clones were treated with different c-Jun-N-terminal kinase (JNK) stimulators. The treatments resulted in a c-Jun increase at RNA and protein levels, and led to a reconstitution of AP-1 binding similar to non-transfected HeLa controls. However, the reconstitution of AP-1 binding levels did not have an inductor effect on the HPV-18 oncogenes, the expression of which has been postulated to be AP-1 dependent. Other classical AP-1 regulated genes such as metalloproteinases were up regulated as expected. In conclusion, the data of this thesis indicate that RARs2 induced a destabilization and accelerated degradation of c-Jun at the protein level responsible for the AP-1 reduction. The mechanism of AP-1 trans-repression in HeLa cells is different from that postulated for other cancer cell models. All changes produced in HeLa cells after RARs2 constitutive expression lead to reduced cell proliferation, which can be associated with the RARs2 tumor suppressor function.
Movement of the Column of Stylidium crassifolium as a Function of Temperature

The column of the flower of S. crassifolium when mechanically stimulated moves through an angle of about 4 rad in 15 ms and then resets more slowly in several hundred seconds. The rates of the firing and resetting as a function of temperature have been investigated. Arrhenius plots of these rates are approximately straight lines yielding energies of activation of ~ 8 kJ mol-1 for firing and ~72 kJ mol-1 for resetting. These results suggest that resetting is the 'active' part of the movement, and is closely linked to the metabolic energy supply. The rate of firing is more likely limited by friction within the cell walls of the motor tissue, or possibly by the viscosity of extracellular water.
Building the human brain

Neurodevelopment As the brain develops, neurons migrate from zones of proliferation to their final locations, where they begin to build circuits. Paredes et al. have discovered that shortly after birth, a group of neurons that proliferates near the ventricles migrates in chains alongside circulatory vessels into the frontal lobes (see the Perspective by McKenzie and Fishell). Young neurons that migrate postnatally into the anterior cingulate cortex then develop features of inhibitory interneurons. The number of migratory cells decreases over the first 7 months of life, and by 2 years of age, migratory cells are not evident. Any damage during migration, such as hypoxia, may affect the child's subsequent physical and behavioral development. Science , this issue p. [81][1]; see also p. [38][2] [1]: http://www.sciencemag. org/content/354/6308/aaf7073.full [2]: /lookup/doi/10.1126/science.aai9379
Influence of Soil Moisture Stress on Vegetative Growth and Mycorrhizal Colonization in Hound's-tongue (Cynoglossum officinale)

Hound's-tongue is an invasive, biennial weed that thrives in dry rangelands of British Columbia. Rosette formation in the first year of growth and a deep root system offer this weed a competitive advantage against associated grasses under dry conditions. To study effects of water stress on seedling growth and mycorrhizal colonization in hound's-tongue, seedlings of this weed were grown in pots in a greenhouse and subjected to four (100, 80, 60, and 40% of field capacity) soil moisture treatments. Effects of soil moisture stress (SMS) on several growth parameters as well as mycorrhizal colonization of roots were studied. The total biomass, shoot and root fresh and dry weights, leaf number, petiole length, leaf area, and specific leaf weight (leaf dry weight per unit leaf area) decreased with increasing SMS; shoot and root water content was not affected. Because of a greater effect of SMS on root compared with the shoot biomass, shoot:root ratio increased as the moisture stress increased. Water stress decreased mycorrhizal colonization and arbuscule and vesicle abundance. A reduction in total biomass, leaf number and leaf area per plant, petiole length, and mycorrhizal colonization may reduce the competitive advantage of hound's-tongue over its neighbors under drought conditions. The effect on plant size may also influence herbivory, by biocontrol agents and other herbivores, and fecundity of this weed. Nomenclature: Hound's-tongue, Cynoglossum officinale L.
Once upon a time? Human menstrual synchrony, offspring survival and female reproductive success

The convergence of the onset dates of human menstrual flow was first documented in 1971 and since then, evidence of human menstrual conversion has been far from anecdotal. However, there is also abundant evidence failing to replicate these results. Criticism hinges on several methodological shortcomings which inherently bias towards synchrony. The purpose of the current study is not to substantiate menstrual synchrony by empirical investigation, but to shift view towards its biological significance. The evolutionary approach posits that concealed ovulation, continuous sexual receptivity, and the potential for menstrual synchrony are all linked to achieve higher gains in paternal investment. However kinship may have been overemphasized for male helpers and underestimated for females. The phenomenon of partible paternity demonstrates that male provisioning need not be contingent on biological fatherhood. At the same time, human life histories assure the availability of well-qualified allomothers such as grandmothers. It is therefore hypothesized that menstrual synchrony in human females represents a redundant life history artifact which has its origins in our primate heritage as cooperative breeders.
Structural and biochemical investigations of the eukaryotic DNA double-strand break repair complex Mre11-Rad50-Nbs1

The Mre11–Rad50 nuclease–ATPase is an evolutionarily conserved multifunctional DNA double-strand break (DSB) repair factor. Mre11–Rad50’s mechanism in the processing, tethering, and signaling of DSBs is unclear, in part because we lack a structural framework for its interaction with DNA in different functional states. We determined the crystal structure of Thermotoga maritima Rad50 (nucleotide-binding domain) in complex with Mre11 (helix-loop-helix domain), AMPPNP, and double-stranded DNA. DNA binds between both coiled-coil domains of the Rad50 dimer with main interactions to a strand-loop-helix motif on the NBD. Our analysis suggests that this motif on Rad50 does not directly recognize DNA ends and binds internal sites on DNA. Functional studies reveal that DNA binding to Rad50 is not critical for DNA double-strand break repair but is important for telomere maintenance. In summary, we provide a structural framework for DNA binding to Rad50 in the ATP-bound state.
Immunohistochemical study on the expression of serotonin and 5HTR3 in gastrointestinal tract of rat embryos and newborns

Serotonin takes part in the regulation of the gastrointestinal motility, secretion and sensitivity. It produces its effects by binding specific receptors thus being one of the important neurotransmitters and signal molecules in the gut. There are different types of specific serotonin receptors, recognized and cloned into seven groups (from 5HT1 to 5HT7) with various subtype numbers. The aim of this work is to determine the presence and localization of immunohistochemical expression of serotonin and serotonin receptor 3 (5-HTR3) in the developing gastrointestinal tract of rats. 20 rat embryos (16 th - 20 th day of gestation) and fragments of the stomach and small intestine of 10 one-day-old rats were used for the study. On paraffin sections immunohistochemical reactions for serotonin (primary antibody rabbit polyclonal antibody, Chemicon, USA) and serotonin receptor 5-HTR3 (primary antibody goat polyclonal antibody, Santa Cruz Biotechnology, USA) were carried out using the ABC. Immunohistochemical expression for serotonin and serotonin receptor 3 (5-HTR3) were not detected in the gastrointestinal tract of rat embryos. In the gastrointestinal tract of the oneday-old rats there was positive reaction for serotonin. Serotonin-producing cells were present in the covering epithelium of the villi in the small intestine. They were small in numbers and separately located. The immunhistochemical reaction for 5-HT3 receptors was positivated in the cytoplasm of a great number of smooth muscle cells in both transverse and longitudinal muscle layer of the stomach wall of the newborn rats. Serotonin production and secretion starts after birth and through its 5-HT3 receptors takes part in the regulation of the morphological and functional maturation of the gastrointestinal tract which starts in the embryonal period but continues postnatally.
Design and Synthesis of Novel 2`(β)-Fluoro-3`(α)-hydroxy-threose Nucleosides: Iso-FMAU Analogues as Potent Antiviral Agents

Novel 2`()-fluoro-3`()-hydroxy-threose nucleosides (iso-FMAU) as antiviral agents were designed and racemically synthesized from Solketal. Condensation successfully proceeded from a glycosyl donor 9 under conditions yielded the nucleoside analogues. Ammonolysis and hydrolysis of isopropylidene protection group gave the desired nucleoside analogues 12, 15, 18, and 19. The antiviral activities of the synthesized compounds were evaluated against the HIV-1, HSV-1, HSV-2 and HCMV. Compound 12 displayed some anti-HCMV activity ($EC_{50}
The complete mitogenome of Colletotrichum lupini var. setosum

Abstract The structure of Colletotrichum lupini mitogenome is typical of a fungus from the genus Colletotrichum similar to C. acutatum and C. lindemuthianum. The sequenced mitogenome has a total length of 36 554 bp. The nucleotide composition in the following genome is: 35.7% – A, 16.5% – C, 13.4% – G and 29.9% – T. In the C. lupini mitogenome we identified 46 genes: 15 protein coding genes, two ribosomal RNAs and 29 tRNA genes.
A comparative analysis of genetic diversity in Portuguese grape germplasm from ampelographic collections fit for quality wine production

Grapevine cultivars diversity is vast and full of synonyms and homonyms. Up to few decades ago characterization of grapevine was based on morphological characters. In the last decades, molecular markers were developed and have been used as tools to study genetic diversity in a range of different plant species. Fifty-six Portuguese accessions representative of ‘Vinhos Verdes’ and ‘Douro’ Controlled Designations of Origin (DOC) were analysed through DNA fingerprints generated by Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR). The study aimed to compare the effectiveness of RAPD and ISSR molecular techniques in the detection of synonyms, homonyms and misnames. RAPD and ISSR analysis enabled the detection of 36 different band patterns, reducing in about 36% the initial material. Several accessions grown under different names, between and within collections, were confirmed as the same genotype, namely Gouveio/Verdelho, Sousao Douro/Vinhao and Arinto Oeste/Pederna. Similarly, some homonyms/misnames were also identified, namely within Azal Tinto and Rabigato accessions. RAPD and ISSR markers revealed to be adequate molecular techniques for grapevine varieties fingerprinting with advantages over other molecular procedures, contributing for a good management of grapevine collections.
Efecto de las micorrizas arbusculares sobre la aclimatación y endurecimiento de microplántulas de mora (Rubus glaucus)

The transfer of Andean blackberry plantlets from in vitro to ex vitro conditions is one of the most critical phases of the micropropagation technique due to the high mortality rate of plantlets (50-90%), as a consequence of a poorly developed cuticle, non-functional stomates and a weak radicle system that facilitates dehydration by water stress. This investigation focused on obtaining clean plantlets originated from tissue culture and hardened with arbuscular mycorrhizas (HMA). The research was performed under controlled conditions; an experimental design of random complete blocks was used with eight treatments, three repetitions and four experimental units as follows; three control treatments without inoculation, without fertilizing (T0), with 50% fertilizing (T50) and with 100% fertilizing (T100), and five treatments inoculated with HMA (MA1, MA2, MA3, MA4 and Mycobiol®) plus T50. The major benefits of inoculation with HMA were achieved with the strain MA4 isolated from Silvania (Cundinamarca) and with native spores classified as Glomus sp. and Acaulospora sp. The inoculated plants showed better adaptation to the environment, reflected in plant size, accumulation of foliar and radicle biomass, wider foliar area, and better nutritional state reflected in a higher absorption of essential nutrients (P, N, Ca, and Mg). The use of the strain MA4 allowed the substitution of 50% of commercial fertilization since it achieved similar values to T100 in the absorption of P and Ca, and higher absorption for N and Mg. The levels of root colonization by the fungus explained this vegetative behavior.
Regulation of Focal Adhesion Dynamics by a Kinesin Motor Kid/KIF22/Kinesin-10

Cell adhesion is one of the fundamental mechanisms cells use to interact with their surrounding environment. It is mediated by multiprotein structures termed focal adhesions (FAs). The formation of FAs and the regulation of their assembly and disassembly dynamics are crucial to cell structure and viability. In my dissertation study, I explored the role of a kinesin motor Kid/kinesin-10/KIF22 in adhesion dynamics. I found that Kid localizes to the sites of FAs and functions as an adhesion disassembly factor by modulating the phosphorylation of two important components of FAs, focal adhesion kinase (FAK) and paxillin. Loss of Kid caused changes in the density, distribution, and size of FAs leading to defects in cell adhesion and migration. This study discovered a novel function of Kid during interphase and expanded our knowledge on how motor proteins play significant roles in adhesion dynamics.
Haemophilus somnus complex: antigenicity and specificity of fractions of Haemophilus somnus.

: Five Haemophilus somnus type 8025 preparations (whole cell, sonicate, crude polysaccharide, purified polysaccharide, and protein) were produced for studies of their antigenicity in rabbits. Bacterial agglutination and passive hemagglutination tests were used to assess the level of antibody produced in rabbits inoculated with the different antigenic preparations. Cross-reactions were seen between the antiserums against the H sumnus 8025 antigens and a variety of related and unrelated bovine pathogens. The strongest cross-reaction occurred between antiserums against H somnus 8025 whole cell and crude polysaccharide antigens and Haemophilus agni and Actinobacillus lignieresii cell suspensions.
Bioaccessibility of Copper, Molybdenum and Zinc from Selected Oilseed Cakes Using Three Stage In Vitro Technique

The study was conducted to determine chemical composition, in vitro dry matter digestibility (IVDMD) and bioaccessibility of (%) of copper (Cu), molybdenum (Mo) and zinc (Zn) in mustard (MC), cotton seed (CSC) and maize germ oil cake (MGOC). The values of DM, OM, CP, EE, NDF, ADF and TA in MC were 92.27, 92.43, 38.36, 8.17, 28.11, 21.32 and 7.57%, respectively and the corresponding values in CSC were 92.16, 92.91, 21.11, 6.26, 38.33, 31.14 and 7.09% and MGOC were 93.72, 96.42, 18.56, 8.86, 34.60, 23.71 and 3.58%. The MC, CSC and MGOC had Cu content of 9.87, 11.28 and 8.62 ppm, Mo content of 1.52, 1.69 and 1.12 ppm and Zn level of 58.94, 38.93 and 28.21 ppm, respectively. IVDMD (%) was found to be the highest for MC (68.42±0.35) and the lowest for CSC (59.71±1.07). Bioaccessibility (%) of Cu and Zn was lower (P<0.05) at ruminal stage than abomasal and intestinal stage in all oilseed cakes. The bioaccessibility of Cu was higher in MC (70.99±0.39%) followed by MGOC (68.66±0.12%) and CSC (65.33±0.19%). The bioaccessibility of Zn was higher (P<0.05) in MC (45.00±1.15), followed by MGOC (42.00±0.57) and CSC (38.03±0.67). Bioaccessibility (%) of Mo was numerically increased from ruminal to intestinal stage and overall bioaccessibility (%) of Mo varied from 83.33±0.84 to 85.00±0.23 in all three oilseed cakes with no significant difference among these oilseed cakes.
Diversity of Nonribosomal Peptide Synthetase Genes in the AnticancerProducing Actinomycetes Isolated from Marine Sediment in Indonesia

Marine actinomycetes is a group of bacteria that is highly potential in producing novel bioactive compound. It has unique characteristics and is different from other terrestrial ones. Extreme environmental condition is suspected to lead marine actinomycetes produce different types of bioactive compound found previously. The aim of this study was to explore the presence and diversity of NRPS genes in 14 anticancer-producing actinomycetes isolated from marine sediment in Indonesia. PCR amplification and restriction fragment analysis of NRPS genes with Hae III from 14 marine actinomycetes were done to assess the diversity of NRPS genes. Genome mining of one species of marine actinomycetes (strain GMY01) also was employed towards this goal. The result showed that NRPS gene sequence diversity in 14 marine actinomycetes could be divided into 4 groups based on NRPS gene restriction patterns. Analysis of 16S rRNA gene sequences of representatives from each group showed that all isolates belong to genus of Streptomyces . Genome mining result showed that strain GMY01 harboring 10 different NRPS gene clusters that encode secondary metabolites, as pure NRPS or hybrid between NRPS and other compounds. These results indicated that marine actinomycetes having a high potential to be developed as source of anticancer drugs development.
Deep divergence and evidence for translocations between Iranian and European populations of the alfalfa weevil (Coleoptera: Curculionidae) based on mitochondrial DNA

Abstract The alfalfa weevil (Hypera postica (Gyllenhal): Coleoptera: Curculionidae) is an invasive pest of alfalfa (Medicago sativa Linnaeus; Fabaceae) in the Holarctic region. Across the wide geographic distribution of the species different local adaptions have been observed. Further, several distinct mitochondrial lineages have been discovered, which have been treated as western and Egyptian/eastern strains. However, our knowledge of the biogeography of H. postica is largely limited to North American and Japanese populations. We sampled the species from four locations in Iran and two countries in Europe (Poland and Czech Republic) and sequenced the mitochondrial COI gene to detect patterns of mitochondrial DNA divergence among Iranian and European strains. We detected two groups separated by a deep molecular split, even justifying the distinction of two molecular operational taxonomic units. Joint analyses with previously published sequences suggest that the European samples may represent the western strain, whereas both the western and Egyptian/eastern strains can be found in Iran. This distribution of genetic lineages may be the result of human-mediated translocations. The directionality, however, cannot be inferred. Our data suggest that translocations may have led to the coexistence of multiple H. postica lineages in some parts of the world, e.g., Iran. We discuss these findings against the background of the current taxonomy of H. postica.