Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of genes involved in rice seed germination at low temperatures

Rice is a model for many genomic studies among crop species. The adaptation to different crop environments is partly the result of traditional breeding combined with molecular assisted selection. Comparative studies between contrasting genotypes can be performed efficiently by the cDNA-AFLP technique, allowing the identification of genes involved in the expression of the target trait. The objective of this study was to identify differentially expressed genes in cultivars contrasting for the character germination at low temperatures. The genotypes used were BRS-Firmeza (Tolerant) and SCSBRS Tio-Taka (Sensitive). Seeds of the two cultivars were sown at 13 and 25°C, respectively. Total RNA was extracted from embryos and cDNAs were synthesized. The cDNAs were analyzed by AFLP (Amplified Fragments Length Polymorphisms) to identify differentially expressed sequences between BRS-Firmeza and SCSBRS Tio-Taka varieties. Four polymorphic fragments were present at 13°C IN BRS-Firmeza molecular profile and absent in SCSBRS Tio-Taka. It is concluded that the technique of AFLP on cDNA as template is efficient to produce and identify fragments of differentially expressed genes in rice during germination under low temperatures. Key words: Oryza sativa, seeds, cDNA-AFLP (cDNA amplified fragment length polymorphism).
Enhancing maintenance control of possum populations using long‐life baits

Abstract Possum populations must be maintained at very low density if the aims of Tb eradication and conservation of particularly vulnerable native species are to be met. The present tactic of initial “knockdown” followed by annual maintenance control allows for reinfestation in between annual operations. Development of toxic baiting methods for “continuous” control of possum populations is therefore desirable. Six bait‐type/presentation‐methods designed for prolonged field life were exposed to field conditions at a forest edge site in Westland. Samples of baits were collected at 2‐monthly intervals for up to 26 months, and assessed for palatability to possums and toxicant concentration. Regression analysis was used to predict the time at which reductions in palatability and toxicity would make the bait ineffective. Field life varied between 2 and >26 months. The most durable option tested was a solid gel bait containing cholecalciferol and presented in a purpose‐designed bait station. This option was selected for assessment in continuous control of possums in forest‐edge habitat in West‐land. Baits were placed up trees beyond the reach of livestock and left in place for 10 months. Trap‐catch monitoring showed these baits did reduce the number of possums, but only after improving the visibility, attractiveness, and accessibility of bait stations. As the study predicted that cholecalciferol gel bait should remain effective for >2 years in the field, there appears to be considerable potential for improving the efficiency (and probably environmental safety) of long‐term control using this new tool.
Treatment of a Petrochemical Industry Wastewater by a Solar Oxidation Process Using The Box-Wilson Experimental Design Method

As an advanced oxidation treatment, the Fe(III)/ H 2 O 2 /Solar-UV process was applied to a petrochemical refinery wastewater in Izmir, Turkey. A solar photocatalytic reactor was used for the advanced oxidation. The Box-Wilson experimental design method was employed to optimize the wastewater flowrate, oxidant and catalyst concentrations as significant factors for maximum organic matter removal. Organic matter removal was monitored throughout the operation period. The maximum reduction in the TOC concentration was 49% with the addition of 2677 mg/L H2O2 and 0.5mM Fe(III) at a 10 L/h flowrate after 8 hours of exposure to solar irradiation.
Shifts in aquatic macroinvertebrate community structure in response to perenniality, southern Cape, South Africa

Stream flow and associated seasonal hydrologic variation is a critical driver affecting the structure of aquatic macroinvertebrate communities. Quarterly aquatic macroinvertebrate sampling was carried out for a single year along the longitudinal axes of two streams in the southern Cape of South Africa. Stones-in-current, marginal vegetation, gravel-sand-mud, and stones-out-of-current biotopes were sampled for aquatic macroinvertebrates. Associations between macroinvertebrate communities and hydrographs were analyzed to investigate whether a non-perennial stream with greater flow variability had a higher prevalence of common or opportunistic species than a perennial one with less variable flow. Macroinvertebrate species richness was greater in the perennial as opposed to the non-perennial stream, where, on a seasonal basis, species richness increased from winter to autumn. Temporal species turnover differed between sites and streams, where reduced flows transformed the more dominant aquatic biotopes from stones-in-current into standing pools. Findings are that aquatic macroinvertebrates respond to changing flow conditions and reduced mean daily flows resulted in the disappearance of flow-dependant taxa and the arrival of non-flow-dependant taxa.
The role of the active site Zn in the catalytic mechanism of the GH38 Golgi α-mannosidase II: Implications from noeuromycin inhibition

Golgi α-mannosidase II (GMII) is a Family 38 glycosyl hydrolase involved in the eukaryotic N-glycosylation pathway in protein synthesis. Understanding of its catalytic mechanism has been of interest for the development of specific inhibitors that could lead to novel anti-metastatic or anti-inflammatory compounds. The active site of GMII has been characterized by structural studies of the Drosophila homologue (dGMII) and unusually contains a Zn atom which forms contacts with substrate analogues, stabilized catalytic intermediates, and other inhibitors observed in the active site. In this contribution, we analyze the structure of the sugar mimetic compound noeuromycin complexed with dGMII. Distortions of the conformation of this inhibitor, together with similar observations from other complexes, have permitted us to propose specific roles for the Zn atom in the chemical mechanism of catalysis of Family 38 glycosidase. Such insights have relevance to efforts to formulate novel, specific inhibitors of GMII.
The role of DNA polymerases, in particular DNA polymerase ε in DNA repair and replication

Analysis of the primary structure of DNA polymerase e B subunit defined similarities to B subunits of eukaryotic DNA polymerases α, δ and e as well as the small subunits of DNA polymerase DI of Euryarchaeota. Multiple sequence alignment of these proteins revealed the presence of 12 conserved motifs and defined a novel protein superfamily. The members of the B subunit family share a common domain architecture, suggesting a similar fold, and arguing for a conserved function among these proteins. The contribution of human DNA polymerase e to nuclear DNA replication was studied using the antibody K18 that specifically inhibits the activity of this enzyme in vitro. This antibody significantly inhibited DNA synthesis both when microinjected into nuclei of exponentially growing human fibroblasts and in isolated HeLa cell nuclei, but did not inhibit SV40 DNA replication in vitro. These results suggest that the human DNA polymerase e contributes substantially to the replicative synthesis of DNA and emphasises the differences between cellular replication and viral model systems. The human DNA polymerases e and δ were found capable of gap-filling DNA synthesis during nucleotide excision repair in vitro. Both enzymes required PCNA and the clamp loader RFC, and in addition, polymerase δ required Fen-1 to prevent excessive displacement synthesis. Nucleotide excision repair of a defined DNA lesion was completely reconstituted utilising largely recombinant proteins, only ligase I and DNA polymerases δ and e provided as highly purified human enzymes. This system was also utilised to study the role of the transcription factor II H during repair. Human non-homologous end joining of model substrates with different DNA end configurations was studied in HeLa cell extracts. This process depended partially on DNA synthesis as an aphidicolin-dependent DNA polymerase was required for the formation of a subset of end joining products. Experiments with neutralising antibodies reveal that DNA polymerase α but not DNA polymerases β or e, may represent this DNA polymerase activity. Our results indicate that DNA synthesis contributes to the stability of DNA ends, and influences both the efficiency and outcome of the end joining event. Furthermore, our results suggest a minor role of PCNA in non-homologous
Influence of transgenic corn (CBH 351, named Starlink) on health condition of dairy cows and transfer of Cry9C protein and cry9C gene to milk, blood, liver and muscle

The influence of transgenic event CBH 351 (Starlink)-derived hybrid corn (SL) on the health condition, physiological function and lactational performance of dairy cows as well as the transfer of the cry9C gene and Cry9C protein present in SL to milk, blood, liver and muscles was examined, and compared with a diet containing non-transgenic (isogenic) control corn (non-SL). After adapting to a diet containing non-SL for 2 weeks, four Holstein cows were assigned to each of the non-SL and SL groups and were fed diets containing non-SL or SL, respectively, for 5 weeks. There were no significant influences on the physiological condition, milk yield or serum biochemical and hematological values after feeding with SL. There was also no influence on pH value, cell density of protozoa, or volatile fatty acid concentration and composition of rumen fluids. In addition, no significant differences were observed on histopathological examination of the major organs and tissues between the SL and non-SL groups. Moreover, the cry9C gene and Cry9C protein were not detected by the polymerase chain reaction method and ELISA in the milk, blood, liver and muscles of the cows at the end of the experiment.
Growth problems in a skeletal sample of children abandoned at Santa Casa da Misericórdia, Faro, Portugal (16th–19th centuries)

In 2006, an excavation at Santa Casa da Misericórdia de Faro, Portugal, revealed a cemetery dating from the 16th–19th centuries with several phases of use, one of which presented 51 sub-adult individuals that had been abandoned at the institution through the ‘foundling wheel’—a device that allowed people to leave unwanted newborns anonymously. Of the 46 individuals for whom it was possible to estimate age-at-death, more than 80% were under two years. Skeletal samples from individuals of these ages are not commonly found in the archaeological record. This Faro sample is also unique in the sense that it is the first time it has been possible to study an osteological assemblage from abandoned children. Considering the assertion that dental development is buffered against environmental insults in comparison to skeletal development, and that discrepancies between dental and skeletal age estimations are suggestive of growth delay, this study aims to investigate if the immature individuals of this institution were exposed to severe environmental restrictions. Skeletal age was estimated according to long bone lengths and epiphyseal fusion. Dental age was calculated on the basis of dental development, namely dental calcification and the sequence of formation and eruption of teeth. Furthermore, a palaeopathological analysis of the sample was conducted. The age estimates obtained by the ossification and fusion of different skeletal elements resulted in too wide intervals and were therefore excluded from subsequent analysis. The age estimates obtained by the dental methods were consistent (100%). By contrast, the estimates obtained by osteometric and dental methods showed some disagreement (osteometric vs. dental calcification: 63.6%; osteometric vs. sequence of formation and eruption of teeth: 80.0%), the osteometric providing younger ages. Regarding the paleopathology, the high frequency of porotic lesions (60.8%) and new bone deposition (37.3%), especially in the individuals previously identified as small for their age, make evident the difficulties experienced by these individuals during their short lives.
Agrobacterium rhizogenes Mediated Hairy Root Induction in Justicia gendarussa Burm.f

Five strains of Agrobacterium rhizogenes (LB510, LB509, YMB072001, A4T, and ATCC 15834) were tested to determine their effects on the induction of hairy root on leaf explants of Justicia gendarussa Burm. f. Leaf explants were sterilized, and then infected within liquid MS medium + sucrose containing A. rhizogenes OD600 = 0.1, for 20 minutes while being shaken gently by hand. Teh explant was co-cultivated on Murashige and Skoog (MS) solid medium at 25°C for 48 hours. After 48 hours of co- cultivation, explants were transferred to MS solid medium with the addition of 250 mg/L cefotaxim, and repeated 1-2 times. Observations were carried out during 6 weeks to observe the specified parameters. Data were analized by Kruskal-Wallis Test and followed by Mann-Whitney Test. All strains of A. rhizogenes were used in this study were able to produce hairy root. The treatment of LB510 and YMB072001 strain was the best strain in the hairy root induction of J. gendarussa Burm. f. The infection frequency of LB510 strain was highest ( 100 % ), longest hairy root (2.23 cm), and highest of hairy root wet weight (0.0243 g). The treatment of YMB072001 strain was the highest number of hairy roots (3.3) per explant and the highest number of hairy roots dry weight (0.0098 g).
ULTRASTRUCTURAL ANALYSIS OF THE INTERACTION BETWEEN PUCCINIA STRIIFORMIS F.SP. TRITICI AND WHEAT AFTER THERMAL INDUCTION OF RESISTANCE

SUMMARY Wheat cultivars with high-temperature resistance shortly exposed to 21°C expressed resistance to stripe rust, Puccinia striiformis f.sp. tritici, after being inoculated with the virulent strain CY29. Observations on the ultrastructural interactions between wheat and the rust fungus demonstrated that marked changes took place in both the fungus and the host mesophyll cells in resistance expression. Hyphae of the fungus were inhibited, and organelles developed vacuoles and disintegrated or collapsed. Development of haustorial mother cells and haustoria was retarded, and these were malformed and necrotized. The extrahaustorial membrane was stained more deeply, wrinkled, and perforated. The extrahaustorial matrix was widened and was coated with large amounts of electron-dense material. Host cells produced defense structures and material related to infection as well as hypersensitive responses. Formation of cell wall appositions, collars or papillae, and encasements of haustoria were essentially observed. In the interaction of the same wheat cultivars with the stripe rust avirulent strain (CY29-mut3) at normal temperature (16°C), the intracellular symptoms of incompatibility were similar to those of thermal induction. In the compatible interaction at 16°C, the pathogen was normal and there were no signs of disorganization or necrosis of infected host cells.
Genetic and physiological data implicating the new human gene G72 and the gene for d-amino acid oxidase in schizophrenia

A map of 191 single-nucleotide polymorphism (SNPs) was built across a 5-Mb segment from chromosome 13q34 that has been genetically linked to schizophrenia. DNA from 213 schizophrenic patients and 241 normal individuals from Canada were genotyped with this marker set. Two 1,400- and 65-kb regions contained markers associated with the disease. Two markers from the 65-kb region were also found to be associated to schizophrenia in a Russian sample. Two overlapping genes G72 and G30 transcribed in brain were experimentally annotated in this 65-kb region. Transfection experiments point to the existence of a 153-aa protein coded by the G72 gene. This protein is rapidly evolving in primates, is localized to endoplasmic reticulum/Golgi in transfected cells, is able to form multimers and specifically binds to carbohydrates. Yeast two-hybrid experiments with the G72 protein identified the enzyme d-amino acid oxidase (DAAO) as an interacting partner. DAAO is expressed in human brain where it oxidizes d-serine, a potent activator of N-methyl-D-aspartate type glutamate receptor. The interaction between G72 and DAAO was confirmed in vitro and resulted in activation of DAAO. Four SNP markers from DAAO were found to be associated with schizophrenia in the Canadian samples. Logistic regression revealed genetic interaction between associated SNPs in vicinity of two genes. The association of both DAAO and a new gene G72 from 13q34 with schizophrenia together with activation of DAAO activity by a G72 protein product points to the involvement of this N-methyl-d-aspartate receptor regulation pathway in schizophrenia.
Cloning of a Zinc-binding Cysteine Proteinase Inhibitor in Citrus Vascular Tissue

A partial cDNA (cvzbp-1) was cloned based on the N-terminal sequence of a citrus (Citrus L.) vascular Zn- binding protein (CVZBP) previously isolated from vascular tissue (Taylor et al., 2002). CVZBP has homology to the Kunitz soybean proteinase inhibitor (KSPI) family. Recombinant protein produced using the cDNA clone inhibited the cysteine proteinase, papain. Metal binding capacity has not been reported for any other member of this family. CVZBP was present in leaves, stems, and roots but not seeds of all citrus species examined. However, CVZBP was present in germinating seeds after the cotyledons had turned green. Within four hrs after wounding, CVZBP was undetectable in the wounded leaf and adjacent leaves. It has been suggested that many members of the KSPI family serve a function in defense. However, the expression of the CVZBP is in direct contrast with those of KSPI members that were implicated in defense response. Though systemically regulated during wounding, we suggest that CVZBP is not a defense protein but rather may function in vascular development.
The Influence of Environmental Estrogens on Early-life Stage Zebrafish Development

iv Acknowledgments . vi List of Figures . vii List of Tables . xiii List of Abbreviations . xiv 1 General Introduction . 1 2 Materials and Methods . 41 2.1 Materials . 41 2.2 Methods . 43 3 The Influence of Bisphenol A on the Early Development of Zebrafish . 59 3.1 Aim of study . 59 3.2 Results . 59 3.2.1 Embryotoxic and teratogenic effects of BPA on the early development of zebrafish . 59 3.2.2 The effects of BPA on the 72 hpf zebrafish liver ultrastructure – pilot study . 69 3.2. 3 The effects of BPA on the 120 hpf zebrafish liver ultrastructure . 94 3.2. 4 The effects of BPA on the expression of vitellogenin 1 mRNA in 120 hpf zebrafish . 125 3.3 Discussion . 126 4 The Influence of Genistein on the Early Development of Zebrafish . 139 4.1 Aim of study . 139 4.2 Results . 139 4.2.1 Embryotoxic and teratogenic effects of genistein on the early development of zebrafish . 139 4.2.2 The effects of genistein on the 120 hpf zebrafish liver ultrastructure . 148 4.2. 3 The effects of genistein on the expression of vitellogenin 1 mRNA in 120 hpf zebrafish . 168 4.3 Discussion . 170 5 The Influence of Bisphenol A and Genistein in Combination on the Early Development of Zebrafish . 177 5.1 Aim of study . 177 5.2 Results . 177 5.2.1 Embryotoxic and teratogenic combined effects of BPA and genistein on the early development of zebrafish . 177
Action and reaction: the arthropod-borne flaviviruses and host interferon responses

The arthropod-borne flaviviruses include tick- and mosquito-borne viruses that are causes of globally significant emerging diseases. These single-stranded RNA viruses are exquisitely sensitive to the antiviral effects of host interferons. However, both the tick- and mosquito-borne flaviviruses are capable of modulating the interferon response. Despite the high degree of similarity among members of the flavivirus genus, the mechanisms employed by individual viruses to modulate interferon responses differ. This review considers the arthropod-borne flaviviruses and the host interferon response as a pair of forces, the action and the reaction. The interaction of these two forces has led to a complex relationship between virus and host. An increased understanding of these interactions will likely facilitate the rational design of novel vaccines and therapeutics.
Convergent adaptive evolution – how insects master the challenge of cardiac glycoside‐containing host plants

Cardiac glycosides are a prime example of highly toxic plant secondary compounds, which block an essential transmembrane carrier in animals, the Na,K‐ATPase. Nevertheless, over 100 insect species from diverse orders are known to feed on plants containing these compounds and in many cases these toxins are additionally sequestered without ill effect. We investigated whether the insects’ adaptations for handling cardiac glycosides are based on a single physiological mechanism or whether various strategies have evolved across groups. We analyzed gene sequences of the Na,K‐ATPase α‐subunit from cardiac glycoside‐adapted insects and screened for amino‐acid substitutions which could alter the affinity of the enzyme toward cardiac glycosides. In representatives from five insect orders, separated by over 300 million years of evolutionary divergence, we uncovered amino‐acid substitutions at identical positions. Especially striking is the convergent substitution of a histidine for the conserved asparagine at position 122, which we report here for the first time in a sawfly, Monophadnus latus Costa (Hymenoptera: Tenthredinidae), and which was previously observed in the orders Lepidoptera, Coleoptera, Hemiptera, and Diptera. Prior in vitro expression and enzyme assays indicated that this substitution as well as combined substitutions with other residues result in a strongly increased cardenolide resistance of the Na,K‐ATPase. The substitutions to threonine111 and histidine122 observed in M. latus are highly effective and were previously known only in lygaeid bugs. However, not all insects dealing with dietary cardenolides rely on target‐site insensitivity as a mechanism of resistance. An impermeable gut or the exclusion of cardenolides from the nervous tissue with the greatest expression of Na,K‐ATPase by the perineurium, the insect blood brain barrier, apparently represent alternative strategies. Immuno‐histochemical data presented here support the existence of P‐glycoprotein‐like efflux transporters in insect gut membranes that might prevent the uptake of allelochemicals like cardenolides.