Miracle-dz/UniFAR-FTUs huggingface dataset:
Mitochondrial genome of Ying hybrid carp (Russian scattered scale mirror carp ♀ × carp-goldfish nucleocytoplasmic hybrid ♂)

Abstract The complete mitogenomes of Ying hybrid carp (Russian scattered scale mirror carp ♀ × Carp-goldfish nucleocytoplasmic hybrid ♂) was sequenced by PCR-based method. The total of the mtDNA was 16,581 bp, and consisted of 13 protein-coding genes, 22 tRNAs, 2rRNA genes, and 1 control region (D-loop region). The overall base composition was as follows: A: 31.9%, T: 24.8%, C: 27.5%, and G: 15.8%, respectively. The overall AT and GC skew were found to be 0.125 and −0.271, respectively. A majority of the genes used ATG as the start codon, except that the codon GTG was found to initiated the CO I gene. Most of the genes ended with the complete stop codon TAA or TAG, while the COII, ND3, ND4, and Cytb genes terminated with the incomplete stop codons ‘T––’.
MAPPING CHARACTERIZATION OF PZNUS SYLVESTRZS VAR. SYLVESTRIFORMZS BASED ON CHLOROPLAST DNA MICROSATELLITE MARKERS

Molecular markers generated by random amplified polymorphic DNA (RAPD) and chloroplast DNA simple sequence repeats (cpDNA SSR) were used to document polymorphisms in Pinus sylvestris (Ps) var. sylvestrifbrmis and to identify putative parental species that include f? densifloru (Pd) var. densfloru collected from Korea (Pd-K) and from China (Pd-C), and Ps var. sylvestris and Ps var. mongolicu. Pinus sylvestris var. sylvestrifbrmis occurs in a very limited region around Baihe, Jilin Province, China where it grows partly overlapping with the habitat of Pd var. densijloru and Ps. var. sylvestris varieties. Dendrogram constructed using RAPD markers showed that Pd var. densifloru (Pd-K and Pd-C) and Ps var. sylvestriformis grouped together in the major cluster and all other varieties of R sylvestris clustered separately. Pinus var. sylvestrifbrmis showed a closer affinity to Pd-K, rather than to Pd-C. In cpDNA SSR analysis, polymorphisms at nine loci (Pt1254, 151 69,2608 1,30204,36480,45002,6371 8,71936, and 102584) were detected from all species. Most marker sizes overlapped between Pd-K and Ps var. sylvestris except loci at Pt15169 and Pt30204. Therefore, these two cpDNA SSR markers were used for paternity test of Ps var. sylvestriformis. The sequence analysis of cpDNA SSR locus at Pt30204 revealed that pollen source of Ps var, sylvestriformis are composed of Pcl-K type which has polyT-C-polyA-polyG type cpDNA SSR and of Ps var. sylvestris which has polyT-polyA-polyG type without C between polyT and polyA and CTAT in SSR. At locus Ptl5169, Ps var. sylvestriJbrmis are composed of Pd-K type which does not have CTAT sequence in SSR and of Ps var. sylvestris type which has CTAT in SSR. This is the first report which confirms the existence of genetic variability in Ps var. sylvestriJbrmis population based on the sequence analysis. Based on the presence of cpDNA SSR, Ps var. sylvestrijormis appears to be an interspecific hybrid, and is the product of introgression involving Pd-K and Ps var. sylvestris. It is suggested to use the hybrid formula, f? densifloru x P. sylvestris for Ps var. sylvestr$ormis rather than an
The SEK-1 p38 MAP kinase pathway modulates Gq signaling in C. elegans

Gq is a heterotrimeric G protein that is widely expressed in neurons and regulates neuronal activity. To identify pathways regulating neuronal Gq signaling we performed a forward genetic screen in Caenorhabditis elegans for suppressors of activated Gq. One of the suppressors is an allele of sek-1, which encodes a mitogen-activated protein kinase kinase (MAPKK) in the p38 MAPK pathway. Here we show that sek-1 mutants have a slow locomotion rate and that sek-1 acts in acetylcholine neurons to modulate both locomotion rate and Gq signaling. Furthermore, we find that sek-1 acts in mature neurons to modulate locomotion. Using genetic and behavioral approaches we demonstrate that other components of the p38 MAPK pathway also play a positive role in modulating locomotion and Gq signaling. Finally, we find that mutants in the SEK-1 p38 MAPK pathway partially suppress an activated mutant of the sodium leak channel NCA-1/NALCN, a downstream target of Gq signaling. Our results suggest that the SEK-1 p38 pathway may modulate the output of Gq signaling through NCA-1.
Agrobacterium-mediated In planta Transformation of Hill Banana for Developing Resistance against Banana Bunchy Top Virus

Banana viruses have had a major negative impact on the production of bananas worldwide. Among banana viruses, Banana Bunchy Top Virus (BBTV) is one of the most destructive viral diseases affecting Hill banana (AAB) which is known for its special flavor and long shelf life and are unique to the lower Pulney hills of Tamil Nadu, India. In transgenics, Pathogen Derived Resistance (PDR) approach is one of the potential strategies for developing virus resistance in crops which has been proven to be difficult to obtain by conventional breeding. Here we have reported a reproducible and efficient in planta transformation method via Agrobacterium- mediated genetic transformation in banana. Three-month-old banana suckers were used as explant and Agrobacterium tumefaciens strain LBA4404 harboring the binary vector pCAMBIA1301:bbtv rep was used in the co-cultivation. The presence and integration of the gus and replicase genes into the banana genome were confirmed by GUS histochemical assay, polymerase chain reaction and Southern blot hybridization. These results suggest that the in planta Agrobacterium-mediated transformation protocol developed in this study for stable integration of rep gene of BBTV is efficient and that this transformation system could be widely adopted for routine transformation in banana for transferring genes.
Plastic Responses in Tree Architecture to Different Light Intensity Habitats: A Case of Chinese Cork Oak

ABSTRACT The capacity of plants to occupy different habitats is made possible by the plastic responses of their presenting in heterogeneous habitats. Light directly influences the plastic responses of plant architectural traits. We measured five years-old saplings of Chinese cork oak growing in different light intensity habitats (forest edge, forest gap and understory). A suite of architectural and leaf morphological attributes indicated a pronounced ability of Chinese cork oak to adapt to shade. Under low light intensity habitats, Chinese cork oak had a significant tendency to invest more in crown growth, characterized by the highest crown area, the lowest crown length ratio and the largest angle of the inclination of the main stem to the vertical. It expressed marked plagiotropic growth in shade indicating a horizontal light-foraging strategy. In addition, Chinese cork oak significantly exhibited the highest specific leaf area and the lowest total leaf area under low light intensity habitats. In shade, they showed some plasticity in displaying most of their leaf area at the top of the crown to minimize self-shading and to enhance light interception. This differentiation can be defined as a plastic phenomenon, likely related to the higher efficiency of light interception and absorption by saplings.
Conserve primers for sequencing complete ungulate mitochondrial cytochrome c oxidase I (COI) gene from problematic and decomposed biological samples

Abstract We describe six novel ungulate-specific conserved primers for sequencing the complete mitochondrial cytochrome c oxidase I (COI) gene of selected threatened species from degraded samples for effective conservation planning. These primers amplified 301–1599 bp DNA fragments in various combinations. The method described may assist in the sequencing of either complete gene from moderate to good quality DNA or shorter fragment from degraded DNA.
Decoding the nonconscious dynamics of thought generation

Much of economics, psychology and neuroscience have focused on thought dynamics and how they control our behavior, from individual moral choices to the irrationality of market dynamics. However, how much of our thoughts we actually control when we feel we make deliberate choices remains unknown. Here we show that the content of thoughts can be decoded from activity patterns as early as 11 seconds before individuals report having formed the volitional thought. Participants freely chose which of two differently oriented and colored gratings to think about. Using functional magnetic resonance imaging (fMRI) and pattern classification methods, we consistently classified the contents of thoughts using activity patterns recorded before and after the thought was reported. We found that activity patterns were predictive as far as 11 seconds before the conscious thought, in visual, frontal and subcortical areas. These predictive patterns contained similar information to the responses evoked by unattended perceptual gratings and were evident in individual visual areas. Interestingly, neural information present before the decision was associated with the vividness of future thoughts, suggesting that preceding nonconscious sensory-like representations can impact the content and strength of future conscious thoughts. Our results suggest that thoughts and their strength can be biased by prior spontaneous nonconscious perception-like representations, advancing theories of free will and models of intrusive and repetitive thought production.
Ecological structure of leaf-beetle assemblages (Coleoptera, Chrysomelidae) of the Bug valley plant communities in the Wlodawa–Koden section

In the years 2005–2007, in the valley of middle Bug, studies on the structure of leaf-beetle assemblages inhabiting, inter alia, typical for this area and environmentally valuable moist habitats, were carried out. In total, the occurrence of 114 species was recorded. Most of them inhabited the riparian zone (49) and the least, mesoxerothermic and psammophilous (35). The highest biodiversity was reached in beetle communities of ruderal (2.88), moist meadows (2.59) whereas the smallest in fresh meadow (1.29). A characteristic feature of Chrysomelidae fauna from this section of the river is a high proportion of hydro, hygro-, and mesohygrophilic species in several plant communities and the complete lack of xerothermic species. Beetle assemblages are species-rich here, however dominated primarily by broad range elements (Holarctic, Palaearctic or Euro-Siberian) with a total of 82 species (71.2%) and 2606 specimens (79.91%). The tested segment of the riverbank is inhabited by a typical lowland fauna of Chrysomelidae, with the presence of very few rare species that were not previously listed either in the area of Belarus, or not distant Polesie National Park.
Aggregated Quantitative Multifactor Dimensionality Reduction

OF DISSERTATION AGGREGATED QUANTITATIVE MULTIFACTOR DIMENSIONALITY REDUCTION We consider the problem of making predictions for quantitative phenotypes based on gene-to-gene interactions among selected Single Nucleotide Polymorphisms (SNPs). Previously, Quantitative Multifactor Dimensionality Reduction (QMDR) has been applied to detect gene-to-gene interactions associated with elevated quantitative phenotypes, by creating a dichotomous predictor from one interaction which has been deemed optimal. We propose an Aggregated Quantitative Multifactor Dimensionality Reduction (AQMDR), which exhaustively considers all k-way interactions among a set of SNPs and replaces the dichotomous predictor from QMDR with a continuous aggregated score. We evaluate this new AQMDR method in a series of simulations for two-way and three-way interactions, comparing the new method with the original QMDR. In simulation, AQMDR yields consistently smaller prediction error than QMDR when more than one significant interaction is present in the simulation model. Theoretical support is provided for the method, and the method is applied on Alzheimer’s Disease (AD) data to identify significant interactions between APOE4 and other AD associated SNPs.
Light Addressable Potentiometric Biosensor for the Detection of Anticholinesterases

Abstract Biotinylated acetylcholinesterase (AChE) from Eel was immobilized to a biotinylated cellulose nitrate membrane via a streptavidin bridge. Using a light addressable potentiometric sensor (LAPS), enzyme activity was determined as a function of substrate concentration (i.e. acetylcholine) and amount of enzyme immobilized to the membrane. This biosensor was also evaluated for its potential to detect organophosphate (OP) anticholinesterases (antiChEs).
Plant growth promotion by Pseudomonas fluorescens

Pseudomonas fluorescens is a Gram-negative rod shaped bacterium that has a versatile metabolism and is widely spread in soil and water. P. fluorescens strain SBW25 (Pf.SBW25) is a well-known model strain to study bacterial evolution, plant colonization and biocontrol of plant diseases. It produces the biosurfactant viscosin, a lipopeptide that plays a key role in motility, biofilm formation and activity against zoospores of Phytophthora infestans and other oomycete pathogens. In addition to viscosin, Pf.SBW25 produces other metabolites with activity against plant pathogens. The production of these yet unknown metabolites appeared to be regulated by the GacS/GacA two-component regulatory system (the Gac-system). The second P. fluorescens strain SS101 (Pf.SS101) studied in this thesis is known for its plant growth-promoting activities but the underlying mechanisms and genes are largely unknown. Therefore, in this study, we aimed to identify novel metabolites and biosynthetic genes in Pf.SBW25 and Pf.SS101, and to investigate their role in plant growth promotion and biocontrol. To this end, a multidisciplinary approach involving bioinformatic analysis of the genome sequences of strains Pf.SBW25 and Pf.SS101, microarray-based expression profiling, screening of genomic libraries, bioactivity assays, mass spectrometric image analysis (MALDI-IMS) and GC/MSMS analysis was adopted. In conclusion, we showed that the GacS/GacA two-component system as a global regulator of the expression of genes play important roles in antagonism of Pseudomonas fluorescens toward plant pathogenic microbes as well as in plant growth promotion and ISR. Growth promotion by P. fluorescens is associated with alterations in auxin biosynthesis and transport, steroid biosynthesis, carbohydrate metabolism and sulfur assimilation. Moreover, advanced chemical profiling allowed us to compare the metabolite profiles of free-living P. fluorescens and P. fluorescens living in association with plant roots. A better understanding of yet unknown mechanisms exploited by the various Pseudomonas fluorescens strains will lead to new opportunities for the discovery and application of natural bioactive compounds for both industrial and agricultural purposes.
Impact of hypoxia on gene expression patterns by the human pathogen, Vibrio vulnificus, and bacterial community composition in a North Carolina estuary

Estuarine environments are continuously being shaped by both natural and anthropogenic sources which directly/indirectly influence the organisms that inhabit these important niches on both individual and community levels. Human infections caused by pathogenic Vibrio species are continuing to rise, and factors associated with global climate change have been suggested to be impacting their abundance and geographical range. Along with temperature, hypoxia has also increased dramatically in the last 40 years, which has led to persistent dead zones worldwide in areas where these infections are increasing. Thus, utilizing membrane diffusion chambers, we investigated the impact of in situ hypoxia on the gene expression of one such bacterium, Vibrio vulnificus, which is an inhabitant of these vulnerable areas worldwide. By coupling these data with multiple abiotic factors, we were able to demonstrate that genes involved in numerous functions, including those involved in virulence, environmental persistence, and stressosome production, were negatively correlated with dissolved oxygen. Furthermore, comparing 16S ribosomal RNA, we found similar overall community compositions during both hypoxia and normoxia. However, unweighted beta diversity analyses revealed that although certain classes of bacteria dominate in both low‐ and high‐oxygen environments, there is the potential for quantitative shifts in lower abundant species, which may be important for effective risk assessment in areas that are becoming increasingly more hypoxic. This study emphasizes the importance of investigating hypoxia as a trigger for gene expression changes by marine Vibrio species and highlights the need for more in depth community analyses during estuarine hypoxia.
DNA hydroxymethylation and methylation dynamics during neural differentiation

5’-methylcytosine (5mC) plays a crucial role in the epigenetic regulation of gene expression and, until recently, was the only known epigenetic mark to result from the chemical modification of bases in mammalian deoxyribonucleic acid (DNA). The discovery of 5’-hydroxymethylcytosine (5hmC) at physiologically significant levels in a wide range of tissues, particularly those of the central nervous system, suggests that this novel epigenetic modification may have a similarly important function to 5mC in transcriptional regulation. The highest levels of 5hmC have been consistently found in fully differentiated cell types, whilst stem cells seem to be characterised by very low or insignificant levels of 5hmC. It therefore appears that loss of pluripotency is associated with a substantial increase in global 5hmC levels and this modification may play a crucial role in this switch in cell fate. The central aim of this project was to investigate the potential role of 5hmC by profiling both 5mC and 5hmC in parallel during the differentiation of embryonic stem cells (ESCs) down a neural lineage, allowing for a deeper understanding of the potential function of 5hmC in the genome. Analysis of genome-wide 5mC and 5hmC patterns in ESCs, neural stem cells (NSCs) and astrocytes supported the hypothesis that dynamic changes in the distribution of both modifications contribute to neural specification. Striking differences in 5hmC levels between in vitro- and in vivo-derived samples were observed, suggesting that cell culture models may not successfully recapitulate 5hmC profiles observed during normal development. Finally, a novel method was successfully developed and validated for genome-wide 5hmC profiling (oxBS-450K), allowing sensitive and reproducible detection of 5hmC at single-base resolution.
An organopalladium(II) compound including enolate oxy­gen- and sp3-carbon-bound 1,3-di­methyl­barbiturate ligands: (1,2-di­amino­ethane)­bis(1,3-di­methyl­barbiturato)­palladium(II) 5.5-hydrate

In the title compound, [Pd(C6H7N2O3)2(C2H8N2)]·5.5H2O, the Pd atom is coordinated by two 1,3-di­methyl­barbiturate anions through a deprotonated tetrahedral carbon and the enolate oxy­gen. The Pd—N bond length of 2.078 (2) A trans to the C atom is shorter than the Pt—N distance of 2.098 (3) A in the Pt analog.
Molecular phylogeny of the tribe Erotini with description of a new genus from China (Coleoptera: Lycidae)

Erotini is a small tribe of net‐winged beetles known from the northern temperate zone. We investigated relationships and limits of tribes and genera using a molecular phylogeny inferred from rrnL, cox1 and nad5 mtDNA fragments. Lopheros Leconte, 1881 and Pseudaplatopterus Kleine, 1940 were inferred in current molecular analyses as terminal lineages within Erotini. Therefore, we consider Lopherotini Kazantsev, 2012 and Pseudaplatopterina Kazantsev, 2012 as junior synonyms of Erotini Leconte, 1881. The Platycis genus group comprises 19 species representing several genus‐group taxa previously placed in Platycis s. l. Konoplatycis Nakane, 1969 was recovered as a deeply rooted lineage of Erotini and we inferred another independent lineage for which we propose a new genus Sinoplatycis gen. nov. Additionally, we studied the diversity of Platycis s. l. in Asia, found their highest diversity in the temperate forest habitats of Eastern Asia and inferred the paraphyletic character of the subgenus Erotides s. str. Five new species are described from China: Sinoplatycis cardinalis sp. nov., S. zhani sp. nov. (type species of Sinoplatycis gen. nov.), Erotides brunnescens sp. nov., E. pusillus sp. nov. and E. slipinskii sp. nov. The molecular phylogeny shows deep splits of Japanese species with respect to the continental Eurasian fauna and the role of shallow seas and mountain systems in the diversification of the Platycis genus group.
Stochastically reduced communities—Microfluidic compartments as model and investigation tool for soil microorganism growth in structured spaces

Microbial community in soil is a complex and dynamic system. Using traditional culture experiments it is difficult to model the stochastic distribution of single organisms of microbial communities in the soil pore's structure. Droplet‐based micro‐segmented flow technique allows the transfer of the principle of stochastic confinement of stochastically reduced communities from soil micro pores into nanoliter droplets. Microfluidics was applied for the investigation and comparison of soil samples from ancient mining areas by highly resolved concentration‐dependent screenings. As results, the generation, incubation, and in situ optical characterization of nanoliter droplets of suspensions of unknown soil microbial communities allowed the identification of different response characteristics toward heavy metal exposition. The investigations proved the high potential of microfluidics for investigations of soil microbial communities. It may be in the future helpful to detect bacteria and consortia with special biosorption characteristics, which could be useful for the development of biological accumulation and detoxification strategies.
Structure of b-Adrenergic Receptors

b-Adrenergic receptors (bARs) control key physiological functions by transducing signals encoded in catecholamine hormones and neurotransmitters to activate intracellular signaling pathways. As members of the large family of G protein-coupled receptors (GPCRs), bARs have a seven-transmembrane helix topology and signal via G proteinand arrestin-dependent pathways. Until 2007, three-dimensional structural information of GPCRs activated by diffusible ligands, including bARs, was limited to homology models that used the related photoreceptor rhodopsin as a template. Over many years, several labs have developed strategies that have finally allowed the structures of the turkey b1AR and the human b2AR to be determined experimentally. The challenges to overcome included heterologous receptor overexpression, design of stabilized and crystallizable modified receptor constructs, ligand-affinity purification of active receptor and the development of novel techniques in crystallization and microcrystallography. The structures of bARs in complex with inverse agonists, antagonists,