Diluted Magnetic DNA Nanowires

DNA, as a natural biological nanowire, could be modified by inorganic atoms, either conducting or semi‐conducting ones, to render feasible for technological applications and sequencing. Magnetic phase transition of modified DNA (M‐DNA) nanowire, similar to diluted magnetic semiconductor (DMS) materials, occurs by changing parameters such as temperature and doping ratio having critical values. Tuning such parameters provide a pleasant control about determination of the magnetic property of M‐DNA, particularly room‐temperature soft ferromagnetism. In this chapter, a fundamental theory for anti‐ferromagnetic Cr3+‐doped M‐DNA nanowire named as diluted magnetic organic structures (DMOS) is tried to figure out the interactions representing the exotic behaviour of these type of organometallics. However, authors detailed preparation of nanowire as a global input and overall procedure of simulation based on Markov chain Monte Carlo (MCMC) method

The relationship between phylogenetic classification, virulence and antibiotic resistance of extraintestinal pathogenic Escherichia coli in İzmir province, Turkey

Background. Extraintestinal pathogenic Escherichia coli (ExPEC) is an important bacterium and responsible for many bloodstream infections, including urinary tract infections and even fatal bacteremia. The aim of this research was to investigate whether ExPEC strains isolated from Turkish blood cultures have a relationship between 16S rRNA based phylogenetic clusters and antibiotic resistance profiles, virulence factors or clonal lineages. Methods. Phenotypically identified ExPEC blood culture isolates (n = 104) were included in this study. The 16S rRNA partial sequence analysis was performed for genotypic identification of ExPEC isolates. Antibiotic susceptibility and Extended Spectrum beta-Lactamase testing of isolates were performed. Phylogenetic classification (A, B1, B2 and D), Multi Locus Sequence Typing analysis and virulence-associated genes were investigated. Results. Based on 16S rRNA partial sequence analysis, 97 out of 104 (93.26%) ExPEC isolates were confirmed as E. coli. Ampicillin (74.22%) and cefuroxime axetil (65.97%) resistances had the highest frequencies among the ExPEC isolates. In terms of phylogenetic classification of ExPEC, D (38.14%, 37/97) was the most prevalent group after A (29.89%, 29/97), B2 (20.61%, 20/97), and B1 (11.34%, 11/97). The sequence types of the 20 ExPEC isolates belonging to the B2 phylogenetic group were analyzed by Multi Locus Sequence Typing. Ten isolates out of 20 (50.0%) were identified as ST131. The other STs were ST95 (n=1), ST14 (n=1), ST10 (n=1), ST69 (n=1), ST1722 (n=2), ST141 (n=1), ST88 (n=1), ST80 (n=1), and ST998 (n=1). Of the ST131 strains, six (60%, 6/10) represented serogroup O25. The most common virulence factor genes were serum resistance factor gene, traT (55.7%) aerobactin siderophore receptor and yersiniabactin encoding genes iutA (45.3%) and fyuA (50.5%), respectively. In addition, PAI (41.2%), iroN (23.7%), hlyA (15.4%), kpsII (13.4%), ompT (13.4%), papG (12.4%), iss (9.3%), cnf1 (7.2%), ibeA (2.06%), and sfaS (2.06%) genes were present in the ExPEC isolates. Conclusion. The 16S rRNA-based phylogenetic relationship tree analysis showed that a large cluster was present among 97 ExPEC isolates along with related reference strains. There were 21 main clusters with 32 closely related subclusters. Based on our findings, different clonal lineages of ExPEC can display different antibiotic susceptibilities and virulence properties. We also concluded that virulence factors were not distributed depending on phylogenetic groups (A, B1, B2, and D). The ExPEC isolates belonging to the same phylogenetic group and sequence type could display different resistance and virulence characteristics.Peer reviewe

Transcriptome Analysis for Non-Model Organism: Current Status and Best-Practices

Since transcriptome analysis provides genome-wide sequence and gene expression information, transcript reconstruction using RNA-Seq sequence reads has become popular during recent years. For non-model organism, as distinct from the reference genome-based mapping, sequence reads are processed via de novo transcriptome assembly approaches to produce large numbers of contigs corresponding to coding or non-coding, but expressed, part of genome. In spite of immense potential of RNA-Seq–based methods, particularly in recovering full-length transcripts and spliced isoforms from short-reads, the accurate results can be only obtained by the procedures to be taken in a step-by-step manner. In this chapter, we aim to provide an overview of the state-of-the-art methods including (i) quality check and pre-processing of raw reads, (ii) the pros and cons of de novo transcriptome assemblers, (iii) generating non-redundant transcript data, (iv) current quality assessment tools for de novo transcriptome assemblies, (v) approaches for transcript abundance and differential expression estimations and finally (vi) further mining of transcriptomic data for particular biological questions. Our intention is to provide an overview and practical guidance for choosing the appropriate approaches to best meet the needs of researchers in this area and also outline the strategies to improve on-going projects

Wellesley College 1875-1975: A Century of Women

https://repository.wellesley.edu/wellesleyhistories/1000/thumbnail.jp

Global Transcriptome Analysis Reveals Differences in Gene Expression Patterns Between Nonhyperhydric and Hyperhydric Peach Leaves

Hyperhydricity is a morphophysiological disorder of plants in tissue culture characterized morphologically by the presence of translucent, thick, curled, and fragile leaves as a result of excessive water intake. Since clonal propagation is a major in vitro technique for multiplying plants vegetatively, the emergence of hyperhydricity-related symptoms causes significant economic losses to agriculture and horticulture. Although numerous efforts have been hitherto devoted to the morphological and anatomical responses of plants to hyperhydricity, the underlying molecular mechanism remains largely unknown. Here, a genome-wide transcriptome analysis was performed to identify differentially expressed genes in hyperhydric and nonhyperhydric leaves of peach [ (L.) Batsch]. The RNA sequencing (RNA-Seq) analysis showed that the expression of >300 transcripts was altered between control and hyperhydric leaf cells. The top 30 differentially expressed transcripts (DETs) were related to the posttranscriptional regulators of organelle gene expression and photosynthesis, cellular elimination, plant cuticle development, and abiotic stress response processes. The expression of 10 DETs was also conformed by quantitative real-time polymerase chain reaction (RT-qPCR) in hyperhydric and nonhyperhydric leaves. As a complex biological process, hyperhydricity alters the expression of various transcripts including transcription factor (), RNA binding protein (pentatricopeptide, ), transporter protein (), and . Thus, this genome-wide transcriptome profiling study may help elucidate the molecular mechanism of hyperhydricity

Boron Stress Responsive MicroRNAs and Their Targets in Barley

Boron stress is an environmental factor affecting plant development and production. Recently, microRNAs (miRNAs) have been found to be involved in several plant processes such as growth regulation and stress responses. In this study, miRNAs associated with boron stress were identified and characterized in barley. miRNA profiles were also comparatively analyzed between root and leave samples. A total of 31 known and 3 new miRNAs were identified in barley; 25 of them were found to respond to boron treatment. Several miRNAs were expressed in a tissue specific manner; for example, miR156d, miR171a, miR397, and miR444a were only detected in leaves. Additionally, a total of 934 barley transcripts were found to be specifically targeted and degraded by miRNAs. In silico analysis of miRNA target genes demonstrated that many miRNA targets are conserved transcription factors such as Squamosa promoter-binding protein, Auxin response factor (ARF), and the MYB transcription factor family. A majority of these targets were responsible for plant growth and response to environmental changes. We also propose that some of the miRNAs in barley such as miRNA408 might play critical roles against boron exposure. In conclusion, barley may use several pathways and cellular processes targeted by miRNAs to cope with boron stress