Development of a Maize Molecular Evolutionary Genomic Database

PANZEA is the first public database for studying maize genomic diversity. It was initiated as a repository of genomic diversity for an NSF Plant Genome project on ‘Maize Evolutionary Genomics’. PANZEA is hosted at the Bioinformatics Research Center, North Carolina State University, and is open to the public (http://statgen.ncsu.edu/panzea). PANZEA is designed to capture the interrelationships between germplasm, molecular diversity, phenotypic diversity and genome structure. It has the ability to store, integrate and visualize DNA sequence, enzymatic, SSR (simple sequence repeat) marker, germplasm and phenotypic data. The relational data model is selected and implemented in Oracle. An automated DNA sequence data submission tool has been created that allows project researchers to remotely submit their DNA sequence data directly to PANZEA. On-line database search forms and reports have been created to allow users to search or download germplasm, DNA sequence, gene/locus data and much more, directly from the web

Computational prediction and molecular confirmation of Helitron transposons in the maize genome

Background: Helitrons represent a new class of transposable elements recently uncovered in plants and animals. One remarkable feature of Helitrons is their ability to capture gene sequences, which makes them of considerable potential evolutionary importance. However, because Helitrons lack the typical structural features of other DNA transposable elements, identifying them is a challenge. Currently, most researchers identify Helitrons manually by comparing sequences. With the maize whole genome sequencing project underway, an automated computational Helitron searching tool is needed. The characterization of Helitron activities in maize needs to be addressed in order to better understand the impact of Helitrons on the organization of the genome. Results: We developed and implemented a heuristic searching algorithm in PERL for identifying Helitrons. Our HelitronFinder program will (i) take FASTA-formatted DNA sequences as input and identify the hairpin looping patterns, and (ii) exploit the consensus 5′ and 3′ end sequences of known Helitrons to identify putative ends. We randomly selected five predicted Helitrons from the program\u27s high quality output for molecular verification. Four out of the five predicted Helitrons were confirmed by PCR assays and DNA sequencing in different maize inbred lines. The HelitronFinder program identified two head-to-head dissimilar Helitrons in a maize BAC sequence. Conclusion: We have identified 140 new Helitron candidates in maize with our computational tool HelitronFinder by searching maize DNA sequences currently available in GenBank. Four out of five candidates were confirmed to be real by empirical methods, thus validating the predictions of HelitronFinder. Additional points to emerge from our study are that Helitrons do not always insert at an AT dinucleotide in the host sequences, that they can insert immediately adjacent to an existing Helitron, and that their movement may cause changes in the flanking region, such as deletions

Surface plasmon resonance under conditions of electromagnetically induced transparency

A scheme for a surface plasmon resonance system under conditions of electromagnetically induced transparency (EIT) is proposed. The system is composed of three layers: a prism, a thin metal film, and a hybrid dielectric consisting of EIT atoms and a background substance. A probe and a coupling laser beam are input. Corresponding analytical formulas are derived for the cases when one or both of the laser beams excite surface plasmon polaritons at the metal/dielectric interface. Under resonance conditions, an extremely sharp dip appears in the reflectivity-frequency spectrum of the probe field, revealing new properties of two-dimensional EIT. The reflectivity is extremely sensitive to shifts in the laser frequencies and atomic levels, and to variations of permittivity of the substrate. This EIT-SPR system may to be used for novel magnetometers and biosensors

Trace element zinc and skin disorders

Zinc is a necessary trace element and an important constituent of proteins and other biological molecules. It has many biological functions, including antioxidant, skin and mucous membrane integrity maintenance, and the promotion of various enzymatic and transcriptional responses. The skin contains the third most zinc in the organism. Zinc deficiency can lead to a range of skin diseases. Except for acrodermatitis enteropathic, a rare genetic zinc deficiency, it has also been reported in other diseases. In recent years, zinc supplementation has been widely used for various skin conditions, including infectious diseases (viral warts, genital herpes, cutaneous leishmaniasis, leprosy), inflammatory diseases (hidradenitis suppurativa, acne vulgaris, rosacea, eczematous dermatitis, seborrheic dermatitis, psoriasis, Behcet's disease, oral lichen planus), pigmentary diseases (vitiligo, melasma), tumor-associated diseases (basal cell carcinoma), endocrine and metabolic diseases (necrolytic migratory erythema, necrolytic acral erythema), hair diseases (alopecia), and so on. We reviewed the literature on zinc application in dermatology to provide references for better use

Overestimation of thermal emittance in solenoid scans due to coupled transverse motion

The solenoid scan is a widely used method for the in-situ measurement of the thermal emittance in a photocathode gun. The popularity of this method is due to its simplicity and convenience since all rf photocathode guns are equipped with an emittance compensation solenoid. This paper shows that the solenoid scan measurement overestimates the thermal emittance in the ordinary measurement configuration due to a weak quadrupole field (present in either the rf gun or gun solenoid) followed by a rotation in the solenoid. This coupled transverse dynamics aberration introduces a correlation between the beam's horizontal and vertical motion leading to an increase in the measured 2D transverse emittance, thus the overestimation of the thermal emittance. This effect was systematically studied using both analytic expressions and numerical simulations. These studies were experimentally verified using an L-band 1.6-cell rf photocathode gun with a cesium telluride cathode, which shows a thermal emittance overestimation of 35% with a rms laser spot size of 2.7 mm. The paper concludes by showing that the accuracy of the solenoid scan can be improved by using a quadrupole magnet corrector, consisting of a pair of normal and skew quadrupole magnets.Comment: 12 pages, 13 figure

Long-read sequencing reveals genomic structural variations that underlie creation of quality protein maize

Mutation of o2 doubles maize endosperm lysine content, but it causes an inferior kernel phenotype. Developing quality protein maize (QPM) by introgressing o2 modifiers (Mo2s) into the o2 mutant benefits millions of people in developing countries where maize is a primary protein source. Here, we report genome sequence and annotation of a South African QPM line K0326Y, which is assembled from single-molecule, real-time shotgun sequencing reads collinear with an optical map. We achieve a N50 contig length of 7.7 million bases (Mb) directly from long-read assembly, compared to those of 1.04 Mb for B73 and 1.48 Mb for Mo17. To characterize Mo2s, we map QTLs to chromosomes 1, 6, 7, and 9 using an F2 population derived from crossing K0326Y and W64Ao2. RNA-seq analysis of QPM and o2 endosperms reveals a group of differentially expressed genes that coincide with Mo2 QTLs, suggesting a potential role in vitreous endosperm formation.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Student Attitudes Contribute to the Effectiveness of a Genomics CURE

The Genomics Education Partnership (GEP) engages students in a course-based undergraduate research experience (CURE). To better understand the student attributes that support success in this CURE, we asked students about their attitudes using previously published scales that measure epistemic beliefs about work and science, interest in science, and grit. We found, in general, that the attitudes students bring with them into the classroom contribute to two outcome measures, namely, learning as assessed by a pre- and postquiz and perceived self-reported benefits. While the GEP CURE produces positive outcomes overall, the students with more positive attitudes toward science, particularly with respect to epistemic beliefs, showed greater gains. The findings indicate the importance of a student\u27s epistemic beliefs to achieving positive learning outcomes

The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students