bluuebunny/crossref_metadata_2025 huggingface dataset:
An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention
Authors: Cavallo Federica , Astolfi Annalisa , Iezzi Manuela , Cordero Francesca , Lollini Pier-Luigi , Forni Guido , Calogero Raffaele
Published: December 2005

Background

Neoplastic transformation is a multistep process in which distinct gene products of specific cell regulatory pathways are involved at each stage. Identification of overexpressed genes provides an unprecedented opportunity to address the immune system against antigens typical of defined stages of neoplastic transformation. HER-2/neu/ERBB2 (Her2) oncogene is a prototype of deregulated oncogenic protein kinase membrane receptors. Mice transgenic for rat Her2 (BALB-neuT mice) were studied to evaluate the stage in which vaccines can prevent the onset of Her2 driven mammary carcinomas. As Her2 is not overexpressed in all mammary carcinomas, definition of an additional set of tumor associated antigens (TAAs) expressed at defined stages by most breast carcinomas would allow a broader coverage of vaccination. To address this question, a meta-analysis was performed on two transcription profile studies [1, 2] to identify a set of new TAA targets to be used instead of or in conjunction with Her2.

Results

The five TAAs identified (Tes, Rcn2, Rnf4, Cradd, Galnt3) are those whose expression is linearly related to the tumor mass increase in BALB-neuT mammary glands. Moreover, they have a low expression in normal tissues and are generally expressed in human breast tumors, though at a lower level than Her2.

Conclusion

Although the number of putative TAAs identified is limited, this pilot study suggests that meta-analysis of expression profiles produces results that could assist in the designing of pre-clinical immunopreventive vaccines.
Secondary structure assignment that accurately reflects physical and evolutionary characteristics
Authors: Cubellis Maria Vittoria , Cailliez Fabien , Lovell Simon C
Published: December 2005

Background

Secondary structure is used in hierarchical classification of protein structures, identification of protein features, such as helix caps and loops, for fold recognition, and as a precursor to ab initio structure prediction. There are several methods available for assigning secondary structure if the three-dimensional structure of the protein is known. Unfortunately they differ in their definitions, particularly in the exact positions of the termini. Additionally, most existing methods rely on hydrogen bonding, which means that important secondary structural classes, such as isolated β-strands and poly-proline helices cannot be identified as they do not have characteristic hydrogen-bonding patterns. For this reason we have developed a more accurate method for assigning secondary structure based on main chain geometry, which also allows a more comprehensive assignment of secondary structure.

Results

We define secondary structure based on a number of geometric parameters. Helices are defined based on whether they fit inside an imaginary cylinder: residues must be within the correct radius of a central axis. Different types of helices (alpha, 310 or π) are assigned on the basis of the angle between successive peptide bonds. β-strands are assigned based on backbone dihedrals and with alternating peptide bonds. Thus hydrogen bonding is not required and β-strands can be within a parallel sheet, antiparallel sheet, or can be isolated. Poly-proline helices are defined similarly, although with three-fold symmetry.

Conclusion

We find that our method better assigns secondary structure than existing methods. Specifically, we find that comparing our methods with those of others, amino-acid trends at helix caps are stronger, secondary structural elements less likely to be concatenated together and secondary structure guided sequence alignment is improved. We conclude, therefore, that secondary structure assignments using our method better reflects physical and evolutionary characteristics of proteins.

The program is available from http://www.bioinf.man.ac.uk/~lovell/segno.shtml
ParPEST: a pipeline for EST data analysis based on parallel computing
Authors: D'Agostino Nunzio , Aversano Mario , Chiusano Maria Luisa
Published: December 2005

Background

Expressed Sequence Tags (ESTs) are short and error-prone DNA sequences generated from the 5' and 3' ends of randomly selected cDNA clones. They provide an important resource for comparative and functional genomic studies and, moreover, represent a reliable information for the annotation of genomic sequences. Because of the advances in biotechnologies, ESTs are daily determined in the form of large datasets. Therefore, suitable and efficient bioinformatic approaches are necessary to organize data related information content for further investigations.

Results

We implemented ParPEST (Par allel P rocessing of EST s), a pipeline based on parallel computing for EST analysis. The results are organized in a suitable data warehouse to provide a starting point to mine expressed sequence datasets. The collected information is useful for investigations on data quality and on data information content, enriched also by a preliminary functional annotation.

Conclusion

The pipeline presented here has been developed to perform an exhaustive and reliable analysis on EST data and to provide a curated set of information based on a relational database. Moreover, it is designed to reduce execution time of the specific steps required for a complete analysis using distributed processes and parallelized software. It is conceived to run on low requiring hardware components, to fulfill increasing demand, typical of the data used, and scalability at affordable costs.
Selection of reference genes for quantitative real-time PCR in bovine preimplantation embryos
Authors: Goossens Karen , Van Poucke Mario , Van Soom Ann , Vandesompele Jo , Van Zeveren Alex , Peelman Luc J
Published: December 2005

Background

Real-time quantitative PCR is a sensitive and very efficient technique to examine gene transcription patterns in preimplantation embryos, in order to gain information about embryo development and to optimize assisted reproductive technologies. Critical to the succesful application of real-time PCR is careful assay design, reaction optimization and validation to maximize sensitivity and accuracy. In most of the studies published GAPD, ACTB or 18S rRNA have been used as a single reference gene without prior verification of their expression stability. Normalization of the data using unstable controls can result in erroneous conclusions, especially when only one reference gene is used.

Results

In this study the transcription levels of 8 commonly used reference genes (ACTB, GAPD, Histone H2A, TBP, HPRT1, SDHA, YWHAZ and 18S rRNA) were determined at different preimplantation stages (2-cell, 8-cell, blastocyst and hatched blastocyst) in order to select the most stable genes to normalize quantitative data within different preimplantation embryo stages.

Conclusion

Using the geNorm application YWHAZ, GAPD and SDHA were found to be the most stable genes across the examined embryonic stages, while the commonly used ACTB was shown to be highly regulated. We recommend the use of the geometric mean of those 3 reference genes as an accurate normalization factor, which allows small expression differences to be reliably measured.
Neogenin expression may be inversely correlated to the tumorigenicity of human breast cancer
Authors: Lee Jeong Eon , Kim Hee Joung , Bae Ji Yeon , Kim Seok Won , Park Joon-Suk , Shin Hyuk Jai , Han Wonshik , Kim Sung-Won , Kang Kyung-Sun , Noh Dong-Young
Published: December 2005

Background

Neogenin is expressed in cap cells that have been suggested to be mammary stem or precursor cells. Neogenin is known to play an important role in mammary morphogenesis; however its relationship to tumorigenesis remains to be elucidated.

Methods

To compare the expression levels of neogenin in cells with different tumorigenicity, the expression levels in M13SV1, M13SV1R2 and M13SV1R2N1 cells, which are immortalized derivatives of type I human breast epithelial cells, were evaluated. Then we measured the expression level of neogenin in paired normal and cancer tissues from eight breast cancer patients. Tissue array analysis was performed for 54 human breast tissue samples with different histology, and the results were divided into four categories (none, weak, moderate, strong) by a single well-trained blinded pathologist and statistically analyzed.

Results

The nontumorigenic M13SV1 cells and normal tissues showed stronger expression of neogenin than the M13SV1R2N1 cells and the paired cancer tissues. In the tissue array, all (8/8) of the normal breast tissues showed strong neogenin expression, while 93.5% (43/46) of breast cancer tissues had either no expression or only moderate levels of neogenin expression. There was a significant difference, in the expression level of neogenin, in comparisons between normal and infiltrating ductal carcinoma (p < 0.001).

Conclusion

Neogenin may play a role in mammary carcinogenesis as well as morphogenesis, and the expression may be inversely correlated with mammary carcinogenicity. The value of neogenin as a potential prognostic factor needs further evaluation.
The transcriptome of Toxoplasma gondii
Authors: Radke Jay R , Behnke Michael S , Mackey Aaron J , Radke Josh B , Roos David S , White Michael W
Published: December 2005

Background

Toxoplasma gondiigives rise to toxoplasmosis, among the most prevalent parasitic diseases of animals and man. Transformation of the tachzyoite stage into the latent bradyzoite-cyst form underlies chronic disease and leads to a lifetime risk of recrudescence in individuals whose immune system becomes compromised. Given the importance of tissue cyst formation, there has been intensive focus on the development of methods to study bradyzoite differentiation, although the molecular basis for the developmental switch is still largely unknown.

Results

We have used serial analysis of gene expression (SAGE) to define theToxoplasma gondiitranscriptome of the intermediate-host life cycle that leads to the formation of the bradyzoite/tissue cyst. A broad view of gene expression is provided by >4-fold coverage from nine distinct libraries (~300,000 SAGE tags) representing key developmental transitions in primary parasite populations and in laboratory strains representing the three canonical genotypes. SAGE tags, and their corresponding mRNAs, were analyzed with respect to abundance, uniqueness, and antisense/sense polarity and chromosome distribution and developmental specificity.

Conclusion

This study demonstrates that phenotypic transitions during parasite development were marked by unique stage-specific mRNAs that accounted for 18% of the total SAGE tags and varied from 1–5% of the tags in each developmental stage. We have also found thatToxoplasmamRNA pools have a unique parasite-specific composition with 1 in 5 transcripts encoding Apicomplexa-specific genes functioning in parasite invasion and transmission. Developmentally co-regulated genes were dispersed across allToxoplasmachromosomes, as were tags representing each abundance class, and a variety of biochemical pathways indicating that trans-acting mechanisms likely control gene expression in this parasite. We observed distinct similarities in the specificity and expression levels of mRNAs in primary populations (Day-6 post-sporozoite infection) that occur prior to the onset of bradyzoite development that were uniquely shared with the virulent Type I-RH laboratory strain suggesting that development of RH may be arrested. By contrast, strains from Type II-Me49B7 and Type III-VEGmsj contain SAGE tags corresponding to bradyzoite genes, which suggests that priming of developmental expression likely plays a role in the greater capacity of these strains to complete bradyzoite development.
Clinical Cancer Advances 2005: Major Research Advances in Cancer Treatment, Prevention, and Screening—A Report From the American Society of Clinical Oncology
Authors: Herbst Roy S. , Bajorin Dean F. , Bleiberg Harry , Blum Diane , Hao Desirée , Johnson Bruce E. , Ozols Robert F. , Demetri George D. , Ganz Patricia A. , Kris Mark G. , Levin Bernard , Markman Maurie , Raghavan Derek , Reaman Gregory H. , Sawaya Raymond , Schuchter Lynn M. , Sweetenham John W. , Vahdat Linda T. , Vokes Everett E. , Winn Rodger J. , Mayer Robert J.
Published: December 2005

A MESSAGE FROM ASCO’s PRESIDENT

This year, for the first time, the American Society of Clinical Oncology (ASCO) is publishing Clinical Cancer Advances 2005: Major Research Advances in Cancer Treatment, Prevention, and Screening, an annual review of the most significant clinical research presented or published over the past year across all cancer types.

ASCO embarked on this project to provide the public, patients, policymakers, and physicians with an accessible summary of the year's most important research advances. While not intended to serve as a comprehensive review, this report provides a year-end snapshot of research that will have the greatest impact on patient care.

As you will read, there is much good news from the front lines of cancer research. These pages report on new chemotherapy regimens that sharply reduce the risk of recurrence for very common cancers; the “coming of age” of targeted cancer therapies; promising studies of drugs to prevent cancer; and improvements in quality of life for people living with the disease, among many other advances.

Survival rates for cancer are on the rise, increasing from 50% to 64% over the last 30 years. Cancer still exacts an enormous toll, however. Nearly 1.4 million Americans will be diagnosed this year, and some 570,000 will die of the disease. Clearly, more research is needed to find effective therapies for the most stubborn cancer types and stages. We need to know more about the long-term effects of newer, more targeted cancer therapies, some of which need to be taken over long periods of time. And we need to devote far greater attention to tracking and improving the care of the nearly 10 million cancer survivors in the United States today.

Despite these and other challenges, the message of this report is one of hope. Through the dedicated, persistent pursuit of clinical research and participation in clinical trials by people with cancer, we steadily uncover new and better ways of treating, diagnosing, and preventing a disease that touches the lives of so many. I want to thank the Editorial Board members, the Specialty Editors, and the ASCO Cancer Communications Committee for their dedicated work to develop this report, and I hope you find it useful.

Sincerely,

Sandra J. Horning, MD

President

American Society of Clinical Oncology
Tubular apocrine adenoma with syringocystadenoma papilliferum arising from the external auditory canal
Authors: Lee Chi-Kyou , Jang Kee-Taek , Cho Yang-Sun
Published: December 2005

Tubular apocrine adenoma (TAA) is a very rare sweat gland tumour. Comprehensive review of the literature reveals that TAA in the external auditory canal (EAC) has not yet been reported. We report a case of TAA in the EAC, together with characteristic histopathological findings.
The laryngeal dissection laboratory
Authors: Effat Kamal G
Published: December 2005

The purpose of this study was to dissect various animal larynges in support of a proposal for a laryngeal dissection laboratory. It was found that although the bovine larynx is larger than the human larynx, the anatomy is similar. Thirty-three bovine larynges were dissected by the author in various simulated phonosurgical and partial laryngectomy procedures. Following each procedure, the specimen was photographed for teaching purposes. The author concludes that dissecting bovine larynges offers a valuable aid to training in the field of laryngeal surgery. It is intended to apply these dissections in the form of a departmental surgical workshop.
Insertion of Provox®2 voice prosthesis using the anterograde technique immediately after the secondary tracheoesophageal puncture
Authors: Ng Raymond W M , Lam Paul , Wong Birgitta Y H
Published: December 2005

Insertion of a voice prosthesis through the tracheoesophageal puncture (TEP) is one way to restore the voice after total laryngectomy. The second generation Provox® voice prosthesis is presently one of the most popular devices. Although TEP can be done primarily, there are many centres that prefer it to be done at a second stage for various reasons. However, secondary TEP for retrograde replacement of prosthesis can be difficult and general anaesthesia is very often necessary. Moreover, the presence of neck stiffness and fibrosis from the surgery or previous radiotherapy could affect the neck extension for proper positioning of the trocar. Similarly, it is difficult to insert the prosthesis if there is stenosis at the pharyngoesophageal segment. We describe a technique in which creation of secondary TEP and insertion of Provox®2 is done with local anaesthesia under the same setting. The procedure is well tolerated and can be safely performed on an out-patient basis.
Pharyngeal perforation with deep neck abscess secondary to isolated hyoid bone fracture
Authors: Sethi Ashwani , Sareen Deepika , Chopra Shamit , Mrig Sumit , Agarwal A K
Published: December 2005

We report the case of a 26-year-old man who presented to us with dysphagia secondary to blunt trauma to the neck. The patient was found to have a hyoid bone fracture with pharyngeal perforation and resultant neck abscess. The patient responded to prompt surgical and medical management. We believe this to be the first report of such a case.
Expression of female sex hormone receptors in human middle-ear cholesteatomas
Authors: Raynov Alexander Markov , Choung Yun-Hoon , Moon Sung-Kyun , Park Keehyun
Published: December 2005

The purpose of this study was to establish the eventual presence of progesterone receptor (PGR) and oestrogen receptor (EGR) in human middle-ear cholesteatoma (MECh) tissues and to compare their expression between male and female patients. An immunohistochemical technique was employed for detection of PGR- and EGR-specific immunoreactivity in MECh samples using formalin-fixed paraffin-embedded tissue sections. The positive results were verified with reverse transcriptase polymerase chain reaction (RT-PCR). The morphological study revealed stable expression of PGR in suprabasal layers of all cholesteatoma samples. Weaker immunoreactivity for PGR was demonstrated in external auditory canal skin (EACS) samples in comparison with MECh, while PGR-specific staining was not observed in retroauricular skin (RAS) samples. EGR was detected only at mRNA levels. Stronger expression of EGR PCR products was disclosed in female cholesteatoma samples, while PGR mRNA was predominantly detected in male cholesteatoma specimens. Our preliminary experimental results give us ground to assume that female sex hormones may stimulate proliferation and affect differentiation of MECh keratinocytes.
Prophylactic Fluconazole Is Effective in Preventing Fungal Colonization and Fungal Systemic Infections in Preterm Neonates: A Single-Center, 6-Year, Retrospective Cohort Study
Authors: Manzoni Paolo , Arisio Riccardo , Mostert Michael , Leonessa MariaLisa , Farina Daniele , Latino Maria Agnese , Gomirato Giovanna
Published: December 2005

OBJECTIVE. Despite the promising preliminary results observed in extremely low birth weight (ELBW) populations, the use of fluconazole to prevent fungal colonization and infection in preterm neonates in the NICU is still an open question and not yet recommended as a standard of care. We have reviewed our 6-year series to assess the effectiveness and safety of this form of prophylaxis.

METHODS. This retrospective study consisted of 465 neonates who weighed <1500 g at birth and were admitted to our NICU in the period 1998–2003. Those who were born between 1998 and 2000 and did not receive fluconazole prophylaxis (group A, n = 240) were compared with those who were born between 2001 and 2003 and treated with fluconazole until the 30th day of life (45th for neonates <1000 g at birth; group B, n = 225). Weekly surveillance cultures were obtained from all patients. Incidence of fungal colonization, incidence of systemic fungal infection (SFI), rate of progression from colonization to infection, and mortality rates attributable to fungi were calculated for both groups and separately for neonates who were <1000 g (ELBW) and were 1001 to 1500 g (NE-VLBW) at birth.

RESULTS. Overall fungal colonization was significantly lower in group B (24.0%) than in group A (43.8%; relative risk [RR]: 0.406; 95% confidence interval [CI]: 0.273–0.605). The same was true of neonates with colonization in multiple sites (2.6% vs 5.8%) and of those with colonization from high-risk sites (5.8% vs 19.2%). SFI incidence was significantly lower in group B (10 of 225 cases; 4.4%) than in group A (40 of 240 cases; 16.7%; RR: 0.233; 95% CI: 0.113–0.447). Reduction of both colonization and SFI in group B was greater in the ELBW neonates and also significant in the NE-VLBW neonates. Rate of progression from colonization to infection was significantly lower in group B (0.17 vs 0.38; RR: 0.369; 95% CI: 0.159–0.815). Crude mortality rate attributable to Candida species was 1.7% (4 of 240) in group A vs 0% (0 of 225) in group B. Overall mortality rate (any cause before hospital discharge) was similar in the two groups (11.2% vs 10.6%), but in colonized infants (n = 159), it was significantly lower in group B (3.7% vs 18.1%; RR: 0.174; 95% CI: 0.039–0.778). The incidence of natively fluconazole-resistant fungal species did not increase over the years, and patterns of sensitivity to fluconazole remained the same. No adverse reaction related to fluconazole occurred.

CONCLUSIONS. Prophylactic fluconazole significantly reduces the incidence of colonization and systemic infection by Candida species in both ELBW and NE-VLBW neonates and decreases the rates of progression from initial colonization to massive colonization and to systemic infection. All VLBW neonates may benefit from fluconazole prophylaxis.
Linear Scleroderma en coup de sabre With Associated Neurologic Abnormalities
Authors: Holland Kristen E. , Steffes Burt , Nocton James J. , Schwabe Michael J. , Jacobson Richard D. , Drolet Beth A.
Published: December 2005

Linear scleroderma represents a unique form of localized scleroderma that primarily affects the pediatric population, with 67% of patients diagnosed before 18 years of age. When linear scleroderma occurs on the head, it is referred to as linear scleroderma en coup de sabre, given the resemblance of the skin lesions to the stroke of a sabre. Here we describe 3 pediatric patients with linear scleroderma en coup de sabre who presented with neurologic abnormalities before or concurrent with the diagnosis of their skin disease. Our patients' cases highlight the underrecognized relationship between neurologic complications and linear scleroderma en coup de sabre and illustrate the importance of a thorough skin examination in patients with unexplained neurologic disease.
Rps8 Maps to a Resistance Gene Rich Region on Soybean Molecular Linkage Group F
Authors: Gordon Stuart G. , St. Martin Steven K. , Dorrance Anne E.
Published: December 2005

Phytophthora root and stem rot caused by Phytophthora sojae M.J. Kaufmann & J.W. Gerdemann is a serious disease of soybean [Glycine max (L.) Merr.] worldwide. Recently, a new locus for resistance to P. sojae, Rps8, was identified and mapped in two small soybean populations. The objective of this study was to verify the genomic location of Rps8 in a larger population. One hundred thirty‐eight F2:3 families from a cross between ‘Williams’ (rps8/rps8) × PI 399073 (Rps8/Rps8) were genotyped by simple sequence repeat (SSR) and restriction fragment length polymorphism (RFLP) markers. From this set of families, 138 and 69 were phenotyped with P. sojae races 1 and 25, respectively. The segregation ratio for each race fit a 3:1 resistant:susceptible, confirming that Rps8 segregated as a single dominant gene. On the basis of linkage analysis with SSR and RFLP markers, Rps8 was located on molecular linkage group F in this population. This region of the soybean genome contains numerous other resistance gene loci as well as pathogen and pest resistance QTL.
Early Generation Testing in Upland Cotton
Authors: Jones Darren G. , Smith C. Wayne
Published: December 2005

Early generation testing (EGT) is often used to identify segregating populations that are expected to contain the greatest frequency of favorable genotypes and to eliminate inferior populations with limited promise. The goal of this study was to determine if EGT methods utilized in cotton (Gossypium hirsutum L.) at College Station (CS) and Weslaco (WS), TX, since 1990 and 1992, respectively, and through 2002, could be used to predict advanced strain performance. Data were collected from 283 unique F2 populations at CS and 146 unique F2 and F3 populations at WS. Correlations of F2 population yield and individual plant selection fiber data suggests that the method used at CS limits the use of EGT for lint yield, yet enhances the use of EGT for the highly heritable fiber traits. Conversely, correlations of F2 population yield and population fiber data suggest that the method used at WS supports EGT for lint yield, but limits the use of EGT for fiber traits. However, by using F3 population fiber yield means and individual plant selection fiber data, EGT is validated at WS. Also, correlations of F2 yield and fiber data with combined yield and fiber data of advanced strains in standard performance trials across multiple locations in central and south Texas indicated that EGT reasonably predicted advanced generation performance.
Cryopreservation of Bermudagrass Germplasm by Encapsulation Dehydration
Authors: Reed Barbara M. , Schumacher Laura , Wang Nan , D'Achino Jeff , Barker Reed E.
Published: December 2005

Genetic conservation of vegetatively‐propagated grasses requires intensive care of pot cultures or carefully separated field plots. Even with intensive care, there is high risk of mechanical contamination and loss of plants to biotic and abiotic stresses. Medium‐ and long‐term storage of this germplasm would be more cost effective and provide a backup for field or greenhouse germplasm collections. Cynodon spp. (bermudagrass and stargrass) germplasm is typically maintained as growing plants in breeders' collections. The development of a long‐term storage protocol for Cynodon in liquid nitrogen (LN) could provide a secure backup of these collections. A diverse group of Cynodon taxa was evaluated for long‐term storage in LN at −196°C. The encapsulation and dehydration (ED) cryopreservation protocol was most effective when combined with a 1‐ to 4‐wk cold‐acclimation period and dehydration to 19 to 23% moisture before exposure to LN. Nineteen of the 25 accessions (76%) had >40% regrowth. Thirty shoot tips of each of 25 Cynodon accessions are now stored at the National Clonal Germplasm Repository (NCGR), Corvallis, and 50 shoot tips are held at the National Center for Germplasm Resources Preservation (NCGRP) in Fort Collins, CO, as a long‐term backup in LN.
Inheritance of High Stearic Acid Content in the Sunflower Mutant CAS‐14
Authors: Pérez‐Vich Begoña , Velasco Leonardo , Muñoz‐Ruz Juan , Fernández‐Martínez José M.
Published: December 2005

A sunflower (Helianthus annuus L.) oil with high concentration of stearic acid has important applications in the food industry. Two sunflower mutants with high stearic acid content, CAS‐3 and CAS‐14, have been developed. In contrast to CAS‐3, high stearic acid expression in CAS‐14 seeds is temperature dependent and nonuniformly distributed in the seed. The trait in CAS‐3 has been found to be governed by two genes, Es1 and Es2. The objective of the present research was to study the inheritance of high stearic acid content in CAS‐14 through crosses with P21, a nuclear male sterile (NMS) line with a wild‐type fatty acid profile, and CAS‐3. The genetic analysis included the evaluation of the F1, F2, F3, BC1F1, and BC1F2 seed generations. Crosses between P21 and CAS‐14 revealed that the high stearic acid trait was recessive and controlled by a single gene, designated Es3. The analysis of the F3 and BC1F2 to P21 generations demonstrated a repulsion‐phase linkage between the Es3 and the Ms loci, the latter conferring the NMS trait. The frequency of recombination between Es3 and Ms was estimated to be 0.09. Crosses between CAS‐3 and CAS‐14 demonstrated that both lines possess alleles for high stearic acid content at different loci, as transgressive segregants with low stearic acid content were observed in all generations. Genetic recombination of es1 and es3 alleles did not result in an increment of the maximum stearic acid content in the seeds compared with the maximum levels produced by the es3 alleles alone.
Effect of Russian Wheat Aphid on Yield and Yield Components of Field Grown Susceptible and Resistant Spring Barley
Authors: Mornhinweg D. W. , Brewer M. J. , Porter D. R.
Published: December 2005

Russian wheat aphid, Diuraphis noxia (Mordvilko) (RWA), can be devastating to barley (Hordeum vulgare L.) in the western USA. RWA‐resistant barley germplasm lines have been developed that control RWA without the use of environmentally detrimental and economically expensive insecticides. This study was conducted to determine if seedling RWA resistance ratings, utilized to develop resistant germplasm lines from greenhouse screenings, accurately predict field performance measured as grain yield and to determine the effect of RWA on yield and yield components of RWA‐resistant barley germplasm lines and cultivars differing in seedling RWA resistant rating. Resistant lines and susceptible cultivars were planted at two field locations in Wyoming. Plots were artificially infested with RWA while controls were kept aphid free with pesticide application. Highly resistant lines maintained or increased yield components and grain yield (average grain yield increase 5%) under RWA feeding pressure. Susceptible cultivars had a large reduction in yield components and grain yield (average reduction 56%). The response of moderately resistant and moderately susceptible lines was intermediate and continuous between the resistant and susceptible lines with an average reduction of 20% in grain yield. Seedling resistance ratings accurately predict field performance, providing a more economical, timely, and efficient means of selecting RWA‐resistant germplasm lines for release.
Soybean Cultivars Resulted from More Recombination Events Than Unselected Lines in the Same Population
Authors: Stefaniak T. R. , Hyten D. L. , Pantalone V. R. , Klarer A. , Pfeiffer T. W.
Published: December 2005

The selection of superior adapted cultivars has contributed to the doubling of soybean [Glycine max (L.) Merr.] yields in the USA since 1930. Genetic variation was required for this selection to be effective. The objective of this study was to evaluate the importance of homologous chromosome meiotic recombination in the creation of soybean cultivars. A set of 10 adapted high yielding cultivars selected from the cross ‘Williams’ × ‘Essex’ was compared with a set of 156 random recombinant inbred lines (RILs) from the same population. Crossover events were identified using 143 simple sequence repeat (SSR) markers spanning all 20 soybean chromosomes. The recombination rates were standardized among chromosomes by dividing the realized crossovers by the potential crossovers. The standardized recombination rate for the entire genome was significantly greater for the 10 cultivars (0.34) than for the RILs (0.29). The cultivars had numerically higher standardized recombination rates for 17 of the 20 chromosomes, significantly higher on chromosomes defined by the molecular linkage groups C2, L, and M. The interaction of linkage groups with the two sets of lines was nonsignificant for standardized recombination. Soybean breeding progress has been accomplished in part by creating and capitalizing on new within_chromosome allele combinations.
Mapping Fiber and Yield QTLs with Main, Epistatic, and QTL × Environment Interaction Effects in Recombinant Inbred Lines of Upland Cotton
Authors: Shen Xinlian , Zhang Tianzhen , Guo Wangzhen , Zhu Xiefei , Zhang Xiaoyang
Published: December 2005

Most agronomic traits of cotton (Gossypium hirsutum L.) are quantitatively inherited and affected by environment. The importance of epistasis as the genetic basis for complex traits has been reported in many crops. In this study, a linkage map was constructed by means of a recombinant inbred line (RIL) population derived from 7235×TM‐1. Main effects, epistatic effects, and environmental interaction effects of quantitative trait loci (QTLs) controlling fiber and yield component traits were determined by mixed linear model based QTL mapping in two to four environments. Sixteen main effect QTLs for 12 traits and 19 digenic interaction QTLs for 12 traits were detected. The amount of variation explained by the QTLs of main effect was larger than the QTLs involved in epistatic interactions. Among seven QTLs having QTL × Environment (QE) interaction effects, five produced significant additive effects and two did not, but only one interaction showed significant additive × additive × environment (AAE) interaction effects. Some QTLs with large effects detected in specific environments could be associated with environmental response elements.
Single‐Plant Selection at Ultra‐Low Density to Improve Stability of a Bread Wheat Cultivar
Authors: Tokatlidis Ioannis S. , Xynias Ioannis N. , Tsialtas John T. , Papadopoulos Ioannis I.
Published: December 2005

The goal of the study was to assess within bread wheat (Triticum aestivum L.) cultivar variation through honeycomb selection, under the ultra‐low density (ULD) of 1.2 plants/m2. Divergent selection of individual plants characterized as providing high (H) and low (L) yield led to 10 H and 10 L first generation families, respectively. Further selection of high yielding plants within H families resulted in 20 second generation families. Progeny evaluation was conducted in two locations, under ULD and the typical crop density (TCD) of 500 plants/m2. Six of the first generation families were also tested, in two locations for two years, across four densities (100, 300, 500, and 700 plants/m2). Intra‐cultivar selection improved yield potential per plant (i.e., expressed under low competition conditions), and there was an indication of overall crop yield potential improvement (i.e., maximum yield per unit area). Compared to the original cultivar at ULD conditions, five of the H first generation and 15 of the second generation families had significantly higher grain yield per plant (by 18 to 53%). Two of the H first generation and four of the second generation families significantly outperformed the original cultivar by 17 to 22% under TCD. Experimentation across the four densities showed that derived families exhibited less density dependence than their original cultivar, a determinant parameter for stability of performance. Results constituted evidence of low densities being more suitable for breeder's seed maintenance, so that any existing or newly developed variation is beneficially exploited.
Chemical Control of Neotyphodium spp. Endophytes in Perennial Ryegrass and Tall Fescue Seeds
Authors: Leyronas C. , Mériaux B. , Raynal G.
Published: December 2005

Seed transmitted Neotyphodium endophytes are widespread in grasses. These fungi may modify agronomic plant traits and induce synthesis of mycotoxins that lead to possible cattle toxicoses. For these reasons, the Technical Permanent Committee for Breeding recommends the grass varieties submitted to the French Official List to contain less than 20% of seeds with living Neotyphodium Several fungicides were tested as seed treatments on perennial ryegrass (Lolium perenne L.) and tall fescue (Festuca arundinacea Schreber). Phytotoxic effects were measured. Their efficacy was evaluated in greenhouse and in field conditions of seed production. Triticonazole [(RS)‐(E)‐5‐(4‐chlorobenzylidene)‐2,2‐dimethyl‐1‐(1H‐1,2,4‐triazol‐1‐ylmethyl)cyclopentanol] was effective but much too phytotoxic. The tested doses of bitertanol [1‐(biphenyl‐4‐yloxy)‐3,3‐dimethyl‐1‐(1H‐1,2,4‐triazol‐ 1‐yl)butan‐2‐ol] and fluquinconazole [3‐(2,4‐dichlorophenyl)‐6‐fluoro‐2‐(1H‐1,2,4‐triazol‐1‐yl)quinazolin‐4(3H)‐one] have few negative effects on germination but very few effects on endophytes. Prochloraz [N‐propyl‐N‐[2‐(2,4,6‐trichlorophenoxy)ethyl]‐1H‐imidazole‐1‐carboxamide] (0.75 g kg−1) represents the best balance between high efficacy and low phytotoxicity on perennial ryegrass and tall fescue seeds. No difference among varieties and species was detected in their response to prochloraz treatment. In greenhouse trials, less than 10% of living endophyte remained in perennial ryegrass and tall fescue seed lots, even in highly infected ones (66% of E+ seeds), when treated with prochloraz. This seed treatment was also efficient in field conditions where the level of endophyte was reduced by more than 60% in highly endophyte‐infected ryegrass seed lots. This study shows that, even if seed germination is a little decreased, prochloraz could be used during grass breeding so that subsequent generations of seed will be free from endophyte with good germination rate.
Cytogenetic and Molecular Characterization of Hybrids between 6x, 4x, and 2x Ploidy Levels in Crested Wheatgrass
Authors: Jensen Kevin B. , Larson Steven R. , Waldron Blair L. , Asay Kay H.
Published: December 2005

The crested wheatgrass cultivar ‘Hycrest,’ which consists of germplasm from an induced tetraploid of Agropuron cristatum (2n = 4x = 28) (L.) Gaertn. and a natural tetraploid (2n = 4x = 28) of A. desertorum (Fisch. Ex Link) Schultes, was hybridized with a promising broadleaf hexaploid (6x‐BL; 2n = 6x = 42) accession of A. cristatum from the USSR. The goal was to combine the wide leaf characteristic and green color retention from the 6x‐BL parent into a common gene pool. The crossability between Hycrest (4x) and 6x‐BL (6x) was excellent; however, chromosome pairing was irregular and chromosome numbers ranged from 2n = 27 to 41. Leaf morphology in Hycrest/6x‐BL hybrids was intermediate to that of the parents. Selected F1 pentaploid progenies (2n = 5x = 35), with leaf widths approaching that of the 6x‐BL parent, were backcrossed to Hycrest (Hycrest*2/6x‐BL), and then crossed among themselves (Hycrest*2/6x‐BL//Hycrest*2/6x‐BL). In the backcross hybrid, chromosome numbers ranged from 2n = 28 to 39. Meiotically, 28 chromosome backcross hybrid plants were more stable than aneuploid backcross hybrids. The broadleaf character was readily detected in the backcross progeny. In Hycrest/6x‐BL//Hycrest/6x‐BL hybrids, chromosome numbers ranged from 2n = 33 to 45. Despite the hybrid origin, all aneuploid hybrids had an increased number of univalents and chromosome associations that involved more than four chromosomes. AFLP analysis reflected genetic introgression from the 6x‐BL parent beyond that observed in Hycrest. Results support earlier conclusions that the crested wheatgrass complex should be treated as a common gene pool.
Safety and Public Acceptance of Transgenic Products
Authors: Byrne Patrick F.
Published: December 2005

Public acceptance of transgenic (genetically engineered, GE) products is influenced by the perception of direct or indirect risks and benefits and the credibility of regulatory agencies that evaluate food and environmental safety. In North America acceptance of GE foods is holding steady, while knowledge about them remains low. Development of transgenic foods with improved nutritional properties or other quality factors will likely be better received than products that primarily benefit the grower or developer of the product. There is continuing unease about biopharming and the association, by some members of the public, of GE crops with corporate agriculture. Several recent reports have reviewed the U.S. regulatory system for transgenic crops and called for a more coordinated and transparent process that allows for greater public participation. For society to benefit from GE crops, we must move away from the polarized positions that have defined the transgenic debate in the past, to positions of mutual respect that allow a rational discussion of the technology's merits and risks.
Defining Sunflower Selection Strategies for a Highly Heterogeneous Target Population of Environments
Authors: de la Vega Abelardo J. , Chapman Scott C.
Published: December 2005

Genotype × environment (G × E) interactions can be a major impediment to genetic progress in sunflower (Helianthus annuus L.) breeding for Argentina. Previous studies revealed that northern and central environments show repeatable differences in genotype discrimination, suggesting some G × E interactions could be accommodated by selecting for specific adaptation. In this study, a trial dataset of 10 hybrids grown over 46 environments was used to validate this megaenvironment definition, to determine the value of division of the sunflower region of Argentina, and to define optimal testing strategies to balance resources between subregions. Pattern analysis confirmed the northern and central megaenvironments. Subdivision of the target region and the testing resources increased the within‐subregion genotype to G × E interaction ratios and did not decrease trial repeatabilities. The genetic correlation between target region and its subregions was 0.36. In contrast to studies for barley in Canada, the calculated ratios of correlated response in a subregion to indirect selection in the undivided target region relative to direct response in the subregion demonstrate that division of the sunflower region is 3× more effective than selecting for broad adaptation to the undivided target region. The unpredictable G × E interactions within subregions should be accommodated by selecting for broad adaptation. In the northern subregion, there is scope to redefine testing strategies by replacing years with locations with no cost in performance predictability. Testing resources can be balanced based on the market value of the two subregions.
Gamete Selection for Resistance to Common and Halo Bacterial Blights in Dry Bean Intergene Pool Populations
Authors: Asensio‐S.‐Manzanera M. Carmen , Asensio Carmen , Singh Shree P.
Published: December 2005

The common [caused by Xanthomonas campestris pv. phaseoli (Smith) Dye (Xcp) and X. campestris pv. phaseoli var. fuscans (Xcpf)] and halo bacterial blights [caused by Pseudomonas syringae pv. phaseolicola (Burkh.) Young et al. (Psp)] are seed‐borne diseases that cause severe yield losses in dry and snap bean (Phaseolus vulgaris L.) worldwide. Use of cultivars resistant to these diseases is pivotal for their integrated control and to facilitate production and distribution of pathogen‐free seed. Our objective was to use gamete selection for resistance to both bacterial blights. Two intergene pool four‐way crosses, namely ZARA III = Wilkinson 2/‘Montcalm’//‘Casasola’/‘Harris’ and ZARA IV = ‘Edmund’/Wilkinson 2//Casasola/BRB 131 were made. Selection for resistance to both bacterial blights was practiced from F1 to F4 in the greenhouse or field at Valladolid, Spain. The F4–derived F5 breeding lines resistant to both blights were screened for Bean common mosaic virus (BCMV), Bean common mosaic necrosis virus (BCMNV), and common bacterial blight in the greenhouse at Kimberly, ID, and for halo blight at Filer, ID, in 2001. They were also evaluated for the two bacterial blights, growth habit, seed color, and 100‐seed weight in the field at Valladolid in 2002. The proportion of resistant, intermediate, and susceptible plants was similar in both F1, and selection was effective from the F1 to F4 for both bacterial blights. Nonetheless, population ZARA IV had relatively lower halo blight scores than ZARA III (1.8–4.1 vs. 2.6–6.5). The contrary occurred for common bacterial blight. Five breeding lines resistant or intermediate to both diseases were obtained from two of 147 F1 plants in ZARA III. ZARA IV produced nine breeding lines resistant to both bacterial blights that originated from four of 128 F1 plants. Some breeding lines had a higher resistance to both bacterial blights than their parents indicating transgressive segregation, and all carried the I allele for resistance to BCMV. We suggest using gamete selection for introgression and pyramiding of resistance to both bacterial blights with multiple‐parent populations in dry bean.
Identification of QTLs Associated with Fusarium Head Blight Resistance in Barley Accession CIho 4196
Authors: Horsley R. D. , Schmierer D. , Maier C. , Kudrna D. , Urrea C. A. , Steffenson B. J. , Schwarz P. B. , Franckowiak J. D. , Green M. J. , Zhang B. , Kleinhofs A.
Published: December 2005

Fusarium head blight (FHB), incited by Fusarium graminearum Schwabe [teleomorph Gibberella zea (Schwein)], reduces quality of harvested barley (Hordeum vulgare L.) because of blighted kernels and the presence of deoxynivalenol (DON), a mycotoxin produced by the pathogen. CIho 4196, a two‐rowed type, is one of the most resistant accessions known in barley; however, it possesses many undesirable agronomic traits. To better understand the genetics of reduced FHB severity and DON accumulation conferred by CIho 4196, a genetic map was generated using a population of recombinant inbred lines derived from a cross between Foster (a six‐rowed malting cultivar) and CIho 4196. Quantitative trait loci (QTL) analyses were performed using data obtained from 10 field environments. The possible associations of resistance QTLs and various agronomic and morphological traits in barley also were investigated. The centromeric region of chromosome 2H flanked by the markers ABG461C and MWG882A (bins 6–10) likely (P < 0.001) contains two QTLs contributing to lower FHB severity and plant height, and one QTL each for DON accumulation, days to heading, and rachis node number. The QTL for low FHB severity in the bin 8 region explained from 3 to 9% of the variation, while the QTL in the bin 10 region explained from 17 to 60% of the variation. A QTL for DON accumulation that explained 9 to 14% of the variation was found in the bin 2 region of chromosome 4H. This may represent a new QTL not present in other FHB resistant sources. Resistance QTLs in the bin 8 region and bin 10 region of chromosome 2HL were provisionally designated Qrgz‐2H‐8 and Qrgz‐2H‐10, respectively. The QTL for DON accumulation in chromosome 4H was provisionally named QDON‐4H‐2.
Variance Component Estimation Using the Additive, Dominance, and Additive × Additive Model When Genotypes Vary across Environments
Authors: Wu Jixiang , Jenkins Johnie N. , McCarty Jack C. , Wu Dongfeng
Published: December 2005

In addition to additive (A) and dominant (D) genetic effects, the A × A interaction (or A × A epistatic) effects that control many quantitative traits are important for genetic and breeding studies. To estimate these genetic variance components, including genotype × environment (G × E) interaction, one usually expects to have data from at least two generations (i.e., F1 and F2) and parents with the same entries in all environments. Practical difficulties may arise in implementing such a design. In this study, we performed Monte Carlo simulations to compare the estimated variance components between four partial and two complete genetic designs (GDs) using the mixed linear model approach. Our definition for GD is different from the traditional definitions of genetic mating designs. Simulation results showed that the estimated genetic variance components for A, A × E, A × A epistatic, and A × A × E effects were unbiased for the six designs. Among four partial designs, two provided the comparable results for D and D × E effects compared with the complete GDs, but with slightly larger mean square errors (MSEs), indicating that some partial GDs can be used when the genetic resources are limited.