Gene B5 in Cotton Confers High and Broad Resistance to Bacterial Blight and Conditions High Amounts of Sesquiterpenoid Phytoalexins.

Bacterial blight resistance gene B5 has received little attention since it was first described in 1950. A near-isogenic line (NIL) of Gossypium hirsutum cotton, AcB5, was generated in an otherwise bacterial-blight-susceptible 'Acala 44' background. The introgressed locus B5 in AcB5 conferred strong and broad-spectrum resistance to bacterial blight. Segregation patterns of test crosses under Oklahoma field conditions indicated that AcB5 is likely homozygous for resistance at two loci with partial dominance gene action. In controlled-environment conditions, two of the four copies of B5 were required for effective resistance. Contrary to expectations of gene-for-gene theory, AcB5 conferred high resistance toward isogenic strains of Xanthomonas citri subsp. malvacearum carrying cloned avirulence genes avrB4, avrb7, avrBIn, avrB101, and avrB102, respectively, and weaker resistance toward the strain carrying cloned avrb6. The hypothesis that each B gene, in the absence of a polygenic complex, triggers sesquiterpenoid phytoalexin production was tested by measurement of cadalene and lacinilene phytoalexins during resistant responses in five NILs carrying different B genes, four other lines carrying multiple resistance genes, as well as susceptible Ac44E. Phytoalexin production was an obvious, but variable, response in all nine resistant lines. AcB5 accumulated an order of magnitude more of all four phytoalexins than any of the other resistant NILs. Its total levels were comparable to those detected in OK1.2, a highly resistant line that possesses several B genes in a polygenic background.

Pro-Inflammatory Oral Microbiota in Juvenile Spondyloarthritis: A Pilot Study.

The role of the microbiota in the pathogenesis of arthritis is gaining increasing attention. While multiple studies have queried the intestinal microbiota, very few have analyzed the contents of the oral microbiota. In this pilot study, we obtained salivary and sub-gingival specimens from a cohort of six healthy controls and five children with well-controlled spondyloarthritis (SpA) and performed 16S sequencing on bacteria obtained from both habitats. The Quantitative Insight into Microbial Ecology tool suite was used to generate operational taxonomic units, Phyloseq was used for diversity analyses, and DeSeq2 was used to compare abundances while adjusting for multiple comparisons. A repeat specimen was obtained from one subject during a flare. Clustering based upon diagnosis was observed from both habitats, with decreased alpha diversity seen within the plaque obtained from the patients vs. controls. Among the differentially abundant taxa were statistically significantly increased plaque Fusobacterium and salivary Rothia mucilaginosa among the patients compared to the controls. Additionally, the abundance of plaque Fusobacterium increased in one patient at the time of a flare. Our data suggest that the oral cavity may harbor bacteria involved in the pathogenesis of spondyloarthritis; additional studies are warranted.

Hyperthermia and radiation therapy for locally advanced or recurrent breast cancer.

INTRODUCTION: This study aims to report the outcome and toxicity of combined hyperthermia (HT) and radiation therapy (RT) in treatment of locally advanced or loco-regionally recurrent breast cancer. PATIENTS AND METHODS: Patients treated with HT and RT from January 1991 to December 2007 were reviewed. RT doses for previously irradiated patients were > 40 Gy and for RT naïve patients > 60 Gy, at 1.8-2 Gy/day. HT was planned for 2 sessions/week, immediately after RT, for a minimum of 20 min and for > 4 sessions. Superficial or interstitial applicators were used with temperature measured by superficial or interstitial thermistors based on target thickness. HT treatment was assessed by thermal equivalent dose (TED), > 42.5 °C and > 43 °C. Endpoints included treatment response, lack of local progression (local control), and survival. RESULTS: 127 patients received HT and RT to 167 sites. These included the intact breast (24.4%), chest wall/skin (67.7%), and breast/chest wall and nodes (7.9%). At a median follow-up of 13 months (mean 30 ± 38), improved overall survival was significantly associated with increasing RT dose (p < 0.0001), median TED 42.5 °C ≥ 200 min (p = 0.003), and local control (p = 0.0002). Local control at last follow-up was seen in 55.1% of patients. Complete response was significantly associated with median TED 42.5 °C ≥ 200 min (p = 0.002) and median TED 43 °C ≥ 100 min (p = 0.03). CONCLUSION: HT and RT are effective for locally advanced or recurrent breast cancer in patients that have been historically difficult to treat by RT alone. Over 50% of patients achieved control of locoregional disease. Overall survival was improved with local control.

Bolus effects on patient awareness of swallowing difficulty and swallow physiology after chemoradiation for head and neck cancer.

BACKGROUND: Patients treated for head and neck cancer frequently develop dysphagia. Bolus characteristics are altered during fluoroscopic swallowing studies to observe the impact on swallowing function. The purpose of this study was to determine bolus volume and consistency effects on oropharyngeal swallowing physiology and patient awareness of swallowing difficulty. METHODS: Twenty-one patients with head and neck cancer were assessed pre-chemoradiation and post-chemoradiation. The Modified Barium Swallow Study (MBSS) was utilized to examine swallow physiology. Each patient provided perceptual ratings of swallowing difficulty after each swallow of varying bolus types. RESULTS: Oral transit times were significantly longer with pudding boluses. There were trends for higher residue percentages as well as perceptual ratings for pudding and cookie boluses. One correlation between perceptual ratings and physiology was significant. CONCLUSION: Patient awareness of swallowing difficulty and aspects of swallowing physiology vary with bolus consistency. Patient awareness does not correlate with observed changes in swallowing physiology.

Pyramiding B genes in cotton achieves broader but not always higher resistance to bacterial blight.

Near-isogenic lines of upland cotton (Gossypium hirsutum) carrying single, race-specific genes B4, BIn, and b7 for resistance to bacterial blight were used to develop a pyramid of lines with all possible combinations of two and three genes to learn whether the pyramid could achieve broad and high resistance approaching that of L. A. Brinkerhoff's exceptional line Im216. Isogenic strains of Xanthomonas axonopodis pv. malvacearum carrying single avirulence (avr) genes were used to identify plants carrying specific resistance (B) genes. Under field conditions in north-central Oklahoma, pyramid lines exhibited broader resistance to individual races and, consequently, higher resistance to a race mixture. It was predicted that lines carrying two or three B genes would also exhibit higher resistance to race 1, which possesses many avr genes. Although some enhancements were observed, they did not approach the level of resistance of Im216. In a growth chamber, bacterial populations attained by race 1 in and on leaves of the pyramid lines decreased significantly with increasing number of B genes in only one of four experiments. The older lines, Im216 and AcHR, exhibited considerably lower bacterial populations than any of the one-, two-, or three-B-gene lines. A spreading collapse of spray-inoculated AcBIn and AcBInb7 leaves appears to be a defense response (conditioned by BIn) that is out of control.

Changes in swallowing physiology and patient perception of swallowing function following chemoradiation for head and neck cancer.

Patients treated with chemoradiation for head and neck cancer often report difficulty with swallowing and are frequently diagnosed with dysphagia. The extent to which patient awareness of dysphagia corresponds to observed physiologic changes in swallowing is unclear. The purpose of this study was to determine how both patient awareness of swallowing function and swallowing physiology individually change following chemoradiation and then to clarify the relationship between them. Twenty-one patients with head and neck cancer treated with chemoradiation were assessed before and after treatment and matched with twenty-one control subjects. The modified barium swallow test was utilized to examine swallowing physiology. Each subject was also given a series of items regarding awareness of specific dysphagia symptoms. Results showed decreased swallow efficiencies, higher percentages of residue, and more occurrences of penetration and aspiration following chemoradiation. Patients also had significantly higher ratings for 4 of the 12 items ("dry mouth," "food sticking in my mouth," "need water to help food go down," and "change in sense of taste"). Only one strong and significant correlation was found between ratings for "I have difficulty swallowing" and swallow efficiency values. Based on these findings, it appears that patients sense a general difficulty with swallowing but have less awareness of specific symptoms of dysphagia.

Nursing genomics: practice implications every nurse should know.

Twenty-first century nurse clinicians, scientists, and educators must be informed of and become proficient in genetic competencies to provide the best available evidenced-based patient care. This article presents a historical context and basic applications of genetics, along with the attendant legal and ethical issues, to provide a framework for understanding genetics and the genomics applications used in clinical nursing practice. The implications of genomics are relevant to all areas of nursing practice, including risk assessment, education, clinical management, and future research.

Predicting reading comprehension of narrative and expository texts among Hebrew-speaking readers with and without a reading disability.

The aim of this study was to investigate which cognitive and reading-related linguistic skills contribute to reading comprehension of narrative and expository texts. The study examined an Israeli national database of Hebrew-speaking readers in fourth grade, from which a subsample of 190 readers with a reading disability (RD) and 190 readers with no reading disability (NRD) was selected. IQ, text reading, reading comprehension, and various linguistic and cognitive skills were assessed. Structural equation modeling results suggested that both groups rely on lower level processes such as text reading accuracy and orthographic knowledge for reading comprehension of both genres. However, RD readers depend more heavily upon these lower level processes compared with NRD for whom higher level processes contribute more to reading comprehension. The various variables accounted for only 25-34% of reading comprehension variance, and possible explanations are discussed. Taken together, these findings highlight the variety of factors influencing reading comprehension and its multidimensional nature.

Oligonucleotide-based microarray for detection of plant viruses employing sequence-independent amplification of targets.

The potential of DNA microarrays for detection of plant viruses is hampered by underutilization of sequence-independent amplification methods for target nucleic acid enrichment. A microarray system is described for an unbiased detection of plant viruses using both short (30 nt) and long (50 and 70 nt) oligonucleotide probes. The assay involves amplification of target nucleic acid using random primers followed by in vitro transcription whose cRNA product is labeled chemically, fragmented and used as target for hybridization. Initial optimization tests with Turnip vein clearing virus and Cauliflower mosaic virus showed increased hybridization efficiency with shorter cDNA targets (100 bp) and longer probes (50 and 70 nt). The system was validated in pure and mixed samples by detection of three Tymovirus species: Asclepias asymptomatic virus, Kennedya yellow mosaic virus and Turnip yellow mosaic virus. The method could detect sequence variants with 70-75% or higher sequence identity, indicating the possible utility of the approach for virus discovery. Array performance comparison of long probes demonstrated the competence of 50-mers to provide a satisfactory balance between detection sensitivity and specificity. The work described is a significant step towards a method to assess, in one assay, the presence of a large diversity of relatives of known viruses of plants.

Uneven Profiles: Language Minority Learners' Word Reading, Vocabulary, and Reading Comprehension Skills.

English reading comprehension skill development was examined in a group of 87 native Spanish-speakers developing English literacy skills, followed from fourth through fifth grade. Specifically, the effects of Spanish (L1) and English (L2) oral language and word reading skills on reading comprehension were investigated. The participants showed average word reading skills and below average comprehension skills, influenced by low oral language skills. Structural equation modeling confirmed that L2 oral language skills had a large, significant effect on L2 reading comprehension, whereas students' word-level reading skills, whether in L1 or L2, were not significantly related to English reading comprehension in three of four models fitted. The results converge with findings from studies with monolinguals demonstrating the influence of oral language on reading comprehension outcomes, and extend these findings by showing that, for language minority learners, L2 oral language exerts a stronger influence than word reading in models of L2 reading.

The conceptual centrality of causal cycles.

How do causal cycles affect judgments of conceptual centrality? Generally, a feature is central to a concept to the extent that other features in the concept depend on it, thereby rendering it immutable from the concept (Sloman, Love, & Ahn, 1998). Previous research on conceptual centrality has focused primarily on features involved in four major types of dependency structures: simple cause-effect relations, causal chains, common-cause structures, and common-effect structures. Causal cycles are a fifth type of dependency structure commonly reported in people's real-life concepts, yet to date, they have been relatively ignored in research on conceptual centrality. The results of six experiments suggest that previously held assumptions about the conceptual representation of cycles are incorrect. We discuss the implications of these findings for our understanding of theory-based concepts.

Light filtering by epidermal flavonoids during the resistant response of cotton to Xanthomonas protects leaf tissue from light-dependent phytoalexin toxicity.

2,7-Dihydroxycadalene and lacinilene C, sesquiterpenoid phytoalexins that accumulate at infection sites during the hypersensitive resistant response of cotton foliage to Xanthomonas campestris pv. malvacearum, have light-dependent toxicity toward host cells, as well as toward the bacterial pathogen. Adaxial epidermal cells surrounding and sometimes covering infection sites turn red. The red cells exhibited 3-4-fold higher absorption at the photoactivating wavelengths of sunlight than nearby colorless epidermal cells. Red epidermal cells protected underlying palisade mesophyll cells from the toxic effects of 2,7-dihydroxycadalene plus sunlight, indicating a role for epidermal pigments in protecting living cells that surround infection sites from toxic effects of the plant's own phytoalexins. A semi-quantitative survey of UV-absorbing substances extracted from epidermal strips from inoculated and mock-inoculated cotyledons indicated that the principal increase in capacity to absorb the photoactivating wavelengths was due to a red anthocyanin and a yellow flavonol, which were identified as cyanidin-3-O-beta-glucoside and quercetin-3-O-beta-glucoside, respectively.

Evidence for novel viruses by analysis of nucleic acids in virus-like particle fractions from Ambrosia psilostachya.

To test the hypothesis that many viruses remain to be discovered in plants, a procedure was developed to sequence nucleic acids cloned randomly from virus-like particle fractions of plant homogenates. As a test of the efficiency of the procedure we targeted Ambrosia psilostachya, western ragweed, plants growing at the Tallgrass Prairie Preserve of northeastern Oklahoma. Amplifiable nucleic acid was found in the fractions from six of twelve specimens and sequences were characterized from four of them. Evidence was obtained for the presence of viruses belonging to two families (Caulimoviridae, Flexiviridae). Multiple viral species were found in two of the four specimens and their level within the isolated nucleic acid population varied from less than 1-37%. None of the sequences were derived from reported sequences of known viruses. Thus, the analysis of nucleic acid from virus-like particles is a useful tool to expand our knowledge of the universe of viruses to non-cultivated species.

Detection and identification of rhamnogalacturonan lyase activity in intercellular spaces of expanding cotton cotyledons.

Rhamnogalacturonan lyase (RG lyase) activity has been detected and its relative activity measured in vivo during the expansion of cotton (Gossypium hirsutum L.) cotyledons. Rhamnogalacturonan (RG) oligomers labeled with a fluorescent tag were injected into the intercellular spaces of cotton cotyledons and, after incubation, the digested substrate was rinsed out. Enzyme digestion products were detected and identified by capillary zone electrophoresis. Rhamnogalacturonan lyase products were identified as such by co-migration with the digestion products of linear RG oligomers when the oligomers were treated with fungal RG lyase but not when treated with fungal RG hydrolase. In addition, reaction of plant RG lyase digestion products of RG oligomers with I(2)/KI, which selectively removes unsaturated galactopyranosyluronic acid (GaLap) residues formed at the non-reducing end of the oligomer, converted the plant digestion products into RG oligomers that co-migrated with fungal RG hydrolase products. The activity of the enzyme in the intercellular spaces of cotton cotyledons is very low and could be detected most easily when not >0.03 nmol of substrate was injected in a approximately 0.7-cm(2) area and incubated in vivo for 2-6 h. Rhamnogalacturonan lyase activity was the highest in rapidly expanding 3- to 4-day-old cotyledons and gradually decreased during the slow-down in expansion over the next 2-3 days. The RG lyase activity was also detected when the APTS (8-aminopyrene-1,3,6-trisulfonic acid, trisodium salt)-labeled substrates were introduced into intercellular spaces by infiltration instead of injection, indicating that the activity was not induced by wounding or released into the apoplast by cell damage. An exo-RG galacturonohydrolase activity was also found, but RG hydrolase and exo-RG rhamnohydrolase were not detected.

Changes in homogalacturonans and enzymes degrading them during cotton cotyledon expansion.

Changes in homogalacturonans (HGs) and enzymes degrading them have been investigated during cotton (Gossypium hirsutum L.) cotyledon expansion. Using an in vivo assay for pectin-degrading enzymes that involves fluorescent labeled oligomers of GalA as substrate and capillary electrophoresis for product analysis, we found that endo- and exo-polygalacturonases are present in the cotyledon extracellular spaces, and there are dramatic changes in the levels of both activities as the cotyledons change their rate of expansion. Capacity for endo-polygalacturonase activity was highest during the initial stages of cotyledon expansion. However, for exo-polygalacturonase activity it was highest in the later stages of expansion. Cell walls were prepared from 3-, 5-, and 7-day-old cotton cotyledons and treated with liquid HF at -23 degrees C. This treatment cleaves the glycosidic linkages of most neutral sugars in the walls without degrading HGs. HGs with a relatively high degree of esterification can then be solubilized with water, and those with low esterification can be solubilized with concentrated imidazole buffer. The majority of HGs were obtained in the water extracts. The degrees of esterification were 57%, 47%, and 47% in water extracts and 34%, 25%, and 27% in imidazole extracts, in 3-, 5-, and 7-day-old cotton cotyledons, respectively. Using a PA100 ion-exchange column, the members of a GalA homologous series up to approximately 70 residues can be separated. The results from HG molecular length distribution analysis indicated that the HG at 3 days was on average shorter than that in the older cotyledons, perhaps reflecting the higher level of endo-polygalacturonase activity at this stage of more rapid growth.

Analysis of ESTs from multiple Gossypium hirsutum tissues and identification of SSRs.

In an effort to expand the Gossypium hirsutum L. (cotton) expressed sequence tag (EST) database, ESTs representing a variety of tissues and treatments were sequenced. Assembly of these sequences with ESTs already in the EST database (dbEST, GenBank) identified 9675 cotton sequences not present in GenBank. Statistical analysis of a subset of these ESTs identified genes likely differentially expressed in stems, cotyledons, and drought-stressed tissues. Annotation of the differentially expressed cDNAs tentatively identified genes involved in lignin metabolism, starch biosynthesis and stress response, consistent with pathways likely to be active in the tissues under investigation. Simple sequence repeats (SSRs) were identified among these ESTs, and an inexpensive method was developed to screen genomic DNA for the presence of these SSRs. At least 69 SSRs potentially useful in mapping were identified. Selected amplified SSRs were isolated and sequenced. The sequences corresponded to the EST containing the SSRs, confirming that these SSRs will potentially map the gene represented by the EST. The ESTs containing SSRs were annotated to help identify the genes that may be mapped using these markers.

A global assembly of cotton ESTs.

Approximately 185,000 Gossypium EST sequences comprising >94,800,000 nucleotides were amassed from 30 cDNA libraries constructed from a variety of tissues and organs under a range of conditions, including drought stress and pathogen challenges. These libraries were derived from allopolyploid cotton (Gossypium hirsutum; A(T) and D(T) genomes) as well as its two diploid progenitors, Gossypium arboreum (A genome) and Gossypium raimondii (D genome). ESTs were assembled using the Program for Assembling and Viewing ESTs (PAVE), resulting in 22,030 contigs and 29,077 singletons (51,107 unigenes). Further comparisons among the singletons and contigs led to recognition of 33,665 exemplar sequences that represent a nonredundant set of putative Gossypium genes containing partial or full-length coding regions and usually one or two UTRs. The assembly, along with their UniProt BLASTX hits, GO annotation, and Pfam analysis results, are freely accessible as a public resource for cotton genomics. Because ESTs from diploid and allotetraploid Gossypium were combined in a single assembly, we were in many cases able to bioinformatically distinguish duplicated genes in allotetraploid cotton and assign them to either the A or D genome. The assembly and associated information provide a framework for future investigation of cotton functional and evolutionary genomics.

Nutrition and physical activity during and after cancer treatment: an American Cancer Society guide for informed choices.

Cancer survivors are often highly motivated to seek information about food choices, physical activity, dietary supplement use, and complementary nutritional therapies to improve their treatment outcomes, quality of life, and survival. To address these concerns, the American Cancer Society (ACS) convened a group of experts in nutrition, physical activity, and cancer to evaluate the scientific evidence and best clinical practices related to optimal nutrition and physical activity after the diagnosis of cancer. This report summarizes their findings and is intended to present health care providers with the best possible information on which to help cancer survivors and their families make informed choices related to nutrition and physical activity. The report discusses nutrition and physical activity issues during the phases of cancer treatment and recovery, living after recovery from treatment, and living with advanced cancer; selected nutritional and physical activity issues such as body weight, food choices, and complementary and alternative nutritional options; and selected issues related to breast, colorectal, lung, prostate, head and neck, and upper gastrointestinal cancers. In addition, handouts containing commonly asked questions and answers and a resource list are provided for survivors and families. Tables that grade the scientific evidence for benefit versus harm related to nutrition and physical activity for breast, colorectal, lung, and prostate cancers are also included for this growing body of knowledge to provide guidance for informed decision making and to identify areas for future research.

Efficacy of irradiation and external hyperthermia in locally advanced, hormone-refractory or radiation recurrent prostate cancer: a preliminary report.

PURPOSE: To present a preliminary report on the feasibility, efficacy, and toxicity of irradiation (RT) and hyperthermia (HT) in patients with locally advanced, hormone-refractory prostate cancer (LAHRPC) who may or may not have received prior RT. METHODS AND MATERIALS: Between 1997 and 2002, 13 consecutive patients with LAHRPC or RT-recurrent prostate cancer were treated with RT and HT on a Phase I-II protocol. Eight patients had RT-recurrent LAHRPC (Group A) and 5 had LAHRPC without prior RT (Group B). All patients had large and clinically symptomatic tumors. The median RT dose was 39.6 Gy and 66.6 Gy in Groups A and B, respectively. External deep HT was delivered using a BSD-2000 Sigma-60 applicator. The median number of HT treatments was 8 in group A and 10 in group B. RESULTS: The median follow-up was 14 and 13 months for Groups A and B, respectively. All patients achieved a complete or partial response (CR/PR) and complete palliation of symptoms. Eleven patients had follow-up CT scans that demonstrated a CR in six and a PR in five. Two patients, who died of metastasis, did not have CT scans and had a PR on digital rectal examination. Two patients demonstrated a biochemical CR. The median duration of the CR/PR among Group A patients was 12 months after therapy. Three patients in Group A developed tumor recurrence at 9, 17, and 27 months after repeat RT to doses of 39.6, 36, and 50 Gy, respectively. At last follow-up, no Group B patient developed local recurrence. Grade 1-2 rectal bleeding was noted in 3 patients. RT and HT were generally well tolerated by all patients who had not previously undergone RT. Of the 8 patients who had, 6 (75%) tolerated retreatment well with minimal or no complications. Two patients in the repeat RT group had severe complications. One patient with lymphoma and factor XI deficiency developed Grade 4 hemorrhagic cystitis. Another previously irradiated patient developed a rectovesical fistula 4 months after retreatment, after disappearance of a large, invasive, and necrotic tumor. CONCLUSION: This preliminary report demonstrates the feasibility and efficacy of RT and HT in patients with LAHRPC, who may or may not have received prior RT. Presently, such patients who have undergone previous RT have no effective treatment options. RT and HT were generally well tolerated by patients who were not previously undergone RT. Of those who had been, most (6 of 8) tolerated retreatment well with minimal or no complications. The high-risk factors for treatment- and tumor regression-related side effects include the presence of large necrotic tumors, previous RT with a large dose/fraction, and the presence of bleeding disorders. Despite the size of these large tumors, RT and HT resulted in significant tumor shrinkage, rapid serum prostate-specific antigen decline, durable treatment responses, and durable palliation of symptoms. Additional clinical studies are warranted.

A Technique for Precise Inoculation of the Internal Phyllosphere of Cotton with Xanthomonas campestris pv. malvacearum.

ABSTRACT A technique was developed to inoculate uniformly and gently the internal phyllosphere from the upper surface of cotton leaves with the phytopathogenic bacterium Xanthomonas campestris pv. malvacearum. The inoculum consisted of 2 to 3 x 10(7) CFU/ml in CaCO(3)-saturated sterile distilled water containing 0.02%, vol/vol, of the wetting agent Silwet L-77. A custom-made inoculation apparatus was employed to immerse a circular area of the adaxial surface of a leaf in inoculum for 90 s. This resulted in uniform, passive entry of bacteria into the substomatal chambers, producing an endophytic bacterial population of 2 x 10(4) CFU/cm(2). Microscopic signs of infection were visible 48 to 72 h after inoculation. In susceptible leaves, uniformly distributed water-soaked spots were observed 7 to 8 days after inoculation. When the technique was used on resistant leaves, the autofluorescence that is characteristic of hypersensitively necrotic cells developed in the guard cells and palisade cells lining substomatal chambers, but not in the underlying spongy mesophyll.