The Amaranth Genome: Genome, Transcriptome, and Physical Map Assembly.

Amaranth ( L.) is an emerging pseudocereal native to the New World that has garnered increased attention in recent years because of its nutritional quality, in particular its seed protein and more specifically its high levels of the essential amino acid lysine. It belongs to the Amaranthaceae family, is an ancient paleopolyploid that shows disomic inheritance (2 = 32), and has an estimated genome size of 466 Mb. Here we present a high-quality draft genome sequence of the grain amaranth. The genome assembly consisted of 377 Mb in 3518 scaffolds with an N of 371 kb. Repetitive element analysis predicted that 48% of the genome is comprised of repeat sequences, of which -like elements were the most commonly classified retrotransposon. A de novo transcriptome consisting of 66,370 contigs was assembled from eight different amaranth tissue and abiotic stress libraries. Annotation of the genome identified 23,059 protein-coding genes. Seven grain amaranths (, , and ) and their putative progenitor () were resequenced. A single nucleotide polymorphism (SNP) phylogeny supported the classification of as the progenitor species of the grain amaranths. Lastly, we generated a de novo physical map for using the BioNano Genomics' Genome Mapping platform. The physical map spanned 340 Mb and a hybrid assembly using the BioNano physical maps nearly doubled the N of the assembly to 697 kb. Moreover, we analyzed synteny between amaranth and sugar beet ( L.) and estimated, using analysis, the age of the most recent polyploidization event in amaranth.

Construction of black (Rubus occidentalis) and red (R. idaeus) raspberry linkage maps and their comparison to the genomes of strawberry, apple, and peach.

The genus Rubus belongs to the Rosaceae and is comprised of 600-800 species distributed world-wide. To date, genetic maps of the genus consist largely of non-transferable markers such as amplified fragment length polymorphisms. An F(1) population developed from a cross between an advanced breeding selection of Rubus occidentalis (96395S1) and R. idaeus 'Latham' was used to construct a new genetic map consisting of DNA sequence-based markers. The genetic linkage maps presented here are constructed of 131 markers on at least one of the two parental maps. The majority of the markers are orthologous, including 14 Rosaceae conserved orthologous set markers, and 60 new gene-based markers developed for raspberry. Thirty-four published raspberry simple sequence repeat markers were used to align the new maps to published raspberry maps. The 96395S1 genetic map consists of six linkage groups (LG) and covers 309 cM with an average of 10 cM between markers; the 'Latham' genetic map consists of seven LG and covers 561 cM with an average of 5 cM between markers. We used BLAST analysis to align the orthologous sequences used to design primer pairs for Rubus genetic mapping with the genome sequences of Fragaria vesca 'Hawaii 4', Malus × domestica 'Golden Delicious', and Prunus 'Lovell'. The alignment of the orthologous markers designed here suggests that the genomes of Rubus and Fragaria have a high degree of synteny and that synteny decreases with phylogenetic distance. Our results give unprecedented insights into the genome evolution of raspberry from the putative ancestral genome of the single ancestor common to Rosaceae.

Characterization of Salt Overly Sensitive 1 (SOS1) gene homoeologs in quinoa (Chenopodium quinoa Willd.).

Salt tolerance is an agronomically important trait that affects plant species around the globe. The Salt Overly Sensitive 1 (SOS1) gene encodes a plasma membrane Na+/H+ antiporter that plays an important role in germination and growth of plants in saline environments. Quinoa (Chenopodium quinoa Willd.) is a halophytic, allotetraploid grain crop of the family Amaranthaceae with impressive nutritional content and an increasing worldwide market. Many quinoa varieties have considerable salt tolerance, and research suggests quinoa may utilize novel mechanisms to confer salt tolerance. Here we report the cloning and characterization of two homoeologous SOS1 loci (cqSOS1A and cqSOS1B) from C. quinoa, including full-length cDNA sequences, genomic sequences, relative expression levels, fluorescent in situ hybridization (FISH) analysis, and a phylogenetic analysis of SOS1 genes from 13 plant taxa. The cqSOS1A and cqSOS1B genes each span 23 exons spread over 3477 bp and 3486 bp of coding sequence, respectively. These sequences share a high level of similarity with SOS1 homologs of other species and contain two conserved domains, a Nhap cation-antiporter domain and a cyclic-nucleotide binding domain. Genomic sequence analysis of two BAC clones (98 357 bp and 132 770 bp) containing the homoeologous SOS1 genes suggests possible conservation of synteny across the C. quinoa sub-genomes. This report represents the first molecular characterization of salt-tolerance genes in a halophytic species in the Amaranthaceae as well as the first comparative analysis of coding and non-coding DNA sequences of the two homoeologous genomes of C. quinoa.

Analyses of a multi-parent population derived from two diverse alfalfa germplasms: testcross evaluations and phenotype-DNA associations.

In a previous study, we showed that the genetic variation present in the Medicago sativa subsp. sativa Peruvian and M. sativa subsp. falcata WISFAL germplasms could be used to improve forage yields when favorable alleles were recombined and used in hybrid combination with cultivated alfalfa. In this paper, we present testcross forage yield and fall growth data for two seasons of a C0 population generated after intermating the Peruvian x WISFAL population for several generations. In addition, we conducted marker-trait association analysis as an attempt to identify Peruvian and WISFAL genomics regions affecting the targeted traits. Five and seven genomic regions were found significantly associated with forage yield and fall growth, respectively. In the case of fall growth, alleles from both accessions were positively associated with plant height. However, more alleles from WISFAL were positively associated with forage yield than from Peruvian. WISFAL is known for its winter hardiness and genomic regions with large effects on winter survival may have masked the effect of forage yield from Peruvian. The fact that most of the genomic regions discovered in this study have been previously associated with traits involved in winter hardiness validates our findings and suggests that associations between DNA fragments and agronomic traits can be detected without the necessity of developing bi-parental mapping populations.

Use of the recto-sigmoid index to diagnose Hirschsprung's disease.

The recto-sigmoid index on barium enema may aid in the diagnosis of Hirschsprung's disease. However, data on its reliability in different age groups are sparse. The recto-sigmoid index and transitional zone were evaluated blindly in 107 patients with diagnostic rectal suction biopsies. Patients were divided into 3 groups: neonates, infants older than 1 month, and children. The recto-sigmoid index and transitional zone agreed with the histopathologic diagnosis in 79% and 87% of the cases, respectively. Their negative predictive values reached clinical significance in infants and children but not in neonates. Their positive predictive values were not significant in any age group. The recto-sigmoid index identified 4 patients with recto-sigmoid Hirschsprung's disease whose diagnosis was missed by evaluating the transitional zone alone.

Nutrition support for pediatric patients with inflammatory bowel disease: a clinical report of the North American Society for Pediatric Gastroenterology, Hepatology And Nutrition.

Impairment of growth and malnutrition are significant complications of inflammatory bowel disease (IBD) in pediatric patients. Since this topic was last reviewed in these pages (), a number of studies have further explored the epidemiology and pathogenesis of these nutritional complications of IBD in an effort to provide more effective interventions to prevent the long-term consequences of chronic nutrient deficiencies in childhood. In addition, during the past 15 years, the use of selected nutrients and microorganisms (probiotics) as primary or adjunctive therapy for the treatment of IBD has become an emerging area of great interest. The following is a Clinical Report from the Nutrition and Inflammatory Bowel Disease Committees of the North American Society for Pediatric Gastroenterology, Hepatology and Nutrition.

Use of infliximab in pediatric patients with inflammatory bowel disease.

BACKGROUND: The concentration of tumor necrosis factor, a proinflammatory cytokine, is increased in the gastrointestinal mucosa of patents with active Crohn's disease (CD) and ulcerative colitis (UC). Neutralization of tumor necrosis factor decreases the mucosal inflammatory response of adults with CD. Little information is available on the use of monoclonal antibody to tumor necrosis factor (infliximab) in children and adolescents with CD or UC. OBJECTIVE: To evaluate the clinical response and side effects of patients to infliximab. METHODS: A retrospective review of data regarding 18 pediatric and adolescent patients with active CD (n = 15) and UC (n = 3) poorly controlled with conventional therapy. All patients received one to six intravenous infusions of infliximab 5 mg/kg, while receiving their usual medications. RESULTS: All patients experienced clinical improvement, including decrease in the frequency of stooling and resolution of extraintestinal symptoms such as arthropathy, malaise, and skin manifestations after treatment with infliximab. All but one patient had a documented decrease in the erythrocyte sedimentation rate. Prednisone dosage was tapered in all but two patients, and discontinued in seven patients. Intravenous infusion of infliximab was well tolerated. One patient developed a rash several days after the infusion. A patient who received six infliximab infusions developed recurrent Staphylococcus aureus infections, as well as septic arthritis and chronic osteomyelitis during the follow-up period, raising the issue of the long-term safety of infliximab. CONCLUSIONS: Treatment of our patients with refractory CD and UC with infliximab was associated with remarkable clinical improvement. Although the drug may have an important role in their management, further assessment of long-term safety and efficacy is needed.

Scaling VO(2) peak in obese and non-obese girls.

OBJECTIVE: The conventional ratio method (milliliters O(2) per mass) typically is used to express VO(2) peak. The goal of the current study was to compare VO(2) peak of obese girls with normal-weight girls by ratio and allometric scaling methods. RESEARCH METHODS AND PROCEDURES: We compared VO(2) peak by ratio and allometric methods in 46 obese and 47 normal-weight girls. Indirect calorimetry was used to measure VO(2) peak during either treadmill running or walking. Regression analysis was used to determine coefficients for mass and stature for each group with ANOVA used to compare data between groups. RESULTS: The obese girls were taller and had higher values of body fatness (p < or = 0.05). Absolute VO(2) peak (liters per minute) was similar between groups; however VO(2) peak relative to mass was 50% lower (p < or = 0.05) in the obese girls. When VO(2) peak (milliliters per minute per kilogram) and mass were correlated, r = -0.48 was found in the obese group. Allometric scaling of logarithmic transformed stature and mass reduced this to r = -0.002, thus eliminating the bias associated with the ratio method. Adjusting VO(2) peak allometrically scaled for mass, stature, and the combination of mass and stature reduced the difference between groups from 50% (ratio method) to 10% to 11% (p < or = 0.05) with higher values found in the normal-weight girls. DISCUSSION: These results demonstrate the bias associated with the ratio method when comparing VO(2) peak in obese girls with VO(2) peak in normal-weight girls. Allometric scaling eliminated the bias and thus may reflect a truer comparative response.

Gastroesophageal reflux and pediatric otolaryngologic disease: the role of antireflux surgery.

OBJECTIVE: To determine the role of antireflux surgery in the treatment of gastroesophageal reflux-induced otolaryngologic disease (GEROD). DESIGN: A retrospective medical record analysis was performed. Patient demographics, otolaryngologic disease secondary to gastroesophageal reflux (GER), method of GER diagnosis, medical treatment used before antireflux surgery, and response to surgical intervention were considered. SETTING: Tertiary care children's hospital. PATIENTS: Among patients undergoing antireflux surgery between January 1, 1996, and December 31, 1999, children with GEROD were included in the study. INTERVENTIONS: Children with GEROD who failed medical therapy underwent antireflux surgery. MAIN OUTCOME MEASURES: The demographics of patients requiring antireflux surgery for treatment of their otolaryngologic disease and their clinical response to surgery were reviewed. RESULTS: Fourteen (17%) of 82 children, ranging in age from 48 days to 3 years (mean age, 9.7 months), who underwent antireflux surgery for GER at our institution between 1996 and 1999 were diagnosed as having GEROD. Twelve (86%) of the 14 patients were found to have upper airway abnormalities, including subglottic edema, fixed subglottic stenosis, reflex apnea, and recurrent croup. Two patients (14%) had severe chronic sinusitis and otitis media. Nine (64%) of the 14 had normal neurologic function for their age vs 5 (36%) who had neurologic impairment. After antireflux surgery, all 14 patients with GEROD had complete resolution of clinical symptoms. CONCLUSIONS: Gastroesophageal reflux has an important role in the cause of numerous otolaryngologic disorders. Although medical management should remain the mainstay of GER therapy, antireflux surgery provided definitive and successful treatment of potentially life-threatening manifestations of GEROD.

Weight loss and growth velocity in obese children after very low calorie diet, exercise, and behavior modification.

UNLABELLED: The prevalence of obesity in American youth is increasing and treatment of the condition is difficult. We have developed a multi-disciplinary weight reduction program that extends over 1 y and includes a very low-calorie diet (VLCD) followed by a hypocaloric diet, exercise, and behavior modification. Based on data collected at baseline, at the end of the acute intervention phase (10-20 wk), and at 1-y evaluation, we assessed the efficacy of this outpatient weight reduction program in treating obese children and adolescents in a follow-up of a series of cases. Furthermore, we examined the impact of the approach on growth velocity and maintenance of weight loss at 1 y. Fifty-six overweight children (aged 7-17 y) were recruited during a period of 18 mo to participate in the weight management program; 52 (93%) completed the acute phase of treatment and 35 (62.5%) successfully completed the 1-y program. There was a significant decrease in body weight and body fat, as assessed by weight determinations and skinfold measurements (p <0.0001; results not corrected for age). The body mass index for the 35 individuals who completed the 1-y program decreased significantly from 32.7 on entry to 28.72 at 1 y (p < 0.0001; results not corrected for age). CONCLUSION: We conclude that a multidisciplinary weight reduction program that combines a VLCD, followed by a balanced hypocaloric diet, with a moderate-intensity progressive exercise program and behavior modification is an effective means for weight reduction in obese children and adolescents.

Impact of significant weight loss on maximal oxygen uptake in obese children and adolescents.

BACKGROUND: The prevalence of pediatric obesity has increased over the past few decades in all ethnic, gender, and age groups. The treatment of obesity, especially in children with moderate to severe conditions, is difficult. In this study, we examined the impact of significant weight loss as a result of participation in a multi-disciplinary weight management program on maximal oxygen uptake (VO2max) in obese children and adolescents. METHODS: Eleven obese children and adolescents (7 to 14 years of age; mean age, 12.3 +/- 1.9 years) were enrolled in a weight management program at the Children's Hospital of New Orleans. The treatment program included a high-protein, very low-calorie diet (VLCD; protein intake, 1.5 to 2.0 g/kg of ideal body weight per day; and 800 kcal/d). Diets were supplemented with extra fluid, minerals, and vitamins. All subjects attended weekly 2-hour clinic sessions. During these sessions, they received nutrition instruction, participated in a moderate-intensity, progressive exercise program, and learned behavior-modification techniques. Weight, height, body mass index ([BMI]; wt/ht2), and VO2max by indirect calorimetry were obtained at enrollment and at the end of 10 weeks of treatment. RESULTS: There was a significant decrease in body weight after 10 weeks. The BMI decreased significantly from 34.1 +/- 4.8 on entry to 29.4 +/- 3.5 (mean +/- SD; P < 0.0001). Despite the significant weight loss, VO2max increased significantly (P < 0.001) from entry (19.2 +/- 3.0 mL/kg/min) to completion of 10 weeks (22.4 +/- 5.8 mL/kg/min). However, absolute VO2max L/min was unchanged. CONCLUSIONS: We conclude that relative VO2max mL/kg/min is significantly improved in obese youth after significant weight loss with a VLCD and moderate-intensity, progressive exercise. However, because absolute VO2max L/min was unchanged, this improvement seems to result from the reduction in total body weight as opposed to the effect of the moderate-intensity exercise intervention.

Zinc, copper, and metallothionein metabolism after jejunoileal bypass surgery or small bowel resection in rats.

Liver dysfunction is a frequent complication of jejunoileal bypass (JIB) surgery, a procedure commonly used until recently to treat morbid obesity. It has been suggested that liver failure in JIB patients is due to bacterial overgrowth and translocation from the bypassed intestine. Because invading microorganisms cause hepatic inflammation these experiments evaluated zinc, copper, and metallothionein (MT) in two experimental rat models of intestinal surgery to determine whether their distribution in plasma and tissues was similar to the highly characteristic pattern observed during an inflammatory response. In the JIB rat model 90 per cent of the small intestine was isolated from the flow of digesta but remained viable in the abdominal cavity. In the small bowel resection (SBR) model 90 per cent of the small intestine was removed and the remaining intestine was resected. Data collected 21 days after surgery showed decreased growth rate and plasma zinc in the SBR and JIB rats that was significantly improved by supplemental zinc. All other measures of zinc, copper, and MT metabolism in the SBR rats were similar to those of controls. In JIB rats, however, liver copper, MT protein, and MT mRNA were significantly elevated, and a high proportion of the intracellular zinc and copper was associated with MT. The pattern of zinc, copper, and MT distribution in systemic circulation and liver of JIB rats suggests hepatic inflammation superimposed on low zinc and copper status. Lack of a similar response in the SBR rats confirms the involvement of the bypassed intestinal segment and supports the hypothesis that bacterial overgrowth and translocation are responsible for liver inflammation and dysfunction in JIB patients.

Safety, feasibility, and efficacy of a resistance training program in preadolescent obese children.

BACKGROUND: Safe and effective exercise programs are needed to prevent and treat chronic diseases in childhood. In particular, preadolescent obese children should participate in activities that are specific to their special needs. Resistance or strength training has been prescribed for adult obese persons. Research is limited concerning the use of resistance training in programs that treat obese preadolescents. METHODS: Nineteen treatment subjects (7-12 years of age) were enrolled in a 10-week weight management program which included diet, behavior modification, and aerobic and flexibility exercises. Forty-eight control subjects (7-12 years of age) participated in the diet, behavior modification program, and a thrice-a-week walking program. The efficacy of the overall weight management program was examined by anthropometry at 10 weeks and 1 year. RESULTS: Fifteen treatment subjects completed the 10-week program (retention rate, 78.9%). Thereafter compliance decreased by approximately 33% for the long-term study. Seventeen control subjects completed the program (retention rate, 35%). Weight, percent of ideal body weight, and body mass index were reduced significantly at 10 weeks (P<0.0001) and did not increase significantly at 1-year follow-up in both treatment and control groups. Height increased significantly at 1 year in both treatment and control subjects. In the treatment subjects, percent fat decreased significantly (P<0.001), whereas fat-free mass did not change significantly (P>0.05). CONCLUSIONS: A resistance-training program may be included safely in a multidisciplinary weight management program for obese preadolescent male and female children. The addition of specific exercise regimes such as resistance training may improve program retention especially in severely obese youth.

Lipid profiles of obese children and adolescents before and after significant weight loss: differences according to sex.

BACKGROUND: Childhood obesity has been associated with elevated serum levels of total cholesterol, triglycerides, and low-density lipoproteins (LDLs). We observed the lipid profiles of obese female subjects versus obese male subjects before and after significant weight loss. METHODS: We studied 29 girls and 21 boys enrolled in a multidisciplinary weight reduction program. RESULTS: Measures were taken at enrollment and at 10 weeks. Significant improvements were observed for changes in percentage of ideal body weight and total cholesterol and triglyceride levels. In addition, LDL decreased significantly in girls but not in boys. CONCLUSIONS: A combination of diet, behavior modification, and exercise, is an effective instrument for lowering total cholesterol and triglyceride levels in obese children. In addition, girls tend to be more susceptible to a decrease in LDL level, which might result in an increased cardiovascular protective effect.

Detection of interferon regulatory factor-1 in lamina propria mononuclear cells in Crohn's disease.

BACKGROUND: The transcription factor, interferon regulatory factor (IRF)-1, is stimulated by interferon-gamma and regulates the expression of several genes implicated in the pathogenesis of inflammatory bowel disease, including interleukin-6, major histocompatibility complex class II molecules, and inducible nitric oxide synthase. Interferon regulatory factor-1 also stimulates naive CD4+ T-cells to differentiate into T-helper-1 cells, the T-cell subset that appears to be upregulated in Crohn's disease. The purpose of this study was to examine the expression of IRF-1 in the nuclei of lamina propria mononuclear cells in situ in colonoscopic biopsy specimens from pediatric patients with Crohn's disease, in patients with ulcerative colitis, and in control patients with no histopathologic abnormalities. METHODS: Archival paraffin-embedded tissue sections were obtained from 25 pediatric patients with Crohn's disease, 6 patients with ulcerative colitis, and 12 control patients who had undergone colonoscopy. Tissue sections were stained with polyclonal rabbit anti-human antisera to IRF-1 and horseradish-peroxidase-conjugated, biotinylated, goat anti-rabbit secondary antibody. Slides were scored and scores compared among patient groups using analysis of variance. RESULTS: Patients with Crohn's disease had significantly higher IRF-1 scores (95% confidence interval [CI], 1.70-2.04) than patients with ulcerative colitis (95% CI, 0.92-1.23) or control subjects (95% CI, 1.11-1.52). CONCLUSIONS: Increased expression of IRF-1 in lamina propria mononuclear cells from patients with Crohn's disease may be relevant to the pathogenesis of Crohn's disease.

Recent advances in the treatment of childhood obesity.

The rapid increase in the prevalence of obesity in the last decade indicates a need for effective treatment programs. We conducted a short-term, repeated-measures, clinical-outcome trial in three groups of children and adolescents in two different locations. Two cohorts (n=34) were enrolled in a 36-wk multi-disciplinary weight-management program at the Children's Hospital of New Orleans. One cohort (n=16) was enrolled in a similar intervention at the General Clinical Research Center (GCRC) at the Medical Center of Louisiana for a 10-wk summer weight-loss program. Subjects were offered a protein-sparing modified fast (PSMF) diet (600-800 kcal/d; 2 g protein/kg body weight), followed by a balanced hypocaloric diet, and they participated in behavior-modification sessions and a moderate-intensity (45-55% volume of oxygen consumed at maximal effort [VO(2)max]), progressive exercise program. The following parameters were examined at baseline, 10 wk, and 36 wk (cohort 1 only): Weight, height, percentage of ideal body weight (%IBW), relative body fat (%fat), fat free body (FFB) mass, estimated VO(2)max mL/kg min(BW) [adjusted for body weight]), blood chemistries, lipid profiles (total cholesterol [TC], triglycerides [TG], low-density lipoprotein [LDL], high-density lipoprotein [HDL], and insulin-like growth factor-1 [IGF-1]). All three groups experienced significant decreases in weight, %IBW and %fat at 10 wk. The weight loss was maintained at 26 wk in cohorts 1 and 2, and at 36 wk in cohort 1. There were no significant decreases in height velocity during the study. In addition, measures of estimated VO(2)max mL/kg/min(BW) and IGF-1 parameters were significantly greater at 10 wk compared to baseline. Measures of TC, TG, and LDL were significantly lower at 10 wk, with no significant changes noted in HDL. We conclude that a multi-disciplinary weight-management program, including PSMF, behavior modification, and exercise, provides an effective method of treatment for obesity in children and adolescents. Long-term, randomized, and controlled clinical trials are needed to confirm the results of this preliminary, short-term observation.

Cow's milk versus formula in older infants: consequences for human nutrition.

Human milk is the preferred feeding for all infants, including premature and sick newborns, with rare exceptions. However, modern technology has produced alternative, "humanized formulae", which closely mimic the composition of human milk. The ingestion of human milk, "humanized formulae" or whole cow's milk has consequences for human nutrition. Gastroesophageal reflux, iron deficiency, calcium and sodium excesses or deficiencies may be influenced by the type and amount of milk fed to the infant. Likewise, neurological development and the likelihood of developing diabetes or cancer may also be influenced by early dietary practices. Until new information is available, we should continue to pattern formulae for older infants after breast milk, but with sufficient protein, calories, lipid and minerals to support optimal growth.

Inclusion of resistance exercise in a multidisciplinary outpatient treatment program for preadolescent obese children.

BACKGROUND: Safe and effective exercise programs are needed to prevent and treat chronic diseases in childhood. In particular, preadolescent obese children should participate in activities that are specific to their special needs. METHODS: We included a moderate intensity, progressive resistance training program in a multidisciplinary weight management program for obese preadolescent children. The program included diet, behavior modification, and aerobic and flexibility exercises. RESULTS: The subjects reported no accidents or injuries and 100% compliance with the minimum required exercise prescription. Weight, percent ideal body weight, body mass index, and percent fat were reduced significantly at 10 weeks and did not increase significantly at 1 year follow-up. Height and lean body mass increased significantly at 1 year. CONCLUSION: A resistance training program may be safely included in a multidisciplinary weight management program for obese preadolescent children.