Microbe associated molecular patterns from rhizosphere bacteria trigger germination and Papaver somniferum metabolism under greenhouse conditions.

Ten PGPR from different backgrounds were assayed on Papaver somniferum var. Madrigal to evaluate their potential as biotic elicitors to increase alkaloid content under the rationale that some microbe associated molecular patterns (MAMPs) are able to trigger plant metabolism. First, the 10 strains and their culture media at two different concentrations were tested for their ability to trigger seed germination. Then, the best three strains were tested for their ability to increase seedling growth and alkaloid levels under greenhouse conditions. Only three strains and their culture media enhanced germination. Then, germination enhancing capacity of these best three strains, N5.18 Stenotrophomonas maltophilia, Aur9 Chryseobacterium balustinum and N21.4 Pseudomonas fluorescens was evaluated in soil. Finally, the three strains were applied on seedlings at two time points, by soil drench or by foliar spray. Photosynthesis was measured, plant height was recorded, capsules were weighted and alkaloids analyzed by HPLC. Only N5.18 delivered by foliar spray significantly increased plant height coupled to an increase in total alkaloids and a significant increase in opium poppy straw dry weight; these increases were supported by a better photosynthetic efficiency. The relative contents of morphine, thebaine, codeine and oripavine were affected by this treatment causing a significant increase in morphine coupled to a decrease in thebaine, demonstrating the effectivity of MAMPs from N5.18 in this plant species. Considering the increase in capsule biomass and alkaloids together with the acceleration of germination, strain N5.18 appears as a good candidate to elicit plant metabolism and consequently, to increase productivity of Papaver somniferum.

Bacterial siderophores efficiently provide iron to iron-starved tomato plants in hydroponics culture.

Iron is one of the essential elements for a proper plant development. Providing plants with an accessible form of iron is crucial when it is scant or unavailable in soils. Chemical chelates are the only current alternative and are highly stable in soils, therefore, posing a threat to drinking water. The aim of this investigation was to quantify siderophores produced by two bacterial strains and to determine if these bacterial siderophores would palliate chlorotic symptoms of iron-starved tomato plants. For this purpose, siderophore production in MM9 medium by two selected bacterial strains was quantified, and the best was used for biological assay. Bacterial culture media free of bacteria (S) and with bacterial cells (BS), both supplemented with Fe were delivered to 12-week-old plants grown under iron starvation in hydroponic conditions; controls with full Hoagland solution, iron-free Hoagland solution and water were also conducted. Treatments were applied twice along the experiment, with a week in between. At harvest, plant yield, chlorophyll content and nutritional status in leaves were measured. Both the bacterial siderophore treatments significantly increased plant yield, chlorophyll and iron content over the positive controls with full Hoagland solution, indicating that siderophores are effective in providing Fe to the plant, either with or without the presence of bacteria. In summary, siderophores from strain Chryseobacterium C138 are effective in supplying Fe to iron-starved tomato plants by the roots, either with or without the presence of bacteria. Based on the amount of siderophores produced, an effective and economically feasible organic Fe chelator could be developed.

Structural and functional study in the rhizosphere of Oryza sativa L. plants growing under biotic and abiotic stress.

AIMS: A structural and functional study has been carried out in the rice production area of the Guadalquivir marshes in southern Spain aiming to increase knowledge of rice rhizosphere structure and function for further application on integrated management practices. METHODS AND RESULTS: Rhizosphere bacterial structure (analysis of 16S rRNA partial sequences from total soil DNA), metabolic diversity (analysed by Biolog FF for fungal community and GN for microbial community) and a screening for putative plant growth-promoting rhizobacteria (PGPR) to identify potential isolates for development of local biofertilizers, and biodiversity of culturable micro-organisms (analysis of 16S rRNA partial sequences) from four areas differing in salinity and Magnaporthe oryzae incidence in two moments of the crop cycle were studied. Results indicate that the dominant taxon in libraries from the four areas was Proteobacteria. Metabolic diversity was higher in areas affected only by salinity or incidence of Magnaporthe than in the control or area affected by both stresses. It seems that rice plants selected, in their rhizosphere, micro-organisms able to affect plant hormonal balance under all conditions, and this activity relied in different bacterial genera depending on the environmental stress. CONCLUSIONS: Bacterial genera for each stress, as well as generalist strains, were found present in all the studied areas. Potential molecular markers and taxonomic markers (Sphingobacteria for salt and Thermococci for Magnaporthe) of the different stress situations have been highlighted, and Class Verrucomicrobiae could be a marker for nonstressed areas. In addition, putative PGPR strains isolated in this study could be used as biofertilizers. SIGNIFICANCE AND IMPACT OF THE STUDY: Rice paddies are great ecologically important ecosystems. The results are very relevant as they may be included in the process of rice production, improving crop conditions with less environmental impact.

Russell-Silver syndrome due to paternal H19/IGF2 hypomethylation in a patient conceived using intracytoplasmic sperm injection.

Epigenetic alterations at several maternal loci have been associated with imprinting disorders in children conceived using assisted reproductive technologies. To date, epimutations at paternal loci have been observed in the spermatozoa of infertile men, but there is little evidence of paternal epimutations in babies conceived using assisted reproductive treatment. This is a report of a female infant with classic Russell-Silver Syndrome (RSS) who was conceived using intracytoplasmic injection of spermatozoa obtained from testicular aspiration. Methylation studies revealed hypomethylation of the paternally derived H19/IGF2 locus. As far as is known, this is the second assisted reproduction treatment-conceived patient with classic RSS and this epigenotype. This case provides further evidence that epimutations affecting paternal alleles might be associated with assisted reproductive treatment.

Silencing of CDKN1C (p57KIP2) is associated with hypomethylation at KvDMR1 in Beckwith-Wiedemann syndrome.

CONTEXT: Beckwith-Wiedemann syndrome (BWS) arises by several genetic and epigenetic mechanisms affecting the balance of imprinted gene expression in chromosome 11p15.5. The most frequent alteration associated with BWS is the absence of methylation at the maternal allele of KvDMR1, an intronic CpG island within the KCNQ1 gene. Targeted deletion of KvDMR1 suggests that this locus is an imprinting control region (ICR) that regulates multiple genes in 11p15.5. Cell culture based enhancer blocking assays indicate that KvDMR1 may function as a methylation modulated chromatin insulator and/or silencer. OBJECTIVE: To determine the potential consequence of loss of methylation (LOM) at KvDMR1 in the development of BWS. METHODS: The steady state levels of CDKN1C gene expression in fibroblast cells from normal individuals, and from persons with BWS who have LOM at KvDMR1, was determined by both real time quantitative polymerase chain reaction (qPCR) and ribonuclease protection assay (RPA). Methylation of the CDKN1C promoter region was assessed by Southern hybridisation using a methylation sensitive restriction endonuclease. RESULTS: Both qPCR and RPA clearly demonstrated a marked decrease (86-93%) in the expression level of the CDKN1C gene in cells derived from patients with BWS, who had LOM at KvDMR1. Southern analysis indicated that downregulation of CDKN1C in these patients was not associated with hypermethylation at the presumptive CDKN1C promoter. CONCLUSIONS: An epimutation at KvDMR1, the absence of maternal methylation, causes the aberrant silencing of CDKN1C, some 180 kb away on the maternal chromosome. Similar to mutations at this locus, this silencing may give rise to BWS.

Clinical spectrum of Denys-Drash and Frasier syndrome.

Denys-Drash syndrome (DDS) and Frasier syndrome (FS) are two related conditions caused by mutations of the Wilms tumor gene, WT1. Both syndromes are characterized by male pseudohermaphroditism, a progressive glomerulopathy, and the development of genitourinary tumors. DDS and FS have previously been distinguished by differences in nephropathy, with DDS patients demonstrating diffuse mesangial sclerosis (DMS) in contrast to focal and segmental glomerulosclerosis (FSGS) in FS patients. The clinicopathological features and genotype analysis of two patients with WT1 mutations are presented in this report. Genotype analysis of the first patient revealed a previously undescribed mutation in exon 8 of the WT1 gene. The second patient presented with a rapidly progressive nephropathy characterized histologically by DMS, but was found to have the genetic mutation seen in FS patients. A summary of all reported patients with the characteristic mutation associated with FS demonstrates the clinical overlap of this syndrome with DDS. This suggests that both these conditions should be considered as part of the spectrum of disease due to WT1 gene mutations rather than as separate diseases. Clinical classification remains important for prognosis, as the underlying renal disease appears to predict the progression of nephropathy independently of the genetic abnormality.

Overexpression of murine WT1 + / + and - / - isoforms has no effect on chemoresistance but delays differentiation in the K562 leukemia cell line.

The Wilms' tumor gene (WT1) encodes a zinc-finger transcription factor that is expressed as four distinct isoforms designated as, + / +, + / -, - / + and - / -. It is expressed in leukemic cells, and is proposed to play a role in their proliferation and differentiation. In this study we have shown that cell lines of the erythroleukemia, K562, overexpressing the murine + / + and - / - WT1 isoforms grow normally and do not exhibit altered responses to the induction of apoptosis by the reagents cisplatin and adriamycin, or to serum withdrawal. However, differentiation of K562 cells with 12-O-tetradecanoylphorbol 13-acetate, modeling aspects of megakaryopoiesis, was partially inhibited by the persistent expression of both the murine + / + and - / - WT1 isoforms. This finding suggests that WT1 plays a role in the regulation of hematopoietic differentiation and is consistent with an oncogenic role for WT1 in leukemogenesis.

Analysis of CDKN1C in Beckwith Wiedemann syndrome.

In this study we have examined 32 patients with Beckwith Wiedemann Syndrome (BWS) for mutations affecting the CDKN1C gene, including seven cases of familial BWS. Mutations were not detected in the coding region of the CDKN1C gene in any individual with BWS. However in two patients, two G/A base substitutions at adjacent positions in the 5'UTR were detected. These substitutions were also found in normal controls. Expression of CDKN1C in somatic tissues was examined in 18 of the 32 cases using semi-quantitative RT-PCR. CDKN1C expression was significantly reduced in the peripheral blood of three cases compared with controls. These results suggest that, although coding region mutations in the CDKN1C gene are rare in BWS, mutations disrupting CDKN1C expression may be found. Three of five informative patients exhibited biallelic CDKN1C expression in lymphocytes, cord blood, and kidney tissue, respectively. Biallelic expression was not associated with overall CDKN1C levels significantly different to those in controls. Patients who expressed CDKN1C biallelically, or who were low CDKN1C expressors, maintained monoallelic methylation in the Differentially Methylated Region 2 (DMR2) of the IGF2 locus. One patient expressing CDKN1C biallelically, maintained imprinted gene expression at the IGF2 locus. These results suggest that biallelic CDKN1C expression does not significantly perturb the overall levels of CDKN1C expression in somatic tissue. They also confirm other studies showing that the mechanisms associated with regulating CDKN1C expression and imprinting are separate from those regulating IGF2 imprinting.

CDKN1C expression in Beckwith-Wiedemann syndrome patients with allele imbalance.

In this study, we have examined CDKN1C expression in BWS patients with allele imbalance (AI) affecting the 11p15 region. Two of two informative patients with AI, attributable to mosaic paternal isodisomy, exhibited reduced levels of CDKN1C expression in the liver and kidney, respectively, relative to expression levels in the equivalent tissues in normal controls. Although overall expression was reduced, some expression from the paternally derived CDKN1C allele was evident, consistent with incomplete paternal imprinting of the gene. One patient showed evidence of maternal allele silencing in addition to AI. These findings show for the first time that CDKN1C expression is reduced in BWS patients with AI and suggest that CDKN1C haploinsufficiency contributes to the BWS phenotype in patients with mosaic paternal isodisomies of chromosome 11.

High frequency of t(12;21) in childhood acute lymphoblastic leukemia detected by RT-PCR.

Recently, a new recurrent translocation, t(12;21)(p13;q22), has been identified in B-cell lineage acute lymphoblastic leukemia (ALL). The translocation results in the fusion of two known genes, ETV6/TEL(12p13) and AML1(21q22), both of which have been shown to be involved in other hematological malignancies. The t(12;21) is virtually undetectable by routine cytogenetics, but the chimeric transcript ETV6-AML1 has been detected in childhood ALL by molecular techniques in up to 36% of cases, making it the most common genetic abnormality in these patients. It has been shown to be associated with a B-precursor phenotype and an excellent prognosis. We tested 66 diagnostic pediatric ALL samples by reverse transcription polymerase chain reaction (RT-PCR) and found evidence of the t(12;21) in 22 (33%). None of these had previously been identified as harboring the t(12;21), although six had karyotypic abnormalities involving either 12p13 or 21q22. ETV6-AML1 expression defined a subgroup of patients characterised by an age of between two and 12 years, B-lineage immunophenotype and non-hyperdiploid DNA content. Our data further support the importance of molecular diagnostic methods in the identification of clinically distinct subgroups of patients with ALL.

Distinct but overlapping expression patterns of two vertebrate slit homologs implies functional roles in CNS development and organogenesis.

The Drosophila slit gene (sli) encodes a secreted leucine-rich repeat-containing protein (slit) expressed by the midline glial cells and required for normal neural development. A putative human sli homolog, SLIT1, has previously been identified by EST database scanning. We have isolated a second human sli homolog, SLIT2, and its murine homolog Slit2. Both SLIT1 and SLIT2 proteins show approximately 40% amino acid identity to slit and 60% identity to each other. In mice, both genes are expressed during CNS development in the floor plate, roof plate and developing motor neurons. As floor plate represents the vertebrate equivalent to the midline glial cells, we predict a conservation of function for these vertebrate homologs. Each gene shows additional but distinct sites of expression outside the CNS suggesting a variety of functions for these proteins.

Allelic imbalance at chromosome 1q21 in Wilms tumor.

The Wilms tumor suppressor gene 1, WT1, located on chromosome 11p13 is mutated in only a subset of Wilms tumors. Cytogenetic studies of Wilms tumors show that the most frequent structural anomalies after those affecting chromosome 11p are rearrangements of 1q, suggesting that there is a gene involved in Wilms tumor etiology in this region. The WT1 target sequence +P5 (D1S3309E), isolated using whole-genome polymerase chain reaction (PCR), binds all WT1 isoforms in vitro and has been mapped to 1q21-22. As +P5 may mark a 1q Wilms tumor gene, constitutional and tumor DNA from 33 Wilms tumor patients (36 tumors) was screened for allele imbalance using microsatellite markers from 1p21 to 1q44. Although no gross rearrangements of the +P5 region were found, this study demonstrates allele imbalance for 1q in 12% of patients (5/36 tumors), defining a smallest region of overlap at 1q21. This finding supports a role for 1q21 in Wilms tumorigenesis.

Mutation analysis of the WT1 gene in sporadic childhood leukaemia.

The 10 coding exons of the WT1 gene, from 39 bp upstream of the translation initiation codon to 12 bp downstream of the stop codon, were examined for point mutations in a panel of 48 sporadic childhood acute leukaemias using the single-stranded conformational polymorphism (SSCP) assay. The panel included 33 cases of acute lymphocytic leukaemia and 15 cases of acute myeloid leukaemia. This is the first study in which sporadic childhood leukaemias have been examined for WT1 point mutations across the entire coding region of the WT1 gene, however, no tumorigenic point mutations or small deletions or insertions could be identified in these patients. A previously described polymorphism in exon 7, resulting in an A to G transition in an arginine codon, was observed at a frequency of 21.5%, equivalent to that seen in the normal population. This study suggests that point mutations in the coding regions of the WT1 occur infrequently in leukaemias of childhood.

A WT1 antisense oligonucleotide inhibits proliferation and induces apoptosis in myeloid leukaemia cell lines.

The response of the CML-BC cell line, K562, the myelomonocytic cell line MM6 and the promyelocytic leukaemia cell line HL-60, to a 15 mer WT1 antisense oligonucleotide, targeted to the translation initiation site of the WT1 mRNA was examined. K562 cells exposed to 0.4 microM antisense oligonucleotide showed markedly reduced proliferation which was associated with reduced cell viability. Sense, scrambled and mutant antisense oligonucleotides had no effect on the proliferation of K562 cells. MM6 cells exposed to 0.4 microM antisense oligonucleotide also showed significantly reduced cellular proliferation which was also accompanied by loss of cell viability. In the K562 and MM6 antisense cultures that exhibited reduced cell viability, both DNA fragmentation and morphological features consistent with apoptosis could be identified. In contrast the growth of HL-60 cells was unaffected by exposure to 0.4 microM antisense oligonucleotide. In each of the cell lines examined, WT1 antisense oligonucleotide abrogated WT1 protein expression, and analysis of WT1 coding sequence in these cells showed that no oncogenic point mutations in the gene were present. We propose therefore that in some myeloid leukaemia cell lines, the expression of a normal WT1 protein is necessary for cell proliferation and that it plays a role in maintaining the viability of some leukaemia cells.

Splicing of exon 5 in the WT1 gene is disrupted in Wilms' tumour.

Using a reverse transcriptase polymerase chain reaction to examine alternate splicing at site I (exon 5) and site II (exon 9) in the Wilms' tumour suppressor gene, WT1, we found that in seven of the 10 Wilms' tumours examined, splicing at site I was disrupted. This is predicted to result in isoform imbalance in Wilms' tumours, with an increase in isoforms in which the 17 amino acids encoded by exon 5 are missing. These observations could not be explained by mutations or rearrangements in flanking introns. Disrupted alternate splicing of exon 5 may play a role in the aetiology of Wilms' tumour.

Homozygous intragenic deletion in the WT1 gene in a sporadic Wilms' tumour associated with high levels of expression of a truncated transcript.

We have examined a panel of 21 sporadic Wilms' tumours for rearrangements in the Wilms' tumour suppressor gene, WT1. In one tumour with specific allele loss in chromosome 11p13, a homozygous deletion in the 3' end of the gene, encompassing exon 10 and the 3' untranslated region, was identified. High levels of a truncated WT1 transcript, predicted to encode a polypeptide missing the fourth zinc finger were expressed in this tumour. All other samples showed normal patterns of digestion on Southern blots. This observation confirms previous findings that large deletions in the gene occur infrequently in sporadic Wilms' tumours and that the zinc-finger region of the encoded polypeptide is critical for correct functioning of the gene.

Analysis of paediatric tumour types associated with hemihyperplasia in childhood.

In order to further explore the relationship between hemihyperplasia in children and the occurrence of embryonal tumours of childhood, the records at St Jude Children's Research Hospital were examined for patients who presented with a malignant tumour and hemihyperplasia. Of 27 evaluable patients, 19 had Wilm's tumour and one had massive bilateral nephroblastomatosis. The tumours were more likely to occur on the side affected by hemihyperplasia than to be found contralaterally. All but five of these patients developed the tumours before the age of six. Twenty-two of the 27 patients developed tumours associated with allelic loss on chromosome band 11p15, suggesting that the locus associated with hemihyperplasia may be also located at chromosome band 11p15.

The insulin-like growth factor 1 receptor gene is normally biallelically expressed in human juvenile tissue and tumours.

We have examined insulin-like growth factor 1 receptor (IGF1R) gene expression for evidence of imprinting in 15 informative patients with embryonal tumours. Biallelic expression was observed in all but one sample of normal juvenile kidney and liver, and in 9/10 associated Wilms' tumours, 3/3 hepatoblastomas and 2/2 adrenal tumours. A single patient with Beckwith-Wiedemann Syndrome (BWS) demonstrated monoallelic expression of the maternally derived IGF1R allele in normal kidney, associated Wilms' tumour and in peripheral blood lymphocytes. The observed biallelic expression of the IGF1R gene in all but one patient strongly suggests that the human gene is not normally imprinted.

Three non-overlapping regions of chromosome arm 11p allele loss identified in infantile tumors of adrenal and liver.

Tumor and constitutional chromosome arm 11p genotypes were compared in 6 hepatoblastoma (HB) patients and 2 adrenal adenoma (AA) patients, with one HB patient and both AA patients displaying clinical features associated with the Beckwith-Wiedemann syndrome (BWS). Using up to 14 chromosome 11 polymorphic markers, loss of constitutional heterozygosity (LOH) was demonstrated in both AA patients and in 4 of 6 HB patients. This identified three distinct and non-overlapping regions of 11p within which LOH occurred, which were defined as lying distal to the gamma-globin locus (11p15.5), proximal to the gamma-globin locus but distal to 11p13 (LOH being detected at 11p15.1), and restricted to the 11p13 region. Specific LOH within each 11p15 region was observed in HB, and this represents the first demonstration by a single study of LOH clearly affecting separate regions of chromosome band 11p15 in a particular tumor type. One AA showed LOH restricted to 11p13 loci, implicating the involvement of the WT1 gene. The second AA patient presented with genitourinary abnormalities and we therefore examined sequences coding for 3 zinc finger domains of WT1 in both AAs. No point mutations were identified in sequence from either patient. Nonetheless our results indicate that 3 separate 11p loci may be significant in the development of tumors which arise in association with BWS.