Is Abdominal Fat Distribution Measured by Axial CT Imaging an Indicator of Complications and Mortality in Acute Pancreatitis?

BACKGROUND

Obesity is an important risk-stratifying co-morbidity for many pathological conditions. Controversy exists about its influence in outcomes after acute pancreatitis (AP). This study assessed abdominal fat distribution (subcutaneous, retroperitoneal and intra-abdominal) measured using computer tomography (CT) images and related it to outcomes in patients with AP.

METHODS

The case notes of patients admitted with AP were identified from computerised records from 2008 to the 2013. Image analysis software was used to assess the individual abdominal fat distributions from CT images.

RESULTS

A total of 79 patients were included. There was no relationship between fat distribution and either severity of, or mortality from, AP. Fat distribution was not found to be an independent risk factor on multivariate analysis. There was, however, a positive correlation between retroperitoneal and intra-abdominal fat with APACHE II scores, Ranson and Glasgow score and Multiple Organ Dysfunction score (MODS) on various days following admission (r = 0.421, p = 0.0008; r = 0.469, p < 0.0001; r = 0.398, p = 0.007; r = 0.336, p = 0.011, respectively). On multiple logistical regression analysis, the only variables associated with mortality were Balthazar Severity Index, MODS and EWS with a p value of <0.0001, 0.0019 and 0.0481, respectively.

CONCLUSIONS

Obese patients have worse predicted outcomes as measured by the EWS, MODS and Ranson scores. Abdominal fat distribution, however, was not shown to be directly related to AP severity or mortality. The addition of fat parameters may be of use in prognostic CT severity index models, but from this data, it does not appear to be an independent risk factor of adverse outcome.

Role of preoperative carbohydrate loading: a systematic review

INTRODUCTION

Surgical stress in the presence of fasting worsens the catabolic state, causes insulin resistance and may delay recovery. Carbohydrate rich drinks given preoperatively may ameliorate these deleterious effects. A systematic review was undertaken to analyse the effect of preoperative carbohydrate loading on insulin resistance, gastric emptying, gastric acidity, patient wellbeing, immunity and nutrition following surgery.

METHODS

All studies identified through PubMed until September 2011 were included. References were cross-checked to ensure capture of cited pertinent articles.

RESULTS

Overall, 17 randomised controlled trials with a total of 1,445 patients who met the inclusion criteria were identified. Preoperative carbohydrate drinks significantly improved insulin resistance and indices of patient comfort following surgery, especially hunger, thirst, malaise, anxiety and nausea. No definite conclusions could be made regarding preservation of muscle mass. Following ingestion of carbohydrate drinks, no adverse events such as apparent or proven aspiration during or after surgery were reported.

CONCLUSIONS

Administration of oral carbohydrate drinks before surgery is probably safe and may have a positive influence on a wide range of perioperative markers of clinical outcome. Further studies are required to determine its cost effectiveness.

Enhanced recovery programmes in hepatobiliary and pancreatic surgery: a systematic review

INTRODUCTION

The terms ‘enhanced recovery after surgery’, ‘enhanced recovery programme’ (ERP) and ‘fast track surgery’ refer to multimodal strategies aiming to streamline peri-operative care pathways, to maximise effectiveness and minimise costs. While the results of ERP in colorectal surgery are well reported, there have been no reviews examining if these concepts could be applied safely to hepatopancreatobiliary (HPB) surgery. The aim of this systematic review was to appraise the current evidence for ERP in HPB surgery.

METHODS

A MEDLINE® literature search was undertaken using the keywords ‘enhanced recovery’, ‘fast-track’, ‘peri-operative’, ‘surgery’, ‘pancreas’ and ‘liver’ and their derivatives such as ‘pancreatic’ or ‘hepatic’. The primary endpoint was length of post-operative hospital stay. Secondary endpoints were morbidity, mortality and readmission rate.

RESULTS

Ten articles were retrieved describing an ERP. ERP protocols varied slightly between studies. A reduction in length of stay was a consistent finding following the incorporation of ERP when compared with historical controls. This was not at the expense of increased rates of readmission, morbidity or mortality in any study.

CONCLUSIONS

The introduction of an ERP in HPB surgery appears safe and feasible. Currently, many of the principles of the multimodal pathway are derived from the colorectal ERP and distinct differences exist, which may impede its implementation in HPB surgery.

Management of acute non-cirrhotic and non-malignant portal vein thrombosis: a systematic review

BACKGROUND

No definitive evidence exists regarding the treatment of acute portal vein thrombosis (PVT). Treatment modalities described include conservative management, anticoagulation, thrombolysis, and thrombectomy. This review examines the impact of such treatment, its outcomes, and the complications resulting from the resultant portal hypertension.

METHODS

A Medline literature search was undertaken using the keywords portal vein thrombosis, anticoagulation, thrombolysis, and thrombectomy. The primary end point was portal vein recanalization. Secondary outcome measures were morbidity and the development of portal hypertension and its sequelae, including variceal bleeding. Data from articles relating to PVT in the context of cirrhosis, malignancy, or liver transplant were excluded.

RESULTS

Early systemic anticoagulation results in complete portal vein recanalization in 38.3% of cases and partial recanalization in 14.0% of cases. Spontaneous recanalization without treatment can only be expected in up to 16.7% of patients. Frequently this is only when associated with self-limiting underlying pathology and/or minimal thrombus extension. Thrombolysis can be associated with major complications in up to 60% of patients.

CONCLUSIONS

The natural history of acute PVT is poorly described. Spontaneous resolution of acute portal vein thrombosis is uncommon. Early anticoagulation results in a satisfactory rate of recanalization with minimal procedure-associated morbidity. Thrombolysis should be used with caution and only considered if the disease is progressive and signs of mesenteric ischemia are present. Further well-designed trials with precise outcome reporting are needed to improve our understanding of the disease.

An observational study into the management of arteriomegaly: a call for a revised classification system

INTRODUCTION

Arteriomegaly is the diffuse ectasia of arteries with or without aneurysmal disease. Patients with arteriomegaly have a higher incidence of morbidity including limb loss compared to patients with other arteriopathies. The aim of this observational study was to review the management of these patients in our institution.

METHODS

Radiologists and surgeons prospectively reviewed aortofemoral angiography. Patients with arteriomegaly were identified. Data relating to demographics, mode of presentation, risk factors, type of arteriomegaly, management and progression of disease were analysed.

RESULTS

Arteriomegaly was identified in 1.3% of patients (n = 69) undergoing lower limb angiography in the study period. Of these, the majority (n = 67) were men. The mean age was 74 years (range: 60-89 years) and 76% were smokers. Co-morbidities included coronary artery disease (55%), diabetes mellitus (20%), hypertension (45%) and cerebrovascular events (6%). Forty-nine patients presented with critical limb ischaemia and eighteen patients were seen electively in the outpatients department with symptoms of intermittent claudication. Data were incomplete for two male patients and were therefore not included. At presentation, 22 patients were classified as Hollier type I, 5 were type II and 9 were type III. Thirty-one patients had arteriomegalic vessels but no aneurysmal disease. After a median follow-up duration of 76 months (range: 6-146 months), 34 patients progressed to type I, 2 to type II and 18 to type III. Thirteen remained without aneurysmal disease. Twenty-nine patients required angioplasty and twenty-eight required bypass surgery during this time. In total, 102 procedures were required for complicated disease. The limb salvage rate was 92%. Although 8 patients in our series died, the remaining 59 are under regular follow up.

CONCLUSIONS

This study illustrates the progressive nature of arteriomegaly. Results of the management of these patients in our institution are similar to those in the literature. We suggest an additional fourth category to Hollier's classification that describes arteriomegalic disease without aneurysmal degeneration as this, too, deserves special management. Regular follow-up visits and early intervention for patients with arteriomegaly is advocated to reduce the high incidence of morbidity.

Factors predicting significant pathology on ultrasonography in women presenting with non-specific lower abdominal pain

INTRODUCTION

Ultrasonography is used frequently to exclude significant pathology in young women presenting with non-specific lower abdominal pain (NSLAP). This study examined parameters that predicted the likelihood of significant findings on ultrasonography. These results could be used to select patients for priority imaging or identify those who could be managed with no ultrasonography.

METHODS

A total of 65 women with NSLAP were identified from 283 admissions. Group 1 (n=42) consisted of patients with normal imaging. Group 2 (n=23) included patients with 'positive' scans requiring treatment. White cell count (WCC), C-reactive protein (CRP) levels, platelet count, age, duration of pain and length of stay in hospital were compared between the groups.

RESULTS

The median WCC and CRP were greater in Group 2 than in Group 1: 15 x 10(9)/l and 123 mg/l versus 11 x 10(9)/l and 72 mg/l respectively (p=0.01 and p=0.05). CRP was a weak predictor of positive pathology on ultrasonography (area under curve [AUC]=0.66, p=0.027) and WCC was a strong predictor of abnormal pathology on ultrasonography (AUC=0.7, p=0.005). A WCC of >12.8 x 10(9)/l was 65% sensitive and 71% specific in predicting subsequent pathology on ultrasonography. The median wait for ultrasonography was 24 hours (range: 1-96 hours).

CONCLUSIONS

This study failed to define any criteria that could select patients not requiring ultrasonography. Since ultrasonography is a relatively cheap and safe investigation, its continued use to screen women with NSLAP is justified. WCC should be used to prioritise imaging.

Can enhanced recovery programmes be further improved by the addition of omega three fatty acids?

AIMS

The term "enhanced recovery programme (ERP)" means applying defined protocols to augment the recovery of patients following surgery. Inflammation is body's response to insults such as infection, injury and surgical procedures. Inflammatory mediators whose function is initially protective may cause undesirable consequences, if the response is unnecessarily prolonged. The principle effects of ERP result from the reduction of the profound stress which results following major surgical procedures.

METHODS

A Pubmed literature search was undertaken using the keywords enhanced recovery, surgery and omega-3. The primary endpoint was whether the addition of omega-3 to ERP improved morbidity and mortality.

RESULTS

Nine randomised trials examining the effect of omega-3 enriched diets following surgery were analysed. Inclusion of omega-3 helps in maintaining a positive nitrogen balance, overcome immune dysfunction, lower the incidence of post-operative infections with the consequence of reduced morbidity and mortality.

CONCLUSIONS

The provision of early or continuous nutrition is one of the cornerstones of an ERP. A theoretically ideal regimen would provide an energy substrate and protein and contain a component which would limit inappropriate inflammation. The beneficial role of omega-3 results from a number of effects which limit the inflammatory response, principally by influencing the production of eicosanoids and modulating cytokines. They also enhance cell-mediated immunity and preserve immune function better than standard dietary formulations. Although ERPs have already produced significant progress, there is sufficient evidence to suggest that the provision of omega-3 fatty acids may result in further improvements.

Pancreaticogastric fistula secondary to intraductal papillary mucinous neoplasia: a case report and review of the literature

Intraductal papillary mucinous neoplasms (IPMNs) are benign cystic lesions of the pancreas with recognised premalignant potential. An occasional feature of IPMNs is fistula formation to surrounding organs. This report describes a case of a pancreaticogastric fistula from a main duct IPMN that produced the complete resolution of the patient's symptoms.

How accurately does a simulation glove reflect function compared to rheumatoid arthritis sufferers?

INTRODUCTION

This study assessed the ability of gloves to simulate rheumatoid arthritis of the hand.

SUBJECTS AND METHODS

Assessments were made in the dominant hand of 24 healthy volunteers with no glove, glove A (simulating stiffness only) and glove B (simulating stiffness and pain). Results were compared to data held on 23 rheumatoid arthritis patients. Sollerman score was used as a standardised measure of hand function and time taken to complete testing was recorded. Grip strength was also measured in volunteers.

RESULTS

Both gloves simulate a reduction in power and prolong time taken to complete Sollerman hand-function testing. The gloves are less able to simulate a matched reduction in function when compared to rheumatoid arthritis sufferers. Sollerman score is 9.7% less in rheumatoid arthritis hands than a healthy volunteer using the glove.

CONCLUSIONS

The glove could, therefore, be used to guide future design of tools and aides that accommodate for hand disorders. More work on the usefulness of such disease simulation in the design of tools for such patients is needed.

Developmentally regulated expression of the bean beta-phaseolin gene in tobacco seed

Recombinant phage lambda177.4 contains a gene for beta phaseolin, a major storage glycoprotein of French bean seed. A 3.8-kilobase Bgl II-BamHI fragment containing the entire 1700-base-pair coding region, together with 863 base pairs of 5' and 1226 base pairs of 3' flanking sequence, was inserted into the A66 Ti plasmid of Agrobacterium tumefaciens and used to transform tobacco. The level of phaseolin in the seeds of plants regenerated from cloned tissue was 1000-fold higher than in other tissues. The molecular weight of the phaseolin RNA transcript in tobacco seeds was identical to that found in bean seeds. The phaseolin protein in tobacco seed was glycosylated and appeared to undergo removal of the signal peptide. However, a large proportion of the phaseolin was cleaved into discrete peptides. These same peptides were formed as phaseolin was degraded during tobacco seed germination. The phaseolin gene appeared to be inserted as a single copy, and the proportion of phaseolin per genome copy in tobacco seeds (up to 3% of the total embryo proteins) resembled that in the bean seeds (40% of total seed protein, expressed from about 14 copies per diploid genome). Furthermore, the transplanted gene was turned on during tobacco seed development, and its protein product, phaseolin, was localized in the embryonic tissues. Finally, the phaseolin gene was inherited as a Mendelian dominant trait in tobacco.

Complete nucleotide sequence of a French bean storage protein gene: Phaseolin

The complete nucleotide sequences of the gene and the mRNA coding for a specific phaseolin type French bean major storage protein have been determined. Comparison of these sequences reveals a phaseolin gene structure consisting of 80 base pairs (bp) of 5' untranslated DNA, 1,263 bp of protein-encoding DNA which is interrupted by five intervening sequences (IVS1, 72 bp; IVS2, 88 bp; IVS3, 124 bp; IVS4, 128 bp; and IVS5, 103 bp), and 135 bp of 3' untranslated DNA. Sequences characteristic of eukaryotic promoters "CCAAT" and "TATA" are present in the 5' flanking DNA, and the eukaryotic poly(A) addition signal A-A-T-A-A-A occurs 16 bp before the first nucleotide of poly(A). The derived amino acid sequence yields an amino acid composition and a molecular weight compatible with those found for the beta-type phaseolin protein. Two regions that probably serve as carbohydrate-peptide linkage recognition sites have been identified. A region of highly hydrophobic amino acids at the NH(2) terminus of the protein suggests the presence of a signal peptide in the newly synthesized phaseolin protein.

Messenger RNA for G1 protein of French bean seeds: Cell-free translation and product characterization

The fraction of poly(A)-containing RNA isolated from ripening bean (Phaseolus vulgaris) cotyledons that sedimented at 16 S in linear logarithmic sucrose gradients was at least as active a messenger as viral RNA when added to a cell-free protein-synthesizing system from wheat germ. The major products synthesized in vitro were polypeptides of about 47,000 and 43,000 daltons, corresponding to two of the three subunits of G1 protein, the most abundant bean seed storage protein. No trace of the largest (53,000 daltons) subunit was found among the polypeptides synthesized in vitro. Proof that the 47,000- and 43,000-dalton polypeptides coded by the 16S RNA were indeed subunits of G1 protein was obtained by immunoprecipitation with monovalent antibody to G1 protein and by electrophoretic mapping of peptides on acrylamide gels after digestion of mixtures of authentic protein and radioactive translation products with protease V8, chymotrypsin, and trypsin. The subunits synthesized in vitro were slightly smaller than the native subunits, probably because they lacked the sugar residues present on the holoprotein.

Laparoscopic cholecystectomy in situs inversus totalis: is it safe?

Situs inversus totalis (SIT) is a rare defect of genetic predisposition. It may cause difficulties in the diagnostic and therapeutic management of abdominal pathology due to the mirror-image anatomy. We report the management of a case of symptomatic cholelithiasis with emphasis on its surgical technique combined with a review of the literature.

How accurately does a simulation glove reflect function compared to rheumatoid arthritis sufferers?

INTRODUCTION

This study assessed the ability of gloves to simulate rheumatoid arthritis of the hand.

SUBJECTS AND METHODS

Assessments were made in the dominant hand of 24 healthy volunteers with no glove, glove A (simulating stiffness only) and glove B (simulating stiffness and pain). Results were compared to data held on 23 rheumatoid arthritis patients. Sollerman score was used as a standardised measure of hand function and time taken to complete testing was recorded. Grip strength was also measured in volunteers.

RESULTS

Both gloves simulate a reduction in power and prolong time taken to complete Sollerman hand-function testing. The gloves are less able to simulate a matched reduction in function when compared to rheumatoid arthritis sufferers. Sollerman score is 9.7% less in rheumatoid arthritis hands than a healthy volunteer using the glove.

CONCLUSIONS

The glove could, therefore, be used to guide future design of tools and aides that accommodate for hand disorders. More work on the usefulness of such disease simulation in the design of tools for such patients is needed.

Use of micrococcal nuclease in the purification of highly template dependent RNA-dependent RNA polymerase from brome mosaic virus-infected barley

The template dependence of RNA-dependent RNA polymerase from brome mosaic virus (BMV)-infected barley was greatly increased by micrococcal nuclease digestion of the endogenous RNA. [32P]UMP incorporation by the nuclease-treated enzyme was stimulated 20-fold when BMV RNA was added as template, while incorporation by the untreated enzyme was stimulated only 5-fold by the addition of BMV RNA. Other properties of BMV polymerase were not changed significantly by nuclease digestion. The extract remained highly active and template specific. Analysis of the products of the reaction showed that separated BMV RNA components could be replicated independently to yield full-length replicative-form RNAs. These data provide strong evidence that the extract is capable of initiating RNA synthesis and that it includes the intact viral replicase. This method should be of general use, allowing the study of cell-free replication of any viral nucleic acid without requiring purification or solubilization of the replicase.

Use of dodecyl-beta-D-maltoside in the purification and stabilization of RNA polymerase from brome mosaic virus-infected barley

The activity and specificity of RNA-dependent RNA polymerase (replicase) isolated from brome mosaic virus-infected barley was enhanced by extraction with the nonionic detergent dodecyl-beta-d-maltoside. The enzyme was stable for at least 8 weeks when stored at -70 degrees . A further 100-fold purification was obtained by centrifugation through sucrose in the presence of detergent. The polymerase activity was associated with the pellet fraction; the template dependence and specificity were similar to those of the enzyme before sucrose purification. SDS-PAGE analysis revealed a 110-kd protein in the purified pellet fraction from infected leaves that was absent from a similar fraction from healthy leaves. The protein had an identical electrophoretic mobility to that of protein la, the product of brome mosaic virus RNA 1 translation in vitro, and the profile of its tryptic polypeptides was very similar to that of protein 1a. These results support data obtained by inoculation of protoplasts with separated BMV RNA components (Kiberstis, et al. (1981), Virology 112, 804-808) that are consistent with the notion that RNA 1 codes for the viral replicase, or a subunit thereof.

Kiddo, a new transposable element family closely associated with rice genes

The promoter region of the rice ubiquitin2 (rubq2) gene was found to be polymorphic between japonica (T309) and indica (IR24) lines as the result of a 270-bp deletion in T309. A TTATA footprint in the T309 rubq2 promoter suggested that an excision event had occurred, and inspection of the 270-bp region present in IR24 revealed that it had all the characteristics of a miniature inverted repeat transposable element (MITE). Database searches showed that this element is a member of a new MITE family, which we have named Kiddo. Thirty-five complete Kiddo sequences were identified in existing rice genomic sequence databases. They could be arranged into four groups, within-group sequence identity was over 90%, with 65-75% identity between groups. The high sequence similarity within a group indicates that some Kiddo members were recently mobile and may still be active. An additional 24 decayed Kiddo sequences were detected. Interestingly, approximately 80% of 18 Kiddo members from annotated accessions lie within 530 bp of a coding sequence. That approximately 40% of Kiddo members present in genic regions reside in introns suggests that Kiddo transposition entails the use of both DNA and RNA intermediates, and may provide some insight into the origins of individual groups. DNA blot analysis showed that Kiddo is a rice-specific element, although one sequence with limited (72%) similarity to Kiddo group A was detected as a wheat EST. Kiddo family members may represent new molecular and phylogenetic markers, as well as representing valuable materials for studying the molecular mechanisms of MITE transposition.

Chromatin structure and phaseolin gene regulation

Chromatin structure, the organized packaging of DNA with histones in the nucleus, is now seen as a dynamic fabric that changes with development. Here, we use studies on the phaseolin (phas) gene that encodes a seed protein to show how chromatin structure interacts with the transcription machinery to accomplish rigorous spatial regulation of expression. In leaf and other vegetative tissues, a nucleosome is rotationally and translationally positioned over an ensemble of three phased TATA boxes, denying access to TBP. Current interest focuses on the mechanisms by which this architecture is remodeled during embryogenesis. The transcription factor PvALF is intrinsically involved, as are other non-histone proteins and abscisic acid. These concepts, and the possible modular nature of phas expression, are summarized together with speculations concerning the re-establishment of the nucleosome over the phas promoter during terminal stages of embryogenesis.

De novo activation of the beta-phaseolin promoter by phosphatase or protein synthesis inhibitors

The promoter for the phaseolin (phas) bean seed protein gene adopts an inactive chromatin structure in leaves of transgenic tobacco. This repressive architecture, which confers stringent spatial regulation, is disrupted upon transcriptional activation during embryogenesis in a process that requires the presence of both a transcription factor (PvALF) and abscisic acid (ABA). Toward determining the need for de novo synthesis of proteins other than PvALF in transcriptional activation we explored the effect of several eukaryotic protein synthesis inhibitors. Surprisingly, cycloheximide (CHX), emetine, and verrucarin A were able to induce transcription from the phas promoter in tobacco and bean leaf tissue in the absence of either PvALF or ABA. This induction was decreased by the replication inhibitors hydroxyurea and aphidicolin but not by genistein or mimosine. Since protein phosphatases and kinases are essential components of the ABA signal transduction pathway, it is conceivable that CHX is also capable of inducing phosphorylation of proteins usually involved in ABA-mediated activation. Interestingly, okadaic acid, an inhibitor of serine/threonine phosphatase, also strongly activated transcription from the phas promoter. In contrast, the protein synthesis inhibitors anisomycin and puromycin did not activate transcription from the phas promoter, nor did the tyrosine phosphatase inhibitors phenylarsine oxide and sodium orthovanadate. These discrete but different results on transcriptional activation may reflect specific modes of action of the inhibitors, or they may reflect differential interactions of the inhibitors or of downstream events resulting from inhibitor activity with presently unknown components of the transcriptional activation system.

The use of FISH in chromosomal localization of transgenes in rice

Chromosomal location and local chromatin structure are thought to play important roles in the stability of transgene expression. Fluorescence in situ hybridization (FISH) is a cytogenetic technique that allows the localization of specific DNA sequences on chromosomes. It provides an excellent means to analyze the chromosomal environment of integrated transgenes, helping to assess the effect of position on gene expression. FISH analyses have been conducted on nuclear chromosomal DNA at metaphase, interphase, meiotic prophase (pachytene) and on extended chromatin fibers (DNA fiber-FISH) and naked DNA molecules. Despite the small size of rice chromosomes, FISH has been successfully accomplished to detect unique and repetitive DNA sequences. A detailed FISH procedure for the detection of small and single copy transgenes within the rice genome is described and the application of FISH to evaluate chromosomal location and the local chromatin structure of transgenes as parameters that could affect their expression is discussed.

Transgene silencing in monocots

Plant gene silencing was originally thought to be a quirk of transformation procedures, but is now recognized to be a facet of vitally important gene regulatory systems, present in all organisms. Monocot plants, especially the grasses, play a foremost role in the agricultural economy of all nations, and their biotechnological manipulation offers great potential for both developed and developing countries. Here, we review reported instances of transgene silencing in monocots and relate the processes of transcriptional and post-transcriptional gene silencing (TGS, PTGS) in perspective to the rapidly burgeoning knowledge of these phenomena in many organisms. Recent findings include the involvement of an RNA-dependent RNA polymerase and a nuclease in PTGS systems and the close relationship between methylation and chromatin structure in TGS events.

Virus recovery is induced in Brome mosaic virus p2 transgenic plants showing synchronous complementation and RNA-2-specific silencing

Nicotiana benthamiana plants expressing Brome mosaic virus (BMV) p2 protein complemented replication of RNAs1 + 3 but, surprisingly, supported little or no replication of RNA-2. Despite this, the p2 transgenic plants were able to support systemic migration of RNAs-1 and -3. Kinetic analyses showed identical degradation rates for RNAs-2 and -3, greatly detracting from the concept of an induction of an RNA-2-specific degradation system. Deletion analysis identified a 200-nucleotide sequence that may contribute to silencing in a context-specific manner. When R1 progeny of a severely silencing p2 transgenic line were tested for virus resistance, three different classes of reactions were observed. In class 1 and class 3 plants, the virus moved systemically and showed various extents of RNA-2 silencing. However, in class 2 plants, there was a stochastic onset of post-transcriptional silencing in the systemic leaves that was reminiscent of virus recovery. Plants showing recovery tended to have a greater number of transgene loci than did those exhibiting component-specific silencing. The induction of silencing did not appear to be dependent solely on the combined steady state levels of the transgene and viral RNA. Some plants transformed with a p2 frameshift construct showed a complete silencing phenotype, but none showed RNA-2-specific silencing. While the relationship between the two types of silencing remains unclear, we speculate that our observations reflect early events in the induction of virus recovery.

Organizational complexity of a rice transgene locus susceptible to methylation-based silencing

Molecular analyses of a rice (Oryza sativa L.) transgene locus introduced using biolistic techniques revealed the presence of multiple copies of rearranged fragments, as well as an intact copy of the supplied constructs. Both the gene of interest (35S-Btt cryIIIA) and the selectable marker used (Ubi1-bar) were methylated and silenced. Additionally, vector sequences were present in great abundance and were also highly methylated, indicating that the entire transgene insert was marked for methylation. The rearrangement of input DNA resulted in interspersion of plasmid backbone regions with the gene of interest. Permutation of segments encoding the gene of interest and the selectable marker was also detected, perhaps explaining why sequences introduced on separate plasmids are frequently found to be inserted at the same locus. The 35S promoter contained several hotspots for fragmentation. These observations strongly support the concept that intrusive DNA is recognized by host surveillance systems and that transgene loci with anomalous structural organization are subjected to inactivation by processes such as methylation.

beta-Phaseolin gene activation is a two-step process: PvALF- facilitated chromatin modification followed by abscisic acid-mediated gene activation

We have shown previously that a rotationally and translationally positioned nucleosome is responsible for the absence of transcriptional expression from the phaseolin (phas) gene promoter in leaf tissue and that the repressive chromatin structure is disrupted on transcriptional activation during embryogenesis. To investigate how the chromatin structure is modified, we ectopically expressed PvALF, a putative seed-specific phas activator, in leaf tissue of a tobacco line transgenic for a chimeric phas/uidA construct. DNase I footprinting in vivo revealed that the ectopic expression of PvALF resulted in remodeling of the chromatin architecture over the TATA region of the phas promoter but did not lead to transcriptional activation in the absence of abscisic acid (ABA). Treatment of the transgenic tobacco leaves with ABA in the absence of PvALF neither alleviated the repressive chromatin architecture nor activated transcription. However, in the presence of PvALF, high levels of beta-glucuronidase expression were obtained on exposure of leaves to ABA. These results reveal that expression from the phas promoter involves at least two discrete steps: chromatin potentiation by PvALF followed by ABA-mediated transcriptional activation.

Footprinting in vivo reveals changing profiles of multiple factor interactions with the beta-phaseolin promoter during embryogenesis

Whereas in vitro techniques are essentially limited to the analysis of interactions with a single or limited number of cis-elements, in vivo footprinting techniques can be used to assess the total profile of factor interactions with a promoter. By probing with dimethylsulphate and using sensitive ligation-mediated PCR analytical techniques, the in vivo status of the phas promoter was determined in transcriptionally active (embryo) and inactive (leaf) tissues. Changes in factor occupancy were detected during embryogenesis, and the greatest complexity seen (at mid-maturation) was in accordance with the many potential binding sites predicted on the basis of sequence comparison. Evidence was obtained that several cis-elements not previously shown to be used for factor binding in plant promoters are occupied. The great complexity of footprints may represent the need for multiple factor interaction to achieve high levels of transcription. Alternatively, it is possible that the differential levels of expression in individual regions of the embryo evident from histochemical analysis of the GUS reporter result from the interaction of relatively few factors, with the overall footprinting pattern representing a summation of patterns from various tissues.

Longevity of 5-azacytidine-mediated gene expression and re-establishment of silencing in transgenic rice

Epigenetic silencing of a bialaphos resistance (bar) gene in R1 progeny of a transgenic rice line was found to be meiotically stable since selfed (R2) progeny were also susceptible and the bar locus highly methylated. A high proportion of R2 seedlings germinated in the presence of 5-azacytidine (AzaC) were herbicide-resistant and also contained at least one unmethylated copy of the bar gene, further establishing the relationship between silencing and methylation. Restored bar gene expression was typically maintained for 20-50 days, but eventual methylation and silencing of the bar locus underscores the ability of the recipient genome to recognize and inactivate intrusive DNA.

Architectural specificity in chromatin structure at the TATA box in vivo: nucleosome displacement upon beta-phaseolin gene activation

Extensive studies of the beta-phaseolin (phas) gene in transgenic tobacco have shown that it is highly active during seed embryogenesis but is completely silent in leaf and other vegetative tissues. In vivo footprinting revealed that the lack of even basal transcriptional activity in vegetative tissues is associated with the presence of a nucleosome that is rotationally positioned with base pair precision over three phased TATA boxes present in the phas promoter. Positioning is sequence-dependent because an identical rotational setting is obtained upon nucleosome reconstitution in vitro. A comparison of DNase I and dimethyl sulfate footprints in vivo and in vitro strongly suggests that this repressive chromatin architecture is remodeled concomitant with gene activation in the developing seed. This leads to the disruption of histone-mediated DNA wrapping and the assembly of the TATA boxes into a transcriptionally competent nucleoprotein complex.

Recurrent onset of epigenetic silencing in rice harboring a multi-copy transgene

Extensive methylation of the Ubi1 promoter has been shown to be associated with transcriptional silencing and bialaphos herbicide sensitivity in several R(1) progeny derived from a transgenic rice line, JKA 52, containing multiple copies of the introduced genes (Kumpatla et al. 1997;Plant Physiol. 115, 361-373). All of the progeny from silenced R(1) lines were silenced, and a proportion (24%) of the R(2) seedlings from JKA 52-6, a non-silenced homozygous R(1) line, were found to be silenced. Several non-silenced (bialaphos-resistant) R(2) progeny derived from the selfed seed of JKA 52-6 were tested at various stages throughout the growth period and found to be resistant to bialaphos, indicating the absence of silencing. Five of these were investigated further to determine whether silencing could recur in subsequent generations. R(3) seedlings were raised from selfed R(2) seed and herbicide sensitivity was detected in 5-40% of the plants in three of the five lines. This silencing was accompanied by methylation of the Ubi1 promoter and the absence of steady-state bar mRNA. This recurrent onset of silencing and instability of expression associated with a transgene locus containing several repeated sequences is undesirable. The data strongly suggest that multi-generation molecular analysis should be undertaken for transgenic lines to be used for agricultural purposes and that lines containing methylated inserts should be carefully evaluated before being included in further breeding strategies.

Epigenetic transcriptional silencing and 5-azacytidine-mediated reactivation of a complex transgene in rice

Despite a growing number of reports indicating non-Mendelian inheritance of transgene expression in monocots, no detailed description of the structure and stability of the transgene exists for transformants generated by direct DNA-transfer techniques, making the cause for these observations difficult to determine. In this paper we describe the complex organization of Btt cryIIIA and bar transgenes in rice (Oryza sativa L.) that displayed aberrant segregation in R1 progeny. Silencing rather than rearrangement of the bar gene was implicated because the herbicide-sensitive R1 plants had a DNA hybridization profile identical to that of the resistant R0 parent and R1 siblings. Genomic DNA analysis revealed substantial methylation of the Ubi1/bar sequences in silenced plants and, to a lesser degree, in herbicide-resistant plants, suggesting that the transgene locus was potentiated for silencing. Nuclease protection and nuclear run-on assays confirmed that silencing was due to transcriptional inactivation. Treatment of R2 progeny of silenced plants with 5-azacytidine resulted in demethylation of the Ubi1 promoter and reactivation of bar gene expression, demonstrating a functional relationship for methylation in gene silencing. These findings indicate that methylation-based silencing may be frequent in cereals transformed by direct DNA protocols that insert multiple, often rearranged sequences.

Paraneoplastic syndromes: mechanisms

Neoplasms may affect distant host tissues, but they always involve normal physiologic mechanisms. Van R. Potter said that "Oncogeny is blocked ontogeny," so tumors are committed to their organ anlagen. Paraneoplastic mediators are appropriate to their blocked anlagen stages. Mediators may have autocrine, paracrine, or endocrine actions. However, their release and distribution depend on the mode of cell death, and the spatial relations to host vascularity. Invasiveness and metastasis are means of normal embryonic development, and not new cancer-specific properties. Nor do human cancers acquire new foreign genetic information; thus, they cannot express neoantigens nor be recognized by the host. However, tumors breach the blood-brain barrier and basement membrane separations of ectoderm from mesenchyme and release "forbidden" self-antigens, to which host immunocytes may respond causing cell- and antibody-mediated autoimmunity. This can damage normal host tissues by a "bystander" effect. Paraneoplastic mechanisms can also be analyzed as arising from three-way interactions between cells blocked in ontogeny, their molecular messengers, and the host tissues they target.

The beta-phaseolin 5' matrix attachment region acts as an enhancer facilitator

MARs found flanking the beta-phaseolin gene (phas) were tested for insulating activity in an enhancer blocking assay. True insulators should block enhancer dependent expression of a reporter gene when placed between the enhancer and a promoter. Insertion of phas 3' MAR or coding sequences lowered CaMV 35S enhancer driven GUS expression from the phas basal promoter, indicating a distance dependence of the 35S enhancer. 5' MAR or 5' MAR core fragments could not act as independent enhancers when fused to the phas basal promoter, and did not lower expression when inserted in the enhancer blocking assay construct, indicating that they facilitated 35S enhancer expression at a distance when located between the enhancer and the promoter.

Analysis of kafirin promoter activity in transgenic tobacco seeds

Sequences corresponding to 855 bp of 5' promoter region and the transit peptide from lambdaGK.1,a genomic clone encoding a 22 kDa alpha-kafirin seed protein from sorghum, were translationally fused to a cloned beta-glucuronidase (GUS) coding sequence from uidA and transferred to tobacco via Agrobacterium tumefaciens-mediated transformation. No GUS expression was detectable at any stage of growth in stems or leaves of these plants. However, GUS expression was detected in both embryo and endosperm tissues of resulting tobacco seeds 10-15 days after flowering. Dissected tissues indicate endosperm expression was localized within the bulk endosperm and not within the parenchyma cell layer underlying the integument. These studies also demonstrate that within dissected tobacco embryos, expression from the kafirin promoter was restricted to the mesocotyl region.

A 68 bp element of the beta-phaseolin promoter functions as a seed-specific enhancer

In beans, expression of the beta-phaseolin gene (phas), encoding the major seed storage protein of bean (Phaseolus vulgaris) is confined to the cotyledons of developing embryos. Phaseolin has not been detected in the endosperm, which remains liquid and is lost early in development. However, fusion constructs between the phas promoter and the gus-coding region yield expression in both embryo and endosperm of developing seeds from transgenic tobacco (Nicotiana tabacum) plants. Although elements extending 1470 bp upstream of the transcription start site are known to modulate phas expression, the proximal 295 bp (p295) are sufficient to drive high levels of seed-specific GUS activity. This region was dissected into three elements: a 68 bp element (seed specific enhancer, SSE: -295 to -227), a middle region (-227 to -109) and a basal phas promoter (-109 to +20: p109). Different promoter constructs containing the SSE or middle region upstream of p109 or a CaMV 35S basal promoter (-64 to +6) were fused to gus. Each construct was expressed in seed, but not in vegetative tissues. Use of the various phas promoter regions yielded notable differences in relative GUS activity in embryo or endosperm. Addition of both the SSE and middle region resulted in higher activity than the sum of adding either element alone to p109, indicating synergistic interaction between these elements. Seeds from plants transformed with the proximal 227 bp of promoter (p227) showed embryo-specific GUS activity. In contrast, constructs containing two copies of the SSE element were preferentially expressed in the endosperm. These results illustrate the modular nature of the proximal phas promoter, where distinct elements contribute to high levels of expression in different parts of the seed.

Intron position affects expression from the tpi promoter in rice

A series of promoter-GUS fusion constructs containing a portion of the rice triosephosphate isomerase (tpi) promoter, the first tpi intron, and the gene encoding bacterial beta-glucuronidase (GUS) were made. These constructs were electroporated into rice protoplasts and transient expression was monitored. Inclusion of the first intron from the rice tpi gene enhanced expression of the GUS gene from the tpi promoter when it was placed 5' of the GUS gene. When the tpi intron was placed in the 3'-untranslated region no enhancement of GUS gene expression was observed, indicating the importance of position in intron-mediated enhancement of gene expression.

Interaction of host proteins with the plus-strand promoter of brome mosaic virus RNA-2

The binding of five barley proteins (Mr: 37, 36, 35, 34, and 30 kDa) to the ICR2 motif present at the 5' end of brome mosaic virus (BMV) RNA-2 was identified using UV cross-linking. Evidence that the interaction is specific included the observation that these proteins did not recognize a similar-size RNA fragment transcribed from a nonviral (beta-glucuronidase) gene, nor did they bind to the 3' end of the plus strand of RNA-3. Replication-defective BMV RNA-2 mutants bearing substitution mutations at nucleotides 9 and 10 of the ICR2 motif were used to show that these positions were involved in the interaction of the five barley proteins with BMV RNA-2. Surprisingly, the profile of barley proteins interacting with the 3' end of the minus strand of RNA-2 was similar to that seen for the 5' end of the plus strand. Further, the profile of proteins binding to minus-sense probes bearing substitution mutations in the ICR2 region differed from that found for the wild-type sequence. These findings support the concept that host proteins are involved in genome replication and that their ability to interact with both plus and minus strands of the viral RNA is probably involved with the initiation of plus-strand synthesis.

Cell Ablation Reveals That Expression from the Phaseolin Promoter Is Confined to Embryogenesis and Microsporogenesis

Most previous studies of the [beta]-phaseolin (phas) gene, which encodes the major storage protein in bean (Phaseolus vulgaris L.), have shown its expression to be rigorously confined to the developing seed, both in bean and transgenic tobacco (Nicotiana tabacum L. cv Xanthi) plants. To confirm unequivocally the lack of phas expression in vegetative tissues, we placed the diphtheria toxin A-chain (DT-A) coding region under the control of [beta]-phaseolin promoter sequences. Tobacco plants transgenic for phas/DT-A were phenotypically normal until flowering, when they produced anthers that were externally normal but contained no viable pollen. Microscopic examination of immature anthers revealed a normal tapetum, but the pollen mother cells did not undergo meiosis and subsequently degenerated, resulting in male-sterile plants. This demonstration of phas expression during microsporogenesis was corroborated by the expression of [beta]-glucuronidase in pollen of plants transformed with comparable phas/uidA constructs. Although these findings suggested that similarities in phas expression may exist between seed and pollen maturation, no phas activity could be detected in bean pollen. After fertilization of the DT-A-transformed plants with pollen from wild-type tobacco, 50% of the resulting embryos aborted at the heart stage, defining this as the earliest time for phas expression during embryogenesis.

Complete sequence of the binary vector Bin 19

Despite the widespread use of Bin 19 as a vector for plant transformation, detailed sequence information on its T-DNA region has only recently become available. We now show that the non-T-DNA region, like the T-DNA region, contains several superfluous insertions and find that some functional elements may not contain optimal sequences. Knowledge of the complete 11,777 bp sequence will aid in the construction of exceptionally efficient derivative vectors of approximately half this size. Precise knowledge of restriction sites and removal of unnecessary sequences will facilitate plasmid manipulations and plant transformation.

Characterization of a rice gene family encoding root-specific proteins

Two cDNA clones (RCc2 and RCc3) corresponding to mRNAs highly expressed only in root tissues of rice (Oryza sativa L.) seedlings were characterized. Respectively, they encode polypeptides of 146 (14.5 kDa) and 133 amino acids (13.4 kDa) that share high (> 70%) sequence similarity with a polypeptide encoded by a cDNA (ZRP3) encoding an mRNA preferentially expressed in young maize roots. Genomic DNA blot analysis revealed that they are members of a small gene family and RCg2, the gene corresponding to RCc2, was isolated. A 1656 bp 5'-upstream sequence of RCg2 was translationally fused to a beta-glucuronidase (GUS) reporter gene and stable introduction of the chimeric construct into rice was confirmed by PCR and genomic DNA blot analyses. Histochemical analysis of transgenic rice plants containing the full-length chimeric gene showed high levels of GUS activity in mature cells and the elongation and maturation zones of primary and secondary roots, and in the root caps, but no GUS activity was detected in root meristematic regions. Surprisingly, high GUS activity was also detected in leaves of the same plants. This raises the possibility that the RCg2 5'-upstream element may not be sufficient for the proper spatial control of root specificity in transgenic rice.

Rice Triosephosphate Isomerase Gene 5[prime] Sequence Directs [beta]-Glucuronidase Activity in Transgenic Tobacco but Requires an Intron for Expression in Rice

In rice (Oryza sativa L.), cytosolic triosephosphate isomerase (TPI) is encoded by a single gene. TPI catalyzes a vital step in glycolysis, and RNA blots showed that the tpi gene is expressed in all vegetative tissues (root, culm, and leaves) and in rice suspension cells. No effect of light on expression was detected, but submergence of rice seedlings resulted in elevated levels of TPI mRNA in roots and culms. The 2767-bp 5[prime] upstream sequence of the tpi gene was fused translationally with the [beta]-glucuronidase (gusA) gene, and the resulting construct, TPI-GUS, was found to express constitutive, high levels of GUS activity in transgenic tobacco (Nicotiana tabacum) plants. However, the same construct yielded no GUS activity in stably transformed rice plants, and RNA blots showed that no GUS mRNA could be detected even though stable integration of functional copies of the construct was confirmed by Southern blot and genomic polymerase chain reaction analyses. Transient assays using particle bombardment yielded high levels of GUS expression from the TPI-GUS construct in tobacco leaves, but essentially no expression in rice, barley, or maize leaves. When the first intron of the tpi gene was included in the construct (TPI-int1-GUS), transient GUS activity was routinely obtained in rice leaves, revealing that the first intron of the rice tpi gene is crucial for its expression in rice. TPI-int1-GUS also directed transient GUS expression in maize and barley leaves, but little or no activity was obtained from this construct in tobacco, tomato, or soybean leaves. These results with the rice tpi promoter are in accordance with mounting evidence that differences in gene expression exist between monocots and dicots.

Cyclophilins are encoded by a small gene family in rice

cDNA clones were isolated and sequenced that encode two related but distinct rice cyclophilins, Cyp1 and Cyp2. The predicted amino acid sequences of each are 72% identical to human T-cell cyclophilin. Genomic DNA gel blot analysis suggests cyclophilins in rice are encoded by a small, 6-10-member gene family. Both Cyp1 and Cyp2 have seven extra amino acid residues in the N-terminal portion of the proteins that are not found in human or other non-plant cyclophilins, suggesting that this is a characteristic of plant cyclophilins. Cyp2 was expressed as 1000 nt transcripts in leaf and root tissues. Cyp1 was expressed as 800 and 900 nt transcripts. Whereas the 900 nt transcript was present in both root and leaf mRNA, the 800 nt transcript was only detectable in root mRNA. A genomic clone of Cyp2 was isolated, sequenced and shown to lack introns. A single transcriptional start site was identified 27 residues downstream of a putative TATA box. The 5' end of the transcript was shown to contain a region rich in adenyl residues (27 of 35). This region would not be conducive to secondary structure formation, which raises the possibility that Cyp2 might be preferentially translated during stress conditions.