The sequence of the human genome

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Phylotranscriptomic analysis of the origin and early diversification of land plants

Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.

Laparoscopic versus open gastric bypass: a randomized study of outcomes, quality of life, and costs

OBJECTIVE

To compare outcomes, quality of life (QOL), and costs of laparoscopic and open gastric bypass (GBP).

SUMMARY BACKGROUND DATA

Laparoscopic GBP has been reported to be a safe and effective approach for the treatment of morbid obesity. The authors performed a prospective randomized trial to compare outcomes, QOL, and costs of laparoscopic GBP with those of open GBP.

METHODS

From May 1999 to March 2001, 155 patients with a body mass index (BMI) of 40 to 60 kg/m2 were randomly assigned to undergo laparoscopic (n = 79) or open (n = 76) GBP. The two groups were similar in age, sex ratio, mean BMI, and comorbidities. Main outcome measures included operative time, estimated blood loss, length of hospital stay, operative complications, percentage of excess body weight loss, and time to return to activities of daily living and work. Changes in QOL were assessed using the SF-36 Health Survey and the bariatric analysis of reporting outcome system (BAROS). Operative and hospital costs of the two operations were also compared.

RESULTS

There were no deaths in either group. Mean operative time was longer for laparoscopic GBP than for open GBP, but operative blood loss was less. Two (2.5%) of the 79 patients in the laparoscopic group required conversion to laparotomy. Median length of hospital stay was shorter for laparoscopic GBP patients (3 vs 4 days). The rate of postoperative anastomotic leak was similar between groups. Wound-related complications such as infection (10.5 vs 1.3%) and incisional hernia (7.9 vs 0%) were more common after open GBP; late anastomotic stricture was less frequent after open GBP (2.6 vs 11.4%). Time to return to activities of daily living and work were shorter after laparoscopic GBP than after open GBP. Weight loss at 1 year was similar between groups. Preoperative SF-36 scores were similar between groups; however, at 1 month after surgery, laparoscopic patients had better physical conditioning, social functioning, general health, and less body pain than open GBP patients. At 6 months, the BAROS outcome was classified as good or better in 97% of laparoscopic GBP patients compared with 82% of open GBP patients. Operative costs were higher for laparoscopic GBP patients, but hospital costs were lower.

CONCLUSIONS

Laparoscopic GBP is a safe and cost-effective alternative to open GBP. Despite a longer operative time, patients undergoing laparoscopic GBP benefited from less blood loss, a shorter hospital stay, and faster convalescence. Laparoscopic GBP patients had comparable weight loss at 1 year but a more rapid improvement in QOL than open GBP patients. The higher initial operative costs for laparoscopic GBP were adequately offset by the lower hospital costs.

Dynamic visualization of local protein synthesis in hippocampal neurons

Using pharmacological approaches, several recent studies suggest that local protein synthesis is required for synaptic plasticity. Convincing demonstrations of bona fide dendritic protein synthesis in mammalian neurons are rare, however. We developed a protein synthesis reporter in which the coding sequence of green fluorescent protein is flanked by the 5' and 3' untranslated regions from CAMKII-alpha, conferring both dendritic mRNA localization and translational regulation. In cultured hippocampal neurons, we show that BDNF, a growth factor involved in synaptic plasticity, stimulates protein synthesis of the reporter in intact, mechanically, or "optically" isolated dendrites. The stimulation of protein synthesis is blocked by anisomycin and not observed in untreated neurons. In addition, dendrites appear to possess translational hot spots, regions near synapses where protein synthesis consistently occurs over time.

Digital ulcers in systemic sclerosis: Prevention by treatment with bosentan, an oral endothelin receptor antagonist

OBJECTIVE

Recurrent digital ulcers are a manifestation of vascular disease in patients with systemic sclerosis (SSc; scleroderma) and lead to pain, impaired function, and tissue loss. We investigated whether treatment with the endothelin receptor antagonist, bosentan, decreased the development of new digital ulcers in patients with SSc.

METHODS

This was a randomized, prospective, placebo-controlled, double-blind study of 122 patients at 17 centers in Europe and North America, evaluating the effect of treatment on prevention of digital ulcers. The primary outcome variable was the number of new digital ulcers developing during the 16-week study period. Secondary assessments included healing of existing digital ulcers and evaluation of hand function using the Scleroderma Health Assessment Questionnaire.

RESULTS

Patients receiving bosentan had a 48% reduction in the mean number of new ulcers during the treatment period (1.4 versus 2.7 new ulcers; P = 0.0083). Patients who had digital ulcers at the time of entry in the study were at higher risk for the development of new ulcers; in this subgroup the mean number of new ulcers was reduced from 3.6 to 1.8 (P = 0.0075). In patients receiving bosentan, a statistically significant improvement in hand function was observed. There was no difference between treatment groups in the healing of existing ulcers. Serum transaminase levels were elevated to >3-fold the upper limit of normal in bosentan-treated patients; this elevation is comparable with that observed in previous studies of this agent. Other side effects were similar in the 2 treatment groups.

CONCLUSION

Endothelins may play an important role in the pathogenesis of vascular disease in patients with SSc. Treatment with the endothelin receptor antagonist bosentan may be effective in preventing new digital ulcers and improving hand function in patients with SSc.

Data access for the 1,000 Plants (1KP) project

The 1,000 plants (1KP) project is an international multi-disciplinary consortium that has generated transcriptome data from over 1,000 plant species, with exemplars for all of the major lineages across the Viridiplantae (green plants) clade. Here, we describe how to access the data used in a phylogenomics analysis of the first 85 species, and how to visualize our gene and species trees. Users can develop computational pipelines to analyse these data, in conjunction with data of their own that they can upload. Computationally estimated protein-protein interactions and biochemical pathways can be visualized at another site. Finally, we comment on our future plans and how they fit within this scalable system for the dissemination, visualization, and analysis of large multi-species data sets.

Circular ecDNA promotes accessible chromatin and high oncogene expression

Oncogenes are commonly amplified on particles of extrachromosomal DNA (ecDNA) in cancer1,2, but our understanding of the structure of ecDNA and its effect on gene regulation is limited. Here, by integrating ultrastructural imaging, long-range optical mapping and computational analysis of whole-genome sequencing, we demonstrate the structure of circular ecDNA. Pan-cancer analyses reveal that oncogenes encoded on ecDNA are among the most highly expressed genes in the transcriptome of the tumours, linking increased copy number with high transcription levels. Quantitative assessment of the chromatin state reveals that although ecDNA is packaged into chromatin with intact domain structure, it lacks higher-order compaction that is typical of chromosomes and displays significantly enhanced chromatin accessibility. Furthermore, ecDNA is shown to have a significantly greater number of ultra-long-range interactions with active chromatin, which provides insight into how the structure of circular ecDNA affects oncogene function, and connects ecDNA biology with modern cancer genomics and epigenetics.

Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics

Culex quinquefasciatus (the southern house mosquito) is an important mosquito vector of viruses such as West Nile virus and St. Louis encephalitis virus, as well as of nematodes that cause lymphatic filariasis. C. quinquefasciatus is one species within the Culex pipiens species complex and can be found throughout tropical and temperate climates of the world. The ability of C. quinquefasciatus to take blood meals from birds, livestock, and humans contributes to its ability to vector pathogens between species. Here, we describe the genomic sequence of C. quinquefasciatus: Its repertoire of 18,883 protein-coding genes is 22% larger than that of Aedes aegypti and 52% larger than that of Anopheles gambiae with multiple gene-family expansions, including olfactory and gustatory receptors, salivary gland genes, and genes associated with xenobiotic detoxification.

PASTA: Ultra-Large Multiple Sequence Alignment for Nucleotide and Amino-Acid Sequences

We introduce PASTA, a new multiple sequence alignment algorithm. PASTA uses a new technique to produce an alignment given a guide tree that enables it to be both highly scalable and very accurate. We present a study on biological and simulated data with up to 200,000 sequences, showing that PASTA produces highly accurate alignments, improving on the accuracy and scalability of the leading alignment methods (including SATé). We also show that trees estimated on PASTA alignments are highly accurate--slightly better than SATé trees, but with substantial improvements relative to other methods. Finally, PASTA is faster than SATé, highly parallelizable, and requires relatively little memory.

Interferon-λ and interleukin 22 act synergistically for the induction of interferon-stimulated genes and control of rotavirus infection

The epithelium is the main entry point for many viruses, but the processes that protect barrier surfaces against viral infections are incompletely understood. Here we identified interleukin 22 (IL-22) produced by innate lymphoid cell group 3 (ILC3) as an amplifier of signaling via interferon-λ (IFN-λ), a synergism needed to curtail the replication of rotavirus, the leading cause of childhood gastroenteritis. Cooperation between the receptor for IL-22 and the receptor for IFN-λ, both of which were 'preferentially' expressed by intestinal epithelial cells (IECs), was required for optimal activation of the transcription factor STAT1 and expression of interferon-stimulated genes (ISGs). These data suggested that epithelial cells are protected against viral replication by co-option of two evolutionarily related cytokine networks. These data may inform the design of novel immunotherapy for viral infections that are sensitive to interferons.

Identification of a novel chemokine (CCL28), which binds CCR10 (GPR2)

We report the identification and characterization of a novel CC chemokine designated CCL28 and its receptor CCR10, known previously as orphan G-protein-coupled receptor GPR2. Human and mouse CCL28 share 83% identity at the amino acid and 76% at the nucleic acid levels. We also identified the mouse homologues of CCL28 and of CCR10, which map to mouse chromosomes 13 and 11, respectively. CCL28 is expressed in a variety of human and mouse tissues, and it appears to be predominantly produced by epithelial cells. Both human and mouse CCL28 induce calcium mobilization in human and mouse CCR10-expressing transfectants. CCL28 desensitized the calcium mobilization induced in CCR10 transfectants by CCL27, indicating that these chemokines share this new chemokine receptor. In vitro, recombinant human CCL28 displays chemotactic activity for resting CD4 or CD8 T cells.

LILRB4 signalling in leukaemia cells mediates T cell suppression and tumour infiltration

Immune checkpoint blockade therapy has been successful in treating some types of cancer but has not shown clinical benefits for treating leukaemia1. This result suggests that leukaemia uses unique mechanisms to evade this therapy. Certain immune inhibitory receptors that are expressed by normal immune cells are also present on leukaemia cells. Whether these receptors can initiate immune-related primary signalling in tumour cells remains unknown. Here we use mouse models and human cells to show that LILRB4, an immunoreceptor tyrosine-based inhibition motif-containing receptor and a marker of monocytic leukaemia, supports tumour cell infiltration into tissues and suppresses T cell activity via a signalling pathway that involves APOE, LILRB4, SHP-2, uPAR and ARG1 in acute myeloid leukaemia (AML) cells. Deletion of LILRB4 or the use of antibodies to block LILRB4 signalling impeded AML development. Thus, LILRB4 orchestrates tumour invasion pathways in monocytic leukaemia cells by creating an immunosuppressive microenvironment. LILRB4 represents a compelling target for the treatment of monocytic AML.

Subsite mapping of the human pancreatic alpha-amylase active site through structural, kinetic, and mutagenesis techniques

We report a multifaceted study of the active site region of human pancreatic alpha-amylase. Through a series of novel kinetic analyses using malto-oligosaccharides and malto-oligosaccharyl fluorides, an overall cleavage action pattern for this enzyme has been developed. The preferred binding/cleavage mode occurs when a maltose residue serves as the leaving group (aglycone sites +1 and +2) and there are three sugars in the glycon (-1, -2, -3) sites. Overall it appears that five binding subsites span the active site, although an additional glycon subsite appears to be a significant factor in the binding of longer substrates. Kinetic parameters for the cleavage of substrates modified at the 2 and 4' ' positions also highlight the importance of these hydroxyl groups for catalysis and identify the rate-determining step. Further kinetic and structural studies pinpoint Asp197 as being the likely nucleophile in catalysis, with substitution of this residue leading to an approximately 10(6)-fold drop in catalytic activity. Structural studies show that the original pseudo-tetrasaccharide structure of acarbose is modified upon binding, presumably through a series of hydrolysis and transglycosylation reactions. The end result is a pseudo-pentasaccharide moiety that spans the active site region with its N-linked "glycosidic" bond positioned at the normal site of cleavage. Interestingly, the side chains of Glu233 and Asp300, along with a water molecule, are aligned about the inhibitor N-linked glycosidic bond in a manner suggesting that these might act individually or collectively in the role of acid/base catalyst in the reaction mechanism. Indeed, kinetic analyses show that substitution of the side chains of either Glu233 or Asp300 leads to as much as a approximately 10(3)-fold decrease in catalytic activity. Structural analyses of the Asp300Asn variant of human pancreatic alpha-amylase and its complex with acarbose clearly demonstrate the importance of Asp300 to the mode of inhibitor binding.

Comparison of minimally invasive esophagectomy with transthoracic and transhiatal esophagectomy

HYPOTHESIS

Minimally invasive esophagectomy can be performed as safely as conventional esophagectomy and has distinct perioperative outcome advantages.

DESIGN

A retrospective comparison of 3 methods of esophagectomy: minimally invasive, transthoracic, and blunt transhiatal.

SETTING

University medical center.

PATIENTS

Eighteen consecutive patients underwent combined thoracoscopic and laparoscopic esophagectomy from October 9, 1998, through January 19, 2000. These patients were compared with 16 patients who underwent transthoracic esophagectomy and 20 patients who underwent blunt transhiatal esophagectomy from June 1, 1993, through August 5, 1998.

MAIN OUTCOME MEASURES

Operative time, amount of blood loss, number of operative transfusions, length of intensive care and hospital stays, complications, and mortality.

RESULTS

Patients who had minimally invasive esophagectomy had shorter operative times, less blood loss, fewer transfusions, and shortened intensive care unit and hospital courses than patients who underwent transthoracic or blunt transhiatal esophagectomy. There was no significant difference in the incidence of anastomotic leak or respiratory complications among the 3 groups.

CONCLUSION

Minimally invasive esophagectomy is safe and provides clinical advantages compared with transthoracic and blunt transhiatal esophagectomy.

Venous Thrombosis in Patients with Solid Tumors: Determination of Frequency and Characteristics

Deep venous thrombosis (DVT) and pulmonary embolism (PE) are well recognized complications of cancer. However, our current knowledge of this association is derived from studies conducted more than a decade ago. In light of the changes in medical practice and the improvement in cancer care in recent years, a re-evaluation of the relationship between malignancy and venous thrombosis is in order. Of a total of 1041 patients with solid tumors admitted to 3 major medical centers, there were 81 (7.8%) diagnosed with DVT/PE. Patients were more likely to develop DVT/PE during chemotherapy (p = .0001). Advanced malignancies (p = .001), renal carcinoma (p = .005), pancreatic (p = .001), gastric (p = .014) and brain tumors (p = .001) were independent variables strongly associated with the occurrence of venous thrombosis. The occurrence of thrombotic events in the population tested in this study did not adversely affect survival (p = .082).

The study identifies subset of patients with cancer at high risk for venous thrombosis. Early prophylaxis with anticoagulants in these patients may be warranted. Most importantly, further clinical trials are desperately awaited to detect possible new trends in the frequency and types of thrombotic events and to better define prevention strategies in cancer patients at risk for thrombosis.

The association between venous thromboembolic disease (VTD) and malignant neoplastic disorders is well known and has been the subject of several reports for more than a century (1–8). There is a general agreement among investigators that thrombotic complications in patients with cancer occur at a rather high frequency, and that other circumstantial factors such as surgery or chemotherapy potentiates this risk (9,10). However, several important considerations pertaining to cancer and thrombosis continue to be shrouded in controversy. For example, there are inexplicable differences in the proportion of patients with cancer diagnosed with deep venous thrombosis (DVT) or pulmonary embolism (PE) reported in the literature (2, 4, 5, 11). In the absence of large well-controlled studies, one may only postulate on the reasons that contributed to these differences. The inclusion of different types of VTD such as superficial, venous, arterial or vascular access device-induced thrombosis may have led to overestimation of the incidence of these events in patients with underlying malignancy. Another possible explanation for this discrepancy relates to the use of a variety of diagnostic and methodological criteria ranging from observation and clinical suspicion to more invasive procedures resulting in considerable differences in the rate of reported clotting events (12). Along the same line of discussion, one may argue whether VTD is a random event or constitutes a complication that occurs more commonly in patients with distinct characteristics and certain tumor types. To further investigate the association between malignancy and thrombosis, we evaluated 1041 patients with solid tumors for the risk of DVT/PE. The main objectives of the study were to determine the frequency of DVT/PE based on validated diagnostic criteria and to identify patients with cancer at high risk for developing these thrombotic episodes. Also, we evaluated the impact of VTD on the survival of these patients.

Sugar ring distortion in the glycosyl-enzyme intermediate of a family G/11 xylanase

The 1.8 A resolution structure of the glycosyl-enzyme intermediate formed on the retaining beta-1,4-xylanase from Bacillus circulans has been determined using X-ray crystallographic techniques. The 2-fluoro-xylose residue bound in the -1 subsite adopts a 2,5B (boat) conformation, allowing atoms C5, O5, C1, and C2 of the sugar to achieve coplanarity as required at the oxocarbenium ion-like transition states of the double-displacement catalytic mechanism. Comparison of this structure to that of a mutant of this same enzyme noncovalently complexed with xylotetraose [Wakarchuk et al. (1994) Protein Sci. 3, 467-475] reveals a number of differences beyond the distortion of the sugar moiety. Most notably, a bifurcated hydrogen bond interaction is formed in the glycosyl-enzyme intermediate involving Heta of Tyr69, the endocyclic oxygen (O5) of the xylose residue in the -1 subsite, and Oepsilon2 of the catalytic nucleophile, Glu78. To gain additional understanding of the role of Tyr69 at the active site of this enzyme, we also determined the 1.5 A resolution structure of the catalytically inactive Tyr69Phe mutant. Interestingly, no significant structural perturbation due to the loss of the phenolic group is observed. These results suggest that the interactions involving the phenolic group of Tyr69, O5 of the proximal saccharide, and Glu78 Oepsilon2 are important for the catalytic mechanism of this enzyme, and it is proposed that, through charge redistribution, these interactions serve to stabilize the oxocarbenium-like ion of the transition state. Studies of the covalent glycosyl-enzyme intermediate of this xylanase also provide insight into specificity, as contacts with C5 of the xylose moiety exclude sugars with hydroxymethyl substituents, and the mechanism of catalysis, including aspects of stereoelectronic theory as applied to glycoside hydrolysis.

Ischemia induces translocation of the insulin-responsive glucose transporter GLUT4 to the plasma membrane of cardiac myocytes

BACKGROUND

Acute myocardial ischemia is accompanied by an increase in glucose uptake and metabolism, which appears to be important in protecting myocardial cells from irreversible ischemic injury. Because insulin augments myocardial glucose uptake by inducing the translocation of glucose transporters from an intracellular compartment to the plasma membrane, we hypothesized that acute ischemia would trigger a similar translocation.

METHODS AND RESULTS

We used a subcellular fractionation method to separate intracellular membrane and plasma membranes from control, ischemic, and hypoxic Langendorff-isolated perfused rat hearts and determined the expression of the major myocardial glucose transporter, GLUT4, in these separated membrane fractions. We found that translocation of GLUT4 molecules occurred in ischemic, hypoxic, and insulin-treated hearts and in hearts that underwent ischemia plus insulin treatment. The percentages of GLUT4 molecules present on the plasma membrane in the different conditions were as follows: control, 18.0 +/- 2.8%; ischemia, 41.3 +/- 9.4%; hypoxia, 31.1 +/- 2.9%; insulin, 61.1 +/- 2.6%; and ischemia plus insulin, 66.8 +/- 5.7%. Among the statistically significant differences in these values were the difference between control and ischemia and the difference between ischemia alone and insulin plus ischemia.

CONCLUSIONS

Ischemia causes substantial translocation of GLUT4 molecules to the plasma membrane of cardiac myocytes. A combination of insulin plus ischemia stimulates an even greater degree of GLUT4 translocation. GLUT4 translocation is likely to mediate at least part of the increased glucose uptake of ischemic myocardium and may be a mechanism for the cardioprotective effect of insulin during acute myocardial ischemia.

Multiple signaling pathways involved in activation of matrix metalloproteinase-9 (MMP-9) by heregulin-beta1 in human breast cancer cells

Matrix metalloproteinase-9 (MMP-9) plays important roles in tumor invasion and angiogenesis. Secretion of MMP-9 has been reported in various cancer types including lung cancer, colon cancer, and breast cancer. In our investigation of MMP-9 regulation by growth factors, MMP-9 was activated by heregulin-beta1 as shown by zymography in both SKBr3 and MCF-7 breast cancer cell lines. Increase in MMP-9 activity was due to increased MMP-9 protein and mRNA levels, which mainly results from transcriptional upregulation of MMP-9 by heregulin-beta1. Heregulin-beta1 activates multiple signaling pathways in breast cancer cells, including Erk, p38 kinase, PKC, and PI3-K pathways. We examined the pathways involved in heregulin-beta1-mediated MMP-9 activation using chemical inhibitors that specifically inhibit each of these heregulin-beta1-activated pathways. The PKC inhibitor RO318220 and p38 kinase inhibitor SB203580 completely blocked heregulin-beta1-mediated activation of MMP-9. MEK-1 inhibitor PD098059 partially blocked MMP-9 activation, whereas PI3-K inhibitor wortmannin had no effect on heregulin-beta1-mediated MMP-9 activation. Therefore, at least three signaling pathways are involved in the activation of MMP-9 by heregulin-beta1. Since MMP-9 is tightly associated with invasion/metastasis and angiogenesis, our studies suggest that blocking heregulin-beta1-mediated activation of MMP-9 by inhibiting the related signaling pathways may provide new strategies for inhibition of cancer metastasis and angiogenesis.

A comparison study of laparoscopic versus open gastric bypass for morbid obesity

BACKGROUND

Laparoscopic Roux-en-Y gastric bypass (GBP) has been previously described, but a comparative study between laparoscopic and open GBP has not been reported. The purpose of this study was to compare surgical outcomes oflaparoscopic GBP with those of open GBP for treatment of morbid obesity.

STUDY DESIGN

From August 1998 to September 1999, we prospectively collected outcome data on 35 patients with body-mass indices between 40 kg/m2 and 60 kg/m2 who underwent laparoscopic GBP. Demographics, operative data, perioperative complications, and weight losses were collected and compared with those obtained from a retrospective chart review of 35 patients with body-mass indices between 40 kg/m2 and 60 kg/m2 who underwent open GBP before August 1998.

RESULTS

Age, gender, preoperative body-mass index, preoperative comorbidity, and earlier abdominal surgery were similar in both groups. All laparoscopic operations were completed without conversion to laparotomy. Mean operative time, operative blood loss, length of intensive care stay, and length of hospital stay were significantly less after laparoscopic GBP than after open GBP (p<0.05). There was no 30-day mortality in either group. At 1-year followup, analysis of the percentage of excess body weight loss showed no significant difference between the two groups (p<0.05).

CONCLUSIONS

Laparoscopic Roux-en-Y gastric bypass is technically feasible and safe. Laparoscopic GBP confers the clinical benefits of laparoscopy and an initial weight loss similar to that of open GBP.

UDP-glucuronosyltransferase activity in human liver and colon

BACKGROUND & AIMS

The contribution of glucuronidation toward human drug metabolism is carried out by the Super gene family of UDP-glucuronosyltransferases (UGTs). Regulation of the human UGT1A locus is tissue specific, resulting in the unique expression of multiple hepatic and extrahepatic gene products. Studies were undertaken to examine UGT1A expression in human hepatic and colonic tissues.

METHODS

UGT1A messenger RNA, protein, catalytic activity, and substrate kinetics were studied in 5 samples of normal hepatic and sigmoid colon tissue using duplex reverse-transcription polymerase chain reaction (RT-PCR), enzymatic and Western blot analysis, and indirect immunofluorescence analysis.

RESULTS

Specific patterns of UGT1A gene expression occur in the liver and colon, which were consistent with different banding patterns as detected by Western blot analysis using a UGT1A-specific antibody. However, microsomal UGT activities in colon were up to 96-fold lower for many phenolic substrates, a finding that was not concordant with RT-PCR and Western blot analysis. Interestingly, UGT activity toward tertiary amines and some steroid hormones was equal.

CONCLUSIONS

Differences of glucuronidation activity between human liver and colon suggest that UGT1A activity may be regulated as a result of the relative presence of individual isoforms with differing catalytic activities or by tissue-specific modulators after gene expression.

An ergonomic evaluation of surgeons' axial skeletal and upper extremity movements during laparoscopic and open surgery

BACKGROUND

Many surgeons have complained of fatigue and musculoskeletal pain after laparoscopic surgery. We evaluated differences in surgeons' axial skeletal and upper extremity movements during laparoscopic and open operations.

METHODS

Five surgeons were videotaped performing 16 operations (8 laparoscopic and 8 open) to record their neck, trunk, shoulder, elbow, and wrist movements during the first hour of surgery. We also compared postprocedural complaints of pain, stiffness, or numbness between the two groups.

RESULTS

Compared with surgeons performing open surgery, surgeons performing laparoscopic surgery exhibited less lateral neck flexion; less trunk flexion; more internal rotation of the shoulders; more elbow flexion; more wrist supination and wrist ulnar and radial deviation. There was a trend of more shoulder stiffness after laparoscopic operations than after open operations.

CONCLUSIONS

Laparoscopic surgery involves a more static posture of the neck and trunk, but more frequent awkward movements of the upper extremities than open surgery. Ergonomic changes in the operating room environment and instrument design could ease the physical stress imposed on surgeons during laparoscopic operations.

Minimally invasive esophagectomy

BACKGROUND

Open esophagectomy can be associated with significant morbidity and delay return to routine activities. Minimally invasive surgery may lower the morbidity of esophagectomy but only a few small series have been published.

METHODS

From August 1996 to September 1999, 77 patients underwent minimally invasive esophagectomy. Initially, esophagectomy was approached totally laparoscopically or with mini-thoracotomy; thoracoscopy subsequently replaced thoracotomy.

RESULTS

Indications included esophageal carcinoma (n = 54), Barrett's high-grade dysplasia or carcinoma in situ (n = 17), and benign miscellaneous (n = 6). There were 50 men and 27 women with an average age of 66 years (range 30 to 94 years). Median operative time was 7.5 hours (4.5 hours with > 20 case experience). Median intensive care unit stay was 1 day (range 0 to 60 days); median length of stay was 7 days (range 4 to 73 days) with no operative or hospital mortalities. There were four nonemergent conversions to open esophagectomy; major and minor complication rates were 27% and 55%, respectively.

CONCLUSIONS

Minimally invasive esophagectomy is technically feasible and safe in our center, which has extensive minimally invasive and open esophageal experience. Open surgery should remain the standard until future studies conclusively demonstrate advantages of minimally invasive approaches.

Recombinant respiratory syncytial viruses with deletions in the NS1, NS2, SH, and M2-2 genes are attenuated in vitro and in vivo

Respiratory syncytial virus (RSV) encodes several proteins that lack well-defined functions; these include NS1, NS2, SH, and M2-2. Previous work has demonstrated that NS2, SH, and M2-2 can each be deleted from RSV genome and thus are considered as accessory proteins. To determine whether RSV can replicate efficiently when two or more transcriptional units are deleted, we removed NS1, NS2, SH, and M2-2 genes individually and in different combinations from an infectious cDNA clone derived from human RSV A2 strain. The following six mutants with two or more genes deleted were obtained: DeltaNS1NS2, DeltaM2-2SH, DeltaM2-2NS2, DeltaSHNS1, DeltaSHNS2, and DeltaSHNS1NS2. Deletion of M2-2 together with NS1 was detrimental to RSV replication. It was not possible to obtain a recombinant RSV when all four genes were deleted. All of the double and triple deletion mutants exhibited reduced replication and small plaque morphology in vitro. Replication of these deletion mutants was more reduced in HEp-2 cells than in Vero cells. Among the 10 single and multiple gene deletion mutants obtained, DeltaM2-2NS2 was most attenuated. DeltaM2-2NS2 formed barely visible plaques in HEp-2 cells and had a reduction of titer of 3 log(10) compared with the wild-type recombinant RSV in infected HEp-2 cells. When inoculated intranasally into cotton rats, all of the deletion mutants were attenuated in the respiratory tract. Our data indicated that the NS1, NS2, SH, and M2-2 proteins, although dispensable for virus replication in vitro, provide auxiliary functions for efficient RSV replication.

Cyclophotocoagulation: a report by the American Academy of Ophthalmology

OBJECTIVE

This document describes cyclophotocoagulation procedures for glaucoma and examines the evidence to answer key questions about patient selection, and efficacy of transscleral and endoscopic techniques.

METHODS

A literature search conducted for the years 1968 to 2000 retrieved 130 citations. The author reviewed 34 of these articles and selected 19 for the panel methodologist to review and rate according to the strength of evidence. A Level I rating is assigned to properly conducted, well-designed, randomized clinical trials; a Level II rating is assigned to well-designed cohort and case-control studies; and a Level III rating is assigned to case series and poorly designed prospective and retrospective studies, including case-control studies.

RESULTS

The predominant problem with all studies on cyclophotocoagulation is the lack of a uniform definition of success, which makes comparisons difficult. One randomized controlled trial (Level I evidence) compared the efficacy of transscleral cyclophotocoagulation with noncontact Nd:YAG and semiconductor diode laser. It found no significant difference between the two, although a significant problem was the variability allowed with laser parameters. Most of the literature consists of noncomparative case series that provide evidence that is limited and often not convincing.

CONCLUSION

Cyclophotocoagulation is indicated for patients with refractory glaucoma who have failed trabeculectomy or tube shunt procedures, patients with minimal useful vision and elevated intraocular pressure, and patients who have no visual potential and need pain relief (based on Level III evidence). It may be useful for patients whose general medical condition precludes invasive surgery or who refuse more aggressive surgery (i.e., filter or tube). It is also useful in emergent situations, such as the acute onset of neovascular glaucoma. There is insufficient evidence to definitively compare the relative efficacy of the cyclophotocoagulation procedures for glaucoma. It is the panel's opinion, however, that semiconductor diode systems appear to possess the best combination of effectiveness (based on Level III evidence), portability, expense, and ease of use at this time.

Comparison of pulmonary function and postoperative pain after laparoscopic versus open gastric bypass: a randomized trial

BACKGROUND

Impairment of pulmonary function is common after upper abdominal operations. The purpose of this study was to compare postoperative pulmonary function and analgesic requirements in patients undergoing either laparoscopic or open Roux-en-Y gastric bypass (GBP).

STUDY DESIGN

Seventy patients with a body mass index of 40 to 60 kg/m2 were randomly assigned to undergo laparoscopic (n = 36) or open (n = 34) GBP. The two groups were similar in age, gender, body mass index, pulmonary history, and baseline pulmonary function. Pulmonary function studies were performed preoperatively and on postoperative days 1, 2, 3, and 7. Oxygen saturation and chest radiographs were performed on both groups preoperatively and on postoperative day 1. Postoperative pain was evaluated using a visual analog scale and the amount of narcotic consumed was recorded. Data are presented as mean +/- standard deviation.

RESULTS

Laparoscopic GBP patients had significantly less impairment of pulmonary function than open GBP patients on the first three postoperative days (p < 0.05). By the 7th postoperative day, all pulmonary function parameters in the laparoscopic GBP group had returned to within preoperative levels, but only one parameter (peak expiratory flow) had returned to preoperative levels in the open GBP group. On the first postoperative day, laparoscopic GBP patients used less morphine than open GBP patients (46 +/- 31 mg versus 76 +/- 39 mg, respectively, p < 0.001), and visual analog scale pain scores at rest and during mobilization were lower after laparoscopic GBP than after open GBP (p < 0.05). Fewer patients after laparoscopic GBP than after open GBP developed hypoxemia (31% versus 76%, p < 0.001) and segmental atelectasis (6% versus 55%, p = 0.003).

CONCLUSION

Laparoscopic gastric bypass resulted in less postoperative suppression of pulmonary function, decreased pain, improved oxygenation, and less atelectasis than open gastric bypass.