Robotic transanal minimally invasive surgery (TAMIS) with the newest robotic surgical platform: a multi-institutional North American experience

BACKGROUND

Transanal minimally invasive surgery (TAMIS) offers intra-luminal full-thickness excision of rectal neoplasia. Robotic TAMIS (RT) allows for greater versatility in motion while operating in the limited space of the rectum. We present our experience with this technique in practice using the DaVinci Xi™ platform.

METHOD

This is a multi-institutional retrospective analysis for patient undergoing Robotic TAMIS for resection of rectal lesions at two tertiary referral hospitals in the United States. Morbidity, mortality, anatomic measurement, and final pathology were analyzed.

RESULTS

Thirty-four patients planned for Robotic TAMIS were identified. Average follow-up was 188 days. The average BMI was 29.5 ± 5.9. All patients had an American Society of Anesthesiologist (ASA) Class of 2 or greater and 21 (62%) were ASA 3 or greater. Rectal lesions located from 2 to 15 cm from the dentate line were successfully resected. Lesions up to 4.5 cm in the longest dimension were successfully resected. The average operative time was 100 ± 70 min, which correlated to a robotic console time of 76 ± 67 min. Patients were placed in Lithotomy in 32 (94%) cases and were prone in only 2 (6%) cases. There were no intraoperative complications or conversions to another technique. The only postoperative complication was a medically managed Clostridium difficile infection in 1 patient. Three patients were upstaged to T2 on final pathology and underwent successful formal resections. BMI was a statistically significant predictor of a longer operation.

CONCLUSIONS

With increased reach and operative range of motion, Robotic TAMIS is a safe and effective method for excising low-risk rectal neoplasia with a wide range of anatomical measurements. Higher BMI is a significant predictor of a longer and likely more challenging operation.

Feasibility of Subcutaneous Gentamicin and Pressurized Irrigation as Adjuvant Strategies to Reduce Surgical Site Infection in Colorectal Surgery: Results of a Pilot Study

Surgical site infections (SSIs) remain a common and costly morbidity after colorectal surgery. This rate remains high even in the setting of strict adherence to Surgical Care Improvement Project Protocols. The aim of our pilot study was to determine the feasibility and safety of subcutaneous gentamicin injection or pressurized irrigation as adjuncts to reduce SSI. A total of 132 patients who underwent colorectal surgery at the VA North Texas Health Care System were prospectively assigned to a pressurized irrigation group (n = 44), a preincision gentamicin injection group (n = 48), or control (n = 40). The primary objective was to assess safety and feasibility of these strategies. Patient demographics were matched among groups. Univariate and multivariate analyses were performed to identify possible predictions of SSI in this cohort. The rate of SSI in the control group was 25 per cent, 13.5 per cent in the pressurized irrigation group, and 12.5 per cent in the gentamicin group ( P = 0.26). Combined, the intervention groups had a 13 per cent SSI versus 25 per cent control ( P = 0.09). Operative time was not increased by the interventions and no intraoperative complications specifically related to the interventions were noted. Postoperative complications were not different between groups. Both albumin and body mass index were associated with SSI. Body mass index was and independent predictor of SSI ( P = 0.006). In conclusion, this pilot study demonstrates the feasibility of the interventions described. There was no detrimental effect of either intervention. There was trend toward a reduction in SSI in the intervention group, which warrants further investigation.

Feasibility of subcutaneous gentamicin and pressurized irrigation as adjuvant strategies to reduce surgical site infection in colorectal surgery: results of a pilot study

Surgical site infections (SSIs) remain a common and costly morbidity after colorectal surgery. This rate remains high even in the setting of strict adherence to Surgical Care Improvement Project Protocols. The aim of our pilot study was to determine the feasibility and safety of subcutaneous gentamicin injection or pressurized irrigation as adjuncts to reduce SSI. A total of 132 patients who underwent colorectal surgery at the VA North Texas Health Care System were prospectively assigned to a pressurized irrigation group (n = 44), a preincision gentamicin injection group (n = 48), or control (n = 40). The primary objective was to assess safety and feasibility of these strategies. Patient demographics were matched among groups. Univariate and multivariate analyses were performed to identify possible predictions of SSI in this cohort. The rate of SSI in the control group was 25 per cent, 13.5 per cent in the pressurized irrigation group, and 12.5 per cent in the gentamicin group (P = 0.26). Combined, the intervention groups had a 13 per cent SSI versus 25 per cent control (P = 0.09). Operative time was not increased by the interventions and no intraoperative complications specifically related to the interventions were noted. Postoperative complications were not different between groups. Both albumin and body mass index were associated with SSI. Body mass index was and independent predictor of SSI (P = 0.006). In conclusion, this pilot study demonstrates the feasibility of the interventions described. There was no detrimental effect of either intervention. There was trend toward a reduction in SSI in the intervention group, which warrants further investigation.

A strategy for reducing surgical backlogs: lessons from a veterans administration hospital

A process was developed to use a nontraditional operative day (Saturday) to increase the number of inguinal herniorrhaphies (IHs) performed. The purpose of this analysis was to compare operating times and outcomes between patients undergoing IH on Saturday versus the weekday. A retrospective review was conducted that included patients who underwent IH from October 2008 to January 2010. This cohort was divided based on the day on which surgery occurred. The outcome measures were operative times, room turnover time, and complication rates. Operative time was shorter for Saturday IHs (50.7 vs. 67.8 min, P ≤ 0.001). The greatest difference between the two groups occurred in turnover times. We considered Saturday turnover time to be zero, which was possible because of multiple support teams and additional room availability. Turnover times during the week averaged 40.5 ± 2 minutes. There was no difference in complication rates for the two groups (Saturday IHs 17.6% vs. 20.9% for weekday IHs, P = 0.75). Elective cases can be accomplished more rapidly during nontraditional operating times if there are multiple support teams and rooms available.

Sexual reproduction and gene flow in the pine pathogen Dothistroma septosporum in British Columbia

Dothistroma septosporum has caused a serious needle blight epidemic in the lodgepole pine forests in northwest British Columbia over the past several years. Although ascocarps had been observed in British Columbia, nothing was known about the contribution of sexual reproduction, gene flow and long-distance dispersal to the epidemic. Amplified fragment length polymorphism and mating-type markers in 19 sites were used to generate population and reproductive data. Overall, evidence suggests a mixed mode of reproduction. Haplotypic diversity was high, with 79 unique and 56 shared haplotypes (possible clones) identified from 192 fungal isolates. Overall, mating-type segregation did not differ significantly from 1:1; however, random mating was rejected in most populations in the index of association and parsimony tree-length permutation analyses using the full data set and, when using clone-corrected data sets, more of the smaller populations showed random mating. Two of the smaller populations consistently showed random mating for both tests using both clone-corrected and noncorrected data. High gene flow is suggested by no differentiation between 14 of the 19 sites, several of which came from young plantations where the pathogen was not likely present prior to the current outbreak. The remaining five sites showed some level of divergence, possibly due to historic separation and endemic pathogen populations. Results indicate a high evolutionary potential and long-distance dispersal in this pathogen, important to consider in future forest management.

Phylogeography and conservation genetics of Lake Qinghai scaleless carp Gymnocypris przewalskii

The objective of this study was to examine the spatial genetic relationships of the Lake Qinghai scaleless carp Gymnocypris przewalskii within the Lake Qinghai system, determining whether genetic evidence supports the current taxonomy of Gymnocypris przewalskii przewalskii and Gymnocypris przewalskii ganzihonensis and whether Gymnocypris przewalskii przewalskii are returning to their natal rivers to spawn. Comparison of mitochondrial (control region) variation (42 haplotypes in 203 fish) of G. przewalskii with the postulated ancestral species found in the Yellow River, Gymnocypris eckloni (10 haplotypes in 23 fish), indicated no haplotype sharing, but incomplete lineage sorting. Consistent with the sub-species status, an AMOVA indicated that the Ganzi River population was significantly different from all other river populations (F(ST) = 0·1671, P < 0·001). No genetic structure was found among the other rivers in the Lake Qinghai catchment. An AMOVA of amplified fragment length polymorphism (AFLP) loci, however, revealed significant genetic differences between most spawning populations (F(ST) = 0·0721, P < 0·001). Both mitochondrial and AFLP data found significant differences among G. p. przewalskii, G. p. ganzihonensis and G. eckloni (F(ST) values of 0·1959 and 0·1431, respectively, P < 0·001). Consistent with the incomplete lineage sorting, Structure analysis of AFLP loci showed evidence of five clusters. One cluster is shared among all sample locations, one is unique to G. p. ganzihonensis and G. eckloni, and the others are mostly found in G. p. przewalskii. Genetic evidence therefore supports the current taxonomy, including the sub-species status of G. p. ganzihonensis, and is consistent with natal homing of most Lake Qinghai populations. These findings have significant implications for the conservation and management of this unique and threatened species. The evidence suggests that G. p. przewalskii should be treated as a single population for conservation purposes. Exchangeability of the populations, however, should not be used to promote homogenization of fish spawning in the different rivers. As some degree of genetic divergence was detected in this study, it is recommended that the spawning groups be treated as separate management units.

Evaluating an evidence-based bundle for preventing surgical site infection: a randomized trial

OBJECTIVE

To determine if an evidence-based practice bundle would result in a significantly lower rate of surgical site infections (SSIs) when compared with standard practice.

DESIGN

Single-institution, randomized controlled trial with blinded assessment of main outcome. The trial opened in April 2007 and was closed in January 2010.

SETTING

Veterans Administration teaching hospital.

PATIENTS

Patients who required elective transabdominal colorectal surgery were eligible. A total of 241 subjects were approached, 211 subjects were randomly allocated to 1 of 2 interventions, and 197 were included in an intention-to-treat analysis.

INTERVENTIONS

Subjects received either a combination of 5 evidenced-based practices (extended arm) or were treated according to our current practice (standard arm). The interventions in the extended arm included (1) omission of mechanical bowel preparation; (2) preoperative and intraoperative warming; (3) supplemental oxygen during and immediately after surgery; (4) intraoperative intravenous fluid restriction; and (5) use of a surgical wound protector.

MAIN OUTCOME MEASURE

Overall SSI rate at 30 days assessed by blinded infection control coordinators using standardized definitions.

RESULTS

The overall rate of SSI was 45% in the extended arm of the study and 24% in the standard arm (P = .003). Most of the increased number of infections in the extended arm were superficial incisional SSIs (36% extended arm vs 19% standard arm; P = .004). Multivariate analysis suggested that allocation to the extended arm of the trial conferred a 2.49-fold risk (95% confidence interval, 1.36-4.56; P = .003) independent of other factors traditionally associated with SSI.

CONCLUSIONS

An evidence-based intervention bundle did not reduce SSIs. The bundling of interventions, even when the constituent interventions have been individually tested, does not have a predictable effect on outcome. Formal testing of bundled approaches should occur prior to implementation.

A report of laryngeal adenocystic carcinoma metastatic to the spleen and the role of splenectomy in the management of metastatic disease: a case report

Introduction

Adenoid cystic carcinoma (ACC) of the larynx is a rare malignancy characterized by an indolent course and late pulmonary metastases. Metastases from the larynx to the spleen are an unusual event. In the present report, we discuss a patient with adenoid cystic carcinoma of the larynx metastatic to the spleen. A review of the literature did not yield any other such incidents. We review the clinical presentation and course of adenoid cystic carcinoma, as well as the role of splenectomy for metastases.

Case presentation

We present a case of laryngeal adenoid cystic carcinoma in a 26-year-old Caucasian man treated with total laryngectomy and ionizing radiation. He initially developed asynchronous pulmonary metastases, which were resected. Our patient subsequently presented with a symptomatic splenic lesion consistent with metastatic disease, for which he underwent laparoscopic splenectomy.

Conclusions

Splenectomy might be indicated for isolated metastases. A splenectomy effectively addresses symptoms and serves as a cytoreduction modality.

Definitive Test to Diagnose Median Arcuate Ligament Syndrome: Injection of Vasodilator During Angiography

The diagnosis of median arcuate ligament (MAL) syndrome and its correlation with symptoms has been controversial since the disease entity was described. The authors describe a technique that will identify patients who will benefit from intervention. Eight patients with isolated celiac artery compression from MAL were identified by the authors. Their technique involved selective cannulation of the superior mesenteric artery (SMA) and injection of a vasodilator during angiography. Symptom reproduction and loss of collateral filling of the celiac territory represented a positive test: 4 of the 8 patients had a positive test and underwent successful surgical treatment of the condition; 3 of them remained asymptomatic at follow-up; 1 patient continues to have mild abdominal discomfort. Of the 4 patients with a negative test, 2 were found to have other conditions causing their symptoms. Vasodilator injection into the SMA is a useful diagnostic test to identify patients with symptomatic MAL syndrome.

Genome organization of glutamine synthetase genes in rainbow trout (Oncorhynchus mykiss)

Unlike mammals, bony fish appear to possess multiple genes encoding glutamine synthetase (GS), the nitrogen metabolism enzyme responsible for the conversion of glutamate and ammonia into glutamine at the expense of ATP. This study reports on the development of genetic markers for each of the four isoforms identified thus far in rainbow trout (Oncorhynchus mykiss) and their genome localization by linkage mapping. We found that genes coding for GS01, GS02, GS03, and GS04 map to four different linkage groups in the trout genome, namely RT-24, RT-23, RT-08, and RT-13, respectively. Linkage groups RT-23 and RT-13 appear to represent distinct chromosomes sharing duplicated marker regions, which lends further support to the previous suggestion that GS02 and GS04 may be duplicate gene copies that evolved from a whole-genome duplication in the trout ancestor. In contrast, there is at present no further evidence that RT-24 and RT-08 share ancestrally homologous segments and additional genomic studies will be needed to clarify the evolutionary origin of genes coding for GS01 and GS03.

Thymocytes between the beta-selection and positive selection checkpoints are nonresponsive to IL-7 as assessed by STAT-5 phosphorylation

Interleukin-7 is widely accepted as a major homeostatic factor involved in T cell development. To assess the IL-7 responsiveness of thymocytes involved in selection processes, we used a new sensitive flow cytometry-based assay to detect intracellular phosphorylation of STAT-5 induced by IL-7 in defined mouse thymocyte subsets. Using this method, we found the earliest thymocyte subset (CD4(-)CD8(-)CD25(-)CD44(+)) to contain both IL-7-responsive and nonresponsive cells. Transition through the next stages of development (CD4(-)CD8(-)CD25(+)CD44(+ and -)) was associated with responsiveness of all thymocytes within these populations. Passage of thymocytes through beta-selection resulted in a significant reduction in IL-7 sensitivity. In the next phases of development (TCR(-) and TCR(low)CD69(-)), thymocytes were completely insensitive to the effects of IL-7. STAT-5 phosphorylation in response to IL-7 was again observed, however, in thymocytes involved in the positive selection process (TCR(low)CD69(+) and TCR(intermediate)). As expected, CD4 and CD8 single-positive thymocytes were responsive to IL-7. These findings delineate an IL-7-insensitive population between the beta-selection and positive selection checkpoints encompassing thymocytes predicted to die by neglect due to failure of positive selection. This pattern of sensitivity suggests a two-signal mechanism by which survival of thymocytes at these checkpoints is governed.

SP600125, an anthrapyrazolone inhibitor of Jun N-terminal kinase

Jun N-terminal kinase (JNK) is a stress-activated protein kinase that can be induced by inflammatory cytokines, bacterial endotoxin, osmotic shock, UV radiation, and hypoxia. We report the identification of an anthrapyrazolone series with significant inhibition of JNK1, -2, and -3 (K(i) = 0.19 microM). SP600125 is a reversible ATP-competitive inhibitor with >20-fold selectivity vs. a range of kinases and enzymes tested. In cells, SP600125 dose dependently inhibited the phosphorylation of c-Jun, the expression of inflammatory genes COX-2, IL-2, IFN-gamma, TNF-alpha, and prevented the activation and differentiation of primary human CD4 cell cultures. In animal studies, SP600125 blocked (bacterial) lipopolysaccharide-induced expression of tumor necrosis factor-alpha and inhibited anti-CD3-induced apoptosis of CD4(+) CD8(+) thymocytes. Our study supports targeting JNK as an important strategy in inflammatory disease, apoptotic cell death, and cancer.

Mechanistic effects of autophosphorylation on receptor tyrosine kinase catalysis: enzymatic characterization of Tie2 and phospho-Tie2

Activation of receptor tyrosine kinases by autophosphorylation is one of the most common and critical transformations in signal transduction, yet its role in catalysis remains controversial. Autophosphorylation of the angiogenic receptor tyrosine kinase Tie2 was studied in terms of the autophosphorylation sites, sequence of phosphorylation at these sites, kinetic effects, and mechanistic consequences. Isoelectric focusing electrophoresis and mass spectrometric analysis of a Tie2 autophosphorylation time course showed that Tyr992 on the putative activation loop was phosphorylated first followed by Tyr1108 in the C-terminal tail (previously unidentified autophosphorylation site). Autophosphorylation of Tie2 to produce pTie2 resulted in a 100-fold increase in k(cat) and a 460-fold increase in k(cat)/K(m). Viscosity studies showed that the unphosphorylated Tie2 was partially limited by product diffusion ((k(cat))(eta) = 0.67 +/- 0.06), while product release was more rate-limiting ((k(cat))(eta) = 0.94 +/- 0.08) for autophosphorylated Tie2 (pTie2). Furthermore, autophosphorylation did not significantly affect the phosphoacceptor dissociation constants. There was a significant (k(cat))(H)/(k(cat))(D) solvent isotope effect (SIE) for unphosphorylated Tie2 (2.42 +/- 0.12) and modest SIE (1.28 +/- 0.04) for pTie2, which is consistent with the chemistry step being more rate-limiting for Tie2 as compared to pTie2. The pH-rate profiles of Tie2 and pTie2 revealed a >0.5 unit shift in the pK(a) values of catalytically relevant ionizable residues upon autophosphorylation. The shift in rate-limiting step will result in a different distribution of enzyme pools (e.g., E, E*S, E*P, etc.) which may modulate the susceptibility to inhibition. Tie2 and pTie2 were profiled with a panel of known ATP-competitive kinase inhibitors. Tie2 activation perturbs catalytic residue ionizations, shifts the rate-limiting step to almost exclusive diffusion-control, and transforms the kinase into a more perfect catalyst.

Conservation of Mhc class III region synteny between zebrafish and human as determined by radiation hybrid mapping

In the HLA, H2, and other mammalian MHC:, the class I and II loci are separated by the so-called class III region comprised of approximately 60 genes that are functionally and evolutionarily unrelated to the class I/II genes. To explore the origin of this island of unrelated loci in the middle of the MHC: 19 homologues of HLA class III genes, we identified 19 homologues of HLA class III genes as well as 21 additional non-class I/II HLA homologues in the zebrafish and mapped them by testing a panel of 94 zebrafish-hamster radiation hybrid cell lines. Six of the HLA class III and eight of the flanking homologues were found to be linked to the zebrafish class I (but not class II) loci in linkage group 19. The remaining homologous loci were found to be scattered over 14 zebrafish linkage groups. The linkage group 19 contains at least 25 genes (not counting the class I loci) that are also syntenic on human chromosome 6. This gene assembly presumably represents the pre-MHC: that existed before the class I/II genes arose. The pre-MHC: may not have contained the complement and other class III genes involved in immune response.

Chemo-enzymatic synthesis of fluorinated sugar nucleotide: useful mechanistic probes for glycosyltransferases

An effective procedure for the synthesis of 2-deoxy-2-fluoro-sugar nucleotides via Select fluor-mediated electrophilic fluorination of glycals with concurrent nucleophilic addition or chemo-enzymatic transformation has been developed, and the fluorinated sugar nucleotides have been used as probes for glycosyltransferases, including fucosyltransferase III, V, VI, and VII, and sialyl transferases. In general, these fluorinated sugar nucleotides act as competitive inhibitors versus sugar nucleotide substrates and form a tight complex with the glycosyltransferase.

Identification of seven genes in the major histocompatibility complex class I region of the zebrafish

Physical linkage of genes whose products are involved in similar physiological pathways may have functional significance. The identification of conserved gene linkage in distantly related organisms can therefore strengthen the hypothesis of selection acting towards keeping genes on a chromosome. We used the cDNA selection technique and the polymerase chain reaction (PCR) with generic primers for the identification of new genes on the genomic clones bearing the major histocompatibility complex (Mhc) class I genes of the zebrafish (Danio rerio). We found six new genes (BING1, DAXX, TAPBP, KNSL2, TAP2B and KE6) whose orthologues are known to be linked to the Mhc class II region in humans and mice. In addition, a new zebrafish Mhc class I gene, termed Dare-UFA, was detected. By contrast, a search for the human leucocyte antigen (HLA)-linked BING3, KE3 and SACM2L genes revealed that these loci are not located on the class I clones of the zebrafish. The zebrafish class I region contains repetitive elements with similarity to the DANA, SATA and LINE repeats, as well as Tc1 transposable elements. Our findings indicate a high degree of linkage conservation between the zebrafish class I and the mammalian class II regions.

Identification and linkage of the proteasome activator complex PA28 subunit genes in zebrafish

PA28 is an activator of the latent 20S proteasome, a large multisubunit complex involved in intracellular proteolysis. Two forms of hexameric PA28 have been identified, PA28-(alphabeta)3 and PA28-(gamma)6, of which the former is of immunological importance. Both the PA28-alpha and PA28-beta subunits are inducible by interferon-gamma (IFN-gamma) and the PA28-(alphabeta)3 complex enhances the ability of the 20S proteasome to produce peptides suited for binding to major histocompatibility complex (Mhc) class I molecules. To identify the homologues of the PA28 subunits in zebrafish we screened a cDNA library and obtained full-length cDNA sequences of the genes PSME1, PSME2 and PSME3 coding for the PA28-alpha, PA28-beta and PA28-gamma subunits, respectively. Phylogenetic analysis indicates the existence of the ancestors of all three genes prior to the divergence of tetrapods and bony fishes. The IFN-gamma-inducible subunits, PA28-alpha and PA28-beta, evolve faster than the presumably older PA28-gamma subunit. Using zebrafish radiation hybrid panels, the genes PSME2 and PSME3 were mapped to linkage group 12 and shown to be separated by a distance of less than 2.4 cM. This observation suggests that an intrachromosomal duplication event created the precursor of the IFN-gamma-inducible genes from a PA28-gamma-like ancestor prior to their recruitment into the Mhc class I peptide presentation pathway.

Major histocompatibility complex class II A genes in cichlid fishes: identification, expression, linkage relationships, and haplotype variation

Two cichlid species, the haplochromine Aulonocara hansbaenschi and the tilapiine Oreochromis niloticus, were used to study the major histocompatibility complex (Mhc) class II A variation within this group. Multiple class II A sequences were recovered from A. hansbaenschi and O. niloticus cDNA libraries and three sequence families, DAA, DBA, and DCA, were identified. Sets of O. niloticus haploid embryo families were used to determine the linkage relationships of these genes. Two independently assorting linkage groups were detected, DAA and DBA/DCA, neither of which is linked to the previously described Mhc class I gene cluster. Three DCA genes and up to four DBA genes were found to segregate in different haplotypes, whereas DAA occurred as a single locus. Four DBA haplotypes, DBA*H1-H4, were identified and shown to co-segregate with the previously described class II B haplotypes. Four DCA haplotypes, DCA*H1-H4, were found at a distance of 37 cM from the DBA/class II B cluster; in one DCA haplotype, DCA*H5, the genes were tightly linked to the DBA/class II B clusters. Transcripts of DAA and DBA genes were found in O. niloticus hepatopancreas and spleen; transcripts of DCA genes were detected in the A. hansbaenschi cDNA library, but not in O. niloticus. These findings provide a basis for using class II haplotypes as markers in the study of adaptive radiation in the cichlid species flocks of the East African Great Lakes.

A contig map of the Mhc class I genomic region in the zebrafish reveals ancient synteny

In contrast to the human and mouse Mhc, in which the clusters of class I and class II loci reside in close vicinity to one another, in the zebrafish, Danio rerio, they are found in different linkage groups. Chromosome walking using BAC (bacterial artificial chromosome) and PAC (P1 artificial chromosome) clones reveals the zebrafish class I region to occupy a segment of approximately 450 kb and to encompass at least 19 loci. These include three class I (Dare-UDA, -UEA, -UFA), five proteasome subunit beta (PSMB8, -9A, -9C, -11, -12), two TAPs (TAP2A, TAP2B), and one TAP binding protein (TAPBP). This arrangement contrasts with the arrangements found in human and mouse Mhc, in which the orthologues of the PSMB, TAP, and TAPBP loci reside within the class II region. In addition to this main zebrafish class I contig, a shorter contig of about 150 kb contains two additional class I (UBA, UCA) and at least five other loci. It probably represents a different haplotype of part of the class I region. The previously identified UAA gene shares an identical 5' part with UEA, but the two genes differ in their 3' parts. One of them is probably the result of an unequal crossing over. The described organization has implications for the persistence of syntenic relationships, coevolution of loci, and interpretation of the origin of the human/mouse Mhc organization.

Nonlinkage of major histocompatibility complex class I and class II loci in bony fishes

In tetrapods, the functional (classical) class I and class II B loci of the major histocompatibility complex (Mhc) are tightly linked in a single chromosomal region. In an earlier study, we demonstrated that in the zebrafish, Danio rerio, order Cypriniformes, the two classes are present on different chromosomes. Here, we show that the situation is similar in the stickleback, Gasterosteus aculeatus, order Gasterosteiformes, the common guppy, Poecilia reticulata, order Cyprinodontiformes, and the cichlid fish Oreochromis niloticus, order Perciformes. These data, together with unpublished results from other laboratories suggest that in all Euteleostei, the classical class I and class II B loci are in separate linkage groups, and that in at least some of these taxa, the class II loci are in two different groups. Since Euteleostei are at least as numerous as tetrapods, in approximately one-half of jawed vertebrates, the class I and class II regions are not linked.

Analysis of a 26-kb region linked to the Mhc in zebrafish: genomic organization of the proteasome component beta/transporter associated with antigen processing-2 gene cluster and identification of five new proteasome beta subunit genes

Sequencing of zebrafish (Danio rerio) bacterial artificial chromosome and P1 artificial chromosome genomic clone fragments and of cDNA clones has led to the identification of five new loci coding for beta subunits of proteasomes (PSMB). Together with the four genes identified previously, nine PSMB genes have now been defined in the zebrafish. Six of the nine genes reside in the zebrafish MHC (Mhc) class I region, four of them reside in a single cluster closely associated with TAP2 on a 26-kb long genomic fragment, and two reside at some distance from the fragment. In addition to homologues of the human genes PSMB5 through PSMB9, two new genes, PSMB11 and PSMB12, have been found for which there are no known corresponding genes in humans. The new genes reside in the PSMB cluster in the Mhc. Homology and promoter region analysis suggest that the Mhc-associated genes might be inducible by IFN-gamma. The zebrafish class I region contains representatives of three phylogenetically distinguishable groups of PSMB genes, X, Y, and Z. It is proposed that these genes were present in the ancestral PSMB region before Mhc class I genes became associated with it.

IkappaB kinase (IKK)-associated protein 1, a common component of the heterogeneous IKK complex

Activation of the transcription factor NF-kappaB is controlled by the sequential phosphorylation, ubiquitination, and degradation of its inhibitory subunit, IkappaB. We recently purified a large multiprotein complex, the IkappaB kinase (IKK) signalsome, which contains two regulated IkappaB kinases, IKK1 and IKK2, that can each phosphorylate IkappaBalpha and IkappaBbeta. The IKK signalsome contains several additional proteins presumably required for the regulation of the NFkappaB signal transduction cascade in vivo. In this report, we demonstrate reconstitution of IkappaB kinase activity in vitro by using purified recombinant IKK1 and IKK2. Recombinant IKK1 or IKK2 forms homo- or heterodimers, suggesting the possibility that similar IKK complexes exist in vivo. Indeed, in HeLa cells we identified two distinct IKK complexes, one containing IKK1-IKK2 heterodimers and the other containing IKK2 homodimers, which display differing levels of activation following tumor necrosis factor alpha stimulation. To better elucidate the nature of the IKK signalsome, we set out to identify IKK-associated proteins. To this end, we purified and cloned a novel component common to both complexes, named IKK-associated protein 1 (IKKAP1). In vitro, IKKAP1 associated specifically with IKK2 but not IKK1. Functional analyses revealed that binding to IKK2 requires sequences contained within the N-terminal domain of IKKAP1. Mutant versions of IKKAP1, which either lack the N-terminal IKK2-binding domain or contain only the IKK2-binding domain, disrupt the NF-kappaB signal transduction pathway. IKKAP1 therefore appears to mediate an essential step of the NF-kappaB signal transduction cascade. Heterogeneity of IKK complexes in vivo may provide a mechanism for differential regulation of NF-kappaB activation.

Isolation of mhc class II DMA and DMB cDNA sequences in a marsupial: the gray short-tailed opossum (Monodelphis domestica)

We report the cDNA sequences for the DMA and DMB family of Mhc genes of the gray short-tailed opossum. Until now DM sequences were available only in eutherian mammals. The marsupial sequences indicate that both members of the family are old and probably diverged from other classical class II families about the time of the radiation of jawed vertebrates some 450 million years ago. We examine the evolutionary rates of equivalent sets of classical and nonclassical genes to check for rate heterogeneity. We find the alpha-1 domain of the DR genes to be untypically conservative in its evolutionary mode. The DM genes appear to evolve at rates typical of other class II genes, indicating that their placement at the root of class II gene evolutionary trees may be justified.

Sequence variation at the major histocompatibility complex DRB loci in beluga (Delphinapterus leucas) and narwhal (Monodon monoceros)

The variation at loci with similarity to DRB class II major histocompatibility complex loci was assessed in 313 beluga collected from 13 sampling locations across North America, and 11 narwhal collected in the Canadian high Arctic. Variation was assessed by amplification of exon 2, which codes for the peptide binding region, via the polymerase chain reaction, followed by either cloning and DNA sequencing or single-stranded conformation polymorphism analysis. Two DRB loci were identified in beluga: DRB1, a polymorphic locus, and, DRB2, a monomorphic locus. Eight alleles representing five distinct lineages (based on sequence similarity) were found at the beluga DRB1 locus. Although the relative number of alleles is low when compared with terrestrial mammals, the amino acid variation found among the lineages is moderate. At the DRB1 locus, the average number of nonsynonymous substitutions per site is greater than the average number of synonymous substitutions per site (0.0806 : 0.0207, respectively; P<0.01). Most of the 31 amino acid substitutions do not conserve the physiochemical properties of the residue, and 21 of these are located at positions implicated as forming pockets responsible for the selective binding of foreign peptide side chains. Only DRB1 variation was examined in 11 narwhal, revealing a low amount of variation. These data are consistent with an important role for the DRB1 locus in the cellular immune response of beluga. In addition, the ratio of nonsynonymous to synonymous substitutions is similar to that among primate alleles, arguing against a reduction in the balancing selection pressure in the marine environment. Two hypotheses may explain the modest amount of Mhc variation when compared with terrestrial mammals: small population sizes at speciation or a reduced neutral substitution rate in cetaceans.

IKK-1 and IKK-2: cytokine-activated IkappaB kinases essential for NF-kappaB activation

Activation of the transcription factor nuclear factor kappa B (NF-kappaB) is controlled by sequential phosphorylation, ubiquitination, and degradation of its inhibitory subunit IkappaB. A large multiprotein complex, the IkappaB kinase (IKK) signalsome, was purified from HeLa cells and found to contain a cytokine-inducible IkappaB kinase activity that phosphorylates IkappaB-alpha and IkappaB-beta. Two components of the IKK signalsome, IKK-1 and IKK-2, were identified as closely related protein serine kinases containing leucine zipper and helix-loop-helix protein interaction motifs. Mutant versions of IKK-2 had pronounced effects on RelA nuclear translocation and NF-kappaB-dependent reporter activity, consistent with a critical role for the IKK kinases in the NF-kappaB signaling pathway.

p38-2, a novel mitogen-activated protein kinase with distinct properties

Mitogen-activated protein (MAP) kinases are involved in many cellular processes. Here we describe the cloning and characterization of a new MAP kinase, p38-2. p38-2 belongs to the p38 subfamily of MAP kinases and shares with it the TGY phosphorylation motif. The complete p38-2 cDNA was isolated by polymerase chain reaction. It encodes a 364-amino acid protein with 73% identity to p38. Two shorter isoforms missing the phosphorylation motif were identified. Analysis of various tissues demonstrated that p38-2 is differently expressed from p38. Highest expression levels were found in heart and skeletal muscle. Like p38, p38-2 is activated by stress-inducing signals and proinflammatory cytokines. The preferred upstream kinase is MEK6. Although p38-2 and p38 phosphorylate the same substrates, the site specificity of phosphorylation can differ as shown by two-dimensional phosphopeptide analysis of Sap-1a. Additionally, kinetic studies showed that p38-2 appears to be about 180 times more active than p38 on certain substrates such as ATF2. Both kinases are inhibited by a class of pyridinyl imidazoles. p38-2 phosphorylation of ATF2 and Sap-1a but not Elk1 results in increased transcriptional activity of these factors. A sequential kinetic mechanism of p38-2 is suggested by steady state kinetic analysis. In conclusion, p38-2 may be an important component of the stress response required for the homeostasis of a cell.

A chemoenzymatic synthesis of UDP-(2-deoxy-2-fluoro)-galactose and evaluation of its interaction with galactosyltransferase

Uridine 5'-diphospho-(2-deoxy-2-fluoro)galactose (UDP-2FGal), prepared and characterized for the first time by a chemoenzymatic method, was found to be a competitive inhibitor of beta-1,4-galactosyltransferase with a Ki value of 149 microM. This study supports that the glycosyltransferase reaction mechanism proceeds through a glycosidic cleavage transition state with sp2 character developed at the anomeric center.

Mechanism of human alpha-1,3-fucosyltransferase V: glycosidic cleavage occurs prior to nucleophilic attack

alpha-1,3-Fucosyltransferase V (FucT V) catalyzes the transfer of 1-fucose from the donor sugar guanosine 5'-diphospho-beta-1-fucose (GDP-Fuc) to an acceptor sugar. A secondary isotope effect on the fucosyltransfer reaction with guanosine 5'-diphospho-[1-2H]-beta-1-fucose (GDP-[1-2H]-Fuc) as the substrate was observed and determined to be Dv = 1.32 +/- 0.13 and DV/K = 1.27 +/- 0.07. Competitive inhibition of FucT V by guanosine 5'-diphospho-2-deoxy-2-fluoro-beta-1-fucose (GDP-2F-Fuc) was observed with an inhibition constant of 4.2 microM which represents the most potent inhibitor of this enzyme to date. Incubation of GDP-2F-Fuc with FucT V and an acceptor molecule prior to the addition of GDP-Fuc had no effect on the potency of inhibition, indicating that GDP-2F-Fuc is neither an inactivator nor a slow substrate. Both the observed secondary isotope effect and the inhibition by GDP-2F-Fuc are consistent with a charged, sp2-hybridized, transition-state structure. A convenient and efficient synthesis of GDP-[1-2H]-Fuc and GDP-2F-Fuc and a nonradioactive, fluorescence assay for fucosyltransferase activity have been developed.

Why is CMP-ketodeoxyoctonate highly unstable?

CMP-ketodeoxyoctonate (CMP-KDO) and analogs, including CMP-5-deoxy-5-fluoro-KDO, CMP-5-deoxy-KDO, and CMP-5-epi-KDO, were prepared from CTP and the corresponding KDO sugars catalyzed by CMP-KDO synthetase. These analogs were found to be much more stable than CMP-KDO (t1/2 = 0.57 h) yet less stable than CMP-sialic acid (t1/2 = 151 h). Fluorination at the 5-position of CMP-KDO has a 200-fold enhanced stability compared to the 156-fold enhancement for the 3R-fluoro analog, probably due to the loss of H-bonding interactions (for the 5-F derivative) and the cause of remote inductive effect (for the 3- and the 5-F analogs) on the glycosidic cleavage. Hydrolysis of CMP-KDO is perhaps facilitated by an intramolecular hydrogen bond from the 5-OH group with the phosphate oxygen as demonstrated by the 3-5-fold enhanced stability of CMP-5-epi-KDO and CMP-5-deoxy-KDO compared to CMP-KDO and by molecular modeling studies of water-solvated CMP-KDO. Hydrolysis of CMP-KDO also was found to be subject to a substantial solvent isotope effect (kH/kD = 2.7), which is significantly different from the reported solvent isotope effect for the hydrolysis of sialyglycosides (kH/kD = 0.86) and dependent on both buffer and magnesium ion concentrations. Considering these results and molecular modeling studies, it is proposed that the hydrolysis of CMP-KDO under neutral conditions proceeds through a glycosidic cleavage which occurs at the electronically favorable twist-boat conformation, facilitated by intramolecular H-bonding interaction of the 4-, 5- and 7- (or 8-) OH groups and the phosphate oxygen and by the leaving group magnesium ion complexation.

Mechanism and specificity of human alpha-1,3-fucosyltransferase V

Human alpha-1,3-fucosyltransferase catalyzes the transfer of the L-fucose moiety from guanosine diphosphate-beta-L-fucose (GDP-Fuc) to acceptor sugars to form biologically important fucoglycoconjugates, including sialyl Lewis x (SLex). Evidence for a general base mechanism is supported by a pH-rate profile that revealed a catalytic residue with a pKa of 4.1. The characterized solvent kinetic isotope effect (Dv = 2.9, Dv/k = 2.1) in a proton inventory study indicates that only one-proton transfer is involved in the catalytic step leading to the formation of the transition state. Evidence for Mn2+ as an electrophilic catalyst was supported by the observation that the nonenzymatic transfer of L-fucose from GDP-Fuc to the hydroxyl group of water in the presence of 10 mM MnCl2 at 20 degrees C was accelerated from K(obs)= 3.5 x 10(-6) to 3.8 x 10(-5) min-1. Using the GDP-Fuc hydrolysis as the nonenzymatic rate, the enzymatic proficiency of FucT V, (Kcat/Ki,GDP-fuc. K(m),1.acNAc)/K(non), was estimated to be 1.2 x 10(10) M-1 with a transition-state affinity of 8.6 x 10(-11) M. The Km for Mn2+ was determined to be 6.1 mM, and alternative divalent metal cofactors were identified as Ca2+, Co2+, and Mg2+. Detailed kinetic characterization of the acceptor sugar specificity indicated that incorporation of hydrophobic functionality [e.g. -O-(CH2)5CO2CH3] to the reducing end of the acceptor sugar substantially decreased the K(m),acceptor by over 100-fold. The role of the nucleotide was investigated by studying the inhibition of nucleotides, including the guanosine series. The inhibitory potency trend (GTP approximately GDP > GMP > > guanosine) is consistent with bidentate chelation of Mn2+ by GDP-Fuc. The role of charge and distance in the synergistic inhibitory effect by the combination of GDP, an aza sugar, and the acceptor sugar was probed. A mechanism for fucosyl transfer incorporating these findings is proposed and discussed.

Forensic identification of ungulate species using restriction digests of PCR-amplified mitochondrial DNA

A survey of mitochondrial D-loop variation in 15 species of ungulates was conducted via amplification by the polymerase chain reaction followed by restriction fragment length polymorphism analysis. This survey included moose (Alces alces), caribou (Rangifer tarandus), mule deer (Odocoileus hemionus hemionus), black-tailed deer (O. h. columbianus), white-tailed deer (O. virginianus), waipiti (Cervus elaphus), pronghorn antelope (Antilocapra americana), bighorn sheep (Ovis canadensis), Stone's sheep (O. dalli), domestic sheep (O. aries), moulflon sheep (O. musimon), mountain goat (Oreamnos americanus), domestic goat (Capra hircus), domestic cattle (Bos taurus), and bison (Bison bison). The results of this preliminary survey indicate that there may be sufficient species specific variation in the D-loop region of the mitochondrial genome of the ungulate species examined here, with the exception of deer (Odocoileus) species, to establish the species origin of the mitochondrial haplotypes of this group. The Odocoileus species are known to hybridize and sharing of mtDNA haplotypes was observed. The chelex DNA extraction technique was successfully used on small blood stains.

Sequence variation at the major histocompatibility complex locus DQ beta in beluga whales (Delphinapterus leucas)

Genetic variation at the Major Histocompatibility Complex locus DQ beta was analyzed in 233 beluga whales (Delphinapterus leucas) from seven populations: St. Lawrence Estuary, eastern Beaufort Sea, eastern Chukchi Sea, western Hudson Bay, eastern Hudson Bay, southeastern Baffin Island, and High Arctic and in 12 narwhals (Monodon monoceros) sympatric with the High Arctic beluga population. Variation was assessed by amplification of the exon coding for the peptide binding region via the polymerase chain reaction, followed by either cloning and DNA sequencing or single-stranded conformation polymorphism analysis. Five alleles were found across the beluga populations and one in the narwhal. Pairwise comparisons of these alleles showed a 5:1 ratio of nonsynonymous to synonymous substitutions per site leading to eight amino acid differences, five of which were nonconservative substitutions, centered around positions previously shown to be important for peptide binding. Although the amount of allelic variation is low when compared with terrestrial mammals, the nature of the substitutions in the peptide binding sites indicates an important role for the DQ beta locus in the cellular immune response of beluga whales. Comparisons of allele frequencies among populations show the High Arctic population to be different (P < or = .005) from the other beluga populations surveyed. In these other populations an allele, Dele-DQ beta*0101-2, was found in 98% of the animals, while in the High Arctic it was found in only 52% of the animals. Two other alleles were found at high frequencies in the High Arctic population, one being very similar to the single allele found in narwhal.

Molecular properties of pyruvate formate-lyase activating enzyme

Pyruvate formate-lyase is a radical-containing enzyme that catalyzes the nonoxidative cleavage of pyruvate via a postulated homolytic mechanism. The formation of this enzymic radical in vitro requires an activating system composed of PFL-activating enzyme, S-adenosylmethionine, ferrous ion, a reduced flavin, DTT, and pyruvate as an allosteric effector. The need for large quantities of PFL-activating enzyme for biochemical and biophysical studies on the mechanism of protein radical formation has prompted us to clone the act gene and overexpress the gene product in Escherichia coli. Using PCR technology, the act gene was isolated and subcloned into various expression vectors. The overexpression of the protein was as high as 30-50% of the total cellular protein. However, the majority of the protein resided in the form of insoluble inclusion bodies. A procedure was developed to denature and isolate the inclusion bodies followed by refolding under anaerobic conditions. This purification method affords 5 mg of purified protein from 1 g of cells. Biochemical characterization demonstrated that the enzyme can bind one Fe(II) per protein monomer, and the protein did not exhibit any visible chromophore as previously observed. Co(II) and Cu(II) can be reconstituted into the protein with similar stoichiometries. Kinetic studies showed that the rate of radical formation was independent of ionic strength and the Km's for SAM and inactive PFL were determined to be 2.8 and 1.2 microM, respectively. Fluorescent binding data revealed that the Kd for SAM binding to the activating enzyme alone was comparable to the Km for SAM in the PFL activation indicating that the binding site for SAM resides on AE.(ABSTRACT TRUNCATED AT 250 WORDS)

Properties of chemical-vapor-deposited silicon carbide for optics applications in severe environments

Important data on chemical-vapor-deposited (CVD) SiC concerning the elastic modulus, polishability, scattering measurement, thermal and cryogenic stability, and degradation owing to the effects of atomic oxygen and electron beams have been obtained with the aim of assessing the suitability of SiC as an optical substrate for severe environments. These measurements show that CVD SiC substrates exhibit excellent polishability (<0.1 nm rms) with low scatter, good retention of mechanical properties up to 1500 degrees C, superior thermal and cryogenic stability (-190 degrees to 1350 degrees C) and high resistance to atomic-oxygen and electron-beam degradation. These results suggest that CVD SiC optical substrates will perform extremely well in severe environments such as outer space, and when used in lasers, combustion, and synchrotron x rays.

A feasibility study of prompt capture gamma in vivo neutron activation analysis

The feasibility of using the information contained in the radiative capture gamma ray spectrum of the neutron-irradiated human body to measure quantitatively total body elemental composition in vivo has been investigated. Results of time dependent Monte Carlo simulations have shown that spectral interference of nonradiative capture origin can be completely eliminated by pulsing the detector/spectrometer system in anticoincidence with the neutron source. Calculations based on the results of the Monte Carlo simulation and on an experimental measurement of the efficiency versus energy characteristics of a Ge(Li) detector suggest that the primary limitation of the proposed technique would be inter-element spectral interference rather than inadequate detector sensitivity. Experimental measurements using a pulsed 14-MeV neutron generator and Ge(Li) gamma-ray spectrometer have produced results that are consistent with the predictions of the theoretical model. A radiative capture gamma-ray spectrum of a tissue-equivalent phantom was measured in pulsed mode and analyzed offline using a computerized spectral analysis procedure. The results were scaled to a proposed facility consisting of a 2.5-MeV pulsed neutron source and a detection system comprising two 50-cm3 (Ge(Li) detectros past which the subject would be scanned. It has been shown that in principle the elements hydrogen, chlorine, calcium, and nitrogen [the latter using large NaI(T1) detectors] could be measured with such a facility at an average body dose level of 0.1 rad. At this dose level the coefficients of variation based on counting statistics alone would be +/- 2%, or better, for these four elements. With an improvement in the detector/spectrometer energy resolution, the elements sulfur and carbon might also be measurable. It is also shown that by modifying the pulsing sequence appropriately and using 14-MeV neutrons, total body oxygen could also be measured at the 0.1 rad dose level via its inelastic neutron scattering deexcitation gamma activity.

Boron neutron capture therapy for the treatment of cerebral gliomas. I. Theoretical evaluation of the efficacy of various neutron beams

The technique of boron neutron capture therapy in the treatment of cerebral gliomas depends upon the selective loading of the tumor with a 10B-enriched compound and subsequent irradiation of the brain with low-energy neutrons. The charged particles produced in the 10B (n,alpha) 7Li reaction have ranges in tissue of less than 10 mum so that the dose distribution closely follows the 10B distribution even to the cellular level. The effectiveness of this therapy procedure is dependent not only on the 10B compound but on the spectral characteristics of the neutron source as well. Hence, an optimization of these characteristics will increase the chances of therapeutic success. Transport calculations using a neutral particle transport code have been made to determine the dose-depth distributions within a simple head phantom for five different incident neutron beams. Comparison of these beams to determine their relative therapeutic efficacy was made by the use of a maximum useable depth criterion. In particular, with presently available compounds, the MIT reactor (MITR) therapy beam (a) is not inferior to a pure thermal neutron beam, (b) would be marginally improved if its gamma-ray contamination were eliminated, (c) is superior to a partially 10B-filtered MITR beam, and (d) produces a maximum useable depth which is strongly dependent upon the tumor-to-blood ratio of 10B concentrations and weakly dependent upon the absolute 10B concentration in tumor. A pure epithermal neutron beam with a mean energy of 37 eV is shown to have close to the optimal characteristics for boron neutron capture therapy. Futhermore, these optimal characteristics can be approximated by a judiciously D2O moderated and 10B-filtered 252Cf neutron source. This tailored 252Cf source would have at least a 1.5 cm greater maximum useable depth than the MITR therapy beam for realistic 10B concentrations. However, at least one gram of 252Cf would be needed to make this a practical therapy source. If the moderated 252Cf source is not 10B filtered, the resultant neutron beam has characteristics similar to those of the MITR beam with no gamma-ray contamination. For usch a beam, 100 mg of 252Cf would produce a flux of 2.4 X 10(8) neutrons/(cm2 sec), which is an intensity suitable for therapy applications.