A striking organization of a large family of human neural cadherin-like cell adhesion genes

We have identified 52 novel human cadherin-like genes organized into three closely linked clusters. Comparison of the genomic DNA sequences with those of representative cDNAs reveals a striking genomic organization similar to that of immunoglobulin and T cell receptor gene clusters. The N-terminal extracellular and transmembrane domains of each cadherin protein are encoded by a distinct and unusually large exon. These exons are organized in a tandem array. By contrast, the C-terminal cytoplasmic domain of each protein is identical and is encoded by three small exons located downstream from the cluster of N-terminal exons. This unusual organization has interesting implications regarding the molecular code required to establish complex networks of neuronal connections in the brain and the mechanisms of cell-specific cadherin-like gene expression.

Structural basis of caspase-7 inhibition by XIAP

The inhibitor of apoptosis (IAP) proteins suppress cell death by inhibiting the catalytic activity of caspases. Here we present the crystal structure of caspase-7 in complex with a potent inhibitory fragment from XIAP at 2.45 A resolution. An 18-residue XIAP peptide binds the catalytic groove of caspase-7, making extensive contacts to the residues that are essential for its catalytic activity. Strikingly, despite a reversal of relative orientation, a subset of interactions between caspase-7 and XIAP closely resemble those between caspase-7 and its tetrapeptide inhibitor DEVD-CHO. Our biochemical and structural analyses reveal that the BIR domains are dispensable for the inhibition of caspase-3 and -7. This study provides a structural basis for the design of the next-generation caspase inhibitors.

Corin, a transmembrane cardiac serine protease, acts as a pro-atrial natriuretic peptide-converting enzyme

Atrial natriuretic peptide (ANP) is a cardiac hormone essential for the regulation of blood pressure. In cardiac myocytes, ANP is synthesized as a precursor, pro-ANP, that is converted to biologically active ANP by an unknown membrane-associated protease. Recently, we cloned a transmembrane serine protease, corin, that is highly expressed in the heart. In this study, we examine effects of corin on pro-ANP processing. Our results show that recombinant human corin converts pro-ANP to ANP and that the cleavage in pro-ANP by corin is highly sequence specific. Our findings suggest that corin is the long-sought pro-ANP-converting enzyme and that the corin-mediated pro-ANP activation may play a role in regulating blood pressure.

NWChem: Past, present, and future

Specialized computational chemistry packages have permanently reshaped the landscape of chemical and materials science by providing tools to support and guide experimental efforts and for the prediction of atomistic and electronic properties. In this regard, electronic structure packages have played a special role by using first-principle-driven methodologies to model complex chemical and materials processes. Over the past few decades, the rapid development of computing technologies and the tremendous increase in computational power have offered a unique chance to study complex transformations using sophisticated and predictive many-body techniques that describe correlated behavior of electrons in molecular and condensed phase systems at different levels of theory. In enabling these simulations, novel parallel algorithms have been able to take advantage of computational resources to address the polynomial scaling of electronic structure methods. In this paper, we briefly review the NWChem computational chemistry suite, including its history, design principles, parallel tools, current capabilities, outreach, and outlook.

A common variant in methionine synthase reductase combined with low cobalamin (vitamin B12) increases risk for spina bifida

Impairment of folate and cobalamin (vitamin B(12)) metabolism has been observed in families with neural tube defects (NTDs). Genetic variants of enzymes in the homocysteine remethylation pathway might act as predisposing factors contributing to NTD risk. The first polymorphism linked to increased NTD risk was the 677C-->T mutation in methylenetetrahydrofolate reductase (MTHFR). We now report a polymorphism in methionine synthase reductase (MTRR), the enzyme that activates cobalamin-dependent methionine synthase. This polymorphorism, 66A-->G (I22M), has an allele frequency of 0.51 and increases NTD risk when cobalamin status is low or when the MTHFR mutant genotype is present. Genotypes and cobalamin status were assessed in 56 patients with spina bifida, 58 mothers of patients, 97 control children, and 89 mothers of controls. Cases and case mothers were almost twice as likely to possess the homozygous mutant genotype when compared to controls, but this difference was not statistically significant. However, when combined with low levels of cobalamin, the risk for mothers increased nearly five times (odds ratio (OR) = 4.8, 95% CI 1.5-15.8); the OR for children with this combination was 2.5 (95% CI 0.63-9.7). In the presence of combined MTHFR and MTRR homozygous mutant genotypes, children and mothers had a fourfold and threefold increase in risk, respectively (OR = 4.1, 95% CI 1.0-16.4; and OR = 2.9, 95% CI 0.58-14.8). This study provides the first genetic link between vitamin B(12) deficiency and NTDs and supports the multifactorial origins of these common birth defects. Investigation of this polymorphism in other disorders associated with altered homocysteine metabolism, such as vascular disease, is clearly warranted.

Acidic stress promotes a glioma stem cell phenotype

Malignant gliomas are lethal cancers that display cellular hierarchies with cancer stem cells at the apex. Glioma stem cells (GSCs) are not uniformly distributed, but rather located in specialized niches, suggesting that the cancer stem cell phenotype is regulated by the tumor microenvironment. Indeed, recent studies show that hypoxia and its molecular responses regulate cancer stem cell maintenance. We now demonstrate that acidic conditions, independent of restricted oxygen, promote the expression of GSC markers, self-renewal and tumor growth. GSCs exert paracrine effects on tumor growth through elaboration of angiogenic factors, and low pH conditions augment this expression associated with induction of hypoxia inducible factor 2α (HIF2α), a GSC-specific regulator. Induction of HIF2α and other GSC markers by acidic stress can be reverted by elevating pH in vitro, suggesting that raising intratumoral pH may be beneficial for targeting the GSC phenotype. Together, our results suggest that exposure to low pH promotes malignancy through the induction of a cancer stem cell phenotype, and that culturing cancer cells at lower pH reflective of endogenous tumor conditions may better retain the cellular heterogeneity found in tumors.

Conformal radiation treatment of prostate cancer using inversely-planned intensity-modulated photon beams produced with dynamic multileaf collimation

PURPOSE

To implement radiotherapy with intensity-modulated beams, based on the inverse method of treatment design and using a multileaf collimation system operating in the dynamic mode.

METHODS AND MATERIALS

An algorithm, based on the inverse technique, has been integrated into the radiotherapy treatment-planning computer system in our Center. This method of computer-assisted treatment design was used to derive intensity-modulated beams to optimize the boost portion of the treatment plan for a patient with a T1c cancer of the prostate. A dose of 72 Gy (in 40 fractions) was given with a six-field plan, and an additional 9 Gy (in five fractions) with six intensity-modulated beams. The intensity-modulated fields were delivered using dynamic multileaf collimation, that is, individual leaves were in motion during radiation delivery, with the treatment machine operating in the clinical mode. Exhaustive quality assurance measurement and monitoring were carried out to ensure safe and accurate implementation.

RESULTS

Dose distribution and dose-volume histogram of the "inverse method" boost plan and of the composite (72 Gy primary + 9 Gy boost) plan were judged clinically acceptable. Compared to a manually designed boost plan, the inverse treatment design gave improved conformality and increased dose homogeneity in the planning target volume. Film and ion chamber dosimetry, performed prior to the first treatment, indicated that each of the six intensity-modulated fields was accurately produced. Thermoluminescent dosimeter (TLD) measurements performed on the patient confirmed that the intended dose was delivered in the treatment. In addition, computer-aided treatment-monitoring programs assured that the multileaf collimator (MLC) position file was executed to the specified precision. In terms of the overall radiation treatment process, there will likely be labor savings in the planning and the treatment phases.

CONCLUSIONS

We have placed into clinical use an integrated system of conformal radiation treatment that incorporated the inverse method of treatment design and the use of dynamic multileaf collimation to deliver intensity-modulated beams. The system can provide better treatment design, which can be implemented reliably and safely. We are hopeful that improved treatment efficacy will result.

Radiobiological considerations in the design of fractionation strategies for intensity-modulated radiation therapy of head and neck cancers

PURPOSE

The dose distributions of intensity-modulated radiotherapy (IMRT) treatment plans can be shown to be significantly superior in terms of higher conformality if designed to simultaneously deliver high dose to the primary disease and lower dose to the subclinical disease or electively treated regions. We use the term "simultaneous integrated boost" (SIB) to define such a treatment. The purpose of this paper is to develop suitable fractionation strategies based on radiobiological principles for clinical trials and routine use of IMRT of head and neck (HN) cancers. The fractionation strategies are intended to allow escalation of tumor dose while adequately sparing normal tissues outside the target volume and considering the tolerances of normal tissues embedded within the primary target volume.

METHODS AND MATERIALS

IMRT fractionation regimens are specified in terms of "normalized total dose" (NTD), i.e., the biologically equivalent dose given in 2 Gy/fx. A linear-quadratic isoeffect formula is applied to convert NTDs into "nominal" prescription doses. Nominal prescription doses for a high dose to the primary disease, an intermediate dose to regional microscopic disease, and lower dose to electively treated nodes are used for optimizing IMRT plans. The resulting nominal dose distributions are converted back into NTD distributions for the evaluation of treatment plans. Similar calculations for critical normal tissues are also performed. Methods developed were applied for the intercomparison of several HN treatment regimens, including conventional regimens used currently and in the past, as well as SIB strategies. This was accomplished by comparing the biologically equivalent NTD values for the gross tumor and regional disease, and bone, muscle, and mucosa embedded in the gross tumor volume.

RESULTS

(1) A schematic HN example was used to demonstrate that dose distributions for SIB IMRT are more conformal compared to dose distributions when IMRT is divided into a large-field phase and a boost phase. Both were shown to be significantly superior compared to dose distributions obtained using conventional beams for the large-field phase followed by IMRT for the boost phase. (2) The relationship between NTD and nominal dose for HN tumors was found to be quite sensitive to the choice of tumor clonogen doubling time but relatively insensitive to other parameters. (3) For late effect normal tissues embedded in the tumor volume and assumed to receive the same dose as the tumor, the biologically equivalent NTD for the SIB IMRT may be significantly higher. (4) Normal tissues outside the target volume receive lower dose due to the higher conformality of the IMRT plans. The biologically equivalent NTDs are even lower due to the lower dose per fraction in the SIB strategy.

CONCLUSIONS

IMRT dose distributions are most conformal when designed to be delivered as SIB. Using isoeffect radiobiological relationships and published HN data, fractionation strategies can be designed in which the nominal dose levels to the primary, regional disease and electively treated volumes are appropriately adjusted, each receiving different dose/fx. Normal tissues outside the treated volumes are at reduced risk in such strategies since they receive lower total dose as well as lower dose/fx. However, the late effect toxicities of tissues embedded within the primary target volume and assumed to receive the same dose as the primary may pose a problem. The efficacy and safety of the proposed fractionation strategies will need to be evaluated with careful clinical trials.

Apoptosis of vascular smooth muscle cells induced by in vitro stimulation with interferon-gamma, tumor necrosis factor-alpha, and interleukin-1 beta

Recent studies have documented evidence for the death of smooth muscle cells (SMCs) within advanced human atheroma. These lesions contain macrophages and T lymphocytes in addition to SMCs. We therefore investigated whether interferon-gamma (IFN-gamma), a cytokine secreted by T lymphocytes, or interleukin-1 beta (IL-1 beta) and tumor necrosis factor-alpha (TNF-alpha), two cytokines characteristically produced by activated macrophages, can trigger apoptosis of vascular SMCs. Simultaneous treatment with IFN-gamma and TNF-alpha and/or IL-1 beta but not with each cytokine alone promoted death of human and rat SMCs. Exposure for 48 hours to a combination of IFN-gamma (400 U/mL), TNF-alpha (400 U/mL), and IL-1 beta (100 U/mL) significantly (P < .001) increased the accumulation of oligonucleosomes comprising DNA fragments and histones in human SMCs. Electrophoresis of genomic DNA showed internucleosomal fragments of genomic DNA isolated from the cytokine-cotreated SMCs of both humans and rats. These cells exhibited morphological changes typical of apoptosis, including cell shrinkage, membrane blebbing, chromatin condensation, and nuclear fragmentation. In situ 3' end labeling of DNA fragments with terminal transferase confirmed the fragmentation of genomic DNA in these cells. Simultaneous treatment with IFN-gamma and TNF-alpha or IL-1 beta induced elaboration of nitrite, an end product of nitric oxide, in rat but not human SMCs. NG-monomethyl-L-arginine inhibited nitrite accumulation and also partly blocked cytokine-induced apoptosis of rat SMCs but had little effect on human SMCs, suggesting operation of both nitric oxide-dependent and -independent mechanisms for cytokine-induced apoptosis in vascular SMCs. Production of immune cytokines by vascular cells and/or infiltrating leukocytes may regulate apoptotic death of SMCs during atherogenesis.

Planning, delivery, and quality assurance of intensity-modulated radiotherapy using dynamic multileaf collimator: a strategy for large-scale implementation for the treatment of carcinoma of the prostate

PURPOSE

To improve the local control of patients with adenocarcinoma of the prostate we have implemented intensity modulated radiation therapy (IMRT) to deliver a prescribed dose of 81 Gy. This method is based on inverse planning and the use of dynamic multileaf collimators (DMLC). Because IMRT is a new modality, a major emphasis was on the quality assurance of each component of the process and on patient safety. In this article we describe in detail our procedures and quality assurance program.

METHODS AND MATERIALS

Using an inverse algorithm, we have developed a treatment plan consisting five intensity-modulated (IM) photon fields that are delivered with DMLC. In the planning stage, the planner specifies the number of beams and their directions, and the desired doses for the target, the normal organs and the "overlap" regions. Then, the inverse algorithm designs intensity profiles that best meet the specified criteria. A second algorithm determines the leaf motion that would produce the designed intensity pattern and produces a DMLC file as input to the MLC control computer. Our quality assurance program for the planning and treatment delivery process includes the following components: 1) verification of the DMLC field boundary on localization port film, 2) verification that the leaf motion of the DMLC file produces the planned dose distribution (with an independent calculation), 3) comparison of dose distribution produced by DMLC in a flat phantom with that calculated by the treatment planning computer for the same experimental condition, 4) comparison of the planned leaf motions with that implemented for the treatment (as recorded on the MLC log files), 5) confirmation of the initial and final positions of the MLC for each field by a record-and-verify system, and 6) in vivo dose measurements.

RESULTS

Using a five-field IMRT plan we have customized dose distribution to conform to and deliver 81 Gy to the PTV. In addition, in the overlap regions between the PTV and the rectum, and between the PTV and the bladder, the dose is kept within the tolerance of the respective organs. Our QA checks show acceptable agreement between the planned and the implemented leaf motions. Correspondingly, film and TLD dosimetry indicates that doses delivered agrees with the planned dose to within 2%. As of September 15, 1996, we have treated eight patients to 81 Gy with IMRT.

CONCLUSION

For complex planning problems where the surrounding normal tissues place severe constraints on the prescription dose, IMRT provides a powerful and efficient solution. Given a comprehensive and rigorous quality-assurance program, the intensity-modulated fields can be efficaciously and accurately delivered using DMLC. IMRT treatment is now ready for routine implementation on a large scale in our clinic.

Phosphorylation of tau at both Thr 231 and Ser 262 is required for maximal inhibition of its binding to microtubules

The paired helical filaments (PHFs) found in Alzheimer's disease (AD) brains are composed primarily of the microtubule-associated protein tau. PHF-tau is in a hyperphosphorylated state and is unable to promote microtubule assembly. We investigated whether the inhibition of tau binding to microtubules is increased when tau is phosphorylated by different kinases in combination with GSK-3. We found that when tau was first phosphorylated by A-kinase, C-kinase, cdk5, or CaM kinase II and then by GSK-3, its binding to microtubules was inhibited by 45, 61, 78, and 79%, respectively. Further, the kinase combinations cdk5/GSK-3 and CaM kinase II/GSK-3 rapidly phosphorylated the sites Thr 231 and Ser 235. When these sites were individually replaced by Ala and the phosphorylation experiments repeated, tau binding to microtubules was inhibited by 54 and 71%, respectively. By comparison, when Ser 262 was replaced by Ala, tau binding to microtubules was inhibited by only 8% after phosphorylation by CaM kinase II. From these observations we estimate that the phosphorylation of Thr 231, Ser 235, and Ser 262 contributes approximately 26, approximately 9, and approximately 33%, respectively, of the overall inhibition of tau binding to microtubules. Together, our results indicate that the binding of tau to microtubules is controlled by the phosphorylation of several sites, among which are Thr 231, Ser 235, and Ser 262.

Number and orientations of beams in intensity-modulated radiation treatments

The fundamental question of how many equispaced coplanar intensity-modulated photon beams are required to obtain an optimum treatment plan is investigated in a dose escalation study for a typical prostate tumor. Furthermore, optimization of beam orientations to improve dose distributions is explored. A dose-based objective function and a fast gradient technique are employed for optimizing the intensity profiles (inverse planning). An exhaustive search and fast simulated annealing techniques (FSA) are used to optimize beam orientations. However, to keep computation times reasonable, the intensity profiles for each beam arrangement are still optimized using inverse planning. A pencil beam convolution algorithm is employed for dose calculation. All calculations are performed in three-dimensional (3D) geometry for 15 MV photons. DVHs, dose displays, TCP, NTCP, and biological score functions are used for evaluation of treatment plans. It is shown that for the prostate case presented here, the minimum required number of equiangular beams depends on the prescription dose level and ranges from three beams for 70 Gy plans to seven to nine beams for 81 Gy plans. For the highest dose level (81 Gy), beam orientations are optimized and compared to equiangular spaced arrangements. It is shown that (1) optimizing beam orientations is most valuable for a small numbers of beams (< or = 5) and the gain diminishes rapidly for higher numbers of beams; (2) if sensitive structures (for example rectum) are partially enclosed by the target volume, beams coming from their direction tend to be preferable, since they allow greater control over dose distributions; (3) while FSA and an exhaustive search lead to the same results, computation times using FSA are reduced by two orders of magnitude to clinically acceptable values. Moreover, characteristics of and demands on biology-based and dose-based objective functions for optimization of intensity-modulated treatments are discussed.

Corin, a mosaic transmembrane serine protease encoded by a novel cDNA from human heart

A novel cDNA has been identified from human heart that encodes an unusual mosaic serine protease, designated corin. Corin has a predicted structure of a type II transmembrane protein and contains two frizzled-like cysteine-rich motifs, seven low density lipoprotein receptor repeats, a macrophage scavenger receptor-like domain, and a trypsin-like protease domain in the extracellular region. Northern analysis showed that corin mRNA was highly expressed in the human heart. In mice, corin mRNA was detected by in situ hybridization in the cardiac myocytes of the embryonic heart as early as embryonic day (E) 9.5. By E11.5-13.5, corin mRNA was most abundant in the primary atrial septum and the trabecular ventricular compartment. Expression in the heart was maintained through the adult. In addition, mouse corin mRNA was also detected in the prehypertrophic chrondrocytes in developing bones. By fluorescent in situ hybridization analysis, the human corin gene was mapped to 4p12-13 where a congenital heart disease locus, total anomalous pulmonary venous return, had been previously localized. The unique domain structure and specific embryonic expression pattern suggest that corin may have a function in cell differentiation during development. The chromosomal localization of the human corin gene makes it an attractive candidate gene for total anomalous pulmonary venous return.

The potential for sparing of parotids and escalation of biologically effective dose with intensity-modulated radiation treatments of head and neck cancers: a treatment design study

PURPOSE

Conventional radiotherapy for cancers of the head and neck (HN) can yield acceptable locoregional tumor control rates, but toxicity of many normal tissues limits our ability to escalate dose. Xerostomia represents one of the most common complications. The purpose of this study is to investigate the potential of intensity-modulated radiotherapy (IMRT) to achieve adequate sparing of parotids and to escalate nominal and/or biologically-effective dose to achieve higher tumor control without exceeding normal tissue tolerances.

METHODS AND MATERIALS

An IMRT optimization system, developed at our institution for research and clinical purposes, and coupled to a commercial radiation treatment planning system, has been applied to a number of cases of HN carcinomas. IMRT plans were designed using dose- and dose-volume-based criteria for 4 and 6 MV coplanar but non-collinear beams ranging in number from 5 to 15 placed at equi-angular steps. Detailed analysis of one of the cases is presented, while the results of the other cases are summarized. For the first case, the IMRT plans are compared with the standard 3D conformal radiation treatment (3DCRT) plan actually used to treat the patient, and with each other. The aim of the 3DCRT plan for this particular case was to deliver 73 Gy to the tumor volume in 5 fractions of 2 Gy and 28 fractions of 2.25 Gy/fx; and 46 Gy to the nodes in 2 Gy/fx while maintaining critical normal tissues to below specified tolerances. The IMRT plans were designed to be delivered as a "simultaneous integrated boost" (SIB) using the "sweeping window" technique with a dynamic MLC. The simultaneous integrated boost strategy was chosen, partly for reasons of efficiency in planning and delivery of IMRT treatments, and partly with the assumption that dose distributions in such treatments are more conformal and spare normal tissues to a greater extent than those with sequential boost strategy. Biologically equivalent dose normalized to 2 Gy/fx, termed here as normalized total dose (NTD), for this strategy was calculated using published head and neck fractionation data.

RESULTS

IMRT plans were more conformal than the 3DCRT plans. For equivalent coverage of the tumor and the nodes, and for the dose to the spinal cord and the brainstem maintained within tolerance limits, the dose to parotids was greatly reduced. For the detailed example presented, it was shown that the tumor and the nodes in the 3DCRT plan receive NTDs of 78 and 46 Gy, respectively. For the IMRT plan, a nominal dose of 70 Gy could be delivered to the tumor in 28 fractions of 2.5 Gy each, simultaneously with 50.4 Gy to nodes with 1.8 Gy/fx. The two are biologically equivalent to 82 and 46 Gy, respectively, if delivered in 2 Gy/fx. Similar computations were carried out for other cases as well. The quality of IMRT plans was found to improve with increasing number of beams, up to 9 beams. Dose-volume-based criteria led to a modest improvement in IMRT plans and required less trial and error.

CONCLUSION

IMRT has the potential to significantly improve radiotherapy of HN cancers by reducing normal tissue dose and simultaneously allowing escalation of dose. SIB strategy is not only more efficient and yields better dose distributions, but may also be biologically more effective. Dose-volume-based criteria is better than purely dose-based criteria. The quality of plans improves with number of beams, reaching a saturation level for a certain number of beams, which for the plans studied was found to be 9.

Comparative DNA sequence analysis of mouse and human protocadherin gene clusters

The genomic organization of the human protocadherin alpha, beta, and gamma gene clusters (designated Pcdh alpha [gene symbol PCDHA], Pcdh beta [PCDHB], and Pcdh gamma [PCDHG]) is remarkably similar to that of immunoglobulin and T-cell receptor genes. The extracellular and transmembrane domains of each protocadherin protein are encoded by an unusually large "variable" region exon, while the intracellular domains are encoded by three small "constant" region exons located downstream from a tandem array of variable region exons. Here we report the results of a comparative DNA sequence analysis of the orthologous human (750 kb) and mouse (900 kb) protocadherin gene clusters. The organization of Pcdh alpha and Pcdh gamma gene clusters in the two species is virtually identical, whereas the mouse Pcdh beta gene cluster is larger and contains more genes than the human Pcdh beta gene cluster. We identified conserved DNA sequences upstream of the variable region exons, and found that these sequences are more conserved between orthologs than between paralogs. Within this region, there is a highly conserved DNA sequence motif located at about the same position upstream of the translation start codon of each variable region exon. In addition, the variable region of each gene cluster contains a rich array of CpG islands, whose location corresponds to the position of each variable region exon. These observations are consistent with the proposal that the expression of each variable region exon is regulated by a distinct promoter, which is highly conserved between orthologous variable region exons in mouse and human.

Observation of electron-antineutrino disappearance at Daya Bay

The Daya Bay Reactor Neutrino Experiment has measured a nonzero value for the neutrino mixing angle θ(13) with a significance of 5.2 standard deviations. Antineutrinos from six 2.9 GWth reactors were detected in six antineutrino detectors deployed in two near (flux-weighted baseline 470 m and 576 m) and one far (1648 m) underground experimental halls. With a 43,000 ton-GWth-day live-time exposure in 55 days, 10,416 (80,376) electron-antineutrino candidates were detected at the far hall (near halls). The ratio of the observed to expected number of antineutrinos at the far hall is R=0.940±0.011(stat.)±0.004(syst.). A rate-only analysis finds sin(2)2θ(13)=0.092±0.016(stat.)±0.005(syst.) in a three-neutrino framework.

Microbial reductive dehalogenation of polychlorinated biphenyls

Under anaerobic conditions, microbial reductive dechlorination of polychlorinated biphenyls (PCBs) occurs in soils and aquatic sediments. In contrast to dechlorination of supplemented single congeners for which frequently ortho dechlorination has been observed, reductive dechlorination mainly attacks meta and/or para chlorines of PCB mixtures in contaminated sediments, although in a few instances ortho dechlorination of PCBs has been observed. Different microorganisms appear to be responsible for different dechlorination activities and the occurrence of various dehalogenation routes. No axenic cultures of an anaerobic microorganism have been obtained so far. Most probable number determinations indicate that the addition of PCB congeners, as potential electron acceptors, stimulates the growth of PCB-dechlorinating microorganisms. A few PCB-dechlorinating enrichment cultures have been obtained and partially characterized. Temperature, pH, availability of naturally occurring or of supplemented carbon sources, and the presence or absence of H(2) or other electron donors and competing electron acceptors influence the dechlorination rate, extent and route of PCB dechlorination. We conclude from the sum of the experimental data that these factors influence apparently the composition of the active microbial community and thus the routes, the rates and the extent of the dehalogenation. The observed effects are due to the specificity of the dehalogenating bacteria which become active as well as changing interactions between the dehalogenating and non-dehalogenating bacteria. Important interactions include the induced changes in the formation and utilization of H(2) by non-dechlorinating and dechlorinating bacteria, competition for substrates and other electron donors and acceptors, and changes in the formation of acidic fermentation products by heterotrophic and autotrophic acidogenic bacteria leading to changes in the pH of the sediments.

Algorithms and functionality of an intensity modulated radiotherapy optimization system

The main purpose of this paper is to describe formalisms, algorithms, and certain unique features of a system for optimization of intensity modulated radiotherapy (IMRT). The system is coupled to a commercial treatment planning system with an accurate dose calculation engine based on the kernel superposition algorithm. The system was designed for use for research as well as for routine clinical practice. It employs dose- and dose-volume-based objective functions. The system can optimize IMRT plans with multiple target volumes simultaneously. Each target volume may be assigned a different prescription dose with constraints on either underdosing, or overdosing, or both. For organs at risk more than one constraint may be applied. This feature allows simultaneous treatment of primary, regional disease and electively treated nodes. The system allows specification of constraints on logical combinations of anatomic structures, such as a region of overlap between the prostate planning target volume and rectum or the volume of lung excluding the tumor. The optimization may also be performed on plans which, in addition to intensity-modulated beams, include other modalities such as non-IMRT photon and electron beams and brachytherapy sources. The various features of the system are illustrated with one phantom example and two clinical examples: a brain stereotactic radiosurgery case and a nasopharynx case. In the cylindrical phantom example, the use of the system for overlap regions is demonstrated. The brain stereotactic radiosurgery example shows the improvement of IMRT plans over the conventional arcs based plan and the three-dimensional conformal plan with multiple fixed gantry angles and demonstrates the application of our system to cases where small grid sizes are important. The nasopharynx example shows the potential of IMRT to simultaneously treat large and boost fields. It also illustrates the power of IMRT to protect normal anatomic structures for highly complex situations and the efficiency in planning and delivery achievable with IMRT. The overall IMRT planning time is typically less than 2 h on a Sun Ultrasparc workstation, most of which is spent in repeated computation of dose distributions.

Crystal structure of a procaspase-7 zymogen: mechanisms of activation and substrate binding

Apoptosis is primarily executed by active caspases, which are derived from the inactive procaspase zymogens through proteolytic cleavage. Here we report the crystal structures of a caspase zymogen, procaspase-7, and an active caspase-7 without any bound inhibitors. Compared to the inhibitor-bound caspase-7, procaspase-7 zymogen exhibits significant structural differences surrounding the catalytic cleft, which precludes the formation of a productive conformation. Proteolytic cleavage between the large and small subunits allows rearrangement of essential loops in the active site, priming active caspase-7 for inhibitor/substrate binding. Strikingly, binding by inhibitors causes a 180 degrees flipping of the N terminus in the small subunit, which interacts with and stabilizes the catalytic cleft. These analyses reveal the structural mechanisms of caspase activation and demonstrate that the inhibitor/substrate binding is a process of induced fit.

Chlamydia psittaci is variably associated with ocular adnexal MALT lymphoma in different geographical regions

Infectious agents play a critical role in MALT lymphoma development. Studies from Italy showed Chlamydia psittaci infection in 87% of ocular adnexal MALT lymphomas and complete or partial regression of the lymphoma after C. psittaci eradication in four of nine cases. However, C. psittaci was not demonstrated in ocular adnexal MALT lymphomas from the USA. This study was thus designed to investigate further the role of C. psittaci, and other infectious agents commonly associated with chronic eye disease, in the development of ocular adnexal MALT lymphoma. The presence of C. psittaci, C. trachomatis, C. pneumoniae, herpes simplex virus 1 and 2 (HSV1, HSV2), and adenovirus 8 and 19 (ADV8, ADV19) was assessed separately by polymerase chain reaction in 142 ocular adnexal MALT lymphomas, 53 non-marginal zone lymphomas, and 51 ocular adnexal biopsies without a lymphoproliferative disorder (LPD), from six geographical regions. C. psittaci was detected at similar low frequencies in non-LPD and non-marginal zone lymphoma groups from different geographical regions (0-14%). Overall, the prevalence of C. psittaci was significantly higher in MALT lymphomas (22%) than in non-LPD (10%, p=0.042) and non-marginal zone lymphoma cases (9%, p=0.033). However, the prevalence of C. psittaci infection in MALT lymphoma showed marked variation among the six geographical regions examined, being most frequent in Germany (47%), followed by the East Coast of the USA (35%) and the Netherlands (29%), but relatively low in Italy (13%), the UK (12%), and Southern China (11%). No significant differences in the detection of C. pneumoniae, C. trachomatis, HSV1, HSV2, ADV8, and ADV19 were found between lymphomas and controls from different geographical regions. In conclusion, our results show that C. psittaci, but not C. pneumoniae, C. trachomatis, HSV1, HSV2, ADV8 or ADV19, is associated with ocular adnexal MALT lymphoma and that this association is variable in different geographical areas.

Newly Emerged Porcine Deltacoronavirus Associated With Diarrhoea in Swine in China: Identification, Prevalence and Full-Length Genome Sequence Analysis

To identify and characterize aetiologic agent(s) associated with an outbreak of a severe diarrhoea in piglets in Jiangxi, China, in March 2015, a nested reverse transcription–polymerase chain reaction (RT‐PCR) for the detection of porcine deltacoronavirus (PDCoV) was developed. A survey based on the nested RT‐PCR established indicated that the monoinfection of PDCoV (33.71%) and coinfection of PDCoV (19.66%) with porcine epidemic diarrhoea virus (PEDV) were common in diarrhoeal pigs in Jiangxi, China. A high prevalence of PDCoV (58.33%) in diarrhoeal samples which were PEDV negative was observed. The complete genome sequence of a representative PDCoV strain, PDCoV/CHJXNI2/2015, was determined. Phylogenetic analysis of complete genome and S protein sequences of PDCoV/CHJXNI2/2015 demonstrated that it was most closely related to Hong Kong and US PDCoVs. To our knowledge, this is the first report on the identification, prevalence, complete genome sequencing and molecular characterizations of PDCoV in diarrhoeal samples in pigs in China.