An updated definition of V(D)J recombination signal sequences revealed by high-throughput recombination assays

In the adaptive immune system, V(D)J recombination initiates the production of a diverse antigen receptor repertoire in developing B and T cells. Recombination activating proteins, RAG1 and RAG2 (RAG1/2), catalyze V(D)J recombination by cleaving adjacent to recombination signal sequences (RSSs) that flank antigen receptor gene segments. Previous studies defined the consensus RSS as containing conserved heptamer and nonamer sequences separated by a less conserved 12 or 23 base-pair spacer sequence. However, many RSSs deviate from the consensus sequence. Here, we developed a cell-based, massively parallel assay to evaluate V(D)J recombination activity on thousands of RSSs where the 12-RSS heptamer and adjoining spacer region contained randomized sequences. While the consensus heptamer sequence (CACAGTG) was marginally preferred, V(D)J recombination was highly active on a wide range of non-consensus sequences. Select purine/pyrimidine motifs that may accommodate heptamer unwinding in the RAG1/2 active site were generally preferred. In addition, while different coding flanks and nonamer sequences affected recombination efficiency, the relative dependency on the purine/pyrimidine motifs in the RSS heptamer remained unchanged. Our results suggest RAG1/2 specificity for RSS heptamers is primarily dictated by DNA structural features dependent on purine/pyrimidine pattern, and to a lesser extent, RAG:RSS base-specific interactions.

Risky business blockade: RAG2 basic region blocks V(D)J recombinase function upon genotoxic stress in DNA damage response

The V(D)J recombinase, composed of the recombination activating gene (RAG) proteins, RAG1 and RAG2, generate functional antigen receptor genes through the repeated generation of DNA double strand breaks and DNA repair. However, this process can lead to increased genomic instability particularly in the presence of excess DNA breaks. Previously, we showed in pre-B cells that full length RAG2, a nuclear protein, will export to the cytoplasm with DNA damage in an ATM-dependent manner with eventual recovery back into the nucleus following DNA repair. We propose that re-localization of RAG2 prevents RAG-mediated DNA cleavage in the presence of excess DNA ends. Here, by using fluorescently tagged RAG proteins, we show that DNA damage-induced export of the V(D)J recombinase can be recapitulated in non-lymphoid cells. Further, we determined that mutations in the intrinsically-disordered region of RAG2 have distinct effects on this process. Specifically, a basic region mutant of RAG2 (K/R 518–524 A) alters the localization pattern of the V(D)J recombinase, and yet its pre-DNA damage localization pattern is re-established upon DNA repair. Conversely, a T490A mutant blocks relocalization of RAG2 following genotoxic stress for both the single T490A mutant and the combined T490A/basic region mutant. Together, these results demonstrate the role of the intrinsically-disordered region in RAG2 in regulating the mobility and subcellular localization of the V(D)J recombinase upon cellular conditions that may be deemed too risky for continued DNA rearrangements.

Supported by NIA T32AG052363, NIH AI128137, OCAST

Destination active chromatin: RAG2 regions that pave the way to V(D)J recombination

V(D)J recombination is required to establish the diversity of antigen receptors in the adaptive immune system. Recombination activating gene 2 (RAG2), a protein subunit of the nuclear V(D)J recombinase, rearranges gene segments to generate functional genes that encode antigen receptors. Based on our previous results, we hypothesized that a negatively charged region (the acidic hinge) in RAG2 functions to regulate localization of the V(D)J recombinase with chromatin. To test this, we generated the acidic hinge mutant 1 (A1; D/E 370–383 A), acidic hinge mutant 2 (A2; D/E 404–410 A), and D400H (a known mutation that causes immunodeficiency) to determine impact on chromatin association and V(D)J recombination activity. Dynamics of RAG2 mobility with the chromatin were determined with fluorescence recovery after photobleaching (FRAP) experiments with stably expressed GFP-tagged wild type (WT) or mutant RAG2 in RAG2−/− pro-B cells. Changes in V(D)J recombination activity and in RAG2 localization was determined for cells expressing the WT versus mutant RAG2 proteins. FRAP experiments indicated that the acidic hinge mutants had more tightly bound interactions with chromatin, as compared to WT RAG2. A1 resulted in increased V(D)J recombination, whereas, A2 and D400H led to decreased V(D)J recombination. Interestingly, these results correlated with an increased and a decreased nuclear localization of A1 and A2, respectively, relative to WT RAG2. These results indicate that the acidic region has a role in the cellular localization of the V(D)J recombinase, affecting its recombination efficiency. However, D400H localized similarly to WT RAG2, indicating the residue has a more direct role in the nuclear function of the V(D)J recombinase.

Full length RAG2 expression enhances the DNA damage response in pre-B cells

V(D)J recombination by the RAG1 and RAG2 protein complex in developing lymphocytes includes DNA double strand break (DSB) intermediates. RAG2 undergoes export from the nucleus and enrichment at the centrosome minutes following production of DSBs by genotoxic stress, suggesting that RAG2 participates in cellular responses to DSBs such as those generated during V(D)J recombination. To determine the effect of RAG2 expression on cell viability following DSB generation, we measured pre-B cells that expressed either full length (FL) wild-type RAG2, or a T490A mutant of RAG2 that has increased stability and fails to undergo nuclear export following generation of DSBs. Each RAG2 construct was labeled with GFP at the N-terminus. Compared to the T490A mutant, cells expressing FL RAG2 exhibited elevated apoptosis by 24 h following irradiation, and this coincided with a greater amount of Caspase 3 cleavage measured in cell lysates. Pre-B cells expressing either RAG2 protein exhibited similar increases in phospho-p53 levels following irradiation. Interestingly, FL RAG2-expressing cells exhibited elevated division relative to the T490A clone beginning ~24 h following irradiation, as well as an increased percentage of cells proceeding through mitosis, suggesting an improved rate of recovery following the initial burst in apoptosis. Altogether, these data show that FL RAG2, but not its stable nuclear export-defective T490A mutant, participates in pre-B cell decisions between apoptosis versus DNA repair and cell cycle progression following DNA damage.

Microscopic Imaging of the Stress Tensor in Diamond Using in Situ Quantum Sensors

The precise measurement of mechanical stress at the nanoscale is of fundamental and technological importance. In principle, all six independent variables of the stress tensor, which describe the direction and magnitude of compression/tension and shear stress in a solid, can be exploited to tune or enhance the properties of materials and devices. However, existing techniques to probe the local stress are generally incapable of measuring the entire stress tensor. Here, we make use of an ensemble of atomic-sized in situ strain sensors in diamond (nitrogen-vacancy defects) to achieve spatial mapping of the full stress tensor, with a submicrometer spatial resolution and a sensitivity of the order of 1 MPa (10 MPa) for the shear (axial) stress components. To illustrate the effectiveness and versatility of the technique, we apply it to a broad range of experimental situations, including mapping the stress induced by localized implantation damage, nanoindents, and scratches. In addition, we observe surprisingly large stress contributions from functional electronic devices fabricated on the diamond and also demonstrate sensitivity to deformations of materials in contact with the diamond. Our technique could enable in situ measurements of the mechanical response of diamond nanostructures under various stimuli, with potential applications in strain engineering for diamond-based quantum technologies and in nanomechanical sensing for on-chip mass spectroscopy.

RAG2 localization and dynamics in the pre-B cell nucleus

RAG2 of the V(D)J recombinase is essential for lymphocyte development. Within the RAG2 noncore region is a plant homeodomain (PHD) that interacts with the modified histone H3K4me3, and this interaction is important for relieving inhibition of the RAG recombinase for V(D)J recombination. However, the effect of the noncore region on RAG2 localization and dynamics in cell nuclei is poorly understood. Here, we used cell imaging to measure the effect of mutating the RAG2 noncore region on properties of the full length protein. We measured GFP-labeled full length RAG2 (FL), the RAG2 core region alone (Core), and a T490A mutant in the noncore region, which has unique regulatory properties. This showed that FL, T490A, and Core localized to nuclear domains that were adjacent to DAPI-rich heterochromatin, and that contained the active chromatin marker H3K4me3. Within the RAG2-enriched regions, T490A exhibited greater colocalization with H3K4me3 than either FL or Core. Furthermore, colocalization of H3K4me3 with FL and T490A, but not Core, increased in conditions that increased H3K4me3 levels. Superresolution imaging showed H3K4me3 was distributed as puncta that RAG2 abutted, and mobility measurements showed that T490A had a significantly lower rate of diffusion within the nucleus than either FL or Core proteins. Finally, mutating Trp453 of the T490A mutant (W453A,T490A), which blocks PHD-dependent interactions with H3K4me3, abolished the T490A-mediated increased colocalization with H3K4me3 and slower mobility compared to FL. Altogether, these data show that Thr490 in the noncore region modulates RAG2 localization and dynamics in the pre-B cell nucleus, such as by affecting RAG2 interactions with H3K4me3.

Abstract P1-06-08: A p53-independent DNA damage response that regulates breast cancer phenotypes

Defects in the DNA damage repair system result in increased genomic instability and have recently been implicated as being drivers of tumorigenesis in both familial and sporadic breast cancers. To maintain genomic integrity, cells have a DNA damage response (DDR) mechanism that functions to repair damaged DNA efficiently and commits cells to death if damage is irreparable. Failure of this mechanism results in genomic instability and cancer predisposition. Widespread chromosomal instability is a characteristic feature of Triple-Negative Breast Cancer (TNBC), making it difficult to decipher between genes that drive cancer development from those that play a bystander role. Little is known about what gives rise to the extensive genomic instability of TNBC, and presents a major deficit in our scientific and clinical knowledge.

Oncogene induced hyper-proliferation results in replication-associated double strand breaks (DSBs) that engage an Mre11-Rad50-Nbs1 complex-dependent DDR. Classically, the oncogene induced DDR is believed to suppress tumorigenesis due to downstream activation of p53. Using genetically engineered primary mammary epithelial cell models, we demonstrate p53-independent effects of the Mre11-dependent DDR in suppressing proliferation and DNA damage induced by diverse oncogenic drivers. Single cell whole genome sequencing in Her2/Neu expressing primary mammary epithelial cells reveals a landscape of stochastic copy number aberrations induced by oncogenic stress that becomes enriched for a genomic scar pattern of larger-size deletions in cells with Mre11 hypomorphism. We identify Mre11 pathway hypomorphism in a subset of basal-like breast cancers (BLBC), which confers vulnerability to specific DNA damaging agents and DDR inhibitors in murine models of p53-deficient BLBC. Thus, assessing the functional status of the Mre11-dependent DDR pathway in p53-mutant breast cancers may provide an opportunity for therapeutic exploitation.

Citation Format: Fagan-Solis KD, Simpson DA, Kapustina M, Martelotto L, Reis-Filho JS, Petrini JH, Gupta GP. A p53-independent DNA damage response that regulates breast cancer phenotypes [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-06-08.

Iatrogenic Creutzfeldt-Jakob disease and its neurosurgical implications

Creutzfeldt-Jakob (CJD) disease has been reported after the insertion of dural homografts. Two Australian cases of CJD, both following posterior fossa craniotomies done in 1982, are reported; the incubation periods were 5 and 12 years. It seems highly probable that the association is causal. CJD infective agents (prions) are resistant to many previously accepted means of sterilisation and it is postulated that cadaver dural material was either derived from subjects with CID, or was contaminated during preparation. In Australia the use of dural homografts in neurosurgery was abandoned in 1987; as the mean incubation period (determined from a world-wide review) has been about 65 months, it is now hoped that this cause of CJD will not recur in the Australian population, although it is premature to state this with confidence. However, precautions against case-to-case transmission remain necessary, and guidelines for this purpose should be enforced in theatre practice and in organ donations.

Dynamic stabilization of the optical resonances of single nitrogen-vacancy centers in diamond

We report electrical tuning by the Stark effect of the excited-state structure of single nitrogen-vacancy (NV) centers located ≲100  nm from the diamond surface. The zero-phonon line (ZPL) emission frequency is controllably varied over a range of 300 GHz. Using high-resolution emission spectroscopy, we observe electrical tuning of the strengths of both cycling and spin-altering transitions. Under resonant excitation, we apply dynamic feedback to stabilize the ZPL frequency. The transition is locked over several minutes and drifts of the peak position on timescales ≳100  ms are reduced to a fraction of the single-scan linewidth, with standard deviation as low as 16 MHz (obtained for an NV in bulk, ultrapure diamond). These techniques should improve the entanglement success probability in quantum communications protocols.

High spatial and temporal resolution wide-field imaging of neuron activity using quantum NV-diamond

A quantitative understanding of the dynamics of biological neural networks is fundamental to gaining insight into information processing in the brain. While techniques exist to measure spatial or temporal properties of these networks, it remains a significant challenge to resolve the neural dynamics with subcellular spatial resolution. In this work we consider a fundamentally new form of wide-field imaging for neuronal networks based on the nanoscale magnetic field sensing properties of optically active spins in a diamond substrate. We analyse the sensitivity of the system to the magnetic field generated by an axon transmembrane potential and confirm these predictions experimentally using electronically-generated neuron signals. By numerical simulation of the time dependent transmembrane potential of a morphologically reconstructed hippocampal CA1 pyramidal neuron, we show that the imaging system is capable of imaging planar neuron activity non-invasively at millisecond temporal resolution and micron spatial resolution over wide-fields.

Quantum measurement and orientation tracking of fluorescent nanodiamonds inside living cells

Fluorescent particles are routinely used to probe biological processes. The quantum properties of single spins within fluorescent particles have been explored in the field of nanoscale magnetometry, but not yet in biological environments. Here, we demonstrate optically detected magnetic resonance of individual fluorescent nanodiamond nitrogen-vacancy centres inside living human HeLa cells, and measure their location, orientation, spin levels and spin coherence times with nanoscale precision. Quantum coherence was measured through Rabi and spin-echo sequences over long (>10 h) periods, and orientation was tracked with effective 1° angular precision over acquisition times of 89 ms. The quantum spin levels served as fingerprints, allowing individual centres with identical fluorescence to be identified and tracked simultaneously. Furthermore, monitoring decoherence rates in response to changes in the local environment may provide new information about intracellular processes. The experiments reported here demonstrate the viability of controlled single spin probes for nanomagnetometry in biological systems, opening up a host of new possibilities for quantum-based imaging in the life sciences.

Topoisomerase IIalpha maintains genomic stability through decatenation G(2) checkpoint signaling

Topoisomerase IIalpha (topoIIalpha) is an essential mammalian enzyme that topologically modifies DNA and is required for chromosome segregation during mitosis. Previous research suggests that inhibition of topoII decatenatory activity triggers a G(2) checkpoint response, which delays mitotic entry because of insufficient decatenation of daughter chromatids. Here we examine the effects of both topoIIalpha and topoIIbeta on decatenatory activity in cell extracts, DNA damage and decatenation G(2) checkpoint function, and the frequencies of p16(INK4A) allele loss and gain. In diploid human fibroblast lines, depletion of topoIIalpha by small-interfering RNA was associated with severely reduced decatenatory activity, delayed progression from G(2) into mitosis and insensitivity to G(2) arrest induced by the topoII catalytic inhibitor ICRF-193. Furthermore, interphase nuclei of topoIIalpha-depleted cells showed increased frequencies of losses and gains of the tumor suppressor genetic locus p16(INK4A). This study shows that the topoIIalpha protein is required for decatenation G(2) checkpoint function, and inactivation of decatenation and the decatenation G(2) checkpoint leads to abnormal chromosome segregation and genomic instability.

Nano-manipulation of diamond-based single photon sources

The ability to manipulate nano-particles at the nano-scale is critical for the development of active quantum systems. This paper presents a technique to manipulate diamond nano-crystals at the nano-scale using a scanning electron microscope, nano-manipulator and custom tapered optical fibre probes. The manipulation of a approximately 300 nm diamond crystal, containing a single nitrogen-vacancy centre, onto the endface of an optical fibre is demonstrated. The emission properties of the single photon source post manipulation are in excellent agreement with those observed on the original substrate.

Dandy-Walker syndrome associated with congenital heart defects: report of three cases

Three cases of Dandy-Walker syndrome associated with congenital heart defects are reported, and their management is described. The various theories concerning the aetiology of the Dandy-Walker syndrome are discussed and it is suggested that the theory of primary developmental atresia of the foramina of Magendie and Luschka is still acceptable. If the child with Dandy-Walker syndrome requires treatment by extracranial CSF drainage it is proposed that a ventriculo-peritoneal shunt is preferable when there is any suspicion of cardiac anomaly. The proximal catheter should be placed in the posterior fossa cyst (dilated fourth ventricle) rather than in the lateral ventricle.

Visible and near infra-red up-conversion in Tm3+/Yb3+ co-doped silica fibers under 980 nm excitation

The spectroscopic properties of Tm(3+)/Yb(3+) co-doped silica fibers under excitation at 980 nm are reported. Three distinct up-conversion fluorescence bands were observed in the visible to near infra-red regions. The blue and red fluorescence bands at 475 and 650 nm, respectively, were found to originate from the (1)G(4) level of Tm(3+). A three step up-conversion process was established as the populating mechanism for these fluorescence bands. The fluorescence band at 800 nm was found to originate from two possible transitions in Tm(3+); one being the transition from the (3)H(4) to (3)H(6) manifold which was found to dominate at low pump powers; the other being the transition from the (1)G(4) to (3)H(6) level which dominates at higher pump powers. The fluorescence lifetime of the (3)H(4) and (3)F(4) levels of Tm(3+) and (2)F(5/2) level of Yb(3+) were studied as a function of Yb(3+) concentration, with no significant energy back transfer from Tm(3+) to Yb(3+) observed.

The visual fields: an interdisciplinary history II. neurosurgeons and quantitative perimetry

When operations for brain tumours became possible, exact charting of visual field defects assumed great importance in diagnosis and in monitoring post-operative progress. This process, known as quantitative perimetry, was energetically practised and taught by Harvey Cushing and by many of his pupils. The advent of non-invasive methods of imaging the brain and the rise of neuro-ophthalmology as an independent discipline were associated with a decline in neurosurgical commitment to quantitative perimetry, but it remains an important branch of the clinical neurosciences.

Kv1.5 is a major component underlying the A-type potassium current in retinal arteriolar smooth muscle

Little is known about the molecular characteristics of the voltage-activated K⁺ (K_v) channels that underlie the A-type K⁺ current in vascular smooth muscle cells of the systemic circulation. We investigated the molecular identity of the A-type K⁺ current in retinal arteriolar myocytes using patch-clamp techniques, RT-PCR, immunohistochemistry, and neutralizing antibody studies. The A-type K⁺ current was resistant to the actions of specific inhibitors for K_v3 and K_v4 channels but was blocked by the K_v1 antagonist correolide. No effects were observed with pharmacological agents against K_v1.1/2/3/6 and 7 channels, but the current was partially blocked by riluzole, a K_v1.4 and K_v1.5 inhibitor. The current was not altered by the removal of extracellular K⁺ but was abolished by flecainide, indicative of K_v1.5 rather than K_v1.4 channels. Transcripts encoding K_v1.5 and not K_v1.4 were identified in freshly isolated retinal arterioles. Immunofluorescence labeling confirmed a lack of K_v1.4 expression and revealed K_v1.5 to be localized to the plasma membrane of the arteriolar smooth muscle cells. Anti-K_v1.5 antibody applied intracellularly inhibited the A-type K⁺ current, whereas anti-K_v1.4 antibody had no effect. Co-expression of K_v1.5 with K_vβ1 or K_vβ3 accessory subunits is known to transform K_v1.5 currents from delayed rectifers into A-type currents. K_vβ1 mRNA expression was detected in retinal arterioles, but K_vβ3 was not observed. K_vβ1 immunofluorescence was detected on the plasma membrane of retinal arteriolar myocytes. The findings of this study suggest that K_v1.5, most likely co-assembled with K_vβ1 subunits, comprises a major component underlying the A-type K⁺ current in retinal arteriolar smooth muscle cells.

Novel and recurrent mutations in lamin A/C in patients with Emery-Dreifuss muscular dystrophy

Emery-Dreifuss muscular dystrophy (EDMD) is characterized by slowly progressive muscle wasting and weakness; early contractures of the elbows, Achilles tendons, and spine; and cardiomyopathy associated with cardiac conduction defects. Clinically indistinguishable X-linked and autosomal forms of EDMD have been described. Mutations in the STA gene, encoding the nuclear envelope protein emerin, are responsible for X-linked EDMD, while mutations in the LMNA gene encoding lamins A and C by alternative splicing have been found in patients with autosomal dominant, autosomal recessive, and sporadic forms of EDMD. We report mutations in LMNA found in four familial and seven sporadic cases of EDMD, including seven novel mutations. Nine missense mutations and two small in-frame deletions were detected distributed throughout the gene. Most mutations (7/11) were detected within the LMNA exons encoding the central rod domain common to both lamins A/C. All of these missense mutations alter residues in the lamin A/C proteins conserved throughout evolution, implying an essential structural and/or functional role of these residues. One severely affected patient possesed two mutations, one specific to lamin A that may modify the phenotype of this patient. Mutations in LMNA were frequently identified among patients with sporadic and familial forms of EDMD. Further studies are needed to identify the factors modifying disease phenotype among patients harboring mutations within lamin A/C and to determine the effect of various mutations on lamin A/C structure and function.

Neuro-ophthalmological sequelae of horse-related accidents

PURPOSE

The aim of this study was to highlight the neuro-ophthalmological dangers associated with horse riding, and working around horses, and the importance of wearing adequate headgear to protect the rider from neuro-ophthalmic injuries. It raises the questions of whether the current laws regarding helmet use are satisfactory, and whether helmets currently used are of an adequate standard.

METHODS

The records over a 20-year period of one neuro-ophthalmologist in Adelaide were reviewed producing 22 patients with neuro-ophthalmological sequelae of head injuries as a result of horse-related accidents.

RESULTS

There were 22 patients (16 female, six male), one of whom was involved in three separate accidents, Of these, seven were professional riders and 15 amateur. In 20 of the 24 accidents, patients were either thrown or fell from the horse. Helmets were worn in 15 of the accidents. All the patients had closed head injuries of varying severity. The most common neuro-ophthalmological complication found was a fourth-nerve palsy in 11 patients. Five patients had a significant loss of vision and two of these were severe enough to warrant a blind pension.

CONCLUSIONS

Horse riding and working around horses constitute an occupation or recreation with inherent dangers. Previous studies have shown that wearing of protective headgear reduces the risk and severity of head injuries, and helmet use should be vigorously promoted. The current laws and practices regarding helmet use are not uniform and seem to be inadequate. The current standard for equestrian safety helmets (AS/NZS 3838:1998) embodies improvements on earlier helmet standards and certainly increases the rider's chances of surviving a severe impact. Nevertheless, serious brain injuries have occurred in wearers of approved helmets, and further research is desirable to ensure the optimum degree of protection compatible with rider acceptance.

Expression of the 67 kDa laminin receptor (67LR) during retinal development: correlations with angiogenesis

Interaction of vascular cells with the laminin component of basement membranes is important for normal cell function. Likewise, abnormal interactions may have a critical role in vascular pathology. It has been previously demonstrated that the 67 kDa laminin receptor (67LR) is expressed at high levels during proliferative retinopathy in a mouse model and in the current study we have examined 67LR in the neonatal mouse to determine if this receptor plays a role in aspects of developmental angiogenesis in the developing murine retina. Groups of C57/BL6 mice were killed at postnatal day P1, P3, P5, P7, P9 and P11 to assess the retinal vasculature. A number of mice were perfused with FITC-dextran and the eyes removed, fixed in 4% paraformaldehyde (PFA) and flat-mounted for confocal scanning laser microscopy. The eyes from the remaining mice were either placed in 4% PFA and embedded in paraffin-wax, or had the neural retina dissected off and total RNA or protein extracted. Immunofluorescence, in situ hybridization, quantitative reverse transcriptase polymerase chain reaction and Western blotting analysis were employed to locate and determine expression levels of 67LR. Both 67LR mRNA and protein expression showed a characteristic bi-phasic expression pattern which correlated with key stages of retinal vascular development in the murine retina. 67LR showed high expression levels at P1 (P < 0.05) (correlating with superficial vascular plexus formation) and at P7 (P < 0.05) (correlating with deep vascular plexus formation). Conversely, 67LR expression was decreased when active angiogenic activity was lowest. Significantly, optical sectioning of retinal flat-mounts revealed high levels of 67LR expression in developing segments of both superficial and deep capillary plexi, a pattern which co-localized strongly with laminin. 67LR is regulated during post-natal development of the retinal vasculature. High levels of 67LR during the two well-defined phases of retinal capillary plexus formation suggests that this receptor may play an important role in retinal angiogenesis.

Retinal VEGF mRNA measured by SYBR green I fluorescence: A versatile approach to quantitative PCR

PURPOSE

To determine whether continuous monitoring of SYBR Green I fluorescence provides a reliable and flexible method of quantitative RT-PCR. Our aims were (i) to test whether SYBR Green I analysis could quantify a wide range of known VEGF template concentrations, (ii) to apply this method in an experimental model, and (iii) to determine whether 20 existing primer pairs could be used to quantify their cognate mRNAs.

METHODS

Real-time quantitative PCR was performed using a LightCycler rapid thermal cycler (Roche). Retinal VEGF mRNA levels were measured in a murine model of oxygen-induced retinopathy during vaso-obliterative and hypoxic phases.

RESULTS

This technique was able to detect as few as 10 control template copies, with quantitative data available routinely for 1000 or more copies. The levels of retinal VEGF mRNA expression followed the hypoxia-induced pattern determined previously by conventional methods. All gene-specific primer pairs which amplify a specific product by conventional PCR were successfully converted to SYBR Green analysis, including those for housekeeping genes glyceraldehyde phosphate dehydrogenase (GAPDH), cyclophilin, and acidic ribosomal phosphoprotein PO (ARP/36B4) and for 28S rRNA. In each case melting curve analysis and agarose gel electrophoresis confirmed the specificity of the amplification product.

CONCLUSIONS

The sequence-independent detection of DNA with SYBR Green I means that it can be used to quantify the amplification of any cDNA using gene-specific primers. This rapid and flexible method is ideally suited for researchers in vision science wishing to quantify mRNAs from many different genes because it does not require investment in gene-specific hybridization probes.

Sindbis-group alphavirus replication in periosteum and endosteum of long bones in adult mice

Several alphaviruses, including the Sindbis-group viruses, Ross River virus, O'nyong-nyong virus, and Chikungunya virus, are associated with outbreaks of acute and persistent arthralgia and arthritis in humans. Mechanisms underlying alphavirus-induced arthralgia and arthritis are not clearly understood, though direct viral replication within or around the affected joints is thought to contribute to disease. S.A.AR86 is a Sindbis-group alphavirus closely related to the arthralgia-associated Ockelbo and Girdwood S.A viruses. Following inoculation with S.A.AR86 derived from a molecular clone, infectious virus was isolated from bone and joint tissue 1 to 6 days postinfection. Studies using either in situ hybridization or S.A.AR86-derived double promoter viruses and replicons expressing green fluorescent protein localized sites of viral replication to the periosteum, tendons, and endosteum within the epiphyses of the long bones adjacent to articular joints. These results demonstrate that alphaviruses associated with arthralgia in humans replicate within bone-associated connective tissue adjacent to articular joints in an adult mouse model.

A single amino acid change in nsP1 attenuates neurovirulence of the Sindbis-group alphavirus S.A.AR86

S.A.AR86, a member of the Sindbis group of alphaviruses, is neurovirulent in adult mice and has a unique threonine at position 538 of nsP1; nonneurovirulent members of this group of alphaviruses encode isoleucine. Isoleucine was introduced at position 538 in the wild-type S.A.AR86 infectious clone, ps55, and virus derived from this mutant clone, ps51, was significantly attenuated for neurovirulence compared to that derived from ps55. Intracranial (i.c. ) s55 infection resulted in severe disease, including hind limb paresis, conjunctivitis, weight loss, and death in 89% of animals. In contrast, s51 caused fewer clinical signs and no mortality. Nevertheless, comparison of the virus derived from the mutant (ps51) and wild-type (ps55) S.A.AR86 molecular clones demonstrated that s51 grew as well as or better than the wild-type s55 virus in tissue culture and that viral titers in the brain following i.c. infection with s51 were equivalent to those of wild-type s55 virus. Analysis of viral replication within the brain by in situ hybridization revealed that both viruses established infection in similar regions of the brain at early times postinfection (12 to 72 h). However, at late times postinfection, the wild-type s55 virus had spread throughout large areas of the brain, while the s51 mutant exhibited a restricted pattern of replication. This suggests that s51 is either defective in spreading throughout the brain at late times postinfection or is cleared more rapidly than s55. Further evidence for the contribution of nsP1 Thr 538 to S.A.AR86 neurovirulence was provided by experiments in which a threonine residue was introduced at nsP1 position 538 of Sindbis virus strain TR339, which is nonneurovirulent in weanling mice. The resulting virus, 39ns1, demonstrated significantly increased neurovirulence and morbidity, including weight loss and hind limb paresis. These results demonstrate a role for alphavirus nonstructural protein genes in adult mouse neurovirulence.

RpmA is required for nonopsonic phagocytosis of Pseudomonas aeruginosa

Pseudomonas aeruginosa causes severe respiratory tract infections in patients with cystic fibrosis (CF). We have been examining nonopsonic phagocytosis of P. aeruginosa by macrophages. To study the P. aeruginosa-macrophage interaction at the molecular level, we have constructed a transposon Tn5G bank in a clinical isolate of P. aeruginosa (strain 4020) and identified mutants resistant to nonopsonic phagocytosis. Phagocytosis-resistant mutants were enriched by passaging the transposon bank over 18 macrophage monolayers. Of 900 individual mutants isolated from this enriched pool in a nonopsonic phagocytosis assay, we identified 85 putative mutants that were resistant to phagocytosis. In this study, we have characterized one of these transposon mutants, P. aeruginosa 4020 H27A, which was poorly ingested. H27A possessed a Tn5G insertion in a gene encoding a protein with homology to the MotA proteins of several species of bacteria. We have called this gene rpmA for required for phagocytosis by macrophages. RpmA is one of two MotA paralogs in P. aeruginosa. This rpmA::Tn5G mutant was motile both on agar plates and in visual examination of wet mounts. The phagocytosis defect was partially complemented by providing the rpmA gene in trans and fully complemented when both rpmA and rpmB were provided. A rpmA null mutant was ingested by macrophages similar to the H27A transposon mutant. These data suggest that the rpmA and rpmB gene products are required for the efficient ingestion of P. aeruginosa by macrophages.

Penetration of clinical isolates of Pseudomonas aeruginosa through MDCK epithelial cell monolayers

Pseudomonas aeruginosa causes both invasive (bacteremic) and chronic noninvasive infections. A simple in vitro system to screen P. aeruginosa clinical isolates for their capacity to penetrate MDCK cell monolayers has been developed. By means of this system, P. aeruginosa clinical isolates, including 32 blood and 45 respiratory isolates, were examined. When monolayers were infected with 3.5x107 cfu of bacteria, significantly more blood (93.7%) than respiratory (54.4%) isolates (P<.001) were detected in the basolateral medium after 3 h. Penetration ability was usually independent of cytotoxicity. Only 8 (4 blood and 4 respiratory) isolates were cytotoxic, possessed exoU, and passed through the monolayer after epithelial cell death, associated with a marked drop in transepithelial electrical resistance. Conversely, noncytotoxic isolates with high penetration ability but without severe epithelial damage were invasive. This system is well suited for screening clinical isolates and their mutants for specific genes conferring the invasiveness phenotype.

Techniques for identifying the applicability of new information management technologies in the clinical setting: an example focusing on handheld computers

This article describes techniques and strategies used to judge the potential applicability of new information management technologies in the clinical setting and to develop specific design recommendations for new features and services. We focus on a project carried out to identify the potential uses of handheld computers (i.e., the Palm Pilot or a small WinCE-based device) in the ambulatory practice setting. We found that the potential for a robust handheld computing device to positively affect the outpatient ambulatory clinical setting is enormous, and that the information derived from the exploratory research project is useful in creating specific design recommendations for further development.

Expression of the VEGF gene family during retinal vaso-obliteration and hypoxia

Vascular insufficiency and retinal ischaemia precede many proliferative retinopathies and stimulate secretion of vasoactive growth factors. Vascular endothelial growth factor (VEGF) plays a major role and we therefore investigated the other members of the VEGF family: Placental growth factor (PlGF), VEGF-B, -C, and -D, and platelet derived growth factors (PDGF) A and B. Neonatal mice were exposed to hyperoxia for 5 days and then returned to room air (resulting in acute retinal ischaemia). RT-PCR demonstrated that all the members of the VEGF family are expressed in the retina and in situ hybridization (ISH) located their mRNAs primarily in ganglion cells. Similarly to VEGF itself, VEGF-C, PDGF-A, and PDGF-B were upregulated during retinal ischaemia (P < 0.05). Only PlGF gene expression increased during hyperoxia (P < 0.01). The expression pattern of these growth factors suggests a role in the normal retina and during vaso-obliterative and ischaemic phases.

Intracellular localization of the Fanconi anemia complementation group A protein

Mutations in the Fanconi anemia (FA) complementation group A (FANCA) gene leads to bone marrow failure, developmental abnormalities and cancer predisposition. To map the intracellular site of FANCA, we constructed a plasmid vector which linked in-frame the enhanced green fluorescent protein (EGFP cDNA) to the 5' end of the FANCA cDNA (pDAS-3). We studied the expression of pDAS-3 in the FANCA mutant fibroblast cell line (GM6914). MMC sensitivity of pDAS-3 transfected cells was comparable to wild-type fibroblasts. The resulting fluorescence pattern in the stable pDAS-3 cell line expressing the fusion protein was primarily nuclear. EGFP-selected cells (lacking FANCA) remain hypersensitive to MMC and maintained a cytoplasmic fluorescence pattern. Using deletion mutants of pDAS-3, a nuclear localization domain was identified at the amino terminus of the polypeptide. Western blot results of FANCA protein confirmed the presence of FANCA in nuclear fractions and FANCA protein levels did not vary during cell cycling. This nuclear trafficking of FANCA should guide future work in defining the function of this protein.

Tonic adrenergic and serotonergic inhibition of a withdrawal reflex in rabbits subjected to different levels of surgical preparation

The excitability of the heel-gastrocnemius withdrawal reflex pathway has been monitored in rabbits undergoing surgical preparation for electrophysiological experimentation under Saffan anaesthesia. Reflexes were evoked by percutaneous electrodes inserted at the heel and recorded as electromyograph signals from the ipsilateral medial gastrocnemius muscle. Two levels of surgery were carried out. The "full surgical" preparation was performed under deep Saffan anaesthesia. The trachea, carotid artery, jugular vein and intrathecal space (via a small laminectomy at L1) were cannulated, the animals were decerebrated by suction, and the left hindlimb was immobilized by screw clamps applied to the tibia and the femur. The sciatic nerve and its branches were exposed by bisection of the posterior biceps muscle and the anaesthetic was withdrawn. In the "reduced surgery" preparation, procedures were carried out with a lighter level of Saffan anaesthesia and operated tissues were infiltrated with local anaesthetic. Only the cannulations were performed in these animals. The excitability of the heel-gastrocnemius reflex declined throughout the full surgical preparation, with the median threshold increasing from 0.8 to 4.2 mA (n=19) and responses to suprathreshold stimuli reducing in size. Most of this effect was reversed after surgery was complete and anaesthesia withdrawn subsequent to decerebration. There were no significant changes in reflex excitability during the reduced surgery preparation (n = 15). Animals prepared by each of these protocols were given increasing intrathecal doses of either the selective alpha2-adrenoceptor antagonist RX 821002 (0.3 to 300 microg) or the serotonin/5-hydroxytryptamine (5-HT)1A-receptor antagonist WAY-100635 (0.01 to 30 microg). Both drugs caused significant, dose-dependent increases in reflex responses, to four to six times pre-drug control in both groups of animals. There were no differences in the effects on reflexes of either drug between the preparations. Thus, surgical preparation of decerebrated rabbits for electrophysiological recording results in depression of hindlimb withdrawal reflexes, although much of this effect did not persist beyond the completion of surgery. Tonic monoaminergic inhibition of reflexes was present to the same extent in both preparations investigated and is not therefore an epiphenomenon of the way in which the animals were prepared.

Advanced glycation end products in vitreous: Structural and functional implications for diabetic vitreopathy

PURPOSE

Advanced glycation end products (AGEs) form irreversible cross-links with many macromolecules and have been shown to accumulate in tissues at an accelerated rate in diabetes. In the present study, AGE formation in vitreous was examined in patients of various ages and in patients with diabetes. Ex vivo investigations were performed on bovine vitreous incubated in glucose to determine AGE formation and cross-linking of vitreous collagen.

METHODS

By means of an AGE-specific enzyme-linked immunosorbent assay (ELISA), AGE formation was investigated in vitreous samples obtained after pars plana vitrectomy in patients with and without diabetes. In addition, vitreous AGEs were investigated in bovine vitreous collagen after incubation in high glucose, high glucose with aminoguanidine, or normal saline for as long as 8 weeks. AGEs and AGE cross-linking was subsequently determined by quantitative and qualitative assays.

RESULTS

There was a significant correlation between AGEs and increasing age in patients without diabetes (r = 0.74). Furthermore, a comparison between age-matched diabetic and nondiabetic vitreous showed a significantly higher level of AGEs in the patients with diabetes (P < 0.005). Collagen purified from bovine vitreous incubated in 0.5 M glucose showed an increase in AGE formation when observed in dot blot analysis, immunogold labeling, and AGE ELISA. Furthermore, there was increased cross-linking of collagen in the glucose-incubated vitreous, when observed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and protein separation. This cross-linking was effectively inhibited by coincubation with 10 mM aminoguanidine.

CONCLUSIONS

This study suggests that AGEs may form in vitreous with increasing age. This process seems to be accelerated in the presence of diabetes and as a consequence of exposure to high glucose. Advanced glycation and AGE cross-linking of the vitreous collagen network may help to explain the vitreous abnormalities characteristic of diabetes.

Expression of vascular endothelial growth factor (VEGF) and its receptors is regulated in eyes with intra-ocular tumours

The immunolocalization and gene expression of vascular endothelial growth factor (VEGF) and its cognate tyrosine kinase receptors, Flt-1 and KDR, has been studied in ocular melanomas and retinoblastomas using in situ hybridization and immunohistochemistry. Tumour-related alterations in VEGF/VEGF-receptor expression have also been examined in separate and uninvolved iris, retina and choroid of the same eyes. Although VEGF immunoreactivity in the normal retina was virtually absent, low-level VEGF expression was evident in the ganglion cell-bodies, Müller cells and in a distinct population of amacrine cells. VEGF gene expression was absent in the iris and choroid of normal eyes. In tumour-bearing eyes, high levels of VEGF protein and gene expression were observed within the vascularized regions of the tumours, while the adjacent retina and choroid showed increased VEGF levels when compared with normals. Flt-1 and KDR gene expression and immunolocalization occurred in VEGF-expressing ganglion, Müller and amacrine cells in normal eyes. Within the intra-ocular tumours, VEGF-receptor gene expression and protein was evident in the endothelial cells and also in cells close to the vessels, while in the adjacent retina, Flt-1 and KDR levels were elevated over normal, especially in the blood vessels. Flt-1 and KDR were both observed at elevated levels in the choroid and iris blood vessels. This study suggests that VEGF, Flt-1 and KDR are expressed by neural, glial and vascular elements within normal human retina. Intra-ocular tumours demonstrate a high level of VEGF and VEGF-receptor expression; within uninvolved, spatially separate retina, choroid and iris in the same eyes, expression is also elevated, especially within the vasculature. Retinal vascular endothelia may respond to high intra-ocular levels of VEGF by increasing expression of their VEGF receptors, a phenomenon which could have relevance to neoplasm-related ocular neovascularization.

The vaccinia virus A18R DNA helicase is a postreplicative negative transcription elongation factor

Loss of vaccinia virus A18R gene function results in an aberrant transcription profile termed promiscuous transcription, defined as transcription within regions of the genome which are normally transcriptionally silent late during infection. Promiscuous transcription results in an increase in the intracellular concentration of double-stranded RNA, which in turn results in activation of the cellular 2-5A pathway and subsequent RNase L-catalyzed degradation of viral and cellular RNAs. One of three hypotheses could account for promiscuous transcription: (i) reactivation of early promoters late during infection, (ii) random transcription initiation, (iii) readthrough transcription from upstream promoters. Transcriptional analysis of several viral genes, presented here, argues strongly against the first two hypotheses. We have tested the readthrough hypothesis by conducting a detailed transcriptional analysis of a region of the vaccinia virus genome which contains three early genes (M1L, M2L, and K1L) positioned directly downstream of the intermediate gene, K2L. The results show that mutation of the A18R gene results in increased readthrough transcription of the M1L gene originating from the K2L intermediate promoter. A18R mutant infection of RNase L knockout mouse fibroblast (KO3) cells does not result in 2-5A pathway activation, yet the virus mutant is defective in late viral gene expression and remains temperature sensitive. These results demonstrate that the A18R gene product is a negative transcription elongation factor for postreplicative viral genes.

Myelodysplasia in adult life: the value of an outreach nursing service

In the state of South Australia, infants with myelodysplasia have been treated by early intervention since 1963, and the majority have survived. Many are now adults, leading active lives despite having severe disabilities. A pilot study confirmed that this population has a high incidence of preventable ill health because of recurrent urinary infections, renal damage, and pressure ulcers. Many of these complications can be prevented by an outreach nursing service aimed at providing education in self-care, counseling, advocacy, and other appropriate nursing interventions, thus allowing clients to avoid hospitalization and maintain their independence. The study also showed that many clients were unaware of important social benefits, the knowledge of which should promote their financial independence. The outreach nursing service is an essential part of an integrated long-term support program for adults with myelodysplasia and other forms of congenital spinal paralysis.

The 67-kd laminin receptor is preferentially expressed by proliferating retinal vessels in a murine model of ischemic retinopathy

Endothelial cell association with vascular basement membranes is complex and plays a critical role in regulation of cell adhesion and proliferation. The interaction between the membrane-associated 67-kd receptor (67LR) and the basement membrane protein laminin has been studied in several cell systems where it was shown to be crucial for adhesion and attachment during angiogenesis. As angiogenesis in the pathological setting of proliferative retinopathy is a major cause of blindness in the Western world we examined the expression of 67LR in a murine model of hyperoxia-induced retinopathy that exhibits retinal neovascularization. Mice exposed to hyperoxia for 5 days starting at postnatal day 7 (P7) and returned to room air (at P12) showed closure of the central retinal vasculature. In response to the ensuing retinal ischemia, there was consistent preretinal neovascularization starting around P17, which persisted until P21, after which the new vessels regressed. Immunohistochemistry was performed on these retinas using an antibody specific for 67LR. At P12, immunoreactivity for 67LR was absent in the retina, but by P17 it was observed in preretinal proliferating vessels and also within the adjacent intraretinal vasculature. Intraretinal 67LR immunoreactivity diminished beyond P17 until by P21 immunoreactivity was almost completely absent, although it persisted in the preretinal vasculature. Control P17 mice (not exposed to hyperoxia) failed to demonstrate any 67LR immunoreactivity in their retinas. Parallel in situ hybridization studies demonstrated 67LR gene expression in the retinal ganglion cells of control and hyperoxia-exposed mice. In addition, the neovascular intra- and preretinal vessels of hyperoxia-treated P17 and P21 mice labeled strongly for 67LR mRNA. This study has characterized 67LR immunolocalization and gene expression in a murine model of ischemic retinopathy. Results suggest that, although the 67LR gene is expressed at high levels in the retinal ganglion cells, the mature receptor protein is preferentially localized to the proliferating retinal vasculature and is almost completely absent from quiescent vessels. The differential expression of 67LR between proliferating and quiescent retinal vessels suggests that this laminin receptor is an important and novel target for future chemotherapeutic intervention during proliferative vasculopathies.

Identification and characterization of a novel DNA marker associated with epidemic Burkholderia cepacia strains recovered from patients with cystic fibrosis

Burkholderia cepacia is a problematic pathogen that may spread among patients with cystic fibrosis (CF). One highly infectious CF strain that causes epidemics in both the United Kingdom and eastern Canada has been shown to possess both the cable pilin subunit gene (cblA) and a unique combination of insertion sequences. However, no genetic markers linking this strain type with other types epidemic at various centers have been identified. Using a randomly amplified polymorphic DNA (RAPD) typing scheme, we identified an apparently conserved 1.4-kb fragment in the DNA fingerprint of epidemic B. cepacia strains. Conservation of the DNA marker among epidemic strains was demonstrated by Southern hybridization, and its prevalence was assessed in a collection of chromosomal DNAs extracted from 627 isolates representative of 132 RAPD-defined B. cepacia strain types. The marker was specifically associated with seven epidemic CF strains, was absent among nonepidemic strains infecting individual patients with CF, and rare among strains recovered from the natural environment. Only one of the seven epidemic CF strain types possessed DNA homologous to cblA. The RAPD marker was designated the "B. cepacia epidemic strain marker" (BCESM). Sequence analysis of chromosomal DNA corresponding to the 1.4-kb RAPD marker revealed the presence of a putative open reading frame (ORF) with significant homology to several negative transcriptional regulators; the ORF was designated the "epidemic strain marker regulator," or esmR. The BCESM DNA is the first genetic marker that has been identified to be specifically associated with and conserved among several epidemic B. cepacia strains which infect multiple patients with CF.

Transcriptional organization and regulation of expression of region 1 of the Escherichia coli K5 capsule gene cluster

The transcriptional organization and regulation of region 1 expression of the Escherichia coli K5 capsule gene cluster were studied. Region 1 was transcribed as an 8.0-kb polycistronic mRNA which was processed to form a separate 1.3-kb transcript encoding the 3'-most gene kpsS. Transcription of region 1 of the E. coli K5 capsule gene cluster was directed from a single promoter 225 bp upstream of a previously unidentified gene, kpsF. The promoter had -35 and -10 consensus sequences typical of an E. coli sigma 70 promoter, with no similarities to binding sites for other sigma factors. Two integration host factor (IHF) binding site consensus sequences were identified 110 bp upstream and 130 bp downstream of the transcription start site. In addition, two AT-rich regions separated by 16 bp identified upstream of the region 1 promoter were conserved upstream of the region 3 promoter. The kpsF gene was 98.8% identical with the kpsF gene identified in the E. coli K1 antigen gene cluster and confirms that the kpsF gene is conserved among group II capsule gene clusters. An intragenic Rho-dependent transcriptional terminator was discovered within the kpsF gene. No essential role for KpsF in the expression of the K5 antigen could be established. The temperature regulation of region 1 expression was at the level of transcription, with no transcription detectable in cells grown at 18 degrees C. Mutations in regulatory genes known to control temperature-dependent expression of a number of virulence genes had no effect on the temperature regulation of region 1 expression. Likewise, RfaH, which is known to regulate expression of E. coli group II capsules had no effect on the expression of region 1. Mutations in the himA and himD genes which encode the subunits of the IHF led to a fivefold reduction in the expression of KpsE at 37 degrees C, confirming a regulatory role for IHF in the expression of region 1 genes.

Complete nucleotide sequence and full-length cDNA clone of S.A.AR86 a South African alphavirus related to Sindbis

S.A.AR86 and Girdwood S.A., two South African Sindbis-like arboviruses, are closely related antigenically to the Swedish isolate, Ockelbo82 [Lundström, J. O., Vene, S., Saluzzo, J. F., and Niklasson, B. (1993) Am. J. Trop. Med. Hyg. 49(5), 531-537]. Each of these viruses is associated with human disease, and Girdwood S.A. was isolated from a human case. In addition, S.A.AR86 is unique among Sindbis-like viruses in that adult mice remain sensitive to lethal infection with S.A.AR86. The complete genomic sequences of S.A.AR86 and Girdwood S.A. were determined. The S.A.AR86 RNA genome contained 11,663 nucleotides, excluding the 5' CAP structure and 3' poly(A) tail. In comparison to the consensus sequence of the prototype Egyptian Sindbis strain AR339, S.A.AR86 differed at 5.57% of the nucleotides, including a 54-nucleotide deletion, two insertions of 6 nucleotides each, and a 3-nucleotide insertion in the 3' terminal one-third of the S.A.AR86 nsP3 gene. S.A.AR86 is one of only three alphaviruses sequenced to date that does not have an opal termination codon between the nsP3 and the nsP4 genes. These genes are separated by a cysteine codon in the S.A.AR86 genome. The genome of Girdwood S.A. was 11,717 nucleotides in length, excluding the 5' CAP and 3' poly(A) tail. Girdwood S.A. contained an opal termination codon between nsP3 and nsP4 and did not have the large 54-nucleotide deletion in nsP3, although Girdwood S.A. did contain the remaining insertions and deletions characteristic of S.A.AR86. S.A.AR86 was more closely related to Girdwood S.A. than to the Egyptian isolate, and the South African isolates as a group were more closely related to the Swedish isolate. Comparison of the S.A.AR86 sequence to that of Ockelbo82, Girdwood S.A., and Sindbis virus AR339 revealed several codons where S.A.AR86 differed from the conserved amino acid encoded by the other three viruses. These changes may be related to the ability of S.A.AR86 to initiate a lethal central nervous system infection in adult mice. To fulfill a prerequisite for testing this hypothesis, a full-length cDNA clone of S.A.AR86 was constructed from which infectious genomic RNA replicas could be derived. The sequence of this clone differed from the S.A.AR86 genomic RNA sequence at four translationally silent positions, and virus derived from the clone reproduced the adult mouse neurovirulence phenotype of its biological progenitor.

Churg-Strauss syndrome

The neurologic manifestations of systemic necrotizing vasculitis are heterogeneous and often complex. Late onset asthma, systemic vasculitis manifest by mononeuritis multiplex, and peripheral eosinophilia-the triad of which is consistent with Churg-Strauss syndrome-developed in a 59-year-old woman. Electromyography and nerve conduction studies showed both myelinating and axonal neuropathy involving multiple nerves. Muscle and nerve biopsy showed neurogenic atrophy, demyelination, and axonal changes involving the sural nerve and inflammatory necrotizing small and medium vessel arterial changes. The patient was treated with high-dose prednisone and improved rapidly. Unusual in this case was the lack of multisystemic involvement. Churg-Strauss syndrome is a disease that is being recognized with increased clinical frequency and responds quickly to methylprednisolone treatment.

Deduced consensus sequence of Sindbis virus strain AR339: mutations contained in laboratory strains which affect cell culture and in vivo phenotypes

The consensus sequence of the Sindbis virus AR339 isolate, the prototype alphavirus, has been deduced. THe results presented here suggest (i) that a substantial proportion of the sequence divergence evident between the consensus sequence and sequences of laboratory strains of AR339 has resulted from selection for efficient growth in cell culture, (ii) that many of these changes affect the virulence of the virus in animal models, and (iii) that such modified genetic backgrounds present in laboratory strains can exert a significant influence on genetic studies of virus pathogenesis and host range. A laboratory strain of Sindbis virus AR339 was sequenced and cloned as a cDNA (pTRSB) from which infectious virus (TRSB) could be derived. The consensus sequence was deduced from the complete sequences of pTRSB and HRsp (E. G. Strauss, C. M. Rice, and J. H. Strauss, Virology 133:92-110, 1984), from partial sequences of the glycoprotein genes of three other AR339 laboratory strains, and by comparison with the sequences of the glycoprotein genes of three other AR339 sequence. HRsp differed form the consensus sequence by eight coding changes, and TRSB differed by three coding changes. In the 5' untranslated region, HRsp differed from the consensus sequence at nucleotide (nt) 5. These differences were likely the result of cell culture passage of the original AR339 isolate. At three of the difference loci (one in TRSB and two in HRsp), selection of cell-culture-adaptive mutations was documented with Sindbis virus or other alphaviruses. Selection in cell culture often results in attenuation of virulence in animals. Considering the TRSB and HRsp sequences together, one noncoding difference from the consensus (an A-for-G substitution in the 5' untranslated region at nt 5) and six coding differences in the glycoprotein genes (at E2 amino acids 1, 3, 70, and 172 and at E1 amino acids 72 and 237) were at loci which, either individually or in combination, significantly affected alphavirus virulence in mice. Although the levels of virulence of isogenic strains containing either nt 5 A or nt 5 G did not differ significantly in neonatal mice, the presence of nt 5 A greatly enhanced the effect of a second attenuating mutation in the E2 gene. These results suggest that minimal differences in the "wild type" genetic background into which an additional mutation is introduced can have a dramatic effect on apparent virulence and pathogenesis phenotypes. A cDNA clone of the consensus AR339 sequence, a sequence devoid of occult attenuating mutations introduced by cell culture passage, will allow the molecular genetic examination of cell culture and in vivo phenotypes of a virus which may best reflect the sequence of Sindbis virus AR339 at the time of its isolation.

Paraneoplastic intestinal pseudo-obstruction, mononeuritis multiplex, and sensory neuropathy/neuronopathy

A patient with diffuse intestinal pseudo-obstruction consisting of gastric paresis and impaired small and large bowel motility, mononeuropathy multiplex, and sensory neuropathy/neuronopathy was found to have small-cell carcinoma of the lung. The clinical symptoms were thought to be consistent with paraneoplastic neuropathy, and high antineuronal and anti-calcium channel antibodies led to the diagnosis of small-cell carcinoma of the lung. Identification of paraneoplastic neuropathy is important, because early treatment may halt the progression of the underlying carcinoma.

Vaccinia virus gene A18R encodes an essential DNA helicase

The vaccinia virus A18R protein is a DNA-dependent ATPase that contains the canonical sequence motifs associated with the DEXH group of DNA and RNA helicases. Investigation of A18R protein function during infection indicated it functions in the early and late phases of vaccinia virus transcription. The A18R protein shares sequence similarity with the mammalian DNA helicase ERCC3. The ERCC3 protein has a dual function: it is a component of the transcription factor TFIIH and is an essential participant in the cellular nucleotide excision repair pathway. Here we present evidence that the A18R protein is a DNA helicase that unwinds duplex DNA in a 3'-to-5' direction. The A18R helicase was inactive on RNA-DNA and RNA-RNA hybrids. The A18R unwinding activity was most efficient on DNA substrates with lengths of 20 nucleotides or less, and its unwinding activity was not stimulated by the addition of Escherichia coli single-strand-binding protein (SSB), the bacteriophage T4 gene 32 SSB, or the vaccinia virus I3L protein, a putative SSB. We have used an electrophoretic gel mobility shift assay to show that the A18R protein forms a stable complex with single-stranded DNA, and to a lesser extent RNA, in a reaction that does not require ATP.

Characterization of Pseudomonas aeruginosa fliO, a gene involved in flagellar biosynthesis and adherence

Pseudomonas aeruginosa binds to eukaryotic cells via both pilus and nonpilus adhesins, while binding of P. aeruginosa to mucin is pilus independent. To characterize genes involved in non-pilus-mediated adherence, transposon mutants of the nonpiliated strain P. aeruginosa PAK-NP that are unable to bind to cells or mucins were isolated. Two such mutants, P. aeruginosa B164 and P. aeruginosa RR18, were identified previously as deficient in binding to eukaryotic cells or mucins as well as nonmotile. The transposon insertion in each of these strains was mapped to the same gene. Sequence analysis of both DNA flanking the transposons and plasmids that could complement the mutations indicated that this open reading frame encodes a putative protein homolog of both Escherichia coli FliO and Erwinia carotovora subsp. atroseptica MopB. The transposons in both of these mutants are nonpolar, since the addition of the P. aeruginosa fliO gene in trans restored adherence to both cells and mucins to these mutants. The cloned fliO gene also complemented the motility defect of both B164 and RR18. A 1.6-kb KpnI fragment from the PAK chromosome that contained the fliO gene was sequenced. The fliO gene appears to be part of an operon with a complete open reading frame upstream of the FliO homolog encoding a putative protein homolog of FliN of both E. coli and Salmonella typhimurium. The partial open reading frame downstream of fliO encodes a putative homolog of both E. coli and S. typhimurium FliP. The fliN gene is flanked on its 5'-end by the 3'-end of a homolog of a fliM gene. The P. aeruginosa FliN protein was identified with a T7 expression system, while all attempts to identify the P. aeruginosa FliO protein were unsuccessful. Homologs of P. aeruginosa FliO are involved in the biosynthesis of flagella, but the function of FliO in this biosynthetic process remains unknown. Further study should reveal the precise role of P. aeruginosa FliO in non-pilus-mediated adherence, which could include regulation of expression or localization of a nonpilus adhesin.

Topography of axonal injury as defined by amyloid precursor protein and the sector scoring method in mild and severe closed head injury

Axonal injury (AI), as defined by amyloid precursor protein (APP) positive axonal swellings, was recorded on a series of line diagrams of standard brain sections divided into 116 sectors to provide an Axonal Injury Sector Score (AISS) ranging from 0 to 116. This sector scoring method of recording axonal damage and providing a topographic overview of AI was applied to a series of 6 mild head injury cases [Glasgow Coma Scale (GCS) 13-15] and six severe head injury cases (GCS 3-8). The AISS ranged from 4 to 107 overall and varied from 4 to 88 in the mildly injured group and 76 to 107 in the severe head injury group, supporting the concept that there is a spectrum of AI in traumatic head injury and that the AISS is a measure of the extent of AI. APP immunostaining demonstrated positive axonal swellings 1.75 h after head injury and analysis of the pattern of AI in the mild and severe head injury groups showed that axons were more vulnerable than blood vessels and that the axons in the corpus callosum and fornices were the most vulnerable of all.