Multiplexed detection of viral antigen and RNA using nanopore sensing and encoded molecular probes

We report on single-molecule nanopore sensing combined with position-encoded DNA molecular probes, with chemistry tuned to simultaneously identify various antigen proteins and multiple RNA gene fragments of SARS-CoV-2 with high sensitivity and selectivity. We show that this sensing strategy can directly detect spike (S) and nucleocapsid (N) proteins in unprocessed human saliva. Moreover, our approach enables the identification of RNA fragments from patient samples using nasal/throat swabs, enabling the identification of critical mutations such as D614G, G446S, or Y144del among viral variants. In particular, it can detect and discriminate between SARS-CoV-2 lineages of wild-type B.1.1.7 (Alpha), B.1.617.2 (Delta), and B.1.1.539 (Omicron) within a single measurement without the need for nucleic acid sequencing. The sensing strategy of the molecular probes is easily adaptable to other viral targets and diseases and can be expanded depending on the application required.

SARS-CoV-2 antibody responses associate with sex, age and disease severity in previously uninfected people admitted to hospital with COVID-19: An ISARIC4C prospective study

The SARS-CoV-2 pandemic enables the analysis of immune responses induced against a novel coronavirus infecting immunologically naïve individuals. This provides an opportunity for analysis of immune responses and associations with age, sex and disease severity. Here we measured an array of solid-phase binding antibody and viral neutralising Ab (nAb) responses in participants (n=337) of the ISARIC4C cohort and characterised their correlation with peak disease severity during acute infection and early convalescence. Overall, the responses in a Double Antigen Binding Assay (DABA) for antibody to the receptor binding domain (anti-RBD) correlated well with IgM as well as IgG responses against viral spike, S1 and nucleocapsid protein (NP) antigens. DABA reactivity also correlated with nAb. As we and others reported previously, there is greater risk of severe disease and death in older men, whilst the sex ratio was found to be equal within each severity grouping in younger people. In older males with severe disease (mean age 68 years), peak antibody levels were found to be delayed by one to two weeks compared with women, and nAb responses were delayed further. Additionally, we demonstrated that solid-phase binding antibody responses reached higher levels in males as measured via DABA and IgM binding against Spike, NP and S1 antigens. In contrast, this was not observed for nAb responses. When measuring SARS-CoV-2 RNA transcripts (as a surrogate for viral shedding) in nasal swabs at recruitment, we saw no significant differences by sex or disease severity status. However, we have shown higher antibody levels associated with low nasal viral RNA indicating a role of antibody responses in controlling viral replication and shedding in the upper airway. In this study, we have shown discernible differences in the humoral immune responses between males and females and these differences associate with age as well as with resultant disease severity.

The Drug-Induced Interface That Drives HIV-1 Integrase Hypermultimerization and Loss of Function

Allosteric HIV-1 integrase (IN) inhibitors (ALLINIs) are an emerging class of small molecules that disrupt viral maturation by inducing the aberrant multimerization of IN. Here, we present cocrystal structures of HIV-1 IN with two potent ALLINIs, namely, BI-D and the drug candidate Pirmitegravir. The structures reveal atomistic details of the ALLINI-induced interface between the HIV-1 IN catalytic core and carboxyl-terminal domains (CCD and CTD). Projecting from their principal binding pocket on the IN CCD dimer, the compounds act as molecular glue by engaging a triad of invariant HIV-1 IN CTD residues, namely, Tyr226, Trp235, and Lys266, to nucleate the CTD-CCD interaction. The drug-induced interface involves the CTD SH3-like fold and extends to the beginning of the IN carboxyl-terminal tail region. We show that mutations of HIV-1 IN CTD residues that participate in the interface with the CCD greatly reduce the IN-aggregation properties of Pirmitegravir. Our results explain the mechanism of the ALLINI-induced condensation of HIV-1 IN and provide a reliable template for the rational development of this series of antiretrovirals through the optimization of their key contacts with the viral target. IMPORTANCE Despite the remarkable success of combination antiretroviral therapy, HIV-1 remains among the major causes of human suffering and loss of life in poor and developing nations. To prevail in this drawn-out battle with the pandemic, it is essential to continue developing advanced antiviral agents to fight drug resistant HIV-1 variants. Allosteric integrase inhibitors (ALLINIs) are an emerging class of HIV-1 antagonists that are orthogonal to the current antiretroviral drugs. These small molecules act as highly specific molecular glue, which triggers the aggregation of HIV-1 integrase. In this work, we present high-resolution crystal structures that reveal the crucial interactions made by two potent ALLINIs, namely, BI-D and Pirmitegravir, with HIV-1 integrase. Our results explain the mechanism of drug action and will inform the development of this promising class of small molecules for future use in antiretroviral regimens.

Multivalent interactions essential for lentiviral integrase function

A multimer of retroviral integrase (IN) synapses viral DNA ends within a stable intasome nucleoprotein complex for integration into a host cell genome. Reconstitution of the intasome from the maedi-visna virus (MVV), an ovine lentivirus, revealed a large assembly containing sixteen IN subunits1. Herein, we report cryo-EM structures of the lentiviral intasome prior to engagement of target DNA and following strand transfer, refined at 3.4 and 3.5 Å resolution, respectively. The structures elucidate details of the protein-protein and protein-DNA interfaces involved in lentiviral intasome formation. We show that the homomeric interfaces involved in IN hexadecamer formation and the α-helical configuration of the linker connecting the C-terminal and catalytic core domains are critical for MVV IN strand transfer activity in vitro and for virus infectivity. Single-molecule microscopy in conjunction with photobleaching reveals that the MVV intasome can bind a variable number, up to sixteen molecules, of the lentivirus-specific host factor LEDGF/p75. Concordantly, ablation of endogenous LEDGF/p75 results in gross redistribution of MVV integration sites in human and ovine cells. Our data confirm the importance of the expanded architecture observed in cryo-EM studies of lentiviral intasomes and suggest that this organization underlies multivalent interactions with chromatin for integration targeting to active genes.

Evaluation of infrared thermography combined with behavioral biometrics for estrus detection in naturally cycling dairy cows

Low estrus detection rates (>50%) are associated to extended calving intervals, low economic profit and reduced longevity in Holstein dairy cows. The objective of this study was to evaluate the accuracy of infrared thermography and behavioral biometrics combined as potential estrus alerts in naturally (not induced) cycling dairy cows housed in a tie-stall barn. Eighteen first lactation cows were subjected to transrectal ultrasonography to determine spontaneous ovulation. The dominant follicle (DF) disappearance was used retrospectively as an indirect indicator of ovulation, and to establish the estrus period (48-24 h prior the DF disappearance). Raw skin temperature (Raw IR) and residual skin temperature (Res IR) were recorded using an infrared camera at the Vulva area with the tail (Vtail), Vulva area without the tail (Vnotail), and Vulva's external lips (Vlips) at AM and PM milking from Day 14 until two days after ovulation was confirmed. Behavioral biometrics were recorded on the same schedule as infrared scan. Behavioral biometrics included large hip movements (L-hip), small hip movements (S-hip), large tail movements and small tail movements to compare behavioral changes between estrus and nonestrus periods. Significant increases in Raw IR skin temperature were observed two days prior to ovulation (Vtail; 35.93 ± 0.27 °C, Vnotail; 35.59 ± 0.27 °C, and Vlips; 35.35 ± 0.27 °C) compared to d -5 (Proestrus; Vtail; 35.29 ± 0.27 °C, Vnotail; 34.93 ± 0.31 °C, and Vlips; 34.68 ± 0.27 °C). No significant changes were found for behavioral parameters with the exception of S-hip movements, which increased at two days before ovulation (d -2; 11.13 ± 1.44 Events/5min) compared to d -5 (7.30 ± 1.02 Events/5min). To evaluate the accuracy of thermal and behavioral biometrics, receiver operating characteristic curve analysis was performed using Youden index (YJ), diagnostic odds ratio, positive likelihood ratio (LR+), Sensitivity, Specificity and Positive predicted value to score the estrus alerts. The greatest accuracy achieved using thermal parameters was for Res IR Vtail PM (YJ = 0.34) and L-hip PM (YJ = 0.27) for behavioral biometrics. Combining thermal and behavioral parameters did not improve the YJ index score but reduced the false-positive occurrence observed by increasing the diagnostic odds ratio (26.62), LR+ (12.47), Specificity (0.97) and positive predicted value (0.90) in a Res IR Vtail PM, S-hip AM, S-hip PM combination. The combination of thermal and behavioral parameters increased the accuracy of estrus detection compared to either thermal or behavioral biometrics, independently in naturally cycling cows during milking.

Long-term Clinical Outcomes in Synovitis, Acne, Pustulosis, Hyperostosis, and Osteitis Syndrome

Objective

To assess the outcome of empirical therapeutic interventions for synovitis, acne, pustulosis, hyperostosis, and osteitis (SAPHO) syndrome.

Methods

The clinical features and treatment outcomes of a cohort of 21 patients diagnosed with SAPHO in Western Australia were reviewed retrospectively.

Results

All 21 patients met published diagnostic criteria; 20 (95%) were Caucasian, and the median age was 47 years. The median follow-up was 6 years (range, 2 to 32 years). Three patients (14%) received no treatment; 18 (86%) required conventional synthetic disease-modifying antirheumatic drug (DMARDs). Thirteen (62%) had an initial good response to methotrexate; 8 relapsed and progressed to biologic DMARDs (bDMARDs) during a period of 14 years. Of the 13 recipients on a tumor necrosis factor inhibitor, 11 (85%) continued treatment for a median of 4 years (range, 1 to 14 years), whereas none of 3 recipients of interleukin 17/23 continued treatment (median, 4 months). Higher Physician Global Assessment scores (better outcomes) were observed in bDMARD recipients (mean, 7.06±2.24 [SD]) compared with non-bDMARD recipients (mean, 5.63±2.50; P=.1672) after a median of 3 years of therapy.

Conclusion

This study describes the broad range of clinical manifestations in SAPHO, variable courses over time, and inconsistent outcomes with diverse empirical therapies. Moderately good long-term treatment outcomes were observed in most recipients of tumor necrosis factor inhibitor. Poorer outcomes were observed with bisphosphonates and interleukin 17/23 axis inhibitors; however, low numbers preclude robust comparison. Suboptimal treatment may be associated with poorer clinical outcomes and greater skeletal damage.

Trial Registration

Australian and New Zealand Clinical Trials Registry: ACTRN12619000445178

SARS-CoV-2 can recruit a heme metabolite to evade antibody immunity

The coronaviral spike is the dominant viral antigen and the target of neutralizing antibodies. We show that SARS-CoV-2 spike binds biliverdin and bilirubin, the tetrapyrrole products of heme metabolism, with nanomolar affinity. Using cryo-electron microscopy and x-ray crystallography, we mapped the tetrapyrrole interaction pocket to a deep cleft on the spike N-terminal domain (NTD). At physiological concentrations, biliverdin significantly dampened the reactivity of SARS-CoV-2 spike with immune sera and inhibited a subset of neutralizing antibodies. Access to the tetrapyrrole-sensitive epitope is gated by a flexible loop on the distal face of the NTD. Accompanied by profound conformational changes in the NTD, antibody binding requires relocation of the gating loop, which folds into the cleft vacated by the metabolite. Our results indicate that SARS-CoV-2 spike NTD harbors a dominant epitope, access to which can be controlled by an allosteric mechanism that is regulated through recruitment of a metabolite.

SARS-CoV-2 recruits a haem metabolite to evade antibody immunity

The coronaviral spike is the dominant viral antigen and the target of neutralizing antibodies. We show that SARS-CoV-2 spike binds biliverdin and bilirubin, the tetrapyrrole products of haem metabolism, with nanomolar affinity. Using cryo-electron microscopy and X-ray crystallography we mapped the tetrapyrrole interaction pocket to a deep cleft on the spike N-terminal domain (NTD). At physiological concentrations, biliverdin significantly dampened the reactivity of SARS-CoV-2 spike with immune sera and inhibited a subset of neutralizing antibodies. Access to the tetrapyrrole-sensitive epitope is gated by a flexible loop on the distal face of the NTD. Accompanied by profound conformational changes in the NTD, antibody binding requires relocation of the gating loop, which folds into the cleft vacated by the metabolite. Our results indicate that the virus co-opts the haem metabolite for the evasion of humoral immunity via allosteric shielding of a sensitive epitope and demonstrate the remarkable structural plasticity of the NTD.

Structural basis of second-generation HIV integrase inhibitor action and viral resistance

Although second-generation HIV integrase strand-transfer inhibitors (INSTIs) are prescribed throughout the world, the mechanistic basis for the superiority of these drugs is poorly understood. We used single-particle cryo-electron microscopy to visualize the mode of action of the advanced INSTIs dolutegravir and bictegravir at near-atomic resolution. Glutamine-148→histidine (Q148H) and glycine-140→serine (G140S) amino acid substitutions in integrase that result in clinical INSTI failure perturb optimal magnesium ion coordination in the enzyme active site. The expanded chemical scaffolds of second-generation compounds mediate interactions with the protein backbone that are critical for antagonizing viruses containing the Q148H and G140S mutations. Our results reveal that binding to magnesium ions underpins a fundamental weakness of the INSTI pharmacophore that is exploited by the virus to engender resistance and provide a structural framework for the development of this class of anti-HIV/AIDS therapeutics.

Structural basis of second-generation HIV integrase inhibitor action and viral resistance

Although second-generation HIV integrase strand-transfer inhibitors (INSTIs) are prescribed throughout the world, the mechanistic basis for the superiority of these drugs is poorly understood. We used single-particle cryo-electron microscopy to visualize the mode of action of the advanced INSTIs dolutegravir and bictegravir at near-atomic resolution. Glutamine-148→histidine (Q148H) and glycine-140→serine (G140S) amino acid substitutions in integrase that result in clinical INSTI failure perturb optimal magnesium ion coordination in the enzyme active site. The expanded chemical scaffolds of second-generation compounds mediate interactions with the protein backbone that are critical for antagonizing viruses containing the Q148H and G140S mutations. Our results reveal that binding to magnesium ions underpins a fundamental weakness of the INSTI pharmacophore that is exploited by the virus to engender resistance and provide a structural framework for the development of this class of anti-HIV/AIDS therapeutics.

Evaluation of infrared thermography compared to rectal temperature to identify illness in early postpartum dairy cows

This study evaluated and compared infrared thermography (IRT) and rectal temperature (RT) as screening tests to identify sick transition dairy cows. Holstein cows (n = 72; 42 primiparous) had RT and IRT temperatures taken daily from 1 to 12 days in milk (DIM). Health examinations were performed daily to diagnose retained fetal membrane, milk fever and metritis, and blood was analyzed for β-hydroxybutyrate at 6 and 9 DIM to diagnose ketosis. Plasma concentrations of cortisol, interleukin-6, tumor necrosis factor α and serum amyloid A at 3, 6, 9 and 12 DIM were included as additional indicators of illness. Cows were categorized as true sick if clinically diagnosed with an illness, or if at least 2 blood parameters were above the normal range. Diagnostic test performances for RT and IRT variables were determined for each variable at a test referent value that provided the highest Youden's (J) index. The best performing screening test depended on the definition of true sickness. In general, the J index for RT was 0.15-0.17 whereas the highest J index for the IRT variables was 0.22 for the mean eye temperature and 0.19 for the mean cheek temperature. Infrared thermography was at least comparable to RT and some IRT variables performed better as a screening tests than RT. Future studies into the automation of IRT for surveillance of early postpartum diseases is warranted.

Differential role for phosphorylation in alternative polyadenylation function versus nuclear import of SR-like protein CPSF6

Cleavage factor I mammalian (CFIm) complex, composed of cleavage and polyadenylation specificity factor 5 (CPSF5) and serine/arginine-like protein CPSF6, regulates alternative polyadenylation (APA). Loss of CFIm function results in proximal polyadenylation site usage, shortening mRNA 3' untranslated regions (UTRs). Although CPSF6 plays additional roles in human disease, its nuclear translocation mechanism remains unresolved. Two β-karyopherins, transportin (TNPO) 1 and TNPO3, can bind CPSF6 in vitro, and we demonstrate here that while the TNPO1 binding site is dispensable for CPSF6 nuclear import, the arginine/serine (RS)-like domain (RSLD) that mediates TNPO3 binding is critical. The crystal structure of the RSLD-TNPO3 complex revealed potential CPSF6 interaction residues, which were confirmed to mediate TNPO3 binding and CPSF6 nuclear import. Both binding and nuclear import were independent of RSLD phosphorylation, though a hyperphosphorylated mimetic mutant failed to bind TNPO3 and mislocalized to the cell cytoplasm. Although hypophosphorylated CPSF6 largely supported normal polyadenylation site usage, a significant number of mRNAs harbored unnaturally extended 3' UTRs, similar to what is observed when other APA regulators, such as CFIIm component proteins, are depleted. Our results clarify the mechanism of CPSF6 nuclear import and highlight differential roles for RSLD phosphorylation in nuclear translocation versus regulation of APA.

Infrared thermography and behavioral biometrics associated with estrus indicators and ovulation in estrus-synchronized dairy cows housed in tiestalls

Most Canadian dairy herds operate in tiestall housing (61%), where average estrus detection rates may be lower than 54%. The objective of this study was to evaluate infrared thermography and behavioral biometrics as indicators of estrus in dairy cows. Eighteen cyclic multiparous cows (Synch) were subjected to an estrus synchronization protocol, and 18 pregnant cows (control) received a sham protocol on the same schedule and frequency as the cyclic cow treatment. A decline in plasma concentrations of progesterone and the appearance of a dominant follicle using transrectal ultrasonography were used as indirect indicators of estrus, and the disappearance of a dominant follicle was used to confirm ovulation. All cows were monitored via visual cameras to determine the frequency of treading, drinking, neighbor interaction, tail movement, lying, and shifting behaviors. Infrared thermograms were recorded at the eye, muzzle, cheek, neck, front right foot, front left foot, rump, flank, vulva area, tail head, and withers. To evaluate the accuracy of behavioral and thermal parameters, a predefined minimum acceptable value (i.e., threshold) for estrus alerts (>0.30 Youden J index and >0.60 area under the curve) was used. Ovulation was confirmed in 14 (77.7%) out of 18 Synch cows. Eye, cheek, neck, rump, flank, vulva area, and wither thermograms exhibited higher temperatures at 48 h [cycle threshold (Δt) = +0.30 to 1.20°C] and 24 h before ovulation compared with 4 d prior to ovulation (Δt = 0.06 to 0.11°C) and during ovulation day (Δt = 0.03 to 0.32°C) in the Synch group. In addition, control cows exhibited greater treading activity per day compared with Synch cows (20.84 ± 0.39 vs. 16.35 events/5 min ± 0.34), and tail movement frequency was greater in Synch cows compared with control cows (14.84 ± 2.7 vs. 10.11 ± 4.7 events/5 min). However, within Synch cows, tail movement was the only behavior that significantly increased in frequency 2 d before ovulation (11.81 ± 1.71 events/5 min) followed by a decrease in frequency 1 d before ovulation (4.67 ± 1.05 events/5 min) compared with ovulation day (0 d; 6.10 ± 1.25 events/5 min) and during luteolysis (3 d before ovulation; 6.01 ± 1.25 events/5 min). Upon evaluation of all variables (thermograms and behavior frequencies) as estrus indicators at 48 and 24 h before ovulation, treading and tail movements before milking and 9 thermal locations satisfied the predefined minimum acceptable value for estrus alerts. This study demonstrates that fluctuations in radiated temperature measured at specific anatomical locations and the frequency of tail movements and treading behaviors can be used as a noninvasive estrus alerts in multiparous cows housed in a tiestall system.

Energy utilization in cattle with steady state and non-steady state methods: the importance of thermal neutrality

The efficiency by which animals utilize dietary energy is fundamental to the cost of production for protein of animal origin and to the carbon footprint an animal industry has. Hence, the development of cost effective methodology for determining these measurements of efficiency is important. The objective of the present study was to investigate the use of infrared thermography in a rapid, non-steady state method for measuring energy loss in cattle. Data from 241 yearling bulls and steers as well as heifers and mature cows are presented. Infrared images were collected following a 24h feed withdrawal period. The infrared thermal response in these animals was significantly ranked (P < 0.03) with conventional measurements of feed efficiency using residual feed intake values for animals demonstrated to be within a thermal neutral zone. When animals were not within a thermal neutral zone there was no significant ranking. The data suggests that the use of a non-steady state approach using infrared thermography for identifying metabolic efficiency in animals may be a more rapid and less expensive method for identifying differences in energy utilization. The data also demonstrates the importance of maintaining thermal neutrality when measuring metabolic efficiency irrespective of the methodology.

A supramolecular assembly mediates lentiviral DNA integration

Retroviral integrase (IN) functions within the intasome nucleoprotein complex to catalyze insertion of viral DNA into cellular chromatin. Using cryo-electron microscopy, we now visualize the functional maedi-visna lentivirus intasome at 4.9 angstrom resolution. The intasome comprises a homo-hexadecamer of IN with a tetramer-of-tetramers architecture featuring eight structurally distinct types of IN protomers supporting two catalytically competent subunits. The conserved intasomal core, previously observed in simpler retroviral systems, is formed between two IN tetramers, with a pair of C-terminal domains from flanking tetramers completing the synaptic interface. Our results explain how HIV-1 IN, which self-associates into higher-order multimers, can form a functional intasome, reconcile the bulk of early HIV-1 IN biochemical and structural data, and provide a lentiviral platform for design of HIV-1 IN inhibitors.

Prophylactic nitric oxide treatment reduces incidence of bovine respiratory disease complex in beef cattle arriving at a feedlot

Bovine respiratory disease complex (BRDc), is a challenging multi-factorial health issue caused by viral/bacterial pathogens and stressors linked with the transport and mixing of cattle, negatively impacting the cattle feedlot industry. Nitric oxide (NO) is a naturally occurring molecule with antimicrobial attributes. This study tests whether NO can prevent the symptoms associated with BRDc. Eighty-five, crossbred, multiple-sourced, commingled commercial weaned beef calves were monitored and scored for temperature, white blood count, clinical score, hematology, cortisol levels and neutrophil/lymphocyte ratio. NO treatment or placebo were given once on arrival to the stockyard. After one week 87.5% of sick animals were from the control while 12.5% from treatment groups and after two weeks 72% and 28% respectively. Treatment was shown to be safe, causing neither distress nor adverse effects on the animals. These data show that NO treatment on arrival to the feedlot significantly decreased the incidence of BRDc in this study.

The non-invasive and automated detection of bovine respiratory disease onset in receiver calves using infrared thermography

Bovine respiratory disease complex (BRD) causes considerable economic loss and biosecurity cost to the beef industry globally and also results in significant degradation to the welfare of affected animals. The successful treatment of this disease depends on the early, timely and cost effective identification of affected animals. The objective of the present study was to investigate the use of an automated, RFID driven, noninvasive infrared thermography technology to determine BRD in cattle. Sixty-five calves averaging 220 kg were exposed to standard industry practices of transport and auction. The animals were monitored for BRD using conventional biometric signs for clinical scores, core temperatures, haematology, serum cortisol and infrared thermal values over 3 weeks. The data collected demonstrated that true positive animals for BRD based on a gold standard including core temperature, clinical score, white blood cell number and neutrophil/lymphocyte ratio displayed higher peak infrared thermal values of 35.7±0.35 °C compared to true negative animals 34.9±0.22 °C (P<0.01). The study also demonstrated that such biometric data can be non-invasively and automatically collected based on a system developed around the animal's water station. It is concluded that the deployment of such systems in the cattle industry would aid animal managers and practitioners in the identification and management of BRD in cattle populations.

Dexamethasone reduces transport-induced weight losses in beef calves

Dexamethasone was administered intramuscularly at two dose levels (Trial 1 = 0.088 mg kg-1; Trial 2 = 10 mg per calf) to beef calves (Trial 1, n = 60; Trial 2, n = 58) prior to transport by road for 10 and 8 h, to test the effect on transport-induced weight losses. Calves lost significant weight over the transport periods (P < 0.001) but dexamethasone-treated calves lost significantly less weight than control animals (P < 0.004). The relationship between salivary dexamethasone concentrations and weight losses in Trial 1 exhibited a significant trend (r = 0.47, P < 0.06). The correlation of administered dose of dexamethasone (mg kg-1) with weight losses in Trial 2 was significant (r = 0.5, P < 0.006). Dexamethasone administration prior to long-haul transport reduced transport-induced weight losses, and may be an effective method of mitigating transport stress.Key words: Transport, beef calves, dexamethasone, weight losses, salivary cortisol, salivary dexamethasone

Mechanistic basis of 5'-3' translocation in SF1B helicases

Superfamily 1B (SF1B) helicases translocate in a 5'-3' direction and are required for a range of cellular activities across all domains of life. However, structural analyses to date have focused on how SF1A helicases achieve 3'-5' movement along nucleic acids. We present crystal structures of the complex between the SF1B helicase RecD2 from Deinococcus radiodurans and ssDNA in the presence and absence of an ATP analog. These snapshots of the reaction pathway reveal a nucleotide binding-induced conformational change of the two motor domains that is broadly reminiscent of changes observed in other SF1 and SF2 helicases. Together with biochemical data, the structures point to a step size for translocation of one base per ATP hydrolyzed. Moreover, the structures also reveal a mechanism for nucleic acid translocation in the 5'-3' direction by SF1B helicases that is surprisingly different from that of 3'-5' translocation by SF1A enzymes, and explains the molecular basis of directionality.

The use of infrared thermography as an early indicator of bovine respiratory disease complex in calves

Bovine respiratory disease (BRD) complex causes considerable distress to domestic livestock and economic hardship to the beef industry. Furthermore, the resulting extensive use of antimicrobial treatments is a growing concern from the perspective of facilitating antibiotic resistant microbes. The earlier detection of BRD would enable an earlier, more targeted treatment regime and earlier isolation of infected individuals. The objective of the present study was to investigate the use of non-invasive infrared thermography in the early detection of BRD in cattle. Studies were conducted on 133 head of weaned calves. Data demonstrated that infrared thermography was able to identify animals at early stages of illness, often several days to over one week before clinical signs were manifest. Data indicated that 4–6 days prior to the onset of clinical symptoms of BRD, greater positive and negative predictive values and test efficiency for infrared thermography (80%, 65% and 71%, respectively) compared to the industry standard practice of clinical scoring (70%, 45% and 55%, respectively).

The use of digital video recorders (DVRs) for capturing digital video files for use in both The Observer and Ethovision

Before switching a laboratory from analog to digital, for the recording of video files for use in Noldus software such as Ethovision and The Observer, researchers need to proceed with caution. There are obvious advantages in moving to digital recording for behavioral work, including increased storage capacity; no requirement to purchase video tapes; immediate search by date, time, or event; digital images are of higher quality; ability to view study sites remotely by Internet connection; and "smart" features, such as motion detection. But before you throw away your time-lapse video recorders, time code generators, and video multiplexors, there are some important cautions to take account of. Some research groups have bought digital surveillance systems on the assumption that they work with Ethovision and The Observer, only to be disappointed. The vast majority of systems depend on proprietary compression software that must then be converted to work properly in Ethovision or The Observer.

Adrenocorticotropic hormone increases hydrolysis of B-6 vitamers in swine adrenal glands

Shipping stress is an economic problem because of its effect on meat quality. Because shipping increases plasma cortisol and pyridoxal 5'-phosphate interacts with steroid hormones, we examined the interaction between adrenocorticotropic hormone (ACTH) and vitamin B-6 metabolism in pigs. Six crossbred pigs with ear vein catheters received 50 IU of porcine ACTH intravenously at 3-h intervals from 0800 to 2100 h on d 1-3 and 100 IU intramuscularly at 0800, 1400 and 2000 h on d 6 and 7. Controls received saline. ACTH had no effect on pyridoxal 5'-phosphate in adrenal tissue but decreased pyridoxamine 5'-phosphate from 6.1 +/- 0.7 to 4.7 +/- 1.0 nmol/g (P < 0.05). Adrenal pyridoxal and pyridoxamine concentrations were 0.4 +/- 0.1 nmol/g in controls and 1.1 +/- 0.3 and 1.3 +/- 0.5 nmol/g, respectively, in ACTH-treated pigs (P < 0.01). Pyridoxal 5'-phosphate phosphatase activity [median (25-75 percentile value)] at pH 7.4 in adrenal tissue was 66.6 (47.8-75.5) nmol/(g. min) in the controls and 764 (626-771) in the ACTH-treated pigs (P < 0.01). There was no significant difference in pyridoxal kinase activity. However, kinase activity in the adrenals was about twice as high as in other tissues. These data suggest an active turnover of vitamin B-6 in adrenal tissue.

Paraspinal abscess following facet joint injection

Injection to the zygapophysial joint is a procedure which is performed frequently for diagnostic or therapeutic reasons in the management of back pain. It is generally considered to be free of significant complications. We report a patient who developed a paraspinal abscess following a lumbar facet joint injection.

Edge enhancement by use of moving gratings in a bismuth silicon oxide crystal and its application to optical correlation

The technique of moving gratings in a photorefractive crystal is applied to the edge enhancement of objects and edge-enhanced optical correlation. The nonlinear dependence of the optimum fringe velocity on the fringe modulation and the variation of the enhancement of the diffraction efficiency with fringe modulation at a fixed fringe velocity appropriate to high fringe modulations are experimentally investigated. It is shown that the diffraction at high fringe modulations, which corresponds to the high-spatial-frequency components of the Fourier spectrum, is enhanced by a factor of approximately 3.7, whereas the diffraction at low fringe modulations is suppressed by a factor of 0.6. The proposed technique has the advantages of real-time enhancement, arbitrary selection of the spatial frequency to be enhanced, and improved stability of the output. Experimental results of the edge enhancement of objects and edge-enhanced correlation are presented.

Characterization of the glycosyltransferase enzyme from the Escherichia coli K5 capsule gene cluster and identification and characterization of the glucuronyl active site

Bacterial capsular polysaccharides play an important role in virulence and survival. The Escherichia coli K5 capsule consists of a repeat structure of -4)GlcA-beta(1,4)-GlcNAc alpha(1-, identical to N-acetylheparosan. A 60-kDa protein, KfiC, has been identified as a bifunctional glycosyltransferase, responsible for the alternating alpha and beta addition of each UDP-sugar to the nonreducing end of the polysaccharide chain. Using hydrophobic cluster analysis, a conserved secondary structure motif characteristic of beta-glycosyltransferases was identified along with two highly conserved aspartic acid residues at positions 301 and 352 within the KfiC protein. Site-directed mutagenesis was used to identify catalytically active amino acids within domain A of the KfiC protein. The conserved aspartic acid residues at 301 and 352 were shown to be critical for the beta addition of UDP-GlcA (uridine diphosphoglucuronic acid) to defined nonreducing end oligosaccharide acceptors, suggesting that these conserved aspartic acid residues are catalytically important for beta-glycosyltransferase activity. A deleted derivative of the kfiC gene was generated, which encoded for a truncated KfiC (kfiC') protein. This protein lacked 139 amino acids at the C terminus. This enzyme had no UDP-GlcA transferase activity but still retained UDP-GlcNAc transferase activity, indicating that two separate active sites are present within the KfiC protein.

Systematic assessment of World Wide Web materials for medical education: online, cooperative peer review

OBJECTIVE

: To develop a generic methodology for the online assessment of medical education materials available on the World Wide Web and to implement it for pilot subject areas.

DESIGN

An online questionnaire was developed, based on an existing scheme for computer-based learning material. It was extended to involve five stages, covering general suitability, local suitability, the user interface, educational style, and a general review. It is available on the Web, so expert reviewers may be recruited from outside the home institution. The methodology was piloted in three subjects areas--clinical chemistry, radiology, and medical physics--concentrating initially on undergraduate teaching.

MEASUREMENTS

The contents of completed questionnaires were stored in an offline database. Selected fields, likely to be of use to students and educators searching for material, were input into an online database.

RESULTS

The online assessment was used successfully in clinical chemistry and medical physics but less well in radiology. Fewer resources were found to fit local needs than expected.

CONCLUSION

The methodology was found to work well for topics where teaching is highly structured and formal and is potentially applicable in other such disciplines. The approach produces more structured and applicable lists of resources than can be obtained from search engines.

Evaluation of high volume extracapsular cataract extraction with posterior chamber lens implantation in Sierra Leone, west Africa

AIMS

Intraocular lens (IOP) implantation in sub-Saharan Africa is not the routine procedure of choice in the treatment of cataract. Previous series consist of small numbers of selected patients. The purpose of this study was to evaluate routine posterior chamber lens implantation in large numbers of consecutive patients.

METHODS

1059 cataract extractions with planned IOL (744 patients) were performed over a 1 year period from August 1993 to July 1994.

RESULTS

94.6% (1002) of eyes showed an improvement in visual acuity. A postoperative uncorrected acuity of 6/18 or better was attained in 41.7% of eyes, while 27.1% attained an uncorrected acuity of < 6/18 to 6/60. The commonest operative complication was posterior capsule rupture (11.4%).

CONCLUSION

Extracapsular cataract extraction with posterior chamber lens implantation, performed in a well equipped clinic, can give satisfactory results in a developing country. Uncorrected visual acuity can be taken as an acceptable endpoint in the majority of cases.

Effects of optical bias on moving gratings in bismuth silicon oxide at large fringe modulation

Optical bias has been applied in the formation of moving gratings in bismuth silicon oxide at large fringe modulations. It is shown that optical bias is an effective method of overcoming the problems associated with the sudden drop in the optimum fringe velocity when the fringe modulation is close to unity. It is experimentally found that within a certain range of optical bias the absolute diffraction efficiency can be higher than that without optical bias, which is not the case when a stationary grating is used.

Dissimilatory iron(III) reduction by Rhodobacter capsulatus

The photosynthetic proteobacterium Rhodobacter capsulatus was shown to be capable of dissimilatory Fe(III) reduction. Activity was expressed during anaerobic phototrophic and microaerobic growth with malate as the carbon source, but not during equivalent aerobic growth. A variety of Fe(III) complexes were demonstrated to act as substrates for intact cells and membrane fractions of strain N22DNAR+ using a ferrozine assay for Fe(II) formation. Rates of reduction appeared to be influenced by the reduction potentials of the Fe(III) complexes. However, Fe(III) complexed by citrate, which is readily reduced by Shewanella putrefaciens, was a poor substrate for dissimilation by R. capsulatus. The Fe(III)-reducing activity of R. capsulatus was located solely in the membrane fraction. The reduction of Fe(III) complexes by intact cells was inhibited by 2-heptyl-4-hydroxyquinoline-N-oxide (HQNO), suggesting the involvement of ubiquinol: cytochrome c oxidoreductases in the electron transport chain. Lack of sensitivity to myxothiazol plus data from mutant strains implies that the cytochrome bc 1 complex and cytochrome c 2 are not obligatory for dissimilation of Fe(III)(maltol)3. Alternative pathways of electron transfer to Fe(III) must hence operate in R. capsulatus. Using strain N22DNAR+, the reduction rate of Fe(III) complexed by nitrilotriacetic acid (NTA) was elevated compared to that of Fe(III)(maltol)3, and moreover was sensitive to myxothiazol. However, these differences were not observed in the absence of the electron donor malate. The governing factor for the reduction rate of Fe(III)(maltol)3 thus appears to be the limited Fe(III)-reducing activity, whilst the reduction rate of Fe(III) complexed by NTA is controlled by the flux of electrons through the respiratory chain. The use of mutant strains confirmed that the role of the cytochrome bc 1 complex in Fe(III) reduction becomes apparent only with the superior substrate. The energy-conserving nature of Fe(III) reduction by R. capsulatus was demonstrated by electrochromic measurements, with the endogenous carotenoid pigments being employed as indicators of membrane potential generation in intact cells. Using Fe(III)EDTA as electron acceptor, periods of membrane potential generation were directly proportional to the quantity of complex added, and were extended in the presence of HQNO. Fe(III)-dependent carotenoid bandshifts were abolished by addition of the protonophoric uncoupler carbonyl cyanide p-trifluoromethoxy-phenylhydrazone.

Oestradiol measurement in women on oral hormone replacement therapy: the validity of commercial test kits

Four commercially available methods for the measurement of oestradiol were used to assay oestradiol concentrations in samples from women receiving oral hormone replacement therapy. Significant differences in results were found between samples that were measured direct and those subjected to an extraction procedure. There was considerable variability in the extraction: direct ratio between methods, indicating that with some methods an extraction procedure should be performed before analysis on samples from women receiving oral hormone replacement therapy. Factors that account for discrepant results between methods probably include increased concentration of sex hormone binding globulin together with cross-reacting metabolites and conjugates.

Spontaneous resolution of pterygium by auto-avulsion

The exact pathogenesis of pterygia is not yet clearly understood. Most recent studies implicate fibroblastic proliferation as the essential histopathology in the condition. A case is presented in which spontaneous avulsion of the head of a pterygium occurred, with rapid resolution of symptoms. Such an avulsion suggests the presence of strong forces being exerted on the cornea by the pterygium. Fibroblastic activity could be responsible for the development of such forces. This case supports existing evidence for the primary nature of fibroblastic proliferation in the development of pterygia.

Incidence, prevalence and possible risk factors for pneumonitis in patients with rheumatoid arthritis receiving methotrexate

OBJECTIVE

Methotrexate (MTX) is being used increasingly to treat rheumatoid arthritis (RA). Pneumonitis is a serious side effect of MTX therapy (P-MTX). Our aim was to determine in patients with RA the incidence and prevalence of P-MTX in Western Australia and identify risk factors for the development of this adverse reaction.

METHODS

Patients with P-MTX were identified by (a) direct communication with rheumatologists in Western Australia, (b) use of a computerized clinical database, (c) questionnaire inquiry of all other rheumatologists in Australia. Possible risk factors for P-MTX were examined using age/sex matched case controls selected from the computerized clinical database.

RESULTS

Ten definite and 3 probable cases of P-MTX were identified. Local incidence of P-MTX was 1/35.4 patient years MTX treatment; if definite and probable cases are included (1/49.6 patient years MTX treatment for definite cases alone). Twelve patients with P-MTX were compared with 24 age/sex matched controls. A shorter duration of MTX treatment and a higher incidence of preexisting lung disease were observed in P-MTX cases but these differences were not statistically significant. No difference was observed between the P-MTX and control patients with respect to rheumatoid factor, duration of RA, use of tobacco, dose of MTX, serum creatinine, creatinine clearance or concurrent treatment with aspirin, nonsteroidal antirheumatic drugs or prednisolone.

CONCLUSION

Our results indicate that in hospital clinic patients with RA pneumonitis is a common adverse reaction. They suggest that hypersensitivity is probably responsible for most cases of pneumonitis associated with MTX, but preexisting lung disease may confer increased risk.

Features of systemic sclerosis (scleroderma) in an identical twin pair

The aetiology of systemic sclerosis (scleroderma) is unknown but it is thought to have both genetic and environmental components. The familial incidence of the disease is very low and we have been able to find only one report of scleroderma in identical twins which was in the Russian literature. We report here on a set of identical twins and their mother who all had features of systemic sclerosis.

Baculovirus-mediated expression of human 65 kDa and 67 kDa glutamic acid decarboxylases in SF9 insect cells and their relevance in diagnosis of insulin-dependent diabetes mellitus

cDNAs coding for the full-length human 65 and 67 kDa glutamic acid decarboxylases (GAD65 and GAD67) were amplified from pancreas and hippocampus cDNA libraries by polymerase chain reaction, respectively. Both cDNAs were inserted into a baculovirus vector which mediated highly efficient expression of the human GAD65 and GAD67 with histidine-hexapeptides as affinity ligands at their C-termini in Spodoptera frugiperda (Sf9) cells. The recombinant GAD proteins were purified to homogeneity by affinity chromatography using a metal-chelating matrix. The infected Sf9 insect cells expressed the recombinant human GAD65 and GAD67 with natural-like conformations, as confirmed by measurement of their enzyme activities as well as their fully restored autoantigenicities. Immunoprecipitation of metabolically labeled infected Sf9 cells demonstrated the autoantigenic potential of the recombinant GAD proteins. The practicability of using recombinant GAD65 and GAD67 derived from the baculovirus expression system for the development of an immunoassay for the diagnosis of insulin-dependent diabetes mellitus is discussed.

Expression of recombinant human thyroid peroxidase by the baculovirus system and its use in ELISA screening for diagnosis of autoimmune thyroid disease

The cDNAs coding for human full-length and soluble thyroid peroxidase (TPO) were constructed, cloned into a baculovirus transfer vector and used for infection of Spodoptera frugiperda (Sf9) cells. The soluble TPO lacking 87 amino acids of the C-terminal transmembrane and intracisternal domains was designed as a fusion protein with a histidine-hexapeptide as an affinity ligand at its C-terminus. Whereas the recombinant full-length TPO was expressed mainly in an insoluble form in Sf9 cells, the recombinant soluble TPO was almost completely secreted into the culture medium. Both the full-length and the soluble TPO were purified by conventional methods and by a specific affinity chromatography using metal chelating matrix respectively, and tested for their autoantigenicity towards anti-TPO autoantibodies. The ELISA established with the purified recombinant soluble TPO as antigen demonstrated its specificity, practicability and reproducibility in screening of anti-TPO autoantibodies in sera of autoimmune thyroid patients. High correlation (r = 0.89, n = 175) was obtained between the soluble TPO and natural TPO prepared from human thyroid glands. Pathological sera (n = 200) were positively assayed with a significance of 91%.

Primary structure and functional expression of the Na/Ca,K-exchanger from bovine rod photoreceptors

Complementary DNA encoding the Na/Ca,K-exchanger was isolated from bovine retina cDNA libraries. The complete full-length cDNA is approximately 4 kb long and contains an open reading frame of 3597 bp. The deduced amino acid sequence corresponds to a protein of 1199 amino acids with a calculated molecular weight of approximately 130 kDa. Hydrophobicity analysis revealed the presence of two alternating sets of hydrophobic and hydrophilic domains. There also exists a hydrophobic region at the N-terminus which may be part of a cleavable signal peptide. The protein shares limited sequence homology with the Na/Ca-exchanger from cardiac sarcolemma. Northern blot analysis indicates that the approximately 6 kb transcript is highly specific for retinal tissue. Insect cells infected with recombinant baculovirus bearing the full-length cDNA express a functional Na/Ca,K-exchanger with an apparent relative molecular weight of approximately 210 kDa, as determined by Western blotting.

Successful reintroduction of methotrexate after pneumonitis in two patients with rheumatoid arthritis

Two patients are described with severe and progressive rheumatoid arthritis in whom methotrexate was reintroduced despite previous methotrexate related pneumonitis. In both patients a marked improvement in disease control occurred without a recurrence of the pneumonitis.

The cGMP-gated channel of rod outer segments is not localized in bipolar cells of the mammalian retina

It has recently been suggested (Nature, 346 (1990) 269-271) that ON-bipolar cells express the same biochemical cascade and guanosine 3',5'-cyclic monophosphate (cGMP)-gated cation channel as rod outer segments. An antibody directed against the cGMP-gated channel of bovine rod outer segments was applied to cryostat sections of rat and cat retinae. No immunocytochemical labelling was found in bipolar cells. Therefore, if those cells express a cGMP-gated channel, it must be immunologically different to the 63 kDa protein constituting the cGMP-gated channel of the outer segment.

Antibodies against synthetic peptides used to determine the topology and site of glycosylation of the cGMP-gated channel from bovine rod photoreceptors

Peptides corresponding to amino acids 321-339 (peptide GS21) and 416-431 (peptide GS31) of the cGMP-gated channel from bovine rod photoreceptors were synthesized and used as antigens for the preparation of polyclonal antibodies. After affinity purification, both antipeptide antibodies were found to bind specifically to the channel protein after Western blotting, but only the antibody against GS21 gave satisfactory results on enzyme-linked immunosorbent assay and electron microscopy. Using immunocytochemistry, we were able to localize amino acids 321-339 to the extracellular side of the rod photoreceptor plasma membrane. By synthesizing heptapeptides corresponding to amino acids 324-330 (peptide GS2s) and 420-426 (peptide GS3s), we were able to affinity purify antibodies specific for two N-glycosylation consensus sites in the channel protein. As assessed by Western blotting, antibodies against GS3s were found to bind to both the glycosylated and deglycosylated channel proteins, whereas antibodies against GS2s only bound to the channel protein after enzymatic deglycosylation. Together, these results allow the refinement of folding models for the cGMP-gated channel and implicate Asn-327 as being the sole site of N-glycosylation.

Detection of IL-2 at mRNA and protein levels in synovial infiltrates from inflammatory arthropathies using biotinylated oligonucleotide probes in situ

A non-radioactive in situ hybridization method for IL-2 mRNA detection based on the use of four biotinylated oligonucleotide probes, plus appropriate positive and negative control probes was developed and applied to synovial surgical and needle biopsies from rheumatoid arthritis (RA), spondyloarthropathy (SpA), psoriatic arthritis (PsA) and juvenile chronic arthritis (JCA) patients. In eight surgical biopsies (six RA, one SpA, one PsA) this non-radioactive system showed similar sensitivity to that of a previously described 32P-labelled probe system, and in addition detected IL-2 mRNA in five out of seven biopsies from SpA and PsA patients and in two out of two JCA needle biopsies. IL-2 mRNA was found in the absence of IL-2 protein in RA biopsies (six surgical, 12 needle), but variable amounts of IL-2 protein were detected in six out of seven needle biopsies from SpA, PsA and JCA patients, where CD3+ lymphoid infiltrates were present. These data suggest differences in IL-2 regulation and expression in RA and non-RA inflammatory arthropathies.

The cGMP-gated channel of the rod photoreceptor cell characterization and orientation of the amino terminus

The molecular properties and orientation of the cGMP-gated cation channel of bovine rod outer segment membranes were studied using biochemical and immunochemical methods. Western blots labeled with anti-channel monoclonal antibodies indicate that the channel has a subunit Mr of 63,000 in bovine rod outer segment membranes prepared in the presence and absence of protease inhibitors and in rod outer segments from other mammalian retinas. The channel has an apparent Mr of 78,000 in both COS-1 cells and Xenopus oocytes expressing the cloned cDNA. NH2-terminal sequence analysis indicates that the lower Mr of the channel in rod outer segments is caused by the absence of the first 92 amino acids predicted by cDNA sequence analysis. Immunofluorescent and immunogold labeling has confirmed that the 63,000 form of the channel is present in rod outer segments. These results indicate that photoreceptor cell-specific co-translational or post-translational cleavage of the NH2-terminal segment of the channel occurs prior or during the incorporation of the channel into the rod outer segment plasma membrane. Immunogold labeling studies using site-directed antibodies also indicate that the NH2-terminal segment of the rod outer segment channel is exposed on the cytoplasmic side of the plasma membrane.

Inadvertent application of silicone foam elastomer catalyst to the eye

Silicone foam elastomer is used extensively to treat granulating wounds. A case is presented in which the catalyst to the polymer was inadvertently applied to the eye. This produced conjunctival and corneal injury, which was slow to heal and resistant to conventional treatment. This form of injury has not previously been described.

Rapid purification and characterization of protein kinase C from bovine retinal rod outer segments

A rapid FPLC procedure for the purification of protein kinase C from bovine rod outer segments is described. The enzyme is essentially homogeneous after purification and exhibits a molecular mass of approximately 85 kDa, as determined by SDS/PAGE. From its chromatographic behaviour on hydroxyapatite, and from Western-blotting experiments using isoenzyme-specific antibodies, we were able to identify the bovine rod outer segment protein kinase C as being of the alpha or type-III form. The purified protein kinase C has a specific activity of 1066 nmol 32P.min-1.mg protein-1, and shows a 30-fold activation upon the addition of the effectors Ca2+, PtdSer and 1,2-diacylglycerol. Arachidonic acid and linoleic acid were also found to enhance significantly the activity of the purified enzyme.