Exploiting the distinctive properties of the bacterial and human MutS homolog sliding clamps on mismatched DNA

MutS homologs (MSHs) are highly conserved core components of DNA mismatch repair. Mismatch recognition provokes ATP-binding by MSH proteins that drives a conformational transition from a short-lived lesion-searching clamp to an extremely stable sliding clamp on the DNA. Here, we have expanded on previous bulk biochemical studies to examine the stability, lifetime, and kinetics of bacterial and human MSH sliding clamps on mismatched DNA using surface plasmon resonance and single-molecule analysis of fluorescently labeled proteins. We found that ATP-bound MSH complexes bound to blocked-end or very long mismatched DNAs were extremely stable over a range of ionic conditions. These observations underpinned the development of a high-throughput Förster resonance energy transfer system that specifically detects the formation of MSH sliding clamps on mismatched DNA. The Förster resonance energy transfer system is capable of distinguishing between HsMSH2-HsMSH3 and HsMSH2-HsMSH6 and appears suitable for chemical inhibitor screens. Taken together, our results provide additional insight into MSH sliding clamps as well as methods to distinguish their functions in mismatch repair.

Sulfated glycan recognition by carbohydrate sulfatases of the human gut microbiota

Sulfated glycans are ubiquitous nutrient sources for microbial communities that have coevolved with eukaryotic hosts. Bacteria metabolize sulfated glycans by deploying carbohydrate sulfatases that remove sulfate esters. Despite the biological importance of sulfatases, the mechanisms underlying their ability to recognize their glycan substrate remain poorly understood. Here, we use structural biology to determine how sulfatases from the human gut microbiota recognize sulfated glycans. We reveal seven new carbohydrate sulfatase structures spanning four S1 sulfatase subfamilies. Structures of S1_16 and S1_46 represent novel structures of these subfamilies. Structures of S1_11 and S1_15 demonstrate how non-conserved regions of the protein drive specificity toward related but distinct glycan targets. Collectively, these data reveal that carbohydrate sulfatases are highly selective for the glycan component of their substrate. These data provide new approaches for probing sulfated glycan metabolism while revealing the roles carbohydrate sulfatases play in host glycan catabolism.

A single sulfatase is required to access colonic mucin by a gut bacterium

Humans have co-evolved with a dense community of microbial symbionts that inhabit the lower intestine. In the colon, secreted mucus creates a barrier that separates these microorganisms from the intestinal epithelium1. Some gut bacteria are able to utilize mucin glycoproteins, the main mucus component, as a nutrient source. However, it remains unclear which bacterial enzymes initiate degradation of the complex O-glycans found in mucins. In the distal colon, these glycans are heavily sulfated, but specific sulfatases that are active on colonic mucins have not been identified. Here we show that sulfatases are essential to the utilization of distal colonic mucin O-glycans by the human gut symbiont Bacteroides thetaiotaomicron. We characterized the activity of 12 different sulfatases produced by this species, showing that they are collectively active on all known sulfate linkages in O-glycans. Crystal structures of three enzymes provide mechanistic insight into the molecular basis of substrate specificity. Unexpectedly, we found that a single sulfatase is essential for utilization of sulfated O-glycans in vitro and also has a major role in vivo. Our results provide insight into the mechanisms of mucin degradation by a prominent group of gut bacteria, an important process for both normal microbial gut colonization2 and diseases such as inflammatory bowel disease3.

Mobility shift-based electrophoresis coupled with fluorescent detection enables real-time enzyme analysis of carbohydrate sulfatase activity

Sulfated carbohydrate metabolism is a fundamental process, which occurs in all domains of life. Carbohydrate sulfatases are enzymes that remove sulfate groups from carbohydrates and are essential to the depolymerisation of complex polysaccharides. Despite their biological importance, carbohydrate sulfatases are poorly studied and challenges remain in accurately assessing the enzymatic activity, specificity and kinetic parameters. Most notably, the separation of desulfated products from sulfated substrates is currently a time-consuming process. In this paper, we describe the development of rapid capillary electrophoresis coupled to substrate fluorescence detection as a high-throughput and facile means of analysing carbohydrate sulfatase activity. The approach has utility for the determination of both kinetic and inhibition parameters and is based on existing microfluidic technology coupled to a new synthetic fluorescent 6S-GlcNAc carbohydrate substrate. Furthermore, we compare this technique, in terms of both time and resources, to high-performance anion exchange chromatography and NMR-based methods, which are the two current 'gold standards' for enzymatic carbohydrate sulfation analysis. Our study clearly demonstrates the advantages of mobility shift assays for the quantification of near real-time carbohydrate desulfation by purified sulfatases, and will support the search for small molecule inhibitors of these disease-associated enzymes.

Synthesis and toxicity profile in 293 human embryonic kidney cells of the β D-glucuronide derivatives of ortho-, meta- and para-cresol

The formation of β-glucuronides is a major route by which mammals detoxify and remove breakdown products, such as l-tyrosine, as well as many xenobiotics, from their systems. In humans, dietary l-tyrosine is broken down largely by the action of the anaerobic gut bacterium C. difficile to p-cresol, providing a competitive advantage in the gut microbiota. Ortho- (o-) and meta- (m-), cresols, also present in the environment, may share a common degradative pathway. Relatively little work has been done on cresyl glucuronides. Here, a direct synthesis of o-, m-, and p-cresyl β-D-glucuronides from methyl 1,2,3,4 tetra-O-acetyl-β-d-glucuronate and the respective cresol employing trimethylsilyltriflate as promoter is presented. The protected intermediates were hydrolysed using aqueous sodium carbonate to yield the cresyl β-glucuronides. The toxicities of the o-, m- and p-cresyl β-D-glucuronides were compared. All three were less toxic to HEK293 cells than their respective cresol precursors: toxicity followed the order o < m < p for Na⁺ salts and o < p < m for Ca²⁺ salts. The m-cresyl-glucuronide Ca²⁺ salt and p-cresyl-glucuronide Na⁺ salt reduced colony formation by 11% and 9% (v. 30% reduction from the aglycone) respectively, whereas o-cresyl-glucuronide (both Na⁺ and Ca²⁺ salts), mildly stimulated HEK293 cell growth.

MutL sliding clamps coordinate exonuclease-independent Escherichia coli mismatch repair

A shared paradigm of mismatch repair (MMR) across biology depicts extensive exonuclease-driven strand-specific excision that begins at a distant single-stranded DNA (ssDNA) break and proceeds back past the mismatched nucleotides. Historical reconstitution studies concluded that Escherichia coli (Ec) MMR employed EcMutS, EcMutL, EcMutH, EcUvrD, EcSSB and one of four ssDNA exonucleases to accomplish excision. Recent single-molecule images demonstrated that EcMutS and EcMutL formed cascading sliding clamps on a mismatched DNA that together assisted EcMutH in introducing ssDNA breaks at distant newly replicated GATC sites. Here we visualize the complete strand-specific excision process and find that long-lived EcMutL sliding clamps capture EcUvrD helicase near the ssDNA break, significantly increasing its unwinding processivity. EcSSB modulates the EcMutL–EcUvrD unwinding dynamics, which is rarely accompanied by extensive ssDNA exonuclease digestion. Together these observations are consistent with an exonuclease-independent MMR strand excision mechanism that relies on EcMutL–EcUvrD helicase-driven displacement of ssDNA segments between adjacent EcMutH–GATC incisions.

The mechanics of MMR strand specific excision that begins at a distant ssDNA break are not yet clear. Here the authors have used multiple single molecule imaging techniques to visualize the behavior of MMR components on mismatched DNA substrates and reveal an exonuclease-independent mechanism for E.coli MMR.

CRISPR/Cas9 Genome Editing to Disable the Latent HIV-1 Provirus

HIV-1 infection can be successfully controlled with anti-retroviral therapy (ART), but is not cured. A reservoir of cells harboring transcriptionally silent integrated provirus is able to reestablish replicating infection if ART is stopped. Latently HIV-1 infected cells are rare, but may persist for decades. Several novel strategies have been proposed to reduce the latent reservoir, including DNA sequence targeted CRISPR/Cas9 genome editing of the HIV-1 provirus. A significant challenge to genome editing is the sequence diversity of HIV-1 quasispecies present in patients. The high level of quasispecies diversity will require targeting of multiple sites in the viral genome and personalized engineering of a CRISPR/Cas9 regimen. The challenges of CRISPR/Cas9 delivery to the rare latently infected cells and quasispecies sequence diversity suggest that effective genome editing of every provirus is unlikely. However, recent evidence from post-treatment controllers, patients with controlled HIV-1 viral burden following interruption of ART, suggests a correlation between a reduced number of intact proviral sequences and control of the virus. The possibility of reducing the intact proviral sequences in patients by a genome editing technology remains intriguing, but requires significant advances in delivery to infected cells and identification of effective target sites.

The influence of unrestricted use of sugammadex on clinical anaesthetic practice in a tertiary teaching hospital

This retrospective casenote audit involving 374 patients requiring intubation for an anaesthetic found that when the availability of sugammadex became unrestricted, its use increased from 7.1 to 65.3% (P <0.0001) of all muscle relaxant reversals, while neostigmine use decreased from 59.6 to 12.5%. Rocuronium use decreased slightly (90.8 to 79.2%, P=0.006) but vecuronium use increased (2.1 to 8.3%, P=0.02). Cisatracurium and suxamethonium use were unchanged. Total rocuronium dose (55.9 ± 24.1 vs 60.4 ± 22.3 mg) and the number of doses (1.9 ± 1.48 to 1.96 ± 1.27) were unchanged, but the time between the last dose and reversal decreased (91.7 ± 68.1 to 62 ± 52.4 minutes, P=0.0002). There appeared to be no change in postoperative nausea and vomiting, or post-anaesthesia care unit time or oxygen saturation levels. Anaesthetic theatre time fell from 143.5 ± 85.8 to 120 ± 71.2 minutes (P=0.01) and remained significant when adjusted for confounding variables (ratio of means 1.17, 95% confidence interval 1.03 to 1.34, P=0.02), although inferences in relation to causality are limited by the retrospective and observational design of the study. Hospital stay also appeared to fall (4.2 ± 3.5 to 3.4 ± 3.0 days, P=0.035), but was not statistically significant when adjusted for confounding variables (ratio of means 1.04, 95% confidence interval 0.89 to 1.2, P=0.59). These observations suggest that the unrestricted availability of sugammadex will change how steroid-based neuromuscular blocking drugs are used and reversed, but further research is needed to determine if patient outcomes will improve.

Mechanism for food avoidance learning in the central pattern generator of feeding behavior of Pleurobranchae californica

Food-avoidance conditioning in the mollusk Pleurobranchaea results in suppression of the feeding response to food stimuli. In conditioned animals, identified interneurons of the central pattern generator (CPG) for feeding behavior, the Int-2s, respond to a food stimulus with greater and more long-lasting excitation than controls. Enhanced Int-2 responsiveness to food stimuli is associated with markedly heightened Int-2 excitability. Sustained activity in the Int-2s arrests motor output of the oscillatory CPG in the protraction/retraction movement cycle of feeding through tonic excitation of a population of retractor interneurons and inhibition of protractors. The CPG locus of the learning mechanism is permissive of sensory excitation of alternative behavior and leaves the possibility open for release of the suppressed behavior in a fully aroused state.

Priorities for improving hospital-based trauma care in an African city

BACKGROUND

This study sought to identify potential cost-effective methods to improve trauma care in hospitals in the developing world.

METHODS

Injured patients admitted to an urban hospital in Ghana over a 1-year period were analyzed prospectively for mechanism of injury, mode of transport to the hospital, injury severity, region of principal injury, operations performed, and mortality. In addition, time from injury until arrival at the hospital and time from arrival at the hospital until emergency surgery were evaluated.

RESULTS

Mortality was 9.4%. Most deaths (65%) occurred within 24 hours of admission. Sixty percent of emergency operations were performed over 6 hours after arrival. Tube thoracostomy was performed on only 13 patients (0.6%). Only 58% of patients received intravenous crystalloid and only 3.6% received 1 or more units of blood.

CONCLUSION

We identified several specific interventions as potential low-cost measures to improve hospital-based trauma care in this setting, including shorter times to emergency surgery and improvements in initial resuscitation. In addition to addressing each of these aspects of trauma care individually, quality improvement programs may represent a feasible and sustainable method to improve trauma care in hospitals in the developing world.

Aboriginal perspectives of diabetes in a remote community in the Northern Territory

This study explores the knowledge and beliefs of diabetes in a group of Aboriginal people from a remote community in the Northern Territory. Information was gathered from participants through a combination of group discussions, semi-structured interviews and informal conversations. The four themes of explanation of diabetes were: worry, food, family and infections. The most common means of preventing or treating diabetes were stopping worry and changing one's diet. Significantly, few of the participants believed that medication was effective, and weight loss and exercise were not mentioned. The results highlight the miscommunication about diabetes that has occurred in this population. For effective communication and management of diabetes, health information must incorporate the contemporary health beliefs of the clients.

Neurocytopathic effects of beta-amyloid-stimulated monocytes: a potential mechanism for central nervous system damage in Alzheimer disease

Growing evidence indicates that cells of the mononuclear phagocyte lineage, which includes peripheral blood monocytes (PBM) and tissue macrophages, participate in a variety of neurodestructive events and may play a pivotal role in neurodegenerative conditions such as Alzheimer disease. The present study sought to determine whether exposure of PBM to beta-amyloid peptide (A beta), the major protein of the amyloid fibrils that accumulate in the brain in Alzheimer disease, could induce cytopathic activity in these cells upon their subsequent incubation with neural tissue. PBM were incubated with A beta for 3 days, centrifuged and washed to remove traces of cell-free A beta, and then applied to organotypic cultures of rat brain for varying periods of time. By using a cell-viability assay to quantitate neurocytopathic effect, an increase in the ratio of dead to live cells was detected in cultures containing A beta-stimulated PBM versus control PBM (stimulated with either bovine serum albumin or reverse A beta peptide) as early as 3 days after coculture. The ratio of dead to live cells increased further by 10 days of coculture. By 30 days of coculture, the dead to live cell ratio remained elevated, and the intensity of neurocytopathic effect was such that large areas of brain mass dissociated from the cultures. These results indicate that stimulation of PBM with A beta significantly heightens their neurocytopathic activity and highlight the possibility that inflammatory reactions in the brain play a role in the neurodegeneration that accompanies Alzheimer disease.

Adherence to zidovudine (AZT) among HIV-infected methadone patients: a pilot study of supervised therapy and dispensing compared to usual care

Twenty-seven HIV-infected methadone maintenance patients who demonstrated problems adhering to zidovudine (AZT) were randomly assigned to a group that received eight weeks of weekday supervised therapy and dispensing of AZT or a group that received usual care of the clinic. Adherence was assessed by self-report, erythrocyte mean corpuscular volume (MCV), Medication Event Monitoring Systems (MEMS), and pill counts. Subjects in the intervention group demonstrated significantly higher MCV levels during the intervention period than usual care subjects, with similar but non-significant trends for the three other adherence measures. MEMS percent indicated significant group differences on weekdays, but not weekend days. There were no differences at a one-month follow-up. Results suggest supervised therapy and dispensing may be an effective strategy for improving AZT adherence, but only while provided. Further research is needed to establish the effects of larger and longer lasting interventions.

Classification of inhibitory responses of the hamster gustatory cortex

Neuronal activity was recorded in the gustatory cortex of the golden Syrian hamster in response to application of taste stimuli to the anterior tongue. Two classes of inhibitory responses were detected: (1) a decrease in activity in response to application of individual taste stimuli: and (2) a decrease in activity in response to application of a mixture of taste stimuli but not in response to application of individual taste stimuli.

Hundreds of neurons in the Aplysia abdominal ganglion are active during the gill-withdrawal reflex

A combination of optical and electrode recording methods was used to obtain an overview of the neuron activity in the Aplysia abdominal ganglion in response to a light touch to the siphon skin. Spike activity was detected in up to 150 different neurons. Habituation and sensitization of the gill-withdrawal reflex was accompanied by large changes in the number of activated neurons. It is likely that these recordings are incomplete; the actual number of activated neurons is estimated to be about 300 in the acutely sensitized preparation. While we presume that not all 300 of these neurons are involved in the gill-withdrawal reflex, the number of neurons is so large that it may be difficult to determine the role of each activated neuron with presently available experimental tools.

Coping with AIDS: strategies for patients and staff in drug abuse treatment programs

HIV infection creates difficulties for patients and staff in drug abuse treatment programs. This article reviews significant problems and coping strategies, drawing on experience in a drug abuse treatment program where a third of the patients are HIV infected. Patient-related problems include denial, anger, depression, and isolation. The coping strategies that patients use can exacerbate their illness. Effective coping strategies may involve the development of mutual-support groups and public education. Staff-related problems include the fear of infection, protecting confidentiality, the need to develop new treatment goals, and recognizing the limitations of drug abuse treatment. To lessen the fears of infection, programs can exercise clear body substance precautions, conduct frequent inservice training, and hold periodic updates for staff. To adequately protect confidentiality, programs can keep up with rapidly changing laws and guidelines. To modify treatment goals, programs can alter admission standards for HIV-infected patients, change treatment methods to minimize the impact of occasional relapses, develop medical referral networks, and give special consideration to counselors who treat HIV-infected patients. To cope with the limitations of drug abuse treatment, programs can support counseling staff in coping with emotionally stressful clinical problems and to avoid burnout.

Optical recordings of the cortical response to whisker stimulation before and after the addition of an epileptogenic agent

Optical recording methods using voltage-sensitive dyes were used to monitor activity in rat somatosensory cortex. We measured evoked signals in response to whisker stimulation before (control) and after the addition of the epileptogenic agent, bicuculline, and also detected spontaneous interictal events that occurred after bicuculline. Bicuculline led to an increase in the size, duration, cortical extent, and, surprisingly, the latency of the evoked responses. These enhanced evoked responses appeared to originate in the region of the control response and propagate outward. In contrast, the spontaneous signals appeared to originate at random cortical positions and had a more variable cortical extent. A transition signal measured just after the addition of bicuculline was larger than the control response but localized and rapid in time course. In most cases, there was a good correlation between the optical recordings and field potential measurements made with a ball electrode on the cortical surface, but there were occasional instances where the optical signal disappeared while the ball electrode signal was unchanged.

Optical monitoring of activity of many neurons in invertebrate ganglia during behaviors

Optical methods for monitoring neuron activity were developed because these methods lend themselves to simultaneous multiple-site measurements. With the use of new voltage-sensitive dyes, the dye-related pharmacology and photodynamic damage appear to be relatively unimportant. Using multiple-site measurements made with a 124-element photodiode array, we estimated that approximately 30 of the 200 neurons present in the Navanax buccal ganglion make action potentials during feeding and that approximately 300 of the 1100 neurons present in the Aplysia abdominal ganglion are active during the gill-withdrawal reflex. The fact that a light mechanical touch to the siphon skin activated such a large number of neurons in the abdominal ganglion suggests that understanding the neuronal basis of the gill-withdrawal reflex and its behavioral plasticity may be forbiddingly difficult.

Simultaneous optical recording of activity from many neurons during feeding in Navanax

Optical methods for monitoring changes in membrane potential have been used to measure action potential activity in the buccal ganglion of an opisthobranch mollusc, Navanax inermis, while the animal was feeding. During feeding activity was detected in 10-15% of the approximately 200 neurons present in the ganglion. Control experiments carried out to determine the completeness of the optical recording showed that activity in at least 70% of the neurons could be detected. Thus, in certain invertebrate ganglia, it is possible to make a reasonably complete recording of the neuron activity responsible for generating relatively complex behaviors.

Functional roles and circuitry in an inhibitory pathway to feeding command neurones in Pleurobranchaea

The paracerebral neurones (PCNs) of the brain of Pleurobranchaea californica serve a command role in the initiation of feeding behaviour (Gillette, Kovac & Davis, 1978). The PCNs are synaptically excited by food stimuli applied to the oral veil of hungry, naive animals. In food avoidance-conditioned animals, the PCNs are inhibited by a barrage of inhibitory postsynaptic potentials concomitant with the suppression of feeding (Davis & Gillette, 1978). In this paper, an interneuronal pathway is described which causes inhibition of the PCNs and potentially mediates the effects of learning. The inhibitory pathway consists of three serially connected interneurones. One population, designated the Interneurone 1s (Int-1s), monosynaptically inhibits the PCNs. A second population, the Interneurone 2s (Int-2s), excites the Int-1 population. They also excite other neurones of the brain including the metacerebral giant neurones. A third population, the Interneurone 3s (Int-3s), monosynaptically excites the Interneurone 2 population. Dual intracellular recordings and current injection show that ipsilateral members of the Int-2 population are electrically coupled via a nonrectifying connection. Contralateral members of the Int-2 population are excitatorily coupled via a polysynaptic pathway. The Int-1 population is phasically active during the rhythmic motor activity that underlies feeding. In the isolated nervous system Int-1 activity is phase-locked with rhythmic PCN activity; Int-1 activity occurs maximally at the end of a PCN burst, during the retraction phase of the cycle. Int-2 activity also occurs during the retraction phase. During actual feeding in the whole animal preparation, the Int-2s are also phasically active; maximal excitation occurs during buccal mass retraction and maximal inhibition during protraction and the bite. Stimulated activity in a single Int-2 can entirely suppress the rhythmic motor activity of the feeding network evoked by electrical stimulation of the stomatogastric nerve. The suppressant effects of Int-2 activity must be mediated widely within the feeding network because the rhythmic motor output so driven is not dependent on PCN spiking. Application of an appetitive chemosensory stimulus to whole and semi-intact animal preparations initiated feeding and elicited excitation of the Int-1 and Int-2 populations. Noxious chemosensory stimuli, such as a dilute soap solution or ethanol, elicited oral veil withdrawal and inhibition of the Int-2s by multiple inhibitory postsynaptic potentials.(ABSTRACT TRUNCATED AT 400 WORDS)

Single cell isolation: a way to examine network interactions

A procedure for isolating identified, small neurons from snail ganglia is described. The technique allows a particular neuron, previously identified by morphological and electrophysiological characteristics, to be marked and then isolated from the ganglia. This procedure was developed to permit the detailed comparison of the electrical characteristics of a neuron before and after isolation from an intact system. An earlier description has appeared. The cell somata is marked intracellularly by the iontophoretic injection of Procion navy blue H3RS which visually differentiates the cell from other cells in the ganglion. The ganglion is then treated with a trypsin-haluronidase solution to soften the ganglion sheath, which is then removed. The cells are gently shaken to isolate them from the ganglion and then examined electrophysiologically. A comparison of membrane properties, such as action potential height, duration and rate of rise and decay was made before and after all treatments were applied to assess deleterious effect. An analysis of network properties, such as burst duration, number of spikes per burst and presynaptic activity was also performed after each phase of the procedure. No significant differences were noted after dye injection, enzyme treatment, and where appropriate, after isolation. An increase in input resistance and corresponding decrease in the slope of the steady state current--voltage plot (I--V plot) were observed after isolation of a cell. These were expected results of removing the 'load' (i.e. axon or electrical coupling) from the cell soma. This method may be applied to many other systems to study the effects of network interactions on the properties of a single cell and should therefore facilitate the analysis of neuronal networks as well as single cell properties.