Transcriptional enhancers at 40: evolution of a viral DNA element to nuclear architectural structures.

Gene regulation by transcriptional enhancers is the dominant mechanism driving cell type- and signal-specific transcriptional diversity in metazoans. However, over four decades since the original discovery, how enhancers operate in the nuclear space remains largely enigmatic. Recent multidisciplinary efforts combining real-time imaging, genome sequencing, and biophysical strategies provide insightful but conflicting models of enhancer-mediated gene control. Here, we review the discovery and progress in enhancer biology, emphasizing the recent findings that acutely activated enhancers assemble regulatory machinery as mesoscale architectural structures with distinct physical properties. These findings help formulate novel models that explain several mysterious features of the assembly of transcriptional enhancers and the mechanisms of spatial control of gene expression.

Expression of Ripk1 and DAM genes correlates with severity and progression of Krabbe disease.

Krabbe disease, an inherited leukodystrophy, is a sphingolipidosis caused by deficiency of ß-galactocerebrosidase: it is characterized by myelin loss, and pathological activation of macrophage/microglia and astrocytes. To define driving pathogenic factors, we explored the expression repertoire of candidate neuroinflammatory genes: upregulation of receptor interacting protein kinase 1 (Ripk1) and disease-associated microglia (DAM) genes, including Cst7 and Ch25h, correlated with severity of Krabbe disease genetically modelled in the twitcher mouse. Upregulation of Ripk1 in Iba1/Mac2-positive microglia/macrophage associated with the pathognomic hypertrophic/globoid phenotype of this disease. Widespread accumulation of ubiquitinin1 in white and grey matter co-localised with p62. In Sandhoff disease, another sphingolipid disorder, neuroinflammation, accumulation of p62 and increased Ripk1 expression was observed. The upregulated DAM genes and macrophage/microglia expression of Ripk1 in the authentic model of Krabbe disease strongly resemble those reported in Alzheimer disease associating with disturbed autophagosomal/lysosomal homeostasis. Activation of this shared molecular repertoire, suggests the potential for therapeutic interdiction at a common activation step, irrespective of proximal causation. To clarify the role of Ripk1 in the pathogenesis of Krabbe disease, we first explored the contribution of its kinase function, by intercrossing twitcher and the K45A kinase-dead Ripk1 mouse and breeding to homozygosity. Genetic ablation of Ripk1 kinase activity neither altered the neuropathological features nor the survival of twitcher mice. We conclude that Ripk1 kinase-dependent inflammatory and degenerative capabilities play no instrumental role in Krabbe disease; however, putative kinase-independent functions of Ripk1 remain formally to be explored in its molecular pathogenesis.

Supporting and Incentivizing Peer Leaders for an Internet-Based Private Peer Community for Youths With Type 1 Diabetes: Social Network and Directed Content Analysis.

BACKGROUND: Youths with type 1 diabetes (T1D) frequently experience stigma. Internet-based peer communities can mitigate this through social support but require leaders to catalyze exchange. Whether nurturing potential leaders translates into a central role has not been well studied. Another issue understudied in such communities is lurking, the viewing of exchanges without commenting or posting. OBJECTIVE: We aimed to assess the centrality of the peer leaders we selected, trained, and incentivized within the Canadian Virtual Peer Network (VPN)-T1D. This is a private Facebook (Meta Platforms, Inc) group that we created for persons aged 14 to 24 years with T1D. We specifically sought to (1) compare a quantitative estimate of network centrality between peer leaders and regular members, (2) assess the proportions of network exchanges that were social support oriented, and (3) assess proportions of high engagement (posts, comments, reactions, and votes) and low engagement (lurking) exchanges. METHODS: We recruited peer leaders and members with T1D from prior study cohorts and clinics. We trained 10 leaders, provided them with a monthly stipend, and encouraged them to post on the private Facebook group we launched on June 21, 2017. We extracted all communications (posts, messages, reactions, polls, votes, and views) that occurred until March 20, 2020. We calculated each member's centrality (80% of higher engagement communications comprising posts, comments, and reactions plus 20% of members with whom they connected). We divided each member's centrality by the highest centrality to compute the relative centrality, and compared the mean values between leaders and members (linear regression). We calculated the proportions of communications that were posts, comments, reactions, and views without reaction. We performed content analysis with a social support framework (informational, emotional, esteem-related, network, and tangible support), applying a maximum of 3 codes per communication. RESULTS: VPN-T1D gained 212 regular members and 10 peer leaders over 33 months; of these 222 members, 26 (11.7%) exited. Peer leaders had 10-fold higher relative centrality than regular members (mean 0.53, SD 0.26 vs mean 0.04, SD 0.05; 0.49 difference; 95% CI 0.44-0.53). Overall, 91.4% (203/222) of the members connected at least once through posts, comments, or reactions. Among the 75,051 communications, there were 5109 (6.81%) posts, comments, and polls, 6233 (8.31%) reactions, and 63,709 (84.9%) views (lurking). Moreover, 54.9% (3430/6253) of codes applied were social support related, 66.4% (2277/3430) of which were informational (eg, insurance and travel preparation), and 20.4% (699/3430) of which were esteem related (eg, relieving blame). CONCLUSIONS: Designating, training, and incentivizing peer leaders may stimulate content exchange and creation. Social support was a key VPN-T1D deliverable. Although lurking accounted for a high proportion of the overall activity, even those demonstrating this type of passive participation likely derived benefits, given that the network exit rate was low. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): RR2-10.2196/18714.

Sample size re-estimation in Phase 2 dose-finding: Conditional power versus Bayesian predictive power.

Unblinded sample size re-estimation (SSR) is often planned in a clinical trial when there is large uncertainty about the true treatment effect. For Proof-of Concept (PoC) in a Phase II dose finding study, contrast test can be adopted to leverage information from all treatment groups. In this article, we propose two-stage SSR designs using frequentist conditional power (CP) and Bayesian predictive power (PP) for both single and multiple contrast tests. The Bayesian SSR can be implemented under a wide range of prior settings to incorporate different prior knowledge. Taking the adaptivity into account, all type I errors of final analysis in this paper are rigorously protected. Simulation studies are carried out to demonstrate the advantages of unblinded SSR in multi-arm trials.

Association Between Financial Distress with Patient and Caregiver Outcomes in Home-Based Palliative Care: A Secondary Analysis of a Clinical Trial.

BACKGROUND: Serious illness often causes financial hardship for patients and families. Home-based palliative care (HBPC) may partly address this. OBJECTIVE: Describe the prevalence and characteristics of patients and family caregivers with high financial distress at HBPC admission and examine the relationship between financial distress and patient and caregiver outcomes. DESIGN, SETTINGS, AND PARTICIPANTS: Data for this cohort study were drawn from a pragmatic comparative-effectiveness trial testing two models of HBPC in Kaiser Permanente. We included 779 patients and 438 caregivers from January 2019 to January 2020. MEASUREMENTS: Financial distress at admission to HBPC was measured using a global question (0-10-point scale: none=0; mild=1-5; moderate/severe=6+). Patient- (Edmonton Symptom Assessment Scale, distress thermometer, PROMIS-10) and caregiver (Preparedness for Caregiving, Zarit-12 Burden, PROMIS-10)-reported outcomes were measured at baseline and 1 month. Hospital utilization was captured using electronic medical records and claims. Mixed-effects adjusted models assessed survey measures and a proportional hazard competing risk model assessed hospital utilization. RESULTS: Half of the patients reported some level of financial distress with younger patients more likely to have moderate/severe financial distress. Patients with moderate/severe financial distress at HBPC admission reported worse symptoms, general distress, and quality of life (QoL), and caregivers reported worse preparedness, burden, and QoL (all, p<.001). Compared to patients with no financial distress, moderate/severe financial distress patients had more social work contacts, improved symptom burden at 1 month (ESAS total score: -4.39; 95% CI: -7.61, -1.17; p<.01), and no increase in hospital-based utilization (adjusted hazard ratio: 1.11; 95% CI: 0.87-1.40; p=.41); their caregivers had improved PROMIS-10 mental scores (+2.68; 95% CI: 0.20, 5.16; p=.03). No other group differences were evident in the caregiver preparedness, burden, and physical QoL change scores. CONCLUSION: These findings highlight the importance and need for routine assessments of financial distress and for provision of social supports required to help families receiving palliative care services.

Spatial Access to Sexual Health Clinics Measured Through a Novel Accessibility Score in Toronto, Canada.

BACKGROUND: Understanding spatial access to sexual health services will provide the foundation for future resource planning and allocation. The purpose of this study was to evaluate the potential geographic access to sexual health services in Toronto, Canada, by developing a novel accessibility index to sexual health clinics. METHODS: We created an accessibility index using the 2-step floating catchment area method to quantify neighborhood-level access to sexual health clinics. The index assumed mixed modes of urban travel through walking and public transit, as well as through driving, and was estimated at the census tract level. RESULTS: Census tracts were grouped into quantiles by the estimated accessibility score. Census tracts with higher accessibility scores were characterized as those with greater residential instability and lower dependency and ethnic concentration. The downtown core area has all census tracts categorized as medium, high, or very high (average [SD] score, 1.320 [0.312]), whereas the noncore area has 56.98%, 302 of 530 census tracts categorized as medium, high, or very high (average [SD] score, -0.105 [0.960]). CONCLUSIONS: We demonstrated the benefit of using statistical methods to quantify the geographical access to sexual health services and identified neighborhoods with high and low levels of access. Findings from this study present an overview of the level of spatial access to sexual health clinics in Toronto based on clinic locations in 2018 and can be further used to characterize neighborhoods with a lower level of access and inform policy and planning decisions in the city.

Complexes between C-Reactive Protein and Very Low Density Lipoprotein Delay Bacterial Clearance in Sepsis.

C-reactive protein (CRP) can increase up to 1000-fold in blood and form complexes with very low density lipoproteins (VLDL). These complexes are associated with worse outcomes for septic patients, and this suggests a potential pathological role in sepsis. Complex formation is heightened when CRP is over 200 mg/l and levels are associated with the severity of sepsis and blood bacterial culture positivity. Using a mouse bacteremia model, blood bacterial clearance can be delayed by i.v. injection of CRP-VLDL complexes. Complexes are more efficiently taken up by activated U937 cells in vitro and Kupffer cells in vivo than VLDL alone. Both in vitro-generated and naturally occurring CRP-VLDL complexes reduce phagocytosis of bacteria by activated U937 cells. Fcγ and scavenger receptors are involved and a competitive mechanism for clearance of CRP-VLDL complexes and bacteria is demonstrated. Interaction of phosphocholine groups on VLDL with CRP is the major driver for complex formation and phosphocholine can disrupt the complexes to reverse their inhibitory effects on phagocytosis and bacterial clearance. Increased formation of CRP-VLDL complexes is therefore harmful and could be a novel target for therapy in sepsis.

Community perspectives on ideal bacterial STI testing services for gay, bisexual, and other men who have sex with men in Toronto, Canada: a qualitative study.

BACKGROUND: Innovation is needed to produce sustained improvements in bacterial sexually transmitted infections (STI) testing given suboptimal access and uptake among sexually active gay, bisexual or other men who have sex with men (GBM). Yet, the STI testing processes and technologies that best address local testing barriers among GBM in Toronto is unknown. We aimed to explore men's perspectives regarding STI testing services for GBM to identify and prioritize new STI testing interventions in Toronto, Ontario, Canada. METHODS: We conducted four focus groups with twenty-seven GBM in 2017: two with cisgender men living with HIV, one with cisgender HIV-negative men, and one with transgender men. Twenty-seven men participated in the focus groups with 40% 18-30 years of age, 48% self-identifying as white, and the remainder self-identifying as Middle Eastern, Latino/Hispanic, Asian/Pacific Islander, South Asian, First Nations, African/Caribbean/Black, or mixed race. 59% of participants self-identified as living with HIV. Participants were asked about their STI testing experiences in Toronto, barriers and facilitators to testing, and ideal STI testing process. Focus groups were audio recorded, transcribed verbatim, and analyzed using thematic analysis. RESULTS: Core concepts included how clinical context, bacterial STI testing delivery, and interactions with healthcare providers can create barriers and recommendations for ways to improve. Regarding clinical context, participants desired more clinics with accessible locations/hours; streamlined testing that minimized use of waiting rooms and wait times; and improved clinic ambience. Bacterial STI testing delivery recommendations included standardization to ensure consistency in sexual history intake, tests offered, follow-up and public health reporting between clinics. Men also recommended reducing the multistep process testing by offering components such as lab requisitions and results online. Participants also recommended interactions with healthcare providers be professional and non-judgmental, offer compassionate and competent care with destigmatizing and lesbian, gay, bisexual and trans (LGBT) affirming communication. CONCLUSION: Concrete and practical solutions for improving existing sexual health services and facilitating optimal STI testing include streamlining testing options and providing patient-centred, LGBT-affirming care to enable optimal STI testing.

A Selective Fluorogenic Peptide Substrate for the Human Mitochondrial ATP-Dependent Protease Complex ClpXP.

The goal of this work is to identify differences in the substrate determinants of two human mitochondrial matrix ATP-dependent proteases, human ClpXP (hClpXP) and human Lon (hLon). This information allows the generation of protease-specific peptide substrates that can be used as chemical biology tools to investigate the physiological functions of hClpXP. These enzymes play a role in protein quality control, but currently the physiological functions of human ClpXP are not well defined. In this study, the degradation profile of casein, an alanine positional scanning decapeptide library, and a specific peptide sequence found in an endogenous substrate of bacterial ClpXP by hClpXP as well as hLon were examined. Based on our findings, we generated a specific fluorogenic peptide substrate, FR-Cleptide, for hClpXP with a kcat of 2.44±0.15 s-1 and Km =262±43 µM, respectively. The FR-Cleptide substrate was successfully used to identify a leucine methyl ketone as a potent lead inhibitor, and to detect endogenous hClpXP activity in HeLa cell lysate. We propose that the fluorogenic peptide substrate is a valuable tool for quantitatively monitoring the activity of hClpXP in cell lysate, as well as mechanistic characterization of hClpXP. The peptide-based chemical tools developed in this study will complement the substrates developed for human Lon in aiding the investigation of the physiological functions of the respective protease.

The Central Role and Possible Mechanisms of Bacterial DNAs in Sepsis Development.

The pathological roles of bacterial DNA have been documented many decades ago. Bacterial DNAs are different from mammalian DNAs; the latter are heavily methylated. Mammalian cells have sensors such as TLR-9 to sense the DNAs with nonmethylated CpGs and distinguish them from host DNAs with methylated CpGs. Further investigation has identified many other types of DNA sensors distributed in a variety of cellular compartments. These sensors not only sense foreign DNAs, including bacterial and viral DNAs, but also sense damaged DNAs from the host cells. The major downstream signalling pathways includeTLR-9-MyD88-IKKa-IRF-7/NF-κB pathways to increase IFN/proinflammatory cytokine production, STING-TBK1-IRF3 pathway to increase IFN-beta, and AIM2-ASC-caspas-1 pathway to release IL-1beta. The major outcome is to activate host immune response by inducing cytokine production. In this review, we focus on the roles and potential mechanisms of DNA sensors and downstream pathways in sepsis. Although bacterial DNAs play important roles in sepsis development, bacterial DNAs alone are unable to cause severe disease nor lead to death. Priming animals with bacterial DNAs facilitate other pathological factors, such as LPS and other virulent factors, to induce severe disease and lethality. We also discuss compartmental distribution of DNA sensors and pathological significance as well as the transport of extracellular DNAs into cells. Understanding the roles of DNA sensors and signal pathways will pave the way for novel therapeutic strategies in many diseases, particularly in sepsis.

Spatial-Temporal Epidemiology of the Syphilis Epidemic in Relation to Neighborhood-Level Structural Factors in British Columbia, 2005-2016.

BACKGROUND: Spatial clusters of syphilis have been observed within several jurisdictions globally; however, the degree to which they are predicted by the spatial distributions of gay, bisexual, and other men who have sex with men (GBM) and testing remains unknown. We sought to describe the spatial-temporal epidemiology of infectious syphilis and identify associations between neighborhood-level factors and rates of syphilis, in British Columbia, Canada. METHODS: We used ArcGIS to map infectious syphilis cases among men (2005 to 2016), SaTScan to detect areas with significantly elevated rates of syphilis, and spatial regression to identify associations between neighborhood-level factors and rates of syphilis. RESULTS: Five clusters were identified: a core in downtown Vancouver (incidence rate ratio [IRR], 18.0; 2007-2016), 2 clusters adjacent to the core (IRR, 3.3; 2012-2016; and IRR, 2.2; 2013-2016), 1 cluster east of Vancouver (IRR, 2.1; 2013-2016), and 1 cluster in Victoria (IRR, 4.3; 2015-2016). Epidemic curves were synchronized across cluster and noncluster regions. Neighborhood-level GBM population estimates and testing rates were both associated with syphilis rates; however, the spatial distribution of syphilis was not fully explained by either of these factors. CONCLUSIONS: We identified two novel ecologic correlates of the spatial distribution of infectious syphilis-density of GBM and rates of syphilis testing-and found that these factors partially, though not entirely, explained the spatial distribution of clusters. Residual spatial autocorrelation suggests that greater syphilis testing coverage may be needed and low-barrier GBM-affirming testing should be expanded to regions outside the core.

Evidence of Significant Ceftriaxone and Quinolone Resistance in Cirrhotics with Spontaneous Bacterial Peritonitis.

OBJECTIVES: There are few studies addressing the impact of cephalosporin and quinolone resistance on hospital length of stay and mortality in spontaneous bacterial peritonitis (SBP). We aim to describe the shifting epidemiology of SBP at our institution and its impact on clinical outcomes. METHODS: We performed a single-center retrospective cohort study of all cases of SBP from 2005 to 2015 at a transplant center. Cases were identified using hospital billing data. Patient data were confirmed using the electronic medical record. Univariate and multivariate logistic regression and Cox proportional hazards models were used to identify factors that were associated with prolonged hospital length of stay and reduced survival. Culture-positive cases (N = 56) were compared to culture-negative cases (N = 104). Subpopulation analysis of the culture-positive cases compared ceftriaxone-resistant (N = 25) to ceftriaxone-susceptible (N = 31) cases. RESULTS: We identified 160 cases of SBP (56 culture positive and 104 culture negative; 21 nosocomial, 79 hospital associated, and 60 community acquired). Forty-five percent (N = 25 total, 13 hospital associated and 6 nosocomial) of bacterial isolates were resistant to ceftriaxone, with 37.5% (N = 21) being gram positive, including 8 methicillin-resistant staphylococcus and 6 vancomycin-resistant enterococcus. Multivariate analysis identified hospital-associated SBP, age, alcoholic cirrhosis, and MELD-Na score as variables associated with worse survival (P < 0.05), with a trend toward worse survival in culture-positive cases (P = 0.123). Only MELD-Na was associated with prolonged length of stay. CONCLUSIONS: The burden of resistant pathogens causing SBP is significant, notably in hospital-associated SBP. Culture-positive SBP may represent a higher risk group compared to culture-negative SBP.

The Feasibility of Automating Assessment of Concordance Between Advance Care Preferences and Care Received Near the End of Life.

BACKGROUND: End-of-life care is patient centered when it is concordant with patient preferences. Concordance has been frequently assessed by interview, chart review, or both. These time-consuming methods can constrain sample sizes, precluding population-level quality assessment. Concordance between preferences and care as measured by automated methods is described. METHODS: Automated processes extracted and analyzed electronic health record (EHR) data to assess concordance between 15 advance care planning preference domains and 232 related end-of-life care events for 388 patients aged 65 years or older with an inpatient encounter at Kaiser Permanente Southern California who died during or after the encounter. Patient preferences were recorded in advance directives or physician orders or reflected in hospital code status. Concordance, assessed in relation to the most recent documents, orders, or code status, occurred when patients received care they preferred or did not receive nonpreferred care. Discordance occurred when patients received care they did not prefer or did not receive care they preferred. RESULTS: Overall concordance for 12,592 observed end-of-life care events was 97.7%. A total of 55 of 4,154 (1.3%) received care events were nonpreferred, according to patient preferences in the EHR. Automated methods could not distinguish between medically nonbeneficial treatments, those that were not medically indicated, and potential undertreatment. CONCLUSION: Automating assessment of concordance between care near the end of life and preferences is feasible but requires model refinement and discrete care preference data. Automated methods may be most valuable as a screening tool to identify potential overtreatment and undertreatment, with chart review to verify discordance.

A retrospective evaluation of nutrition support in relation to clinical outcomes in critically ill patients with an open abdomen.

BACKGROUND: Optimising nutrition support in critically ill patients with an open abdomen is challenging. OBJECTIVES: The aims of this study were to (i) quantify the amount and adequacy of nutrition support administered and (ii) determine any relationships that exist between mode of nutrition support delivery and clinical outcomes in critically ill patients with an open abdomen. METHODS: A retrospective review of critically ill patients mechanically ventilated for at least 48 h with an open abdomen in a mixed quaternary referral intensive care unit. Enteral and parenteral nutrition (ml) administered daily to patients was recorded for up to 21 days. Length of stay in the intensive care unit and hospital and duration of mechanical ventilation (days) were reported. RESULTS: Thirty patients were studied [14 male, 68 y (15-90 y), body mass index 25 kg/m2 (11-51 kg/m2), Acute Physiology and Chronic Health Evaluation II score 20 (7-41), energy goal 1860 kcal/d (1250-2712 kcal/d)]. Patients received 55% (0-117%) of energy goal and 56% (0-105%) protein goal from either enteral or parenteral nutrition. When enteral nutrition was delivered alone or in combination with parenteral nutrition, patients received 48% (0-146%) of their energy and 59% (19-105%) of their protein goal. Patients fed parenteral nutrition, either alone or as supplementary to enteral nutrition (n = 18), received more energy when compared with those who only received enteral nutrition (n = 9) [65 (27-117) vs 49 (15-89) % energy goal, P = 0.025]. Parenteral nutrition was associated with an increased length of stay in hospital [63 (45-156) vs 45 (17-93) d, P = 0.037]. CONCLUSION: Patients with an open abdomen receive about half of their nutrition requirements when fed exclusively via the enteral route. Providing combination enteral and parenteral nutrition to reach nutritional goals may not result in better clinical outcomes for patients with an open abdomen.

Cobalamin-dependent radical S-adenosyl-l-methionine enzymes in natural product biosynthesis.

Covering: 2011 to 2018 This highlight summarizes the investigation of cobalamin (Cbl)- and radical S-adenosyl-l-methionine (SAM)-dependent enzymes found in natural product biosynthesis to date and suggests some possibilities for the future. Though some mechanistic aspects are apparently shared, the overall diversity of this family's functions and abilities is significant and may be tailored to the specific substrate and/or reaction being catalyzed. A little over a year ago, the first crystal structure of a Cbl- and radical SAM-dependent enzyme was solved, providing the first insight into what may be the shared scaffolding of these enzymes.

Conceptualizing Geosexual Archetypes: Mapping the Sexual Travels and Egocentric Sexual Networks of Gay and Bisexual Men in Toronto, Canada.

BACKGROUND: There are complex, synergistic, and persistent sexually transmitted infection (STI) epidemics affecting gay, bisexual and other men who have sex with men (gbMSM) in every major urban centre across North America. We explored the spatial architecture of egocentric sexual networks for gbMSM in Toronto, Canada. METHODS: Our integrative mixed methods study included in-depth interviews with 31 gbMSM between May and July 2016. During interviews, participants mapped their egocentric sexual network for the preceding 3 months geographically. At the end, a self-administered survey was used to collect sociodemographic characteristics, online technology use, and STI testing and history. RESULTS: We identified 6 geosexual archetypes: hosters, house-callers, privates, rovers, travellers, and geoflexibles. Hosters always, or almost always (≥80%), hosted sex at their home. House-callers always, or almost always (≥80%), had sex at their partner's home. Rovers always or almost always (≥80%) had sex at public venues (eg, bath houses, sex clubs) and other public spaces (eg, parks, cruising sites). Privates had sex in private-their own home or their partner's (part hoster, part house-caller). Travellers had sex away from their home, either at a partner's home or some other venue or public space (part house-caller, part rover). Geoflexibles had sex in a variety of locations-their home, their partner's home, or public venues. All hosters and rovers, and to a lesser extent, geoflexibles, reported a history of syphilis and human immunodeficiency virus. CONCLUSIONS: Prioritizing interventions to hosters, rovers, and geoflexibles may have an important impact on reducing STI transmission.

Resolution of the uncertainty in the kinetic mechanism for the trans-3-Chloroacrylic acid dehalogenase-catalyzed reaction.

trans- and cis-3-Chloroacrylic acid dehalogenase (CaaD and cis-CaaD, respectively) catalyze the hydrolytic dehalogenation of their respective isomers and represent key steps in the bacterial conversion of 1,3-dichloropropene to acetaldehyde. In prior work, a kinetic mechanism for the CaaD-catalyzed reaction could not be unequivocally determined because (1) the order of product release could not be determined and (2) the fluorescence factor for the enzyme species, E*PQ (where P = bromide and Q = malonate semialdehyde, the two products of the reaction) could not be assigned. The ambiguities in the model have now been resolved by stopped-flow experiments following the reaction using an active site fluorescent probe, αY60W-CaaD and 3-bromopropiolate, previously shown to be a mechanism-based inhibitor of CaaD, coupled with the rate of bromide release in the course of CaaD inactivation. A global fit of the combined datasets provides a complete minimal model for the reaction of αY60W-CaaD and 3-bromoacrylate. In addition, the global fit produces kinetic constants for CaaD inactivation by 3-bromopropiolate and implicates the acyl bromide as the inactivating species. Finally, a comparison of the model with that for cis-CaaD shows that for both enzymes turnover is limited by product release and not chemistry.

Reversibility of neuropathology in Tay-Sachs-related diseases.

The GM2 gangliosidoses are progressive neurodegenerative disorders due to defects in the lysosomal ß-N-acetylhexosaminidase system. Accumulation of ß-hexosaminidases A and B substrates is presumed to cause this fatal condition. An authentic mouse model of Sandhoff disease (SD) with pathological characteristics resembling those noted in infantile GM2 gangliosidosis has been described. We have shown that expression of ß-hexosaminidase by intracranial delivery of recombinant adeno-associated viral vectors to young adult SD mice can prevent many features of the disease and extends lifespan. To investigate the nature of the neurological injury in GM2 gangliosidosis and the extent of its reversibility, we have examined the evolution of disease in the SD mouse; we have moreover explored the effects of gene transfer delivered at key times during the course of the illness. Here we report greatly increased survival only when the therapeutic genes are expressed either before the disease is apparent or during its early manifestations. However, irrespective of when treatment was administered, widespread and abundant expression of ß-hexosaminidase with consequent clearance of glycoconjugates, α-synuclein and ubiquitinated proteins, and abrogation of inflammatory responses and neuronal loss was observed. We also show that defects in myelination occur in early life and cannot be easily resolved when treatment is given to the adult brain. These results indicate that there is a limited temporal opportunity in which function and survival can be improved-but regardless of resolution of the cardinal pathological features of GM2 gangliosidosis, a point is reached when functional deterioration and death cannot be prevented.

ITGB6 loss-of-function mutations cause autosomal recessive amelogenesis imperfecta.

Integrins are cell-surface adhesion receptors that bind to extracellular matrices (ECM) and mediate cell-ECM interactions. Some integrins are known to play critical roles in dental enamel formation. We recruited two Hispanic families with generalized hypoplastic amelogenesis imperfecta (AI). Analysis of whole-exome sequences identified three integrin beta 6 (ITGB6) mutations responsible for their enamel malformations. The female proband of Family 1 was a compound heterozygote with an ITGB6 transition mutation in Exon 4 (g.4545G > A c.427G > A p.Ala143Thr) and an ITGB6 transversion mutation in Exon 6 (g.27415T > A c.825T > A p.His275Gln). The male proband of Family 2 was homozygous for an ITGB6 transition mutation in Exon 11 (g.73664C > T c.1846C > T p.Arg616*) and hemizygous for a transition mutation in Exon 6 of Nance-Horan Syndrome (NHS Xp22.13; g.355444T > C c.1697T > C p.Met566Thr). These are the first disease-causing ITGB6 mutations to be reported. Immunohistochemistry of mouse mandibular incisors localized ITGB6 to the distal membrane of differentiating ameloblasts and pre-ameloblasts, and then ITGB6 appeared to be internalized by secretory stage ameloblasts. ITGB6 expression was strongest in the maturation stage and its localization was associated with ameloblast modulation. Our findings demonstrate that early and late amelogenesis depend upon cell-matrix interactions. Our approach (from knockout mouse phenotype to human disease) demonstrates the power of mouse reverse genetics in mutational analysis of human genetic disorders and attests to the need for a careful dental phenotyping in large-scale knockout mouse projects.

Genetic effects of multiple asthma loci identified by genomewide association studies on asthma and spirometric indices.

BACKGROUND: Genomewide association study (GWAS) published by GABRIEL consortium identified 10 asthma-associated loci. However, their relationship with lung functions is unclear. This study investigated the association between asthma traits and single-nucleotide polymorphisms (SNPs) of these GWAS loci. METHODS: Rs3894194 and rs9273349 were not genotyped due to unavailable TaqMan assays. Genetic associations of remaining eight SNPs were investigated in 903 school-age asthmatics and 1205 non-allergic controls. Four significant SNPs were then replicated in 479 adult asthmatics and 746 adult controls, and 1341 Chinese preschool children. Meta-analyses were performed by combining data from school-age children and adults. Generalized multifactor dimensionality reduction (GMDR) was used to analyze their interactions for asthma traits. RESULTS: Childhood asthma was associated with GSDMB_rs2305480 (odds ratio [OR] 0.69, 95% confidence interval [CI] 0.57-0.83). IL13_rs1295686 was associated with all asthma (OR 1.64, 95% CI 1.16-2.32) and early-onset asthma (OR 1.92, 95% CI 1.20-3.06) in adults, whereas GSDMB_rs2305480 was only associated with early-onset asthma (OR 0.69, 95% CI 0.49-0.96). According to meta-analyses, the minor allele of rs2305480 was inversely associated with FEV1 , FVC, and FEV1 /FVC (p < 0.01). GMDR analyses revealed 2-locus models of SLC22A5 with SMAD3 to modulate FEVt /FVC in both preschool children and adults, with IL13 to determine FVC in both school-age children and adults, and with IL2RB to modulate FEV1 /FVC in school-age children. CONCLUSIONS: IL13 and GSDMB are replicated as asthma genes. Rs2305480 of GSDMB is also associated with low FEV1 , FVC, and FEV1 /FVC among asthmatics. Moreover, SLC22A5, IL13, SMAD3, and GSDMB interact to modulate spirometric indices.