Addressing food insecurity in rural primary care: a mixed-methods evaluation of barriers and facilitators

BACKGROUND

Food insecurity (FI) is associated with negative health outcomes and increased healthcare utilization. Rural populations face increased rates of FI and encounter additional barriers to achieving food security. We sought to identify barriers and facilitators to screening and interventions for FI in rural primary care practices.

METHODS

We conducted a mixed-methods study using surveys and semi-structured interviews of providers and staff members from rural primary care practices in northern New England. Survey data were analyzed descriptively, and thematic analysis was used to identify salient interview themes.

RESULTS

Participants from 24 rural practices completed the survey, and 13 subsequently completed an interview. Most survey respondents (54%) reported their practices systematically screen for FI and 71% reported food needs were "very important" for their patients and communities. Time and resource constraints were the most frequently cited barriers to screening for and addressing FI in practices based on survey results. Interview themes were categorized by screening and intervention procedures, community factors, patient factors, external factors, practice factors, process and implementation factors, and impact of FI screening and interventions. Time and resource constraints were a major theme in interviews, and factors attributed to rural practice settings included geographically large service areas, stigma from loss of privacy in small communities, and availability of food resources through farming.

CONCLUSIONS

Rural primary care practices placed a high value on addressing food needs but faced a variety of barriers to implementing and sustaining FI screening and interventions. Strategies that utilize practice strengths and address time and resource constraints, stigma, and large service areas could promote the adoption of novel interventions to address FI.

Needs for Successful Engagement in Telemedicine Among Rural Older US Veterans and Their Caregivers: Qualitative Study

BACKGROUND

Telemedicine is an important option for rural older adults who often must travel far distances to clinics or forgo essential care. In 2014, the Geriatric Research, Education, and Clinical Centers (GRECC) of the US Veterans Health Administration (VA) established a national telemedicine network called GRECC Connect. This network increased access to geriatric specialty care for the 1.4 million rural VA-enrolled veterans aged 65 years or older. The use of telemedicine skyrocketed during the COVID-19 pandemic, which disproportionately impacted older adults, exacerbating disparities in specialty care access as overburdened systems shut down in-person services. This surge presented a unique opportunity to study the supports necessary for those who would forgo telemedicine if in-person care were available.

OBJECTIVE

In spring 2021, we interviewed veterans and their informal caregivers to (1) elicit their experiences attempting to prepare for a video visit with a GRECC Connect geriatric specialist and (2) explore facilitators and barriers to successful engagement in a telemedicine visit.

METHODS

We conducted a cross-sectional qualitative evaluation with patients and their caregivers who agreed to participate in at least 1 GRECC Connect telemedicine visit in the previous 3 months. A total of 30 participants from 6 geographically diverse GRECC Connect hub sites agreed to participate. Semistructured interviews were conducted through telephone or the VA's videoconference platform for home telemedicine visits (VA Video Connect) per participant preference. We observed challenges and, when needed, provided real-time technical support to facilitate VA Video Connect use for interviews. All interviews were recorded with permission and professionally transcribed. A team of 5 researchers experienced in qualitative research analyzed interview transcripts using rapid qualitative analysis.

RESULTS

From 30 participant interviews, we identified the following 4 categories of supports participants described regarding successful engagement in telemedicine, as defined by visit completion, satisfaction, and willingness to engage in telemedicine in the future: (1) caregiver presence to facilitate technology setup and communication; (2) flexibility in visit modality (eg, video from home or a clinic or telephone); (3) technology support (eg, determining device compatibility or providing instruction and on-demand assistance); and (4) assurance of comfort with web-based communication, including orientation to features like closed captioning. Supports were needed at multiple points before the visit, and participants stressed the importance of eliciting the varying needs and preferences of each patient-caregiver dyad. Though many initially agreed to a telemedicine visit because of pandemic-related clinic closures, participants were satisfied with telemedicine and willing to use it for other types of health care visits.

CONCLUSIONS

To close gaps in telemedicine use among rural older adults, supports must be tailored to individuals, accounting for technology availability and comfort, as well as availability of and need for caregiver involvement. Comprehensive scaffolding of support starts well before the first telemedicine visit.

"Everyone's struggling right now": Impact of COVID-19 on addressing food insecurity in rural primary care

BACKGROUND

Primary care practices can address food insecurity (FI) through routine screening, practice-based food programmes, and referrals to community resources. The COVID-19 pandemic had disproportionate impacts on health outcomes for food-insecure households.

OBJECTIVE

To describe the impact of the COVID-19 pandemic on FI screening and interventions in rural primary care practices in northern New England.

METHODS

We conducted semi-structured interviews with thirteen providers and staff regarding changes to FI screening and interventions, community resources and partnerships, and patient food needs during the pandemic. Themes and exemplar quotations were identified through iterative discussion.

RESULTS

Practices reported more frequent informal discussions with patients about FI during the pandemic. Despite limitations in site operations, practices created programmes to distribute food at practice locations or through food deliveries. The adoption of telemedicine had variable impacts on FI screening, creating challenges for some while facilitating screening outside of scheduled visits for others. Practices reported increased food availability due to new or expanded community programmes, but lack of transportation and delivery availability were challenges. New and stronger connections formed between practices and community partners. Increased awareness of FI among both patients and practice staff resulted in decreased stigma.

CONCLUSION

Screening for and addressing FI was a priority for rural primary care practices during the pandemic. The implementation of practice-based FI interventions was supported by stronger practice-community connections and a decrease in stigma. The experiences of providers and staff during the pandemic provide insight into best practices for engaging primary care practices in reducing FI.

Behavioral Activation: Values-Aligned Activity Engagement as a Transdiagnostic Intervention for Common Geriatric Conditions

Scalable, transdiagnostic interventions are needed to meet the needs of a growing population of older adults experiencing multimorbidity and functional decline. Behavioral activation (BA) is a pragmatic, empirically supported treatment for depression that focuses on increasing engagement in values-aligned activities. We propose BA is an ideal transdiagnostic intervention approach for older adults because it (a) specifically targets activity restriction, a shared characteristic of common conditions of aging; and (b) has strong potential for scalability through delivery by a broad range of clinician and nonclinician interventionists and via telehealth. We describe the history of BA and review recent literature demonstrating impacts beyond depression including on cognition, social isolation, and disability. We also describe the feasibility of delivering BA across interventionists, settings, and modalities. Our approach advances scholarship by proposing BA as a scalable, transdiagnostic behavioral intervention to address functional decline in older adults with common geriatric conditions.

The role of Department of Veterans Affairs community-based outpatient clinics in enhancing rural access to geriatrics telemedicine specialty care

BACKGROUND

Half of the 4.7 M veterans who reside in rural communities and rely on U.S. Department of Veterans Affairs (VA) health care are older (≥65). Their rurality presents unique challenges, including a shortage of clinicians skilled in geriatric medicine. Community-based outpatient clinics (CBOCs) help extend VA's geographic reach but are typically located in under-resourced settings. Telemedicine may increase access to care, but little is known about CBOCs' capacity to leverage telemedicine to meet older patients' needs. We identified organizational barriers and facilitators to the use of geriatric telemedicine specialty care from the perspective of rural clinicians and staff.

METHODS

From February-April 2020, we interviewed CBOC clinicians and staff (N = 50) from 13 rural CBOCs affiliated with four VA Geriatric Research Education and Clinical Centers. Semi-structured interviews addressed patient population characteristics; CBOC location, staffing, and in-house resources; use of VA specialty care services; and telemedicine use. We developed a codebook using an iterative process and Gale's Framework Method thematically organize and analyze data.

RESULTS

Respondents perceived that their CBOCs serve a predominantly older patient population. Four characteristics enabled CBOCs to offer geriatric telemedicine specialty care: partnerships with larger VA Medical Center teams; social worker/telehealth clinical technician knowledge of geriatrics and telehealth resources; periodic outreach/education from geriatric specialists; and routine use of other telehealth services. Barriers included: constraints on clinic space and unstable internet for telemedicine visits; staffing challenges leading to limited familiarity with telemedicine resources; and clinician and staff perceptions of older veterans' preference for in-person visits.

CONCLUSIONS

Telemedicine is an important modality to enhance access to care for an increasingly older and medically complex patient population. Although rural CBOCs provide a large portion of care to VA's growing geriatric population, staff are insufficiently trained in geriatrics, work in resource-poor settings, and are largely unaware of VA telemedicine programs designed to support them.

The Development and Use of a New Visual Tool (REVISIT) to Support Participant Recall: Web-Based Interview Study Among Older Adults

BACKGROUND

Qualitative health services research often relies on semistructured or in-depth interviews to develop a deeper understanding of patient experiences, motivations, and perspectives. The quality of data gathered is contingent upon a patient's recall capacity; yet, studies have shown that recall of medical information is low. Threats to generating rich and detailed interview data may be more prevalent when interviewing older adults.

OBJECTIVE

We developed and studied the feasibility of using a tool, Remembering Healthcare Encounters Visually and Interactively (REVISIT), which has been created to aid the recall of a specific telemedicine encounter to provide health services research teams with a visual tool, to improve qualitative interviews with older adults.

METHODS

The REVISIT visual appointment summary was developed to facilitate web-based interviews with our participants as part of an evaluation of a geriatric telemedicine program. Our primary aims were to aid participant recall, maintain focus on the index visit, and establish a shared understanding of the visit between participants and interviewers. The authors' experiences and observations developing REVISIT and using it during videoconference interviews (N=16) were systematically documented and synthesized. We discuss these experiences with REVISIT and suggest considerations for broader implementation and future research to expand upon this preliminary work.

RESULTS

REVISIT enhanced the interview process by providing a focus and catalyst for discussion and supporting rapport-building with participants. REVISIT appeared to support older patients' and caregivers' recollection of a clinical visit, helping them to share additional details about their experience. REVISIT was difficult to read for some participants, however, and could not be used for phone interviews.

CONCLUSIONS

REVISIT is a promising tool to enhance the quality of data collected during interviews with older, rural adults and caregivers about a health care encounter. This novel tool may aid recall of health care experiences for those groups for whom it may be more challenging to collect accurate, rich qualitative data (eg, those with cognitive impairment or complex medical care), allowing health services research to include more diverse patient experiences.

Implementing a Social Needs Screening and Referral Program Among Veterans: Assessing Circumstances & Offering Resources for Needs (ACORN)

BACKGROUND

The Department of Veterans Affairs (VA) healthcare system routinely screens Veterans for food insecurity, housing instability, and intimate partner violence, but does not systematically screen for other health-related social needs (HRSNs).

OBJECTIVES

To (1) develop a process for systematically identifying and addressing Veterans' HRSNs, (2) determine reported prevalence of HRSNs, and (3) assess the acceptability of HRSN screening among Veterans.

DESIGN

"Assessing Circumstances and Offering Resources for Needs" (ACORN) is a Veteran-tailored HRSN screening and referral quality improvement initiative. Veterans were screened via electronic tablet for nine HRSNs (food, housing, utilities, transportation, legal needs, social isolation, interpersonal violence, employment, and education) and provided geographically tailored resource guides for identified needs. Two-week follow-up interviews with a purposive sample of Veterans explored screening experiences.

PARTICIPANTS

Convenience sample of Veterans presenting for primary care at a VA urban women's health clinic and suburban community-based outpatient clinic (October 2019-May 2020).

MAIN MEASURES

Primary outcomes included prevalence of HRSNs, Veteran-reported acceptability of screening, and use of resources guides. Data were analyzed using descriptive statistics, chi-square tests, and rapid qualitative analysis.

KEY RESULTS

Of 268 Veterans screened, 50% reported one or more HRSNs. Social isolation was endorsed most frequently (29%), followed by educational needs (19%), interpersonal violence (12%), housing instability (9%), and utility concerns (7%). One in five Veterans reported at least one form of material hardship. In follow-up interviews (n = 15), Veterans found screening acceptable and felt VA should continue screening. No Veterans interviewed had contacted recommended resources at two-week follow-up, although several planned to use resource guides in the future.

CONCLUSION

In a VA HRSN screening and referral program, Veterans frequently reported HRSNs, felt screening was important, and thought VA should continue to screen for these needs. Screening for HRSNs is a critical step towards connecting patients with services, identifying gaps in service delivery, and informing future resource allocation.

An ecological and epidemiological single-season survey of Anaplasma and Ehrlichia positive ticks in Victoria Falls National Park, Zimbabwe

There is an urgent need for continued research on the ecology of tick-borne diseases in Africa. Our objective was to provide a preliminary description of the ecology and epidemiology of tick species, tick-borne pathogens, and animal hosts in Zimbabwe, focusing efforts at Victoria Falls National Park, for a single season. We tested the hypothesis that tick surveillance and pathogen screening data can be used to model associations among ticks, hosts, and pathogens. We collected ticks from domesticated animals and wildlife in Zimbabwe and screened the ticks for the presence of Anaplasma and Ehrlichia bacteria. Nearly 30% of the screened ticks were PCR-positive; 89% of tick species were PCR-positive, and 88% of animal species carried at least one PCR-positive tick. We sequenced a subset of amplicons that were similar to three Anaplasma species and three Ehrlichia species. The odds of a tick being PCR-positive increased when many ticks were collected from the host or the tick was collected from a cow (domesticated animal). Tick species shared host species more often than expected. We demonstrate that ticks in northwestern Zimbabwe present a One Health problem for nearby wildlife and humans.

Integrating CFIR-ERIC and e-Delphi Methods to Increase Telegeriatrics Uptake

BACKGROUND AND OBJECTIVES

Participatory implementation methods are needed in geriatric health care to improve care and services for a growing population of older adults. We describe an efficient participatory approach to improve uptake of Geriatric Research Education and Clinical Center (GRECC) Connect, a national geriatrics outpatient consultation service using telehealth technology to connect geriatric specialists to rural, older veterans though community-based clinics.

RESEARCH DESIGN AND METHODS

We designed a three-phase participatory method to identify high-priority implementation strategies to support the uptake of GRECC Connect. We used the Consolidated Framework for Implementation Research-Expert Recommendations for Implementing Change (CFIR-ERIC) Strategy Matching Tool to derive expert-recommended implementation strategies informed by qualitative interviews with both GRECC Connect staff and clinicians at community-based clinics. We engaged expert panelists in a participatory two-step modified e-Delphi process using confidential surveys and discussion to prioritize strategies nationally.

RESULTS

Qualitative interviews revealed barriers, facilitators, and recommendations for program uptake. Many strategies recommended by CFIR-ERIC addressed multiple barriers but needed to be tailored to our specific context. In our two-step e-Delphi process, expert panelists shared previous experience with the strategies presented, views on the importance and feasibility of each, and arrived at a consensus about which strategies to prioritize nationally.

DISCUSSION AND IMPLICATIONS

We demonstrate the feasibility and benefits of engaging subject matter experts to identify strategies to be tested on a national level. Future considerations include weighting of survey responses, accounting for regional differences, and sensitivity of Likert scales used in the e-Delphi process.

Perceived benefits of geriatric specialty telemedicine among rural patients and caregivers

OBJECTIVE

Explore the perceived benefits of a Veterans Health Administration (VHA) geriatric specialty telemedicine service (GRECC Connect) among rural, older patients and caregivers to contribute to an assessment of its quality and value.

DATA SOURCES

In Spring 2021, we interviewed a geographically diverse sample of rural, older patients and their caregivers who participated in GRECC Connect telemedicine visits.

STUDY DESIGN

A cross-sectional qualitative study focused on patient and caregiver experiences with telemedicine, including perceived benefits and challenges.

DATA COLLECTION

We conducted 30 semi-structured qualitative interviews with rural, older (≥65) patients enrolled in the VHA and their caregivers via videoconference or phone. Interviews were recorded, transcribed, and analyzed using a rapid qualitative analysis approach.

PRINCIPAL FINDINGS

Participants described geriatric specialty telemedicine visits focused on cognitive assessments, tailored physical therapy, medication management, education on disease progression, support for managing multiple comorbidities, and suggestions to improve physical functioning. Participants reported that, in addition to prescribing medications and ordering tests, clinicians expedited referrals, coordinated care, and listened to and validated both patient and caregiver concerns. Perceived benefits included improved patient health; increased patient and caregiver understanding and confidence around symptom management; and greater feelings of empowerment, hopefulness, and support. Challenges included difficulty accessing some recommended programs and services, uncertainty related to instructions or follow-up, and not receiving as much information or treatment as desired. The content of visits was well aligned with the domains of the Age-Friendly Health Systems and Geriatric 5Ms frameworks (Medication, Mentation, Mobility, what Matters most, and Multi-complexity).

CONCLUSIONS

Alignment of patient and caregiver experiences with widely-used models of comprehensive geriatric care indicates that high-quality geriatric care can be provided through virtual modalities. Additional work is needed to develop strategies to address challenges and optimize and expand access to geriatric specialty telemedicine.

The effects of loneliness and psychological flexibility on veterans' substance use and physical and mental health functioning during the COVID-19 pandemic

During the COVID-19 pandemic, social isolation was a common experience as people were trying to keep themselves and others safe from infection. Veterans with problematic substance use are at particular risk of the consequences of social isolation. This study evaluated the nature of social interactions during the COVID-19 pandemic and the effects of loneliness and psychological flexibility on self-reported substance use and physical and mental health functioning among U.S. veterans who reported problematic substance use. Data from 409 veterans with self-reported substance use concerns were obtained via a cross-sectional online survey. Results showed that many veterans who engaged in problematic substance use during the COVID-19 pandemic reported a number of social supports during this period and frequent communication with others, but still felt lonelier during the pandemic. In regression analyses, higher levels of loneliness were associated with more negative impacts of the pandemic, greater substance use, and poorer physical and mental health functioning. Psychological flexibility demonstrated significant unique variance in explaining mental health functioning during the pandemic after accounting for loneliness, but not for substance use or physical functioning. For veterans with high levels of loneliness, high levels of psychological flexibility were associated with a lower negative impact on quality of life due to the pandemic, but for veterans with low levels of loneliness, differing levels of psychological flexibility were not significantly associated with the negative impact of COVID-19. Overall, loneliness and psychological flexibility appear to be highly associated with the negative impact of COVID-19 on veterans with problematic substance use.

Missed opportunities to improve food security for pregnant people: a qualitative study of prenatal care settings in Northern New England during the COVID-19 pandemic

Background

Food insecurity during pregnancy has important implications for maternal and newborn health. There is increasing commitment to screening for social needs within health care settings. However, little is known about current screening processes or the capacity for prenatal care clinics to address food insecurity among their patients. We aimed to assess barriers and facilitators prenatal care clinics face in addressing food insecurity among pregnant people and to identify opportunities to improve food security among this population.

Methods

We conducted a qualitative study among prenatal care clinics in New Hampshire and Vermont. Staff and clinicians engaged in food security screening and intervention processes at clinics affiliated with the Northern New England Perinatal Quality Improvement Network (NNEPQIN) were recruited to participate in key informant interviews. Thematic analysis was used to identify prominent themes in the interview data.

Results

Nine staff members or clinicians were enrolled and participated in key informant interviews. Key barriers to food security screening and interventions included lack of protocols and dedicated staff at the clinic as well as community factors such as availability of food distribution services and transportation. Facilitators of screening and intervention included a supportive culture at the clinic, trusting relationships between patients and clinicians, and availability of clinic-based and community resources.

Conclusion

Prenatal care settings present an important opportunity to identify and address food insecurity among pregnant people, yet most practices lack specific protocols for screening. Our findings indicate that more systematic processes for screening and referrals, dedicated staff, and onsite food programs that address transportation and other access barriers could improve the capacity of prenatal care clinics to improve food security during pregnancy.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40795-022-00499-7.

The Impact of the COVID-19 Pandemic on Food Insecurity in Northern New England Primary and Prenatal Care Settings

INTRODUCTION AND OBJECTIVE

Food insecurity (FI) is associated with adverse health outcomes across the lifespan. Primary care and prenatal practices can identify and address FI among patients through screening and interventions. It is unclear how practices and communities responded to FI during the COVID-19 pandemic, and how the pandemic may have impacted practices' FI strategies. We aimed to understand how practices providing primary care or prenatal care in northern New England experienced changes in FI during the COVID-19 pandemic.

METHODS

We conducted a web-based survey of clinicians and staff from 43 unique practices providing primary care or prenatal care in northern New England.

RESULTS

Most practices (59.5%) reported at least 1 new food program in the practice or community since the pandemic began. Practices reporting new practice- or community-based food programs were more likely to be rural, federally qualified health centers, and have greater confidence in practice and community capacity to address FI (chi-square tests, P < .05).

CONCLUSION

Results suggest that practices and surrounding communities in northern New England responded to FI during the pandemic by increasing food support programs. Future work is needed to examine the impact of food programs initiated during the pandemic and determine optimal strategies for practices to address FI among patients.

Adaptation of a social risk screening and referral initiative across clinical populations, settings, and contexts in the Department of Veterans Affairs Health System

Identifying and addressing social risks and social needs in healthcare settings is an important step towards achieving health equity. Assessing Circumstances and Offering Resources for Needs (ACORN) is a Department of Veterans Affairs (VA) social risk screening and referral model that aims to systematically identify and address social needs. Since initial piloting in 2018, our team has collaborated with clinical and operations partners to implement ACORN across multiple VA clinical settings while adapting and tailoring the initiative to meet the needs of different populations, specialties, and individuals administering screening. Given ACORN's complexity as a growing initiative with multiple partners and frequent real-time modifications within a large national healthcare system, we recognized a need to systematically document the rationale and process of adaptations over time. We looked to three implementation frameworks-RE-AIM, the Adaptome, and FRAME-to describe the rationale for adaptations, the nature of and context within which adaptations were made, and the details of each adaptation. In this manuscript, we uniquely interweave these three frameworks to document adaptations to ACORN across diverse VA clinical settings, with a focus on how adaptations support the promotion of heath equity in the Veteran population.

Community health worker interventions for older adults with complex health needs: A systematic review

BACKGROUND/OBJECTIVES

The number of older adults with complex health needs is growing, and this population experiences disproportionate morbidity and mortality. Interventions led by community health workers (CHWs) can improve clinical outcomes in the general adult population with multimorbidity, but few studies have investigated CHW-delivered interventions in older adults.

DESIGN

We systematically reviewed the impact of CHW interventions on health outcomes among older adults with complex health needs. We searched for English-language articles from database inception through April 2020 using seven databases. PROSPERO protocol registration CRD42019118761.

SETTING

Any U.S. or international setting, including clinical and community-based settings.

PARTICIPANTS

Adults aged 60 years or older with complex health needs, defined in this review as multimorbidity, frailty, disability, or high-utilization.

INTERVENTIONS

Interventions led by a CHW or similar role consistent with the American Public Health Association's definition of CHWs.

MEASUREMENTS

Pre-defined health outcomes (chronic disease measures, general health measures, treatment adherence, quality of life, or functional measures) as well as qualitative findings.

RESULTS

Of 5671 unique records, nine studies met eligibility criteria, including four randomized controlled trials, three quasi-experimental studies, and two qualitative studies. Target population and intervention characteristics were variable, and studies were generally of low-to-moderate methodological quality. Outcomes included mood, functional status and disability, social support, well-being and quality of life, medication knowledge, and certain health conditions (e.g., falls, cognition). Results were mixed with several studies demonstrating significant effects on mood and function, including one high-quality RCT, while others noted no significant intervention effects on outcomes.

CONCLUSION

CHW-led interventions may have benefit for older adults with complex health needs, but additional high-quality studies are needed to definitively determine the effectiveness of CHW interventions in this population. Integration of CHWs into geriatric clinical settings may be a strategy to deliver evidence-based interventions and improve clinical outcomes in complex older adults.

Mind, Mood, Mobility: Supporting Independence Among Rural Older Adults at Risk for Functional Decline

Rural communities need access to effective interventions that can prevent functional decline among a growing population of older adults. We describe the conceptual framework and rationale for a multicomponent intervention ("Mind, Mood, Mobility") delivered by Area Agency on Aging staff for rural older adults at risk for functional decline due to early impairments in cognition, mood, or mobility. Our proposed model utilizes primary care to identify at-risk older adults, combines evidence-based interventions that address multiple risk factors simultaneously, and leverages a community-based aging services workforce for intervention delivery.

A proof-of-principle study of the short-term effects of 3,4-methylenedioxymethamphetamine (MDMA) on tinnitus and neural connectivity

Background: This study was conducted to investigate the short-term behavioural and neurophysiological effects of 3,4-methylenedioxymethamphetamine (MDMA) on tinnitus perception.Methods: A double-blind randomized controlled cross-over design. Part 1. Behavioural measures of tinnitus following 30 mg MDMA or placebo administration (N = 5 participants) and Part 2. Behavioural measures of tinnitus and correlations between pairs of apriori regions of interest (ROI) using resting-state functional magnetic resonance imaging (rs-fMRI) before and after 70 mg of MDMA or placebo (N = 8 participants).Results: The results to MDMA were similar to placebo. For the 70 mg dose, there was a significant reduction after 4 h in annoyance and ignore ratings. RsMRI showed decreased connectivity compared with placebo administration between the left hippocampal, right hippocampal, left amygdala and right amygdala regions, and between the right posterior parahippocampal cortex and the left amygdala after two hours of 70 mg MDMA administration. Increased connectivity compared to placebo administration was found post MDMA between the right post-central gyrus and right posterior and superior temporal gyrus, and between the thalamus and frontoparietal network.Conclusions: Following 70 mg of MDMA two tinnitus rating scales significantly improved. There was, however, a placebo effect. Compared with placebo the rsMRI following the MDMA showed reductions in connectivity between the amygdala, hippocampus and parahippocampal gyrus. There is sufficient proof of concept to support future investigation of MDMA as a treatment for tinnitus.

Nanopore sequencing of the glucocerebrosidase (GBA) gene in a New Zealand Parkinson's disease cohort

INTRODUCTION

Bi-allelic mutations in the gene for glucocerebrosidase (GBA) cause Gaucher disease, an autosomal recessive lysosomal storage disorder. Gaucher disease causing GBA mutations in the heterozygous state are also high risk factors for Parkinson's disease (PD). GBA analysis is challenging due to a related pseudogene and structural variations (SVs) that can occur at this locus. We have applied and refined a recently developed nanopore DNA sequencing method to analyze GBA variants in a clinically assessed New Zealand longitudinal cohort of PD.

METHOD

We examined amplicons encompassing the coding region of GBA (8.9 kb) from 229 PD cases and 50 healthy controls using the GridION nanopore sequencing platform, and Sanger validation.

RESULTS

We detected 23 variants in 21 PD cases (9.2% of patients). We detected modest PD risk variant p.N409S (rs76763715) in one case, p.E365K (rs2230288) in 12 cases, and p.T408 M (rs75548401) in seven cases, one of whom also had p.E365K. We additionally detected the possible risk variants p.R78C (rs146774384) in one case, p.D179H (rs147138516) in one case which occurred on the same haplotype as p.E365K, and one novel variant c.335C > T or p.(L335 = ), that potentially impacts splicing of GBA transcripts. Additionally, we found a higher prevalence of dementia among patients with GBA variants.

CONCLUSION

This work confirmed the utility of nanopore sequencing as a high-throughput method to identify known and novel GBA variants, and to assign precise haplotypes. Our observations may contribute to improved understanding of the effects of variants on disease pathogenesis, and to the development of more targeted treatments.

Effectiveness of Ambulatory Telemedicine Care in Older Adults: A Systematic Review

BACKGROUND

Disparities in healthcare access and delivery, caused by transportation and health workforce difficulties, negatively impact individuals living in rural areas. These challenges are especially prominent in older adults.

DESIGN

We systematically evaluated the feasibility, acceptability, and effectiveness in providing telemedicine (TMed), searching the English-language literature for studies (January 2012 to July 2018) in the following databases: Medline (PubMed); Cochrane Library (Wiley); Web of Science; CINAHL; EMBASE (Ovid); and PsycINFO (EBSCO).

PARTICIPANTS

Older adults (mean age = 65 years or older, and none were younger than 60 years).

INTERVENTIONS

Interventions consisted of live, synchronous, two-way videoconferencing communication in nonhospital settings. All medical interventions were included.

MEASUREMENTS

Quality assessment, using the Cochrane Collaboration's Risk-of-Bias Tool, was applied on all included articles, including a qualitative summary of all articles.

RESULTS

Of 6616 citations, we reviewed the full text of 1173 articles, excluding 1047 that did not meet criteria. Of the 17 randomized controlled trials, the United States was the country with the most trials (6 [35%]), with cohort sizes ranging from 3 to 844 (median = 35) participants. Risk of bias among included studies varied from low to high. Our qualitative analysis suggests that TMed can improve health outcomes in older adults and that it could be used in this population.

CONCLUSIONS

TMed is feasible and acceptable in delivering care to older adults. Research should focus on well-designed randomized trials to overcome the high degree of bias observed in our synthesis. Clinicians should consider using TMed in routine practice to overcome barriers of distance and access to care. J Am Geriatr Soc 67:1737-1749, 2019.

Prevalence and significance of CYP2C19*2 and CYP2C19*17 alleles in a New Zealand acute coronary syndrome population

BACKGROUND

High on-treatment platelet reactivity has been associated with poor outcomes following acute coronary syndromes (ACS). Both the loss of function CYP2C19*2 allele and the gain of function CYP2C19*17 allele along with a range of clinical characteristics have been associated with variation in the response to clopidogrel.

AIM

The study aims to examine the frequency of CYP2C19 variants and understand the factors associated with on-treatment platelet reactivity in a New Zealand ACS population.

METHODS

We prospectively enrolled 312 ACS patients. We collected clinical characteristics and measured on-treatment platelet reactivity using two validated point-of-care assays, VerifyNow and Multiplate. DNA was extracted and CYP2C19*2 and *17 alleles were identified using real-time polymerase chain reaction.

RESULTS

CYP2C19*2 or CYP2C19*17 alleles were observed in 101 (32%) and 106 (34%) of patients, respectively, with significant differences in distribution by ethnicity. In Maori and Pacific Island patients, 47% (confidence interval (CI) 31-63%) had CYP2C19*2 and 11% (CI 4-19%) CYP2C19*17 compared with 26% (CI 19-32%) and 41% (CI 32-49%) in white people. Carriage of CYP2C19*2 alleles was associated with higher levels of platelet reactivity measured by either assay, but we observed no relationship between platelet reactivity and CYP2C19*17. In multivariate analysis diabetes, clopidogrel dose and CYP2C19*2 status were all significant independent predictors of platelet reactivity.

CONCLUSIONS

Both CYP2C19*2 and *17 were common in a New Zealand ACS population, with CYP2C19*2 observed in almost half the Maori and Pacific Island patients. CYP2C19*2, diabetes and clopidogrel dose were independent contributors to on-treatment platelet reactivity.

Extensive variation at MHC DRB in the New Zealand sea lion (Phocarctos hookeri) provides evidence for balancing selection

Marine mammals are often reported to possess reduced variation of major histocompatibility complex (MHC) genes compared with their terrestrial counterparts. We evaluated diversity at two MHC class II B genes, DQB and DRB, in the New Zealand sea lion (Phocarctos hookeri, NZSL) a species that has suffered high mortality owing to bacterial epizootics, using Sanger sequencing and haplotype reconstruction, together with next-generation sequencing. Despite this species' prolonged history of small population size and highly restricted distribution, we demonstrate extensive diversity at MHC DRB with 26 alleles, whereas MHC DQB is dimorphic. We identify four DRB codons, predicted to be involved in antigen binding, that are evolving under adaptive evolution. Our data suggest diversity at DRB may be maintained by balancing selection, consistent with the role of this locus as an antigen-binding region and the species' recent history of mass mortality during a series of bacterial epizootics. Phylogenetic analyses of DQB and DRB sequences from pinnipeds and other carnivores revealed significant allelic diversity, but little phylogenetic depth or structure among pinniped alleles; thus, we could neither confirm nor refute the possibility of trans-species polymorphism in this group. The phylogenetic pattern observed however, suggests some significant evolutionary constraint on these loci in the recent past, with the pattern consistent with that expected following an epizootic event. These data may help further elucidate some of the genetic factors underlying the unusually high susceptibility to bacterial infection of the threatened NZSL, and help us to better understand the extent and pattern of MHC diversity in pinnipeds.

Current State and Future Prospects of Direct-to-Consumer Pharmacogenetics

Direct-to-consumer (DTC) DNA testing has grown from contentious beginnings into a global industry, by providing a wide range of personal genomic information directly to its clients. These companies, typified by the well-established 23andMe, generally carry out a gene-chip analysis of single-nucleotide polymorphisms (SNPs) using DNA extracted from a saliva sample. These genetic data are then assimilated and provided direct to the client, with varying degrees of interpretation. Although much debate has focused on the limitations and ethical aspects of providing genotypes for disease risk alleles, the provision of pharmacogenetic results by DTC companies is less studied. We set out to evaluate current DTC pharmacogenetics offerings, and then to consider how these services might best evolve and adapt in order to play a potentially useful future role in delivery of personalized medicine.

A polymorphism of the GTP-cyclohydrolase I feedback regulator gene alters transcriptional activity and may affect response to SSRI antidepressants

Tetrahydrobiopterin (BH(4)) is an essential cofactor for synthesis of many neurotransmitters including serotonin. In serotonergic neurons, BH(4) is tightly regulated by GTP-cyclohydrolase I feedback regulator (GFRP). Given the pivotal role of the serotonergic system in mood disorders and selective serotonin reuptake inhibitors (SSRIs) antidepressant function, we tested the hypothesis that GFRP gene (GCHFR) variants would modify response to antidepressants in subjects with major depression. Two single nucleotide polymorphisms (rs7164342 and rs7163862) in the GCHFR promoter were identified and occurred as two haplotypes (GA or TT). A multiple regression analysis revealed that homozygous individuals for the TT haplotype were less likely to respond to the SSRI fluoxetine than to the tricyclic antidepressant nortriptyline (P = 0.037). Moreover, the TT haplotype showed a reduced transcription rate in luciferase reporter gene assays, which may impact on BH(4)-mediated neurotransmitter production, thus suggesting a biological process through which GCHFR promoter variants might influence antidepressant response.

Proteomic analysis of rat hippocampus exposed to the antidepressant paroxetine

Antidepressant drugs can exert significant effects on the mood of a patient suffering major depression and other disorders. These drugs generally have pharmacological actions on the uptake or metabolism of the neurotransmitters serotonin, noradrenaline and, to a lesser extent, dopamine. However, there are many aspects of antidepressant action we do not understand. We have applied proteomic analysis in a rat hippocampal model in an attempt to identify relevant molecules that operate in pathways functionally relevant to antidepressant action. Rats were administered either 5 mg/kg daily of the antidepressant paroxetine or vehicle for 12 days, then hippocampal protein was recovered and resolved by 2-D gel electrophoresis. After antidepressant exposure, we observed increased expression or modification of cytochrome c oxidase, subunit Va, cyclin-dependent kinase inhibitor 2A interacting protein, dynein, axonemal, heavy polypeptide 3 and RHO GDP-dissociation inhibitor alpha. Decreased expression or modification was observed for complexin 1 (CPLX1), alpha-synuclein, parvalbumin, ribosomal protein large P2, prohibitin, nerve growth factor, beta subunit (NGFB), peroxiredoxin 6 (PRDX6), 1-acylglycerol-3-phosphate O-acyltransferase 2_predicted, cystatin B (CYTB) and lysosomal membrane glycoprotein 1. CPLX1, the most strongly regulated protein observed, mediates the fusion of cellular transport vesicles with their target membranes and has been implicated in the pathophysiology of mood disorders, as well as antidepressant action. CPLX1 and the other proteins identified may represent links into molecular processes of importance to mood dysregulation and control, and their respective genes may represent novel candidates for studies of antidepressant pharmacogenetics.

Upstream genetic variant near INSIG2, influences response to carnitine supplementation in bipolar patients with valproate-induced weight gain

BACKGROUND

The protein product of INSIG2 is involved in cholesterol and triglyceride metabolism and homeostasis. Variation at rs7566605 near the gene INSIG2 has been associated with increased BMI.

OBJECTIVE

To evaluate the effect of rs7566605/INSIG2 genotype on the ability of valproate-treated bipolar patients (BMI ≥ 25 kg/m2) to lose weight using carnitine supplementation during a 26-week lifestyle intervention study.

DESIGN

Forty-eight bipolar patients with clinically significant treatment emergent weight gain were genotyped at the rs7566605 SNP. Participants were randomised to l-carnitine (15 mg/kg/day) or placebo for 26 weeks in conjunction with a moderately energy restricted, low-fat diet. Weight and body fat percent were measured fortnightly. Waist circumference measurements and dual-energy X-ray absorptiometry were used to assess changes in body composition. Obesity-related biomarkers were measured at baseline and 26 weeks.

RESULTS

There was a significant interaction between rs7566605/INSIG2 genetic status and treatment with carnitine or placebo. Carnitine had no significant effect on body composition measures in G allele homozygous patients who lost between 0.97 and 2.23 kg of fat. However C allele carriers on average gained 2.28 kg when given a placebo. Carnitine supplementation in this group enabled average weight loss of 2.22 kg of fat (p = 0.01). Approximately half of this mass was in the vital truncal compartment (p = 0.002). Bioinformatic analysis detected that the SNP lies in a highly conserved 336 bp sequence which potentially affects INSIG2 gene expression.

CONCLUSIONS

C-carriers at rs7566605, possibly regulating the homeostasis gene INSIG2, lost significantly less weight in this lifestyle intervention study. This effect was reversed by carnitine supplementation.

Improvement of the duty cycle of an orthogonal acceleration time-of-flight mass spectrometer using ion gates

A method to control the duty cycle of a time-of-flight mass spectrometer is described. The method relies on one or more ion gates placed in the beam path that have the function to transmit or stop the beam. These ion gates can switch from the open state to the closed state in tens of nanoseconds and effectively select portions of the mass range. The method is useful in circumstances where recording the complete mass spectrum is not an essential requirement, for example, in the analysis of known compounds where sensitivity and speed of operation are more important. It will be of benefit for applications in separation sciences with techniques involving fast chromatographic separations, where hundreds of mass spectra may be required per second. In such circumstances analytical identification may require only a limited number of masses (or mass regions) to be continuously monitored. Improvement of the duty cycle is particularly important for orthogonal-acceleration time-of-flight (oa-TOF) mass spectrometry instruments whose performance suffers from a low duty cycle. The duty cycle is not a constant for an instrument design but is a mass-dependent function and is least for smaller masses. The method described here is capable of raising the duty cycle to 100%. A theory is developed for one or more ion gate arrangements, for both linear- and reflectron-TOF systems. For a two-gate system the relationship between the positions of the first and second gates is described by a '2/3 rule'. Experimental results are shown for one-gate and two-gate operation, both in linear and in reflectron modes of operation, on an oa-TOF system built in-house.

IMPDH1 promoter mutations in a patient exhibiting azathioprine resistance

Around 9% of inflammatory bowel disease (IBD) patients are resistant to azathioprine. We hypothesized that these patients may carry mutations within inosine-5'-monophosphate dehydrogenase (IMPDH). To test this hypothesis, we screened 20 azathioprine-resistant patients for variations in the two IMPDH genes (IMPDH1 and IMPDH2) using dHPLC and DNA sequencing. A 9 bp insertion within the IMPDH1 P3 promoter was found in a patient exhibiting severe azathioprine resistance. The insertion is predicted to abolish a cAMP-response element (CRE) and was found to significantly reduce IMPDH1 P3 promoter activity in a luciferase reporter gene assay (P-value <0.001). This in vitro assay suggests the variant promoter has altered function in vivo and consequently may have contributed to the thiopurine resistance observed in this patient. The absence of functional variants within the other patients indicates that if IMPDH genetic variability contributes to azathioprine resistance it does so infrequently.

Glycosylphosphatidylinositol-specific phospholipase D immunoreactivity is present in islet amyloid in type 2 diabetes

Numerous apolipoproteins associate with amyloid plaques. A minor high-density lipoprotein-associated protein, glycosylphosphatidylinositol-specific phospholipase D (GPI-PLD), has recently been described by the authors and others. Since GPI-PLD is synthesized by, and secreted from, pancreatic islet beta cells, the present study examined the hypothesis that GPI-PLD associates with islet amyloid. GPI-PLD immunoreactivity was examined in pancreatic tissues from type 2 diabetic and non-diabetic humans. GPI-PLD binding to heparan sulphate proteoglycan was determined in the absence or presence of heparan sulphate or heparin. Fibril formation from human islet amyloid polypeptide was determined in the absence or presence of GPI-PLD. In non-diabetics, GPI-PLD immunoreactivity was present and co-localized with insulin, as opposed to co-localizing with amyloid in diabetics. No immunoreactivity for apolipoprotein A-I was present in islet cells or islet amyloid. Heparan sulphate proteoglycan, which is commonly present in most amyloid, bound GPI-PLD in vitro. GPI-PLD inhibited the formation of amyloid fibrils from synthetic islet amyloid polypeptide in vitro. GPI-PLD is therefore present in islet amyloid and appears to derive from local production from islets. This localization likely derives from interaction between GPI-PLD and heparan sulphate proteoglycan. Since GPI-PLD also inhibited islet amyloid polypeptide fibril formation in vitro, it is concluded that GPI-PLD may play a role in islet amyloid formation in type 2 diabetes.

NMR structure determination and structure-based functional characterization of conserved hypothetical protein MTH1175 from Methanobacterium thermoautotrophicum

The solution structure of MTH1175, a 124-residue protein from the archaeon Methanobacterium thermoautotrophicum has been determined by NMR spectroscopy. MTH1175 is part of a family of conserved hypothetical proteins (COG1433) with unknown functions which contains multiple paralogs from all complete archaeal genomes and the archaeal gene-rich bacterium Thermotoga maritima. Sequence similarity indicates this protein family may be related to the nitrogen fixation proteins NifB and NifX. MTH1175 adopts an alpha/beta topology with a single mixed beta-sheet, and contains two flexible loops and an unstructured C-terminal tail. The fold resembles that of Ribonuclease H and similar proteins, but differs from these in several respects, and is not likely to have a nuclease activity.

Thiopurine S-methyltransferase (TPMT) genotype does not predict adverse drug reactions to thiopurine drugs in patients with inflammatory bowel disease

BACKGROUND

Azathioprine and mercaptopurine (MP) are well established treatments for inflammatory bowel disease but they have severe adverse effects that prevent their use in some patients. The likelihood and type of adverse effect may relate to thiopurine methyltransferase (TPMT) enzyme activity and genotype.

AIM

To compare the TPMT genotype frequencies in patients with inflammatory bowel disease who have had severe adverse effects to those who tolerate azathioprine or MP (controls).

METHODS

Patients with inflammatory bowel disease who had been treated with azathioprine or MP in Christchurch between 1996 and 2002 were identified. Patients with adverse effects, and controls, were invited to provide a peripheral blood sample for analysis of TPMT genotype. The genotype frequencies were then compared between the two groups.

RESULTS

Fifty-six patients were identified with adverse effects requiring cessation of therapy, of which 50 were genotyped. Reactions included allergic-type (25%), hepatitis (33%), nausea/vomiting (14%), bone marrow suppression (10%), pancreatitis (6%) and other (12%). Five of 50 patients with reactions had TPMT genotype *1/*3, one had *3/*3, and the rest had the wildtype genotype *1/*1. The patient with genotype *3/*3 had severe pancytopenia requiring hospitalization. Three of 50 controls had the *1/*3 genotype and the rest were *1/*1.

CONCLUSIONS

The TPMT allele frequency in our population with inflammatory bowel disease is similar to that reported elsewhere. There was a slight trend for more frequent TPMT mutations in the patients with adverse reactions, but this was not statistically significant. Most patients with reactions did not have gene mutations.

Schizophrenia and bipolar affective disorder: perspectives for the development of therapeutics

Schizophrenia and bipolar disorder remain two of the most severe and difficult to treat psychotic disorders hampered by our poor understanding of their pathologies. The development of typical antipsychotic drugs opened an avenue of investigation through the dopamine D2 receptor in schizophrenia. With the reintroduction of the atypical antipsychotic clozapine came the development of a new generation of atypical agents and hypotheses challenging the centrality of this receptor in explaining antipsychotic effects. Evaluation of these competing theories does not provide sufficient evidence to displace the importance of the dopamine D2 receptor in antipsychotic efficacy, but does raise limitations of it as an explanatory hypothesis. Further, the treatment of other symptom domains in schizophrenia remains relatively neglected and open for the development of novel therapies. Similar to schizophrenia, bipolar disorder presents a diversity of clinical states but unlike schizophrenia, its mainstay of treatment, lithium, has not had a clear receptor target impeding understanding of the disorder's pathology and treatment. This has pushed investigation into other domains emphasising a number of intracellular signalling pathways and glial-neuronal interactions. The heavy genetic loading of bipolar disorder has allowed linkage analyses to identify a number of putative regions, however, the diversity of phenotypes complicates such studies. Polymorphisms of candidate genes have yielded potential leads such as dopamine beta hydroxylase in mood disorder and the serotonin transporter for treatment response. It is anticipated that combiningthe above approaches may hold promise for the development of more effective treatments.

A common P-glycoprotein polymorphism is associated with nortriptyline-induced postural hypotension in patients treated for major depression

The multi-drug resistance gene ABCB1 (or MDR1) encodes a P-glycoprotein (P-gp) that regulates passage of many substances across the blood-brain barrier. The antidepressant amitriptyline and its metabolites (including nortriptyline) are substrates for P-gp, and in mice lacking P-gp, penetration of amitriptyline, but not fluoxetine, into the brain is enhanced. We reasoned that polymorphic variation of P-gp may contribute to differing responses of patients to antidepressant drugs. A single nucleotide polymorphism (SNP) of ABCB1 (3435C>T) was recently correlated with expression levels and in vivo function of P-gp. We examined this SNP in patients with major depression enrolled in a randomized antidepressant treatment trial of nortriptyline and fluoxetine, and observed a significant association between nortriptyline-induced postural hypotension and 3435C>T (chi(2) = 6.78, df = 2, P = 0.034). Our results suggest that homozygosity for 3435T alleles of ABCB1 is a risk factor for occurrence of nortriptyline-induced postural hypotension (OR = 1.37, P = 0.042, 95% CI 1.01-1.86).

Genetic variation of the beta(2)-adrenoceptor: its functional and clinical importance in bronchial asthma

Asthma is a polygenic disease for which no clear genotype-phenotype relationships have emerged. In contrast, although not associated with the diagnosis of asthma per se, variant forms of the beta(2)-adrenoceptor (beta2-AR) gene (ADRB2) display functional effects that may be clinically relevant. Single nucleotide polymorphisms (SNPs) of ADBR2 are common and result in amino acid substitutions at positions 16, 27, and 164 of the receptor as well as position 19 of its 5' upstream peptide. These SNPs influence receptor function in vitro, although evidence regarding exact relationships is conflicting. This has raised the possibility that phenotypes such as bronchial hyper-responsiveness (BHR) and responses to (beta2)-agonist drugs may be genetically determined. To date, no unequivocal relationships between SNPs and phenotype have been identified. In some studies the Gly(16) allele has been associated with increased BHR and asthma severity. In others, the Arg(16) allele has been shown to determine acute bronchodilator response and adverse events during long term beta(2)-agonist therapy. The latter may provide the basis for clinical application of this new knowledge. More recently, a small number of frequently occurring, functionally relevant ADRB2 haplotype pairs have been confirmed. These combinations of alleles may be more important in determining genotype/phenotype relationships than individual SNPs, and may explain why earlier investigations have yielded contrasting results. Future studies will be required to clarify the pharmacodynamic effects of ADRB2haplotypes both in vitro and in vivo.

Solution structure of Pyrobaculum aerophilum DsrC, an archaeal homologue of the gamma subunit of dissimilatory sulfite reductase

The solution structure of DsrC, an archaeal homologue of the gamma subunit of dissimilatory sulfite reductase, has been determined by NMR spectroscopy. This 12.7-kDa protein from the hyperthermophilic archaeon Pyrobaculum aerophilum adopts a novel fold consisting of an orthogonal helical bundle with a beta hairpin along one side. A portion of the structure resembles the helix-turn-helix DNA-binding motif common in transcriptional regulator proteins. The protein contains two disulfide bonds but remains folded following reduction of the disulfides. DsrC proteins from organisms other than Pyrobaculum species do not contain these disulfide bonds. A conserved cysteine next to the C-terminus, which is not involved in the disulfide bonds, is located on a seven-residue C-terminal arm that is not part of the globular protein and is likely to dynamically sample more than one conformation.

Characterization of the human ABCG1 gene: liver X receptor activates an internal promoter that produces a novel transcript encoding an alternative form of the protein

The human ABCG1 gene encodes a member of the ATP-binding cassette (ABC) superfamily of transporter proteins and is highly induced when macrophages are incubated with oxysterols. Using mRNA from oxysterol-treated human THP-1 cells together with 5'-rapid amplification of cDNA ends and polymerase chain reaction, we identified a novel ABCG1 transcript that encodes a putative protein of 786 residues containing a new amino terminus of 203 amino acids. Characterization of the genomic organization and structure of the human ABCG1 gene demonstrates that: (i) the gene consists of 23 exons spanning 98 kilobase pairs (kb) on chromosome 21q22.3, (ii) the 203 amino acids are encoded on three previously unidentified exons, 8-10, and (iii) a promoter, containing a TATA box and two liver X receptor (LXR) alpha response elements (LXREs), is located upstream of exon 8. Northern analysis using exon-specific probes confirms that oxysterol treatment results in >10-fold induction of ABCG1 transcripts that are derived from either exons 8-23 or exons 5, 7, and 11-23. Electromobility shift assays demonstrate that LXRalpha and retinoid X receptor alpha bind to the two LXREs in intron 7. Cells were transiently transfected with reporter luciferase constructs under the control of either (i) 9 kb of genomic DNA corresponding to intron 7 and part of exon 8 and containing either wild-type or mutant LXREs or (ii) two copies of the wild-type or mutant LXRE. In all cases, the wild-type construct was regulated in an LXR- and oxysterol-dependent manner, and this regulation was attenuated when the LXREs were mutated. In conclusion, the human ABCG1 gene contains multiple promoters, spans more than 98 kb and comprises 23 exons that give rise to alternative transcripts encoding proteins with different amino-terminal sequences. Elucidation of the various roles of different ABCG1 isoforms will be important for our understanding of mammalian cholesterol homeostasis.

Reducing the progression of myopia with atropine: a long term cohort study of Olmsted County students

BACKGROUND

Myopia is an important public health problem because it is common and is associated with increased risk for chorioretinal degeneration, retinal detachment, and other vision- threatening abnormalities. In animals, ocular elongation and myopia progression can be lessened with atropine treatment. This study provides information about progression of myopia and atropine therapy for myopia in humans.

METHODS

A total of 214 residents of Olmsted County, Minnesota (118 girls and 96 boys, median age, 11 years; range 6 to 15 years) received atropine for myopia from 1967 through 1974. Control subjects were matched by age, sex, refractive error, and date of baseline examination to 194 of those receiving atropine. Duration of treatment with atropine ranged from 18 weeks to 11.5 years (median 3.5 years).

RESULTS

Median followup from initial to last refraction in the atropine group (11.7 years) was similar to that in the control group (12.4 years). Photophobia and blurred vision were frequently reported, but no serious adverse effects were associated with atropine therapy. Mean myopia progression during atropine treatment adjusted for age and refractive error (0.05 diopters per year) was significantly less than that among control subjects (0.36 diopters per year)(P<.001). Final refractions standardized to the age of 20 years showed a greater mean level of myopia in the control group (3.78 diopters) than in the atropine group (2.79 diopters) (P<.001).

CONCLUSIONS

The data support the view that atropine therapy is associated with decreased progression of myopia and that beneficial effects remain after treatment has been discontinued.

DNA-XPA interactions: a (31)P NMR and molecular modeling study of dCCAATAACC association with the minimal DNA-binding domain (M98-F219) of the nucleotide excision repair protein XPA

Recent NMR-based, chemical shift mapping experiments with the minimal DNA-binding domain of XPA (XPA-MBD: M98-F219) suggest that a basic cleft located in the loop-rich subdomain plays a role in DNA-binding. Here, XPA-DNA interactions are further characterized by NMR spectroscopy from the vantage point of the DNA using a single-stranded DNA nonamer, dCCAATAACC (d9). Up to 2.5 molar equivalents of XPA-MBD was titrated into a solution of d9. A subset of (31)P resonances of d9 were observed to broaden and/or shift providing direct evidence that XPA-MBD binds d9 by a mechanism that perturbs the phosphodiester backbone of d9. The interior five residues of d9 broadened and/or shifted before (31)P resonances of phosphate groups at the termini, suggesting that when d9 is bound to XPA-MBD the internal residues assume a correlation time that is characteristic of the molecular weight of the complex while the residues at the termini undergo a fraying motion away from the surface of the protein on a timescale such that the line widths are more characteristic of the molecular weight of ssDNA. A molecular model of the XPA-MBD complex with d9 was calculated based on the (15)N (XPA-MBD) and (31)P (d9) chemical shift mapping studies and on the assumption that electrostatic interactions drive the complex formation. The model shows that a nine residue DNA oligomer fully covers the DNA-binding surface of XPA and that there may be an energetic advantage to binding DNA in the 3'-->5' direction rather than in the 5'-->3' direction (relative to XPA-MBD alpha-helix-3).

Is cytochrome P450 2C9 genotype associated with NSAID gastric ulceration?

AIMS

The aim of this study was to explore whether genetic variation of cytochrome P450 2C9 (CYP2C9) contributes to NSAID-associated gastric ulceration. The hypothesis tested was that CYP2C9 poor metabolizer genotype would predict higher risk of gastric ulceration in patients on NSAIDs that are metabolized by CYP2C9, due to higher plasma NSAID concentrations.

METHODS

Peripheral blood DNA samples from 23 people with a history of gastric ulceration attributed to NSAIDs metabolized by CYP2C9, and from 32 people on NSAIDs without gastropathy, were analysed to determine CYP2C9 genotype.

RESULTS

The following genotypes were found: *1/*1 (wild type) in 70% of cases and 58% of controls, *1/*2 in 17% of cases and 29% of controls, *1/*3 in 13% of cases and 13% of controls. The difference between case and control nonwild-type genotype frequency was 11.5% (95% CI -14,37%), with the direction of the difference being against the hypothesis. No individuals with homozygote poor metaboliser genotype were identified. The differences in genotype frequencies between the two groups were not significant and the frequencies were similar to those in a large published population study. Ninety-five percent binomial confidence interval analysis confirms that there is no apparent clinically significant relationship between CYP2C9 genotype and risk of gastric ulceration although a small difference in risk in poor metabolizers cannot be excluded.

CONCLUSIONS

These results do not support the hypothesis that gastric ulceration resulting from NSAID usage is linked to the poor metabolizing genotypes of CYP2C9.

Human nucleotide excision repair protein XPA: NMR spectroscopic studies of an XPA fragment containing the ERCC1-binding region and the minimal DNA-binding domain (M59-F219)

XPA is a central protein component of nucleotide excision repair (NER), a ubiquitous, multi-component cellular pathway responsible for the removal and repair of many structurally distinct DNA lesions from the eukaryotic genome. The solution structure of the minimal DNA-binding domain of XPA (XPA-MBD: M98-F219) has recently been determined and chemical shift mapping experiments with 15N-labeled XPA-MBD show that XPA binds DNA along a basic surface located in the C-terminal loop-rich subdomain. Here, XPA-DNA interactions are further characterized using an XPA fragment containing the minimal DNA-binding domain plus the ERCC1-binding region (XPA-EM: M59-F219). The 15N/1H HSQC spectrum of XPA-EM closely maps onto the 15N/1H HSQC spectrum of XPA-MBD, suggesting the DNA-binding domain is intact in the larger XPA fragment. Such a conclusion is corroborated by chemical shift mapping experiments of XPA-EM with a single strand DNA oligomer, dCCAATAACC (d9), that show the same set of 15N/1H HSQC cross peaks are effected by the addition of DNA. However, relative to DNA-free XPA-MBD, the 15N/1H HSQC cross peaks of many of the basic residues in the loop-rich subdomain of DNA-free XPA-EM are less intense, or gone altogether, suggesting the acidic ERRC1-binding region of XPA-EM may associate transiently with the basic DNA-binding surface. While the DNA-binding domain in XPA-EM is structured and functional, 15N-edited NOESY spectra of XPA-EM indicate that the acidic ERRC1-binding region is unstructured. If the structural features observed for XPA-EM persist in XPA, transient intramolecular association of the ERCC1-binding domain with the DNA-binding region may play a role in the sequential assembly of the NER components.

Positive and negative regulation of squalene synthase (ERG9), an ergosterol biosynthetic gene, in Saccharomyces cerevisiae

To identify regulatory cis-elements in the proximal promoter of the yeast ERG9 squalene synthase gene, promoter deletion analysis was performed. This approach identified two regulatory elements, one an upstream repressing cis-element (URS), and the other an upstream activating cis-element (UAS). Electromobility shift assays (EMSAs) demonstrated that distinct proteins bind each element. Genetic screens were performed to identify yeast mutants that altered expression of ERG9 promoter-reporter gene fusions. Three non-ergosterol biosynthetic pathway genes were identified. A mutation in TPO1(YLL028W) led to a 5.5-fold increase in ERG9 expression while mutations in YER064C and SLK19 (YOR195W) led to a 3.1- and 5.6-fold decrease, respectively. Deletion analysis of these genes demonstrated that TPO1 and SLK19 specifically regulated ERG9 expression when tested with several different promoter-reporter gene fusions. Additionally, EMSAs demonstrated that extracts derived from the TPO1 deletion strain was unable to shift the repressing cis-element while protein extracts from the SLK19 deletion strain had a reduced shift of the activating cis-element. Furthermore, these two mutants showed quantitative differences in sterols and antifungal drug susceptibilities consistent with their role in regulating ERG9 expression.

Spectroscopic studies of zinc(II)- and cobalt(II)-associated Escherichia coli formamidopyrimidine-DNA glycosylase: extended X-ray absorption fine structure evidence for a metal-binding domain

Formamidopyrimidine-DNA glycosylase (Fpg) is a 30.2 kDa protein that plays an important role in the base excision repair of oxidatively damaged DNA in Escherichia coli. Sequence analysis and genetic evidence suggest that zinc is associated with a C4-type motif, C(244)-X(2)-C(247)-X(16)-C(264)-X(2)-C(267), located at the C-terminus of the protein. The zinc-associated motif has been shown to be essential for damaged DNA recognition. Extended X-ray absorption fine structure (EXAFS) spectra collected on the zinc-associated protein (ZnFpg) in the lyophilized state and in 10% frozen aqueous glycerol solution show directly that the metal is coordinated to the sulfur atom of four cysteine residues. The average Zn-S bond length is 2.33 +/- 0.01 and 2.34 +/- 0.01 A, respectively, in the lyophilized state and in 10% frozen aqueous glycerol solution. Fpg was also expressed in minimal medium supplemented with cobalt nitrate to yield a blue-colored protein that was primarily cobalt-associated (CoFpg). The profiles of the circular dichroism spectra for CoFpg and ZnFpg are identical, suggesting that the substitution of Co(2+) for Zn(2+) does not alter the structure of Fpg. A similar conclusion is reached upon the analysis of two-dimensional (15)N/(1)H HSQC spectra of uniformly (15)N-labeled samples of ZnFpg and CoFpg; the spectra are similar and display features characteristic of a structured protein. Biochemical assays with a 54 nt DNA oligomer containing 7, 8-dihydro-8-oxoguanine at a specific location show that CoFpg and ZnFpg are equally active at cleaving the DNA at the site of the oxidized guanine. EXAFS spectra of CoFpg indicate that the cobalt is coordinated to the sulfur atom of four cysteine residues with an average Co-S bond length of 2.28 +/- 0.01 and 2.29 +/- 0.01 A, respectively, in the lyophilized state and in 10% frozen aqueous glycerol solution. The structural similarity between CoFpg and ZnFpg suggests that it is biologically relevant to use the paramagnetic properties of Co(2+) as a structural probe.

A comprehensive approach for accurate measurement of proton-proton coupling constants in the sugar ring of DNA

Stereo-selectivedeuteration has been explored as an approach for improving the accuracy of NMR-derived, three-bond vicinal proton-proton coupling constants in the 12-base-pair DNA Dickerson sequence [d(CGCGAATTCGCG)(2)]. The coupling constants are useful for DNA structure determination in restrained molecular dynamics calculations. Specifically, the A5 and A6 residues were prepared with the H2" proton stereo-selectively replaced with a deuteron. Deuteration of the H2" leads to a 42-fold reduction in the transverse cross-relaxation rate of the H2' spin, effectively negating the contribution of transverse cross relaxation to the cross peak frequencies and phases. Calculated linewidth and polarization transfer functions indicated that the reduced dipolar interaction is also expected to result in a significant increase in intensity for all cross peaks involving the H1', H2', or H3' spin. The spectral complexity is also reduced by selective deuteration. Time-shared homonuclear decoupling of passive spins during acquisition was implemented, reducing the spin system, in some cases, to an effectively isolated two-spin system. This enables the use of a 90 degrees mixing pulse instead of the 35 degrees pulse commonly used in standard P.E.COSY experiments, leading to an additional 75% increase in signal intensity. Selective excitation pulses were used to reduce the number of increments required in the indirect dimension by as much as a factor of 4. The cumulative improvement in sensitivity is striking, approaching three orders of magnitude per unit time. Separate experiments, referred to as Stripe-COSY and Superstripe-COSY, were optimized for each coupling constant measured. Finally, J-doubling was used to obtain the most accurate peak separations. This comprehensive approach shows promise as an effective method for extracting highly accurate homonuclear vicinal coupling constants in DNA.

Structural proteomics of an archaeon

A set of 424 nonmembrane proteins from Methanobacterium thermoautotrophicum were cloned, expressed and purified for structural studies. Of these, approximately 20% were found to be suitable candidates for X-ray crystallographic or NMR spectroscopic analysis without further optimization of conditions, providing an estimate of the number of the most accessible structural targets in the proteome. A retrospective analysis of the experimental behavior of these proteins suggested some simple relations between sequence and solubility, implying that data bases of protein properties will be useful in optimizing high throughput strategies. Of the first 10 structures determined, several provided clues to biochemical functions that were not detectable from sequence analysis, and in many cases these putative functions could be readily confirmed by biochemical methods. This demonstrates that structural proteomics is feasible and can play a central role in functional genomics.

Structure-based functional classification of hypothetical protein MTH538 from Methanobacterium thermoautotrophicum

The structure of MTH538, a previously uncharacterized hypothetical protein from Methanobacterium thermoautotrophicum, has been determined by NMR spectroscopy. MTH538 is one of numerous structural genomics targets selected in a genome-wide survey of uncharacterized sequences from this organism. MTH538 is a so-called singleton, a sequence not closely related to any other (known) sequences. The structure of MTH538 closely resembles the known structures of receiver domains from two component response regulator systems, such as CheY, and is similar to the structures of flavodoxins and GTP-binding proteins. Tests on MTH538 for characteristic activities of CheY and flavodoxin were negative. MTH538 did not become phosphorylated in the presence of acetyl phosphate and Mg(2+), although it appeared to bind Mg(2+). MTH538 also did not bind flavin mononucleotide (FMN) or coenzyme F(420). Nevertheless, sequence and structure parallels between MTH538/CheY and two families of ATPase/phosphatase proteins suggest that MTH538 may have a role in a phosphorylation-independent two-component response regulator system.