Stressful life events and co-occurring depression,substance abuse and suicidality among American Indian and Alaska Native adolescents

Depression, suicidality and substance abuse disorders are examined with special emphasis on the role of stressful life events in predicting severity and patterns of comorbidity among American Indian and Alaska Native adolescents in boarding school environments. Both amount and severity of comorbidity increase with age and specific patterns of comorbidity are associated with gender. Different types and amounts of stressful life events predict specific combinations of comorbidity. These outcomes are interpretable with respect to associated cultural dynamics and the ecology of mental health services delivery for Indian and Native adolescents. Theoretical and methodological issues are discussed in relation to the use of stressful life events in examining cultural factors related to comorbidity among culturally different populations.     

Why was Standing Rock and the #NoDAPL campaign so historic? Factors affecting American Indian participation in social movement collaborations and coalitions

ABSTRACT

Is the #NoDAPL mobilization, which was historically unusual as a national scale grassroots campaign featuring American Indians grassroots activists and tribal governments in coalition with others, an indicator of future similar efforts? Or, will the Standing Rock resistance be a relative aberration, based on a unique set of circumstances? To explore these questions, I draw upon theory and historical scholarship about American settler colonialism; cross-group collaborations and social movement coalitions; and American Indian movements. A variety of within-group, intergroup and larger structural factors pose significant obstacles to American Indian participation in grassroots social movement coalitions. However, striking threats, the existence of social ties between American Indian movements and environmental movements, and overlap between ideologies and frames generated by each movement were sufficient to generate robust coalitional mobilization.     

Surfing waves of data in San Diego: sophisticated analyses provide a broad view of human genetic diversity

A report on the 64th annual American Society of Human Genetics meeting held in San Diego, USA, 18-22 October, 2014.Fueled by rapid technological innovations, the ability of geneticists to assay accurately not only genetic data but also gene expression levels, epigenetic markers, biomarker levels and microbiome composition has expanded the field of human genetics vastly. Alongside this expansion, the annual American Society of Human Genetics (ASHG) conference has grown to draw over 6,500 scientific participants with a broad range of interests. Here, we focus on some of the most notable advances made in the area of population genetics that were presented at the 64^th annual ASHG meeting. This year, the sophistication of the analysis methods employed was striking, particularly for drawing inferences from subtle differences in human genetic variation.     

The Politics of Reintegrating Australian Aboriginal and American Indian Indigenous Knowledge into Resource Management: The Dynamics of Resource Appropriation and Cultural Revival

As the United States and Australia struggle with contemporary crises over competing uses of rapidly depleting natural resources, there are striking parallels between American Indian and Australian Aboriginal communities demanding a place at the management table and offering culturally based understandings of and solutions for the ecosystems at risk. These efforts to integrate indigenous knowledge into mainstream natural resource management are part of larger legal and political debates over land tenure, the locus of control, indigenous self-governance, and holistic ecosystems management.     

Karma, reincarnation, and medicine: Hindu perspectives on biomedical research

Prior to the completion of the Human Genome Project, bioethicists and other academics debated the impact of this new genetic information on medicine, health care, group identification, and peoples’ lives. A major issue is the potential for unintended and intended adverse consequences to groups and individuals. When conducting research in, for instance, American Indian and Alaskan native (AI/AN) populations, political, cultural, religious and historical issues must be considered. Among African Americans, the Tuskegee Syphilis Experiment is a reminder of racism and discrimination in this country. The goal of the current study is to understand reasons for participating, or not, in genetic research such as the HapMap project and other genetic/medical research from the perspective of the Indian American community in Houston, Texas. In this article, we report on a topic central to this discussion among Indian Americans: karma and reincarnation. Both concepts are important beliefs when considering the body and what should happen to it. Karma and reincarnation are also important considerations in participation in medical and genetic research because, according to karma, what is done to the body can affect future existences and the health of future descendants. Such views of genetic and medical research are culturally mediated. Spiritual beliefs about the body, tissue, and fluids and what happens to them when separated from the body can influence ideas about the utility and acceptability of genetic research and thereby affect the recruitment process. Within this community it is understood that genetic and environmental factors contribute to complex diseases such as diabetes, hypertension, and cancer; and acknowledgment of the significance of environmental stressors in the production of disease. A commitment to service, i.e. “betterment of humanity,” karmic beliefs, and targeting environmental stressors could be prominent avenues for public health campaigns in this population. This study suggests that minority status does not automatically indicate unwillingness to participate in genetic or medical research. Indian Americans were not skeptical about the potential benefits of biomedical research in comparison to other ethnic minority communities in the United States.     

Biotechnological interventions in sea buckthorn (Hippophae L.): current status and future prospects

Sea buckthorn (Hippophae L., Elaeagnaceae) is an economically and ecologically important medicinal plant comprising of species which are winter hardy, dioecious, wind-pollinated multipurpose shrubs bearing yellow or orange berries with nitrogen-fixing ability. It grows widely in cold regions of Indian Himalayas, China, Russia, Europe and many other countries. It is commonly known as ‘cold desert gold’ due to its high potential as a bio-resource for land reclamation, reducing soil erosion and its multifarious uses. The wild populations are being used for harvesting economic benefits with negligible plantation efforts. Although this plant has many excellent traits, it is still in an early phase of domestication. This woody plant is prone to many pests and diseases which destroy the plants and halt its commercial production. Limited progress has been made for improvement of sea buckthorn through breeding programs due to long juvenile period and lack of QTL linkage map, which makes screening of mapping populations a time-consuming and labor-intensive task. Conventional propagation methods, i.e. seeds, softwood and hardwood cuttings, and suckers are in place but are cumbersome and season dependent. Therefore, application of modern tools of biotechnology needs to be standardized for harnessing maximum benefits from this nutraceutical plant. Improvement of this genus through genetic transformation requires an efficient regeneration system, which is yet to be standardized. Taxonomic status of the genus is controversial and requires more inputs. Taxonomic delineation of species and subspecies and also the breeding programs can be more robustly addressed using molecular markers. This review summarizes the progress made and suggests some future directions of research for this important fruit species.     

Aldehyde dehydrogenase polymorphism in North American, South American, and Mexican Indian populations.

While about 40% of the South American Indian populations (Atacameños, Mapuche, Shuara) were found to be deficient in aldehyde dehydrogenase isozyme I (ALDH2 or E2), preliminary investigations showed very low incidence of isozyme deficiency among North American natives (Sioux, Navajo) and Mexican Indians (mestizo). Possible implications of such trait differences on cross-cultural behavioral response to alcohol drinking are discussed.     

The Brazilian Xavante Indians revisited: New protein genetic studies

A total of 94 individuals from the Xavante village of Rio das Mortes were variously studied in relation to 28 protein genetic systems. No variation was observed for 15 of them, in accordance with previous studies. Of the remaining 13, four (Rh, Duffy, acid phosphatase, and GC) showed significant departures from the averages obtained in 32 other South American Indian populations. If studies performed in the 1960s are considered, there is indication that no significant changes in this village's gene pool has occurred in the last 30 years. Comparison with two other Xavante populations included nine systems with variation, and for three of them (MNSs, Rh, and Duffy) significant differences were found. Genetically the Rio das Mortes are closer to the São Marcos than to the Simões Lopes Xavantes. A dendrogram considering 25 genetic systems and 33 South American Indian populations was constructed. There the Xavante were grouped together, in two neighboring clusters, with three other tribes who speak Ge languages. But these clusters also present populations who speak other languages, and the reproducibility of the tree is low. South American Indians, at least with this set of markers, do not seem to be clearly classified into defined subgroups. Am J Phys Anthropol 104:23–34, 1997. © 1997 Wiley-Liss, Inc.     

Why the Indian Subcontinent Holds the Key to Global Tiger Recovery

With only ~3,000 wild individuals surviving restricted to just 7% of their historical range, tigers are now a globally threatened species. Therefore, conservation efforts must prioritize regions that harbor more tigers, as well try to capture most of the remaining genetic variation and habitat diversity. Only such prioritization based on demographic, genetic, and ecological considerations can ensure species recovery and retention of evolutionary flexibility in the face of ongoing global changes. Although scientific understanding of ecological and demographic aspects of extant wild tiger populations has improved recently, little is known about their genetic composition and variability. We sampled 73 individual tigers from 28 reserves spread across a diversity of habitats in the Indian subcontinent to obtain 1,263 bp of mitochondrial DNA and 10 microsatellite loci. Our analyses reveals that Indian tigers retain more than half of the extant genetic diversity in the species. Coalescent simulations attribute this high genetic diversity to a historically large population size of about 58,200 tigers for peninsular India south of the Gangetic plains. Furthermore, our analyses indicate a precipitous, possibly human-induced population crash ~200 years ago in India, which is in concordance with historical records. Our results suggest that only 1.7% (with an upper limit of 13% and a lower limit of 0.2%) of tiger numbers in historical times remain now. In the global conservation context our results suggest that, based on genetic, demographic, and ecological considerations, the Indian subcontinent holds the key to global survival and recovery of wild tigers.     

Multi-dimensional classification of biomedical text: toward automated, practical provision of high-utility text to diverse users

MOTIVATION: Much current research in biomedical text mining is concerned with serving biologists by extracting certain information from scientific text. We note that there is no 'average biologist' client; different users have distinct needs. For instance, as noted in past evaluation efforts (BioCreative, TREC, KDD) database curators are often interested in sentences showing experimental evidence and methods. Conversely, lab scientists searching for known information about a protein may seek facts, typically stated with high confidence. Text-mining systems can target specific end-users and become more effective, if the system can first identify text regions rich in the type of scientific content that is of interest to the user, retrieve documents that have many such regions, and focus on fact extraction from these regions. Here, we study the ability to characterize and classify such text automatically. We have recently introduced a multi-dimensional categorization and annotation scheme, developed to be applicable to a wide variety of biomedical documents and scientific statements, while intended to support specific biomedical retrieval and extraction tasks. RESULTS: The annotation scheme was applied to a large corpus in a controlled effort by eight independent annotators, where three individual annotators independently tagged each sentence. We then trained and tested machine learning classifiers to automatically categorize sentence fragments based on the annotation. We discuss here the issues involved in this task, and present an overview of the results. The latter strongly suggest that automatic annotation along most of the dimensions is highly feasible, and that this new framework for scientific sentence categorization is applicable in practice.     

Bridging molecular genetics and participatory research: how access and benefit‐sharing stimulate interdisciplinary research for tropical biology and conservation

Molecular genetics research can benefit efforts to conserve the genetic diversity of tropical plant species. Clear and efficient procedures are needed to access DNA samples, while respecting tropical countries’ and local communities’ rights on genetic resource usage. The Nagoya Protocol on Access and Benefit‐Sharing, which took effect in 2014, provides an opportunity to establish such procedures. However, scientists are concerned that its emphasis on monetary gains restricts research focused on scientific, societal, and environmental benefits. Despite much political and scientific debate, few concrete cases have demonstrated the practical functioning of the Nagoya Protocol. This paper describes the first application of the Protocol in Guatemala, where it was used to grant permission to a non‐commercial study on gene flow in mahogany (Swietenia macrophylla King) populations in the Maya Biosphere Reserve of Petén. On the basis of this study, we discuss five strategies to enhance the application of molecular genetics to conservation biology under the Nagoya Protocol: (1) generate short and standardized procedures; (2) enable science communication; (3) cultivate a common understanding between users, providers, and potential beneficiaries; (4) involve local research and practitioner organizations; and (5) integrate participatory research. Positive societal views on the application of molecular genetics to conservation biology generate further support for work in this discipline and promote adoption of research results for the conservation of genetic diversity of tropical plant species.     

Artificial interproximal grooving of the teeth in American Indians

Artificial grooves about 2 mm in width have been observed on the cervical region of teeth of American Indian populations which come from widespread localities and which extend through considerable time depth. The grooves appear to have been made ante-mortem and to show a close relationship with interproximal caries and peridontal bone resorption. It is conjectured that the grooves represent efforts of a therapeutic or, at least, palliative nature.     

On the origins of New World paleopathology

Many of the lesions found in American Indian bones do not resemble those found in human bones from the Old World, suggesting that the American Indians suffered from a distinct group of illnesses. If Old World pathogens did not follow man to the New World, what were the sources of pre-Columbian Indian diseases? As in the Old World, humans were susceptible to diseases endemic in the local animal populations. Exposure to these diseases varied with culturally conditioned animal contacts. As the New World population increased, the probability for disease increased, to the point where it is likely that even in pre-Columbian times, disease rather than war or climatic changes may have been a major influence in changing settlement patterns. The generalization that the only Old World plants and animals found in the New were those brought by man seems to hold as true for the pre-Columbian disease organisms as it is for larger forms of life.     

Assessing Accuracy of Genotype Imputation in American Indians

Background

Genotype imputation is commonly used in genetic association studies to test untyped variants using information on linkage disequilibrium (LD) with typed markers. Imputing genotypes requires a suitable reference population in which the LD pattern is known, most often one selected from HapMap. However, some populations, such as American Indians, are not represented in HapMap. In the present study, we assessed accuracy of imputation using HapMap reference populations in a genome-wide association study in Pima Indians.

Results

Data from six randomly selected chromosomes were used. Genotypes in the study population were masked (either 1% or 20% of SNPs available for a given chromosome). The masked genotypes were then imputed using the software Markov Chain Haplotyping Algorithm. Using four HapMap reference populations, average genotype error rates ranged from 7.86% for Mexican Americans to 22.30% for Yoruba. In contrast, use of the original Pima Indian data as a reference resulted in an average error rate of 1.73%.

Conclusions

Our results suggest that the use of HapMap reference populations results in substantial inaccuracy in the imputation of genotypes in American Indians. A possible solution would be to densely genotype or sequence a reference American Indian population.     

No aging in India: The uses of gerontology

This paper develops a critique of international gerontology through an ethnography and analysis of gerontological practice in India. The central theme of Indian gerontology — that of an imminent demographic and social explosion of an aging population who will tax the country's slender resources — misrepresents available data and fails to signify the experience of most Indian old people. Narrative and deconstructive techniques are deployed to examine the language of crisis and the complex sources of this misrepresentation. Three sources are explored: local disjunctions of class and gender in India, neocolonial biases in the structure of knowledge on aging central to international discourse, and subaltern strategies within India for subverting Western and elite Indian imperatives of what it means to be old.A variety of textual, ethnographic, and historical materials are examined: Indian and American literature pertaining to the 1982 World Assembly on Aging, a series of sociological texts each entitled Aging in India, and four contemporary Indian institutions designed to meet the needs of old people: a social service agency, a geriatric clinic, a retirement community, and an old age home.     

Peopling of the Americas: paleobiological evidence.

A subjective and bivariate analysis of 8500-10,000-year-old human fossil remains from North America substantiates that the fossils' closest affinities are with Asian populations. Within North American prehistoric Indian populations, increasing brachycephalization and the possible development of a larger, broader face are two structural trends that can be identified. In those respects where Paleo-Indian specimens differ from modern northern Asians and North American Indians, they tend to resemble southern Asian and European populations. These assessments generally support the inference that populations entered the New World relatively recently but before the modern northern Asian and North American features were fully developed. Based on the data examined, no date can be specified for time of entrance of the first populations, nor can the number of founding populations be discerned.     

Are there morally acceptable alternatives to blastocyst derived ESC?

ESC derivation, use and SCNT have raised many moral and ethical issues. In this opinion piece I have focused on the argument that morally less ambiguous alternatives to ESC derived from the ICM of blastocysts exist. These possibilities range from using multiple adult stem cell populations each of which is uniquely suited for a particular disease target or identifying adult ESC-like populations, using transdifferentiated ESC-like cells or alternate methods of deriving ESC. I suggest that while it is important to support such efforts, current results do not provide sufficient compelling data to allow one to stop the use of ESC and perhaps adult cells will never be a reliable alternative. All options need to be fully explored and decisions need to be made with scientific rigor and respect for each individual's moral compass.     

The McGill-Mouse-Miniscope platform: A standardized approach for high-throughput imaging of neuronal dynamics during behavior

Understanding the rules that govern neuronal dynamics throughout the brain to subserve behavior and cognition remains one of the biggest challenges in neuroscience research. Recent technical advances enable the recording of increasingly larger neuronal populations to produce increasingly more sophisticated datasets. Despite bold and important open-science and data-sharing policies, these datasets tend to include unique data acquisition methods, behaviors, and file structures. Discrepancies between experimental protocols present key challenges in comparing data between laboratories and across different brain regions and species. Here, we discuss our recent efforts to create a standardized and high-throughput research platform to address these issues. The McGill-Mouse-Miniscope (M3) platform is an initiative to combine miniscope calcium imaging with standardized touchscreen-based animal behavioral testing. The goal is to curate an open-source and standardized framework for acquiring, analyzing, and accessing high-quality data of the neuronal dynamics that underly cognition throughout the brain in mice, marmosets, and models of disease. We end with a discussion of future developments and a call for users to adopt this standardized approach.     

Developing success criteria and goals for evaluating oyster reef restoration: Ecological function or resource exploitation?

Habitat restoration encompasses a broad range of activities, emphasizing very different issues, goals, and approaches depending on the operational definition of ‘restoration’. This is particularly true for many shellfish (molluscan) dominated systems (e.g. oyster reefs, mussel beds, vermetid gastropod reefs). In contrast to other well-studied biogenic habitats, such as seagrasses, mangroves, or salt marshes, bivalves are directly consumed as a resource. Hence resource extraction has direct consequences for habitat health. Restoration objectives have typically included reduction of public health risks through improved water quality to increase harvest. Restoration or enhancement of populations of commercially exploited shellfish depressed by overharvesting and/or reduced environmental quality remains the principal motivation behind most shellfish ‘restoration’ efforts. Direct and indirect ecosystem services (e.g. filtering capacity, benthic–pelagic coupling, nutrient dynamics, sediment stabilization, provision of habitat, etc.) derived from oyster habitat have been largely ignored or underestimated. Only recently, the restoration of lost ecological function associated with shellfish communities has been included in our discussions and related research examining habitat development and function through a scientific approach. The former area has been reviewed extensively and will not be our focus here. In this review, we examine some of the restoration efforts made in the name of fisheries enhancement, address their effectiveness, and discuss some of the issues associated with realizing the broader goal of ecological restoration. We note the importance of linking success criteria to specific goals and make the case for a greater need in clarifying the ecological functions of shellfish and shellfish habitats. We recognize the limitations of existing datasets and summarize ongoing attempts to address oyster habitat restoration throughout the broad geographic distribution of the American oyster, Crassostrea virginica (Gmelin). In many ways this topic parallels the ongoing debate over ‘attraction versus production’ associated with artificial reef management. We consider how local conditions (e.g. tidal range, bottom topography, turbidity, salinity) and resulting habitat traits affect restoration strategies. We also discuss the underappreciated value of shellfish populations from those areas designated as closed to harvesting due to their intrinsic worth as habitat/larval reserves. The necessity of ecosystem (adaptive) management strategies emerges from this discussion. Finally, this overview supports our contention that shellfish habitat should be included in discussions of ‘essential fish habitats’ (or EFH).     

Genetic landscape of the people of India: a canvas for disease gene exploration

Analyses of frequency profiles of markers on disease or drug-response related genes in diverse populations are important for the dissection of common diseases. We report the results of analyses of data on 405 SNPs from 75 such genes and a 5.2 Mb chromosome, 22 genomic region in 1871 individuals from diverse 55 endogamous Indian populations. These include 32 large (> 10 million individuals) and 23 isolated populations, representing a large fraction of the people of India. We observe high levels of genetic divergence between groups of populations that cluster largely on the basis of ethnicity and language. Indian populations not only overlap with the diversity of HapMap populations, but also contain population groups that are genetically distinct. These data and results are useful for addressing stratification and study design issues in complex traits especially for heterogeneous populations. For complete authors’ list of the Indian Genome Variation Database Consortium please see Appendix. For correspondence. E-mail: skb@igib.res.in; Functional Genomics Unit, Institute of Genomics and Integrative Biology (CSIR), Mall Road, New Delhi 110 007, India.