Ontogeny and function of the circadian clock in intestinal organoids.

Circadian rhythms regulate diverse aspects of gastrointestinal physiology ranging from the composition of microbiota to motility. However, development of the intestinal circadian clock and detailed mechanisms regulating circadian physiology of the intestine remain largely unknown. In this report, we show that both pluripotent stem cell-derived human intestinal organoids engrafted into mice and patient-derived human intestinal enteroids possess circadian rhythms and demonstrate circadian phase-dependent necrotic cell death responses to Clostridium difficile toxin B (TcdB). Intriguingly, mouse and human enteroids demonstrate anti-phasic necrotic cell death responses to TcdB. RNA-Seq analysis shows that ~3-10% of the detectable transcripts are rhythmically expressed in mouse and human enteroids. Remarkably, we observe anti-phasic gene expression of Rac1, a small GTPase directly inactivated by TcdB, between mouse and human enteroids, and disruption of Rac1 abolishes clock-dependent necrotic cell death responses. Our findings uncover robust functions of circadian rhythms regulating clock-controlled genes in both mouse and human enteroids governing organism-specific, circadian phase-dependent necrotic cell death responses, and lay a foundation for human organ- and disease-specific investigation of clock functions using human organoids for translational applications.

Affect, Values and Problems Assessing Decision-Making Capacity.

The dominant approach to assessing decision-making capacity in medicine focuses on determining the extent to which individuals possess certain core cognitive abilities. Critics have argued that this model delivers the wrong verdict in certain cases where patient values that are the product of mental disorder or disordered affective states undermine decision-making without undermining cognition. I argue for a re-conceptualization of what it is to possess the capacity to make medical treatment decisions. It is, I argue, the ability to track one's own personal interests at least as well as most people can. Using this idea, I demonstrate that it is possible to craft a solution for the problem cases-one that neither alters existing criteria in dangerous ways (e.g. does not open the door to various kinds of abuse) nor violates the spirit of widely accepted ethical constraints on decision-making assessment.

The Overdose Crisis and Using Alone: Perspectives of People Who Use Drugs in Rural and Semi-Urban Areas of British Columbia.

Background: A significant rise in the rate of overdose deaths in British Columbia (BC), driven by fentanyl contamination of the illicit drug supply, led to the declaration of a public health emergency in 2016. Those at greatest risk of death are people who use alone. This community-based participatory action research study based in the Fraser East region of BC study aimed to overview underlying factors that contribute to unwitnessed overdoses in semi-urban and rural settings. Methods: This descriptive study used a community-based participatory action research model with peer research associates (PRAs) involved at various research stages. In total, 22 interviews were conducted with participants aged 19 and over who used illicit drugs in the Fraser East since the start of the public health emergency in 2016. A collaborative data analysis approach was taken for data interpretation, and content analysis was performed to explore themes surrounding using alone. Results: Among people who use drugs (PWUD), using alone was found to be influenced by (a) the availability of drugs and personal funds, (b) personal safety, (c) stigma and shame, (d) protecting privacy, (e) mental health conditions and addiction, and (f) the lack of engagement with harm reduction services. At times, using alone was due to unforeseen, episode-specific situations. Conclusion: A multi-dimentional and context-specific approach is needed in overdose prevention and response for people who use drugs alone. There is need for enhanced approaches that address or include support services for families to reduce stigma and isolation of those at risk of an overdose.

Increased Programmed Death-Ligand 1 is an Early Epithelial Cell Response to Helicobacter pylori Infection.

Helicobacter pylori (H. pylori) is the major risk factor for the development of gastric cancer. Our laboratory has reported that the Sonic Hedgehog (Shh) signaling pathway is an early response to infection that is fundamental to the initiation of H. pylori-induced gastritis. H. pylori also induces programmed death ligand 1 (PD-L1) expression on gastric epithelial cells, yet the mechanism is unknown. We hypothesize that H. pylori-induced PD-L1 expression within the gastric epithelium is mediated by the Shh signaling pathway during infection. To identify the role of Shh signaling as a mediator of H. pylori-induced PD-L1 expression, human gastric organoids generated from either induced pluripotent stem cells (HGOs) or tissue (huFGOs) were microinjected with bacteria and treated with Hedgehog/Gli inhibitor GANT61. Gastric epithelial monolayers generated from the huFGOs were also infected with H. pylori and treated with GANT61 to study the role of Hedgehog signaling as a mediator of induced PD-1 expression. A patient-derived organoid/autologous immune cell co-culture system infected with H. pylori and treated with PD-1 inhibitor (PD-1Inh) was developed to study the protective mechanism of PD-L1 in response to bacterial infection. H. pylori significantly increased PD-L1 expression in organoid cultures 48 hours post-infection when compared to uninfected controls. The mechanism was cytotoxic associated gene A (CagA) dependent. This response was blocked by pretreatment with GANT61. Anti-PD-L1 treatment of H. pylori infected huFGOs, co-cultured with autologous patient cytotoxic T lymphocytes and dendritic cells, induced organoid death. H. pylori-induced PD-L1 expression is mediated by the Shh signaling pathway within the gastric epithelium. Cells infected with H. pylori that express PD-L1 may be protected from the immune response, creating premalignant lesions progressing to gastric cancer.

Differences in microbial community response to nitrogen fertilization result in unique enzyme shifts between arbuscular and ectomycorrhizal-dominated soils.

While the effect of nitrogen (N) deposition on belowground carbon (C) cycling varies, emerging evidence shows that forest soils dominated by trees that associate with ectomycorrhizal fungi (ECM) store more C than soils dominated by trees that associate with arbuscular mycorrhizae (AM) with increasing N deposition. We hypothesized that this is due to unique nutrient cycling responses to N between AM and ECM-dominated soils. ECM trees primarily obtain N through fungal mining of soil organic matter subsidized by root-C. As such, we expected the largest N-induced responses of C and N cycling to occur in ECM rhizospheres and be driven by fungi. Conversely, as AM trees rely on bacterial scavengers in bulk soils to cycle N, we predicted the largest AM responses to be driven by shifts in bacteria and occur in bulk soils. To test this hypothesis, we measured microbial community composition, metatranscriptome profiles, and extracellular enzyme activity in bulk, rhizosphere, and organic horizon (OH) soils in AM and ECM-dominated soils at Bear Brook Watershed in Maine, USA. After 27 years of N fertilization, fungal community composition shifted across ECM soils, but bacterial communities shifted across AM soils. These shifts were mirrored by enhanced C relative to N mining enzyme activities in both mycorrhizal types, but this occurred in different soil fractions. In ECM stands these shifts occurred in rhizosphere soils, but in AM stands they occurred in bulk soils. Additionally, ECM OH soils exhibited the opposite response with declines in C relative to N mining. As rhizosphere soils account for only a small portion of total soil volume relative to bulk soils, coupled with declines in C to N enzyme activity in ECM OH soils, we posit that this may partly explain why ECM soils store more C than AM soils as N inputs increase.

Substance use and overdose risk: documenting the perspectives of formerly incarcerated persons in the Fraser East region of BC.

BACKGROUND: The relationship between incarceration and risk of overdose has been well-documented in the literature, but few studies document the perspectives of persons at risk of overdose who were incarcerated. This sub-inquiry aimed to understand the experiences of persons with a history of substance use and incarceration in the Fraser East region of BC and how involvement with the criminal justice system affected their drug use and perceived risk of overdose. METHODS: The Fraser East Overdose Response project utilized a community-based participatory action approach that included peer researchers with lived experience in all parts of the research process. This qualitative pilot study aimed to better understand individuals at risk of an unwitnessed overdose in order to prevent deaths and identify effective local responses. A snowball sampling technique was used to recruit persons aged 19 and over who used illicit drugs over the past 3 years in the Fraser East since 2016. In total, 22 participants were interviewed. Of these, 13 participants identified a history of incarceration. Interviews were analyzed using a framework analysis approach. RESULTS: The perspectives that participants shared revealed that impacts from incarceration are influenced by policies but also highly individualized. Our inquiry found three broader themes, within which were situated differing and sometimes conflicting interpretations and experiences of systemic environments: (1) incarceration was associated with harms and was perceived to increase risk of overdose following release, (2) incarceration was perceived to have limited impact on substance use and overdose risk, and (3) incarceration was associated with a perceived reduction of substance use and overdose risk. CONCLUSIONS: Understanding the complexities of the perceptions of those with lived experience of substance use and incarceration is of importance to better inform interventions in this population. The existing knowledge base urgently requires further inquiry into the intersections between qualitative perspectives, environments and policies, and quantitative outcomes of overdose vís-a-vís correctional institution.

Theory Without Theories: Well-Being, Ethics, and Medicine.

Medical ethics would be better if people were taught to think more clearly about well-being or (what I take to be the same thing) the concept of what is good for a person. Yet for a variety of reasons, bioethicists have generally paid little attention to this concept. Here, I argue, first, that focusing on general theories of welfare is not useful for practical medical ethics. I argue, second, for what I call the "theory-without-theories approach" to welfare in practical contexts. The first element of this approach is a focus on examining important and relatively uncontroversial constituents of welfare as opposed to general theories. The second key element is a framework for thinking about choice in relation to welfare, a framework I refer to as "the mild objectivity framework." I conclude with illustrations of the way in which the "theory without theories approach" can improve thinking in medicine.

Further Reflections: Surrogate Decisionmaking When Significant Mental Capacities are Retained.

Mackenzie Graham has made an important contribution to the literature on decisionmaking for patients with disorders of consciousness. He argues, and I agree, that decisions for unresponsive patients who are known to retain some degree of covert awareness ought to focus on current interests, since such patients likely retain the kinds of mental capacities that in ordinary life command our current respect and attention. If he is right, then it is not appropriate to make decisions for such patients by appealing to the values they had in the past, either the values expressed in an advance directive or the values recalled by a surrogate. There are two things I wish to add to the discussion. My first point is somewhat critical, for although I agree with his general conclusion about how, ideally, such decisions should be approached, I remain skeptical about whether his conclusion offers decisionmakers real practical help. The problem with these cases is that the evidence we have about the nature of the patient's current interests is minimal or nonexistent. However-and this is important-Graham's conclusion will be extremely relevant if in the future, our ability to communicate with such patients improves, as I hope it will. This leads to my second point. Graham's conclusion illustrates a more general problem with our standard framework for decisionmaking for previously competent patients, a problem that has not been adequately recognized. So, in what follows, I explain the problem I see and offer some brief thoughts about solutions.

Phenotypic and physiological responses to salt exposure in Sorghum reveal diversity among domesticated landraces.

PREMISE: Soil salinity negatively impacts plant function, development, and yield. To overcome this impediment to agricultural productivity, variation in morphological and physiological response to salinity among genotypes of important crops should be explored. Sorghum bicolor is a staple crop that has adapted to a variety of environmental conditions and contains a significant amount of standing genetic diversity, making it an exemplary species to study variation in salinity tolerance. METHODS: Twenty-one diverse Sorghum accessions were treated with nonsaline water or 75 mM sodium chloride. Salinity tolerance was assessed via changes in biomass between control and salt-treated individuals. Accessions were first rank-ordered for salinity tolerance, and then individuals spanning a wide range of responses were analyzed for foliar proline and ion accumulation. Tolerance rankings were then overlaid on a neighbor-joining tree. RESULTS: We found that, while proline is often a good indicator of osmotic adjustment and is historically associated with increased salt tolerance in many species, proline accumulation in sorghum reflects a stress response injury rather than acclimation. When combining ion profiles with stress tolerance indices, the variation observed in tolerance was not a sole result of Na+ accumulation, but rather reflected accession-specific mechanisms. CONCLUSIONS: We identified significant variation in salinity tolerance among Sorghum accessions that may be a result of the domestication history of Sorghum. When we compared our results with known phylogenetic relationships within sorghum, the most parsimonious explanation for our findings is that salinity tolerance was acquired early during domestication and subsequently lost in accessions growing in areas varying in soil salinity.

Impaired ß-Oxidation and Altered Complex Lipid Fatty Acid Partitioning with Advancing CKD.

Studies of lipids in CKD, including ESRD, have been limited to measures of conventional lipid profiles. We aimed to systematically identify 17 different lipid classes and associate the abundance thereof with alterations in acylcarnitines, a metric of ß-oxidation, across stages of CKD. From the Clinical Phenotyping Resource and Biobank Core (CPROBE) cohort of 1235 adults, we selected a panel of 214 participants: 36 with stage 1 or 2 CKD, 99 with stage 3 CKD, 61 with stage 4 CKD, and 18 with stage 5 CKD. Among participants, 110 were men (51.4%), 64 were black (29.9%), and 150 were white (70.1%), and the mean (SD) age was 60 (16) years old. We measured plasma lipids and acylcarnitines using liquid chromatography-mass spectrometry. Overall, we identified 330 different lipids across 17 different classes. Compared with earlier stages, stage 5 CKD associated with a higher abundance of saturated C16-C20 free fatty acids (FFAs) and long polyunsaturated complex lipids. Long-chain-to-intermediate-chain acylcarnitine ratio, a marker of efficiency of ß-oxidation, exhibited a graded decrease from stage 2 to 5 CKD (P<0.001). Additionally, multiple linear regression revealed that the long-chain-to-intermediate-chain acylcarnitine ratio inversely associated with polyunsaturated long complex lipid subclasses and the C16-C20 FFAs but directly associated with short complex lipids with fewer double bonds. We conclude that increased abundance of saturated C16-C20 FFAs coupled with impaired ß-oxidation of FFAs and inverse partitioning into complex lipids may be mechanisms underpinning lipid metabolism changes that typify advancing CKD.

GDF-15, Galectin 3, Soluble ST2, and Risk of Mortality and Cardiovascular Events in CKD.

RATIONALE & OBJECTIVE: Inflammation, cardiac remodeling, and fibrosis may explain in part the excess risk for cardiovascular disease (CVD) in patients with chronic kidney disease (CKD). Growth differentiation factor 15 (GDF-15), galectin 3 (Gal-3), and soluble ST2 (sST2) are possible biomarkers of these pathways in patients with CKD. STUDY DESIGN: Observational cohort study. SETTING & PARTICIPANTS: Individuals with CKD enrolled in either of 2 multicenter CKD cohort studies: the Seattle Kidney Study or C-PROBE (Clinical Phenotyping and Resource Biobank Study). EXPOSURES: Circulating GDF-15, Gal-3, and sST2 measured at baseline. OUTCOMES: Primary outcome was all-cause mortality. Secondary outcomes included hospitalization for physician-adjudicated heart failure and the atherosclerotic CVD events of myocardial infarction and cerebrovascular accident. ANALYTIC APPROACH: Cox proportional hazards models used to test the association of each biomarker with each outcome, adjusting for demographics, CVD risk factors, and kidney function. RESULTS: Among 883 participants, mean estimated glomerular filtration rate was 49±19mL/min/1.73m2. Higher GDF-15 (adjusted HR [aHR] per 1-SD higher, 1.87; 95% CI, 1.53-2.29), Gal-3 (aHR per 1-SD higher, 1.51; 95% CI, 1.36-1.78), and sST2 (aHR per 1-SD higher, 1.36; 95% CI, 1.17-1.58) concentrations were significantly associated with mortality. Only GDF-15 level was also associated with heart failure events (HR per 1-SD higher, 1.56; 95% CI, 1.12-2.16). There were no detectable associations between GDF-15, Gal-3, or sST2 concentrations and atherosclerotic CVD events. LIMITATIONS: Event rates for heart failure and atherosclerotic CVD were low. CONCLUSIONS: Adults with CKD and higher circulating GDF-15, Gal-3, and sST2 concentrations experienced greater mortality. Elevated GDF-15 concentration was also associated with an increased rate of heart failure. Further work is needed to elucidate the mechanisms linking these circulating biomarkers with CVD in patients with CKD.

Interactions among plants, bacteria, and fungi reduce extracellular enzyme activities under long-term N fertilization.

Atmospheric nitrogen (N) deposition has enhanced soil carbon (C) stocks in temperate forests. Most research has posited that these soil C gains are driven primarily by shifts in fungal community composition with elevated N leading to declines in lignin degrading Basidiomycetes. Recent research, however, suggests that plants and soil microbes are dynamically intertwined, whereby plants send C subsidies to rhizosphere microbes to enhance enzyme production and the mobilization of N. Thus, under elevated N, trees may reduce belowground C allocation leading to cascading impacts on the ability of microbes to degrade soil organic matter through a shift in microbial species and/or a change in plant-microbe interactions. The objective of this study was to determine the extent to which couplings among plant, fungal, and bacterial responses to N fertilization alter the activity of enzymes that are the primary agents of soil decomposition. We measured fungal and bacterial community composition, root-microbial interactions, and extracellular enzyme activity in the rhizosphere, bulk, and organic horizon of soils sampled from a long-term (>25 years), whole-watershed, N fertilization experiment at the Fernow Experimental Forest in West Virginia, USA. We observed significant declines in plant C investment to fine root biomass (24.7%), root morphology, and arbuscular mycorrhizal (AM) colonization (55.9%). Moreover, we found that declines in extracellular enzyme activity were significantly correlated with a shift in bacterial community composition, but not fungal community composition. This bacterial community shift was also correlated with reduced AM fungal colonization indicating that declines in plant investment belowground drive the response of bacterial community structure and function to N fertilization. Collectively, we find that enzyme activity responses to N fertilization are not solely driven by fungi, but instead reflect a whole ecosystem response, whereby declines in the strength of belowground C investment to gain N cascade through the soil environment.

CD44 variant isoform 9 emerges in response to injury and contributes to the regeneration of the gastric epithelium.

The CD44 gene encodes several protein isoforms due to alternative splicing and post translational modifications. Given that CD44 variant isoform 9 (CD44v9) is expressed within Spasmolytic Polypeptide/TFF2-Expressing Metaplasia (SPEM) glands during repair, CD44v9 may be play a funcitonal role during the process of regeneration of the gastric epithelium. Here we hypothesize that CD44v9 marks a regenerative cell lineage responsive to infiltrating macrophages during regeneration of the gastric epithelium. Ulcers were induced in CD44-deficient (CD44KO) and C57BL/6 (BL6) mice by a localized application of acetic acid to the serosal surface of the stomach. Gastric organoids expressing CD44v9 were derived from mouse stomachs and transplanted at the ulcer site of CD44KO mice. Ulcers, CD44v9 expression, proliferation and histology were measured 1, 3, 5 and 7-days post-injury. Human-derived gastric organoids were generated from stomach tissue collected from elderly (>55 years) or young (14-20 years) patients. Organoids were transplanted into the stomachs of NOD scid gamma (NSG) mice at the site of injury. Gastric injury was induced in NRG-SGM3 (NRGS) mice harboring human-derived immune cells (hnNRGS) and the immune profile anlayzed by CyTOF. CD44v9 expression emerged within regenerating glands the ulcer margin in response to injury. While ulcers in BL6 mice healed within 7-days post-injury, CD44KO mice exhibited loss of repair and epithelial regeneration. Ulcer healing was promoted in CD44KO mice by transplanted CD55v9-expressing gastric organoids. NSG mice exhibited loss of CD44v9 expression and gastric repair. Transplantation of human-derived gastric organoids from young, but not aged stomachs promoted repair in NSG mouse stomachs in response to injury. Finally, compared to NRGS mice, huNRGS animals exhibited reduced ulcer sizes, an infiltration of human CD162+ macrophages and an emergence of CD44v9 expression in SPEM. Thus, during repair of the gastic epithelium CD44v9 emerges within a regenerative cell lineage that coincides with macrophage inflitration within the injured mucosa. Copyright © 2017 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

Growth Differentiation Factor-15 and Risk of CKD Progression.

Growth differentiation factor-15 (GDF-15) is a member of the TGF-ß cytokine superfamily that is widely expressed and may be induced in response to tissue injury. Elevations in GDF-15 may identify a novel pathway involved in loss of kidney function among patients with CKD. Among participants in the Clinical Phenotyping and Resource Biobank (C-PROBE) study and the Seattle Kidney Study (SKS), we tested whether kidney tissue expression of GDF15 mRNA correlates with circulating levels of GDF-15 and whether elevations in circulating GDF-15 are associated with decline in kidney function. In matching samples of 24 patients with CKD from the C-PROBE study, circulating GDF-15 levels significantly correlated with intrarenal GDF15 transcript levels (r=0.54, P=0.01). Among the 224 C-PROBE and 297 SKS participants, 72 (32.1%) and 94 (32.0%) patients, respectively, reached a composite end point of 30% decline in eGFR or progression to ESRD over a median of 1.8 and 2.0 years of follow up, respectively. In multivariable models, after adjusting for potential confounders, every doubling of GDF-15 level associated with a 72% higher (95% confidence interval, 1.21 to 4.45; P=0.003) and 65% higher (95% confidence interval, 1.08 to 2.50; P=0.02) risk of progression of kidney disease in C-PROBE and SKS participants, respectively. These results show that circulating GDF-15 levels strongly correlated with intrarenal expression of GDF15 and significantly associated with increased risk of CKD progression in two independent cohorts. Circulating GDF-15 may be a marker for intrarenal GDF15-related signaling pathways associated with CKD and CKD progression.

Epithelial PIK3R1 (p85) and TP53 Regulate Survivin Expression during Adaptation to Ileocecal Resection.

Intestinal adaptation to small-bowel resection (SBR) after necrotizing enterocolitis expands absorptive surface areas and promotes enteral autonomy. Survivin increases proliferation and blunts apoptosis. The current study examines survivin in intestinal epithelial cells after ileocecal resection. Wild-type and epithelial Pik3r1 (p85α)-deficient mice underwent sham surgery or 30% resection. RNA and protein were isolated from small bowel to determine levels of ß-catenin target gene expression, activated caspase-3, survivin, p85α, and Trp53. Healthy and post-resection human infant small-bowel sections were analyzed for survivin, Ki-67, and TP53 by immunohistochemistry. Five days after ileocecal resection, epithelial levels of survivin increased relative to sham-operated on mice, which correlated with reduced cleaved caspase-3, p85α, and Trp53. At baseline, p85α-deficient intestinal epithelial cells had less Trp53 and more survivin, and relative responses to resection were blunted compared with wild-type. In infant small bowel, survivin in transit amplifying cells increased 71% after SBR. Resection increased proliferation and decreased numbers of TP53-positive epithelial cells. Data suggest that ileocecal resection reduces p85α, which lowers TP53 activation and releases survivin promoter repression. The subsequent increase in survivin among transit amplifying cells promotes epithelial cell proliferation and lengthens crypts. These findings suggest that SBR reduces p85α and TP53, which increases survivin and intestinal epithelial cell expansion during therapeutic adaptation in patients with short bowel syndrome.

The human milk oligosaccharide 2'-fucosyllactose augments the adaptive response to extensive intestinal.

Intestinal resection resulting in short bowel syndrome (SBS) carries a heavy burden of long-term morbidity, mortality, and cost of care, which can be attenuated with strategies that improve intestinal adaptation. SBS infants fed human milk, compared with formula, have more rapid intestinal adaptation. We tested the hypothesis that the major noncaloric human milk oligosaccharide 2'-fucosyllactose (2'-FL) contributes to the adaptive response after intestinal resection. Using a previously described murine model of intestinal adaptation, we demonstrated increased weight gain from 21 to 56 days (P < 0.001) and crypt depth at 56 days (P < 0.0095) with 2'-FL supplementation after ileocecal resection. Furthermore, 2'-FL increased small bowel luminal content microbial alpha diversity following resection (P < 0.005) and stimulated a bloom in organisms of the genus Parabacteroides (log2-fold = 4.1, P = 0.035). Finally, transcriptional analysis of the intestine revealed enriched ontologies and pathways related to antimicrobial peptides, metabolism, and energy processing. We conclude that 2'-FL supplementation following ileocecal resection increases weight gain, energy availability through microbial community modulation, and histological changes consistent with improved adaptation.

Methods for accurate quantification of LTR-retrotransposon copy number using short-read sequence data: a case study in Sorghum.

Transposable elements (TEs) are ubiquitous in eukaryotic genomes and their mobility impacts genome structure and function in myriad ways. Because of their abundance, activity, and repetitive nature, the characterization and analysis of TEs remain challenging, particularly from short-read sequencing projects. To overcome this difficulty, we have developed a method that estimates TE copy number from short-read sequences. To test the accuracy of our method, we first performed an in silico analysis of the reference Sorghum bicolor genome, using both reference-based and de novo approaches. The resulting TE copy number estimates were strikingly similar to the annotated numbers. We then tested our method on real short-read data by estimating TE copy numbers in several accessions of S. bicolor and its close relative S. propinquum. Both methods effectively identify and rank similar TE families from highest to lowest abundance. We found that de novo characterization was effective at capturing qualitative variation, but underestimated the abundance of some TE families, specifically families of more ancient origin. Also, interspecific reference-based mapping of S. propinquum reads to the S. bicolor database failed to fully describe TE content in S. propinquum, indicative of recent TE activity leading to changes in the respective repetitive landscapes over very short evolutionary timescales. We conclude that reference-based analyses are best suited for within-species comparisons, while de novo approaches are more reliable for evolutionarily distant comparisons.

Trusting Social Media as a Source of Health Information: Online Surveys Comparing the United States, Korea, and Hong Kong.

BACKGROUND: The Internet has increasingly become a popular source of health information by connecting individuals with health content, experts, and support. More and more, individuals turn to social media and Internet sites to share health information and experiences. Although online health information seeking occurs worldwide, limited empirical studies exist examining cross-cultural differences in perceptions about user-generated, experience-based information compared to expertise-based information sources. OBJECTIVE: To investigate if cultural variations exist in patterns of online health information seeking, specifically in perceptions of online health information sources. It was hypothesized that Koreans and Hongkongers, compared to Americans, would be more likely to trust and use experience-based knowledge shared in social Internet sites, such as social media and online support groups. Conversely, Americans, compared to Koreans and Hongkongers, would value expertise-based knowledge prepared and approved by doctors or professional health providers more. METHODS: Survey questionnaires were developed in English first and then translated into Korean and Chinese. The back-translation method ensured the standardization of questions. Surveys were administered using a standardized recruitment strategy and data collection methods. RESULTS: A total of 826 participants living in metropolitan areas from the United States (n=301), Korea (n=179), and Hong Kong (n=337) participated in the study. We found significant cultural differences in information processing preferences for online health information. A planned contrast test revealed that Koreans and Hongkongers showed more trust in experience-based health information sources (blogs: t451.50=11.21, P<.001; online support group: t455.71=9.30, P<.001; social networking sites [SNS]: t466.75=11.36, P<.001) and also reported using blogs (t515.31=6.67, P<.001) and SNS (t529.22=4.51, P<.001) more frequently than Americans. Americans showed a stronger preference for using expertise-based information sources (eg, WebMD and CDC) compared to Koreans and Hongkongers (t360.02=3.01, P=.003). Trust in expertise-based information sources was universal, demonstrating no cultural differences (Brown-Forsythe F2,654=1.82, P=.16). Culture also contributed significantly to differences in searching information on behalf of family members (t480.38=5.99, P<.001) as well as to the goals of information searching. CONCLUSIONS: This research found significant cultural differences in information processing preferences for online health information. Further discussion is included regarding effective communication strategies in providing quality health information.

Variation in allelic expression associated with a recombination hotspot in Zea mays.

Gene expression is a complex process, requiring precise spatial and temporal regulation of transcription factor activity; however, modifications of individual cis- and trans-acting modules can be molded by natural selection to create a sizeable number of novel phenotypes. Results from decades of research indicate that developmental and phenotypic divergence among eukaryotic organisms is driven primarily by variation in levels of gene expression that are dictated by mutations, either in structural or regulatory regions, of genes. The relative contributions and interplay of cis- and trans-acting regulatory factors to this evolutionary process, however, remain poorly understood. Analysis of eight genes in the Bz1-Sh1 interval of Zea mays (maize) indicates significant allele-specific expression biases in at least one tissue for all genes, ranging from 1.3-fold to 36-fold. All detected effects were cis-regulatory in nature, although genetic background may also influence the level of expression bias and tissue specificity for some allelic combinations. Most allelic pairs exhibited the same direction and approximate intensity of bias across all four tissues; however, a subset of allelic pairs show alternating dominance across different tissue types or variation in the degree of bias in different tissues. In addition, the genes showing the most striking levels of allelic bias co-localize with a previously described recombination hotspot in this region, suggesting a naturally occurring genetic mechanism for creating regulatory variability for a subset of plant genes that may ultimately lead to evolutionary diversification.

Phylogenetic reconstruction using four low-copy nuclear loci strongly supports a polyphyletic origin of the genus Sorghum.

BACKGROUND AND AIMS: Sorghum is an essential grain crop whose evolutionary placement within the Andropogoneae has been the subject of scrutiny for decades. Early studies using cytogenetic and morphological data point to a poly- or paraphyletic origin of the genus; however, acceptance of poly- or paraphyly has been met with resistance. This study aimed to address the species relationships within Sorghum, in addition to the placement of Sorghum within the tribe, using a phylogenetic approach and employing broad taxon sampling. METHODS: From 16 diverse Sorghum species, eight low-copy nuclear loci were sequenced that are known to play a role in morphological diversity and have been previously used to study evolutionary relationships in grasses. Further, the data for four of these loci were combined with those from 57 members of the Andropogoneae in order to determine the placement of Sorghum within the tribe. Both maximum likelihood and Bayesian analyses were performed on multilocus concatenated data matrices. KEY RESULTS: The Sorghum-specific topology provides strong support for two major lineages, in alignment with earlier studies employing chloroplast and internal transcribed spacer (ITS) markers. Clade I is composed of the Eu-, Chaeto- and Heterosorghum, while clade II contains the Stipo- and Parasorghum. When combined with data from the Andropogoneae, Clade II resolves as sister to a clade containing Miscanthus and Saccharum with high posterior probability and bootstrap support, and to the exclusion of Clade I. CONCLUSIONS: The results provide compelling evidence for a two-lineage polyphyletic ancestry of Sorghum within the larger Andropogoneae, i.e. the derivation of the two major Sorghum clades from a unique common ancestor. Rejection of monophyly in previous molecular studies is probably due to limited taxon sampling outside of the genus. The clade consisting of Para- and Stiposorghum resolves as sister to Miscanthus and Saccharum with strong node support.