• Obesity and Sexual Functioning

      Center for Obesity Research and Education (Temple University) (2018-09-15)
    • Objectively measured sedentary time and cardiovascular risk factor control in US Hispanics/Latinos with diabetes mellitus: Results from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL)

      Wang, X; Strizich, G; Hua, S; Sotres-Alvarez, D; Buelna, C; Gallo, LC; Gellman, MD; Mossavar-Rahmani, Y; O'Brien, MJ; Stoutenberg, M; Wang, T; Larissa Avilés-Santa, M; Kaplan, RC; Qi, Q; Stoutenberg, Mark|0000-0001-5206-7627 (2017-06-01)
      © 2017 The Authors. Background--Cardiovascular disease (CVD) risk factor control is a cornerstone of diabetes mellitus management. Little is known about relationships of objectively measured sedentary time and physical activity with major CVD risk factor control in individuals with diabetes mellitus. We examined associations of objectively measured sedentary time and moderate-to-vigorous physical activity with reaching major CVD risk factor control goals among US Hispanic/Latino adults with diabetes mellitus. Methods and Results--This cross-sectional analysis included 1699 participants with diabetes mellitus from the Hispanic Community Health Study/Study of Latinos (2008-2011). Logistic regression models were used to estimate the odds ratios (ORs) of meeting the following 5 major CVD risk factor control goals: hemoglobin A1c < 7.0%; systolic/diastolic blood pressure < 140/ 80 mm Hg; triglycerides < 150 mg/dL; low-density lipoprotein cholesterol < 100 mg/dL; and high-density lipoprotein cholesterol > 40/50 mg/dL for men/women. After adjustment for covariates including moderate-to-vigorous physical activity, less sedentary time was associated with increased odds of reaching hemoglobin A1c (OR=1.76 [95% CI: 1.10, 2.82]) and triglyceride control goals (OR=2.16 [1.36, 3.46]), and reaching ≥ 3 CVD risk factor control goals (OR=2.08 [1.34, 3.23]) (all ORs for comparisons of extreme tertiles of sedentary time). Moderate-to-vigorous physical activity was not associated with reaching any CVD risk factor control goals. Substituting 60-min/day of sedentary time with light-intensity physical activity was associated with increased odds of reaching hemoglobin A1c (OR=1.18 [1.04, 1.35]), high-density lipoprotein cholesterol (OR=1.17 [1.04, 1.32]), and triglyceride (OR=1.20 [1.05, 1.36]) control goals. Conclusions--Among US Hispanic/Latino adults with diabetes mellitus, less sedentary time, but not moderate-to-vigorous physical activity, was associated with improved CVD risk factor control, specifically in reaching hemoglobin A1c and triglyceride control goals.
    • Observation of superconducting vortex clusters in S/F hybrids

      Di Giorgio, C; Bobba, F; Cucolo, AM; Scarfato, A; Moore, SA; Karapetrov, G; D'Agostino, D; Novosad, V; Yefremenko, V; Iavarone, M (2016-12-09)
      © 2016 The Author(s). While Abrikosov vortices repel each other and form a uniform vortex lattice in bulk type-II superconductors, strong confinement potential profoundly affects their spatial distribution eventually leading to vortex cluster formation. The confinement could be induced by the geometric boundaries in mesoscopic-size superconductors or by the spatial modulation of the magnetic field in superconductor/ferromagnet (S/F) hybrids. Here we study the vortex confinement in S/F thin film heterostructures and we observe that vortex clusters appear near magnetization inhomogeneities in the ferromagnet, called bifurcations. We use magnetic force microscopy to image magnetic bifurcations and superconducting vortices, while high resolution scanning tunneling microscopy is used to obtain detailed information of the local electronic density of states outside and inside the vortex cluster. We find an intervortex spacing at the bifurcation shorter than the one predicted for the same superconductor in a uniform magnetic field equal to the thermodynamical upper critical field H c2. This result is due to a local enhanced stray field and a competition between vortex-vortex repulsion and Lorentz force. Our findings suggest that special magnetic topologies could result in S/F hybrids that support superconductivity even when locally the vortex density exceeds the thermodynamic critical threshold value beyond which the superconductivity is destroyed.
    • Observational study of coagulation activation in early breast cancer: Development of a prognostic model based on data from the real world setting

      Mandoj, C; Pizzuti, L; Sergi, D; Sperduti, I; Mazzotta, M; Di Lauro, L; Amodio, A; Carpano, S; Di Benedetto, A; Botti, C; Ferranti, F; Antenucci, A; D'Alessandro, MG; Marchetti, P; Tomao, S; Sanguineti, G; Giordano, A; Maugeri-Saccà, M; Ciliberto, G; Conti, L; Vici, P; Barba, M; Giordano, Antonio|0000-0002-5959-016X (2018-05-16)
      © 2018 The Author(s). Background: Cancer and coagulation activation are tightly related. The extent to which factors related to both these pathologic conditions concur to patient prognosis intensely animates the inherent research areas. The study herein presented aimed to the development of a tool for the assessment and stratification of risk of death and disease recurrence in early breast cancer. Methods: Between 2008 and 2010, two hundreds thirty-five (N: 235) patients diagnosed with stage I-IIA breast cancer were included. Data on patient demographics and clinic-pathologic features were collected in course of face-to-face interviews or actively retrieved from clinical charts. Plasma levels of plasminogen activator inhibitor type 1 (PAI-1), fragment 1 + 2 (F1 + 2), thrombin antithrombin complex (TAT), factor VIII (FVIII), and D-dimer (DD) were measured at breast cancer diagnosis and prior to any therapeutic procedure, including breast surgery. The risk of death was computed in terms of overall survival (OS), which was the primary outcome. For a subset of patients (N = 62), disease free survival (DFS) was also assessed as a measure of risk of disease recurrence. Results: Median follow up was 95 months (range 6-112 months). Mean age at diagnosis was 60.3 ± 13.4 years. Cancer cases were more commonly intraductal carcinomas (N: 204; 86.8%), pT1 (131; 55.7%), pN0 (141; 60%) and G2 (126; 53.6%). Elevated levels of PAI-1 (113; 48.1%) represented the most frequent coagulation abnormality, followed by higher levels of F1 + 2 (97; 41.3%), DD (63; 27.0%), TAT (34; 40%), and FVIII (29; 12.3%). In univariate models of OS, age, pT, DD, FVIII were prognostically relevant. In multivariate models of OS, age (p = 0.043), pT (p = 0.001), levels of DD (p = 0.029) and FVIII (p = 0.087) were confirmed. In the smaller subgroup of 62 patients, lymph node involvement, percent expression of estrogen receptors and levels of FVIII impacted DFS significantly. Conclusions: We developed a risk assessment tool for OS including patient- and cancer-related features along with biomarkers of coagulation activation in a cohort of early BC patients. Further studies are warranted to validate our prognostic model in the early setting and eventually extend its application to risk evaluation in the advanced setting for breast and other cancers.
    • Occupational physical activity and body mass index: Results from the hispanic community health study / study of Latinos

      Singer, RH; Stoutenberg, M; Gellman, MD; Archer, E; Davis, SM; Gotman, N; Marquez, DX; Buelna, C; Deng, Y; Hosgood, HD; Zambrana, RE; Stoutenberg, Mark|0000-0001-5206-7627 (2016-03-01)
      © 2016 Singer et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Purpose: To examine the associations between overweight/obesity and occupation among Hispanics/Latinos, the largest minority population in the U.S. Methods: This study included 7,409 employed individuals in the Hispanic Community Health Study/Study of Latinos (HCHS/SOL), a prospective study of Hispanic/Latino individuals aged 18-74 in four communities in the U.S. We independently examined the relationships between BMI, Occupational Activity (OA), and Total Hours Worked, quantified via self-reported hours worked per week and occupation-assigned Metabolic Equivalents (METs). Results: More than three quarters of the participants were either overweight (39.3%) or obese (37.8%). Individuals with a primary occupation and those employed in a secondary occupation worked an average of 36.8 and 14.6 hrs/wk, respectively. The overall adjusted odds for being obese compared to normal weight were 3.2% (AOR = 1.03, 95% CI 1.01, 1.05) and 14.4% (AOR = 1.14 95% Cl 1.07, 1.23) greater for each 10 MET·hrs/wk unit of increased OA, and each 10-hrs/wk unit of Total Hours Worked, respectively. Conclusion: This study presents the first findings on the association between OA with overweight/obesity among Hispanic/Latino individuals in the U.S. Increasing OA and Total Hours Worked per week were independently associated with increasing odds of overweight/obesity suggesting that the workplace is only one part of the overall energy expenditure dynamic. Our findings point to the need to emphasize engaging employed individuals in greater levels of PA outside of the work environment to impact overweight/obesity.
    • Offspring of Mothers With Histories of Chronic and Non-chronic Depression: Symptom Trajectories From Ages 6 to 15

      Silver, J; Olino, TM; Carlson, GA; Klein, DN (2020-11-19)
      © Copyright © 2020 Silver, Olino, Carlson and Klein. Several studies have reported that individuals with chronic depression have higher rates of depressive disorders, and particularly chronic depression, in their first-degree relatives, compared to those with non-chronic (episodic) major depression. In addition, a few studies have suggested that offspring of parents with chronic depression have elevated rates of depression and other psychopathology. Most of this work uses the Diagnostic and Statistical Manual of Mental Disorders (DSM), which defines chronicity as persistence for at least 2 years. An alternative is a life-course, approach, which evaluates overall course since first onset. We examined the trajectories of depressive, anxiety, and externalizing symptoms in a community sample of 577 offspring of mothers with histories of chronic depression, non-chronic (or episodic) major depression, and no depression using prospective, multi-informant assessments from age 6 to age 15. Offspring of mothers with a history of depression exhibited higher levels of depression, anxiety, and externalizing symptoms than offspring of mothers who were never depressed. Moreover, the effects of maternal depression on offspring depression, anxiety, and externalizing symptoms were more pronounced for mothers with histories of chronic than non-chronic depression, particularly when the life-course approach to classifying chronicity was used. These data suggest that research that combines chronic and non-chronic depressions includes significant heterogeneity that may hinder understanding of etiology and reduce the likelihood of developing a cumulative and replicable literature. In addition, these findings have significant implications for prevention and treatment.
    • On dynamic pitch benefit for speech recognition in speech masker

      Shen, J; Souza, PE (2018-10-22)
      © 2018 Shen and Souza. Previous work demonstrated that dynamic pitch (i.e., pitch variation in speech) aids speech recognition in various types of noises. While this finding suggests dynamic pitch enhancement in target speech can benefit speech recognition in noise, it is of importance to know what noise characteristics affect dynamic pitch benefit, and who will benefit from enhanced dynamic pitch cues. Following our recent finding that temporal modulation in noise influences dynamic pitch benefit, we examined the effect of speech masker characteristics on dynamic pitch benefit. Specifically, the first goal of the study was to test the hypothesis that dynamic pitch benefit varies depending on the availability of pitch cues in the masker and the intelligibility of masker. The second goal of this study was to investigate whether older listeners as a group can benefit from dynamic pitch for speech recognition in speech maskers. In addition, individual factors of hearing loss and working memory capacity were examined for their impact on older listeners' dynamic pitch benefit. Twenty-three younger listeners with normal hearing and 37 older listeners with varying levels of hearing sensitivity participated the study, in which speech reception thresholds were measured with sentences in speech maskers. While we did not find an effect of masker characteristics on dynamic pitch benefit, the results showed older listeners can benefit from dynamic pitch for recognizing speech in speech maskers. The data also suggest that among those older listeners with hearing loss, dynamic pitch benefit is stronger for individuals with higher working memory capacity. This can be attributed to their ability to exploit facilitated lexical access in processing of degraded speech signal.
    • On Objects, Trauma, and Loss: An Interview with Laura Levitt

      Handelman, Kali; Levitt, Laura S. (2021-02-04)
    • On Seams and Seamlessness

      Alpert, Rebecca; 0000-0001-7536-9695 (1995)
      When Laura Levitt, my friend and colleague at Temple University, asked me to participate in this forum, my first response was a categorical no. Laura and I have talked about our different perspectives about postmodern approaches to Jewish feminism infrequently over the last several years. The conversations always end with us restating our differences, agreeing to disagree. Because my feelings are so strong about this subject, I was reluctant to have this conversation in public. Yet Laura persuaded me to consider participation, in full knowledge that this would be an airing of our differences, and I have taken the risk to do so. My contribution, a letter to Laura, is an effort to bring my love for her into the context of what is, for me, a passionate and acrimonious intellectual debate that has important implicationsfor the future ofJewish feminism.
    • On the diversity of malaria parasites in African apes and the origin of Plasmodium falciparum from bonobos

      Krief, S; Escalante, AA; Pacheco, MA; Mugisha, L; André, C; Halbwax, M; Fischer, A; Krief, JM; Kasenene, JM; Crandfield, M; Cornejo, OE; Chavatte, JM; Lin, C; Letourneur, F; Grüner, AC; McCutchan, TF; Rénia, L; Snounou, G (2010-02-01)
      The origin of Plasmodium falciparum, the etiological agent of the most dangerous forms of human malaria, remains controversial. Although investigations of homologous parasites in African Apes are crucial to resolve this issue, studies have been restricted to a chimpanzee parasite related to P. falciparum, P. reichenowi, for which a single isolate was available until very recently. Using PCR amplification, we detected Plasmodium parasites in blood samples from 18 of 91 individuals of the genus Pan, including six chimpanzees (three Pan troglodytes troglodytes, three Pan t. schweinfurthii) and twelve bonobos (Pan paniscus). We obtained sequences of the parasites' mitochondrial genomes and/or from two nuclear genes from 14 samples. In addition to P. reichenowi, three other hitherto unknown lineages were found in the chimpanzees. One is related to P. vivax and two to P. falciparum that are likely to belong to distinct species. In the bonobos we found P. falciparum parasites whose mitochondrial genomes indicated that they were distinct from those present in humans, and another parasite lineage related to P. malariae. Phylogenetic analyses based on this diverse set of Plasmodium parasites in African Apes shed new light on the evolutionary history of P. falciparum. The data suggested that P. falciparum did not originate from P. reichenowi of chimpanzees (Pan troglodytes), but rather evolved in bonobos (Pan paniscus), from which it subsequently colonized humans by a host-switch. Finally, our data and that of others indicated that chimpanzees and bonobos maintain malaria parasites, to which humans are susceptible, a factor of some relevance to the renewed efforts to eradicate malaria.
    • On the number of new world founders: A population genetic portrait of the peopling of the Americas

      Hey, J (2005-01-01)
      The founding of New World populations by Asian peoples is the focus of considerable archaeological and genetic research, and there persist important questions on when and how these events occurred. Genetic data offer great potential for the study of human population history, but there are significant challenges in discerning distinct demographic processes. A new method for the study of diverging populations was applied to questions on the founding and history of Amerind-speaking Native American populations. The model permits estimation of founding population sizes, changes in population size, time of population formation, and gene flow. Analyses of data from nine loci are consistent with the general portrait that has emerged from archaeological and other kinds of evidence. The estimated effective size of the founding population for the New World is fewer than 80 individuals, approximately 1% of the effective size of the estimated ancestral Asian population. By adding a splitting parameter to population divergence models it becomes possible to develop detailed portraits of human demographic history. Analyses of Asian and New World data support a model of a recent founding of the New World by a population of quite small effective size. © 2005 Jody Hey.
    • Open versus Traditional Textbooks: A Comparison of Student Engagement and Performance

      Chang, Isabelle (2020)
      This study compared student engagement and performance in both open educational resources (OER) (n[open textbook users fall 2018] = 72) and traditional textbook (n[traditional textbook users fall 2017] = 66) classes. Data were drawn from the Learning Management System (LMS). Results show (1) final grades in the OER class were on a par with the traditional textbook class, and (2) OER equalize student engagement and performance by narrowing the dispersions of page views, on-time assignment submissions (OTAS), attendance, and final grades. (3) OER increased attendance and lessened excessive dependence on LMS course materials recorded in the traditional class. (4) The indirect effect of attendance on final grades was stronger than the direct effect of OTAS in the OER class. Attendance provided the opportunity for the instructor and students to be on the “same page,” which helps students better assimilate course content and comprehend lectures. (5) The availability of textbooks appears to be a factor influencing student course success. However, it remains unknown how much of the variance was explained by OER. It is apparent that OER are more important than ever in elevating overall student academic success.
    • Opioid use prior to knee arthroplasty in patients who catastrophize about their pain: Preoperative data from a multisite randomized clinical trial

      Riddle, DL; Slover, JD; Ang, DC; Bair, MJ; Kroenke, K; Perera, RA; Dumenci, L (2018-01-01)
      © 2018 Riddle et al. Background: Opioid use rates prior to knee arthroplasty (KA) among people who catastrophize about their pain are unknown. We determined prevalence of opioid use and compared patterns of preoperative opioid use and oral morphine equivalent (OME), a measure of daily opioid dose, across varied geographic sites. We also determined which baseline variables were associated with opioid use and OME. Patients and methods: Preoperative opioid use data described type of opioid, dosage, and frequency among 397 patients scheduled for KA. Demographic, knee-related pain, and psychological distress dimensions were examined to identify variables associated with opioid use and opioid dose (OME). Opioid use prevalence and OME were compared across the four sites. A three-level censored regression determined variables associated with opioid use and OME. Results: The overall opioid use prevalence was 31.7% (95% confidence interval [CI] = 27.0, 36.3) and varied across sites from 15.9% (95% CI = 9.0, 22.8) to 51.2% (95% CI = 40.5, 61.9). After adjustment, patients using opioids were more likely to be younger, African American, and have higher self-efficacy and comorbidity scores (P < 0.05). The only variable independently associated with OME was lower depressive symptoms (P < 0.05). Conclusion: People who catastrophized prior to KA did not demonstrate increased preoperative opioid use based on current evidence, but variation in the prevalence of opioid use across study sites was substantial. Variables associated with opioid use were non-modifiable demographic and comorbidity variables.
    • Optimal, minimax and admissible two-stage design for phase II oncology clinical trials

      Qin, F; Wu, J; Chen, F; Wei, Y; Zhao, Y; Jiang, Z; Bai, J; Yu, H (2020-05-20)
      © 2020 The Author(s). Background: The article aims to compare the efficiency of minimax, optimal and admissible criteria in Simon's and Fleming's two-stage design. Methods: Three parameter settings (p 1-p 0 = 0.25-0.05, 0.30-0.10, 0.50-0.30) are designed to compare the maximum sample size, the critical values and the expected sample size for minimax, optimal and admissible designs. Type I & II error constraints (α, β) vary across (0.10, 0.10), (0.05, 0.20) and (0.05, 0.10), respectively. Results: In both Simon's and Fleming's two-stage designs, the maximum sample size of admissible design is smaller than optimal design but larger than minimax design. Meanwhile, the expected samples size of admissible design is smaller than minimax design but larger than optimal design. Mostly, the maximum sample size and expected sample size in Fleming's designs are considerably smaller than that of Simon's designs. Conclusions: Whenever (p 0, p 1) is pre-specified, it is better to explore in the range of probability q, based on relative importance between maximum sample size and expected sample size, and determine which design to choose. When q is unknown, optimal design may be more favorable for drugs with limited efficacy. Contrarily, minimax design is recommended if treatment demonstrates impressive efficacy.
    • Organization and differential expression of the GACA/GATA tagged somatic and spermatozoal transcriptomes in Buffalo Bubalus bubalis

      Srivastava, J; Premi, S; Kumar, S; Ali, S; Kumar, Sudhir|0000-0002-9918-8212 (2008-03-20)
      Background: Simple sequence repeats (SSRs) of GACA/GATA have been implicated with differentiation of sex-chromosomes and speciation. However, the organization of these repeats within genomes and transcriptomes, even in the best characterized organisms including human, remains unclear. The main objective of this study was to explore the buffalo transcriptome for its association with GACA/GATA repeats, and study the structural organization and differential expression of the GACA/GATA repeat tagged transcripts. Moreover, the distribution of GACA and GATA repeats in the prokaryotic and eukaryotic genomes was studied to highlight their significance in genome evolution. Results: We explored several genomes and transcriptomes, and observed total absence of these repeats in the prokaryotes, with their gradual accumulation in higher eukaryotes. Further, employing novel microsatellite associated sequence amplification (MASA) approach using varying length oligos based on GACA and GATA repeats; we identified and characterized 44 types of known and novel mRNA transcripts tagged with these repeats from different somatic tissues, gonads and spermatozoa of water buffalo Bubalus bubalis. GACA was found to be associated with higher number of transcripts compared to that with GATA. Exclusive presence of several GACA-tagged transcripts in a tissue or spermatozoa, and absence of the GATA-tagged ones in lung/heart highlights their tissue-specific significance. Of all the GACA/GATA tagged transcripts, ∼30% demonstrated inter-tissue and/or tissue-spermatozoal sequence polymorphisms. Significantly, ∼60% of the GACA-tagged and all the GATA-tagged transcripts showed highest or unique expression in the testis and/or spermatozoa. Moreover, ∼75% GACA-tagged and all the GATA-tagged transcripts were found to be conserved across the species. Conclusion: Present study is a pioneer attempt exploring GACA/GATA tagged transcriptome in any mammalian species highlighting their tissue, stage and species-specific expression profiles. Comparative analysis suggests the gradual accumulation of these repeats in the higher eukaryotes, and establishes the GACA richness of the buffalo transcriptome. This is envisaged to establish the roles of integral simple sequence repeats and tagged transcripts in gene expression or regulation. © 2008 Srivastava et al; licensee BioMed Central Ltd.
    • Origin and evolution of sulfadoxine resistant Plasmodium falciparum

      Vinayak, S; Alam, T; Mixson-Hayden, T; McCollum, AM; Sem, R; Shah, NK; Lim, P; Muth, S; Rogers, WO; Fandeur, T; Barnwell, JW; Escalante, AA; Wongsrichanalai, C; Ariey, F; Meshnick, SR; Udhayakumar, V (2010-03-01)
      The Thailand-Cambodia border is the epicenter for drug-resistant falciparum malaria. Previous studies have shown that chloroquine (CQ) and pyrimethamine resistance originated in this region and eventually spread to other Asian countries and Africa. However, there is a dearth in understanding the origin and evolution of dhps alleles associated with sulfadoxine resistance. The present study was designed to reveal the origin(s) of sulfadoxine resistance in Cambodia and its evolutionary relationship to African and South American dhps alleles. We sequenced 234 Cambodian Plasmodium falciparum isolates for the dhps codons S436A/F, A437G, K540E, A581G and A613S/T implicated in sulfadoxine resistance. We also genotyped 10 microsatellite loci around dhps to determine the genetic backgrounds of various alleles and compared them with the backgrounds of alleles prevalent in Africa and South America. In addition to previously known highly-resistant triple mutant dhps alleles SGEGA and AGEAA (codons 436, 437, 540, 581, 613 are sequentially indicated), a large proportion of the isolates (19.3%) contained a 540N mutation in association with 437G/581G yielding a previously unreported triple mutant allele, SGNGA. Microsatellite data strongly suggest the strength of selection was greater on triple mutant dhps alleles followed by the double and single mutants. We provide evidence for at least three independent origins for the double mutants, one each for the SGKGA, AGKAA and SGEAA alleles. Our data suggest that the triple mutant allele SGEGA and the novel allele SGNGA have common origin on the SGKGA background, whereas the AGEAA triple mutant was derived from AGKAA on multiple, albeit limited, genetic backgrounds. The SGEAA did not share haplotypes with any of the triple mutants. Comparative analysis of the microsatellite haplotypes flanking dhps alleles from Cambodia, Kenya, Cameroon and Venezuela revealed an independent origin of sulfadoxine resistant alleles in each of these regions.
    • Origins and Evolution of MicroRNA Genes in Drosophila Species

      Nozawa, Masafumi; Miura, Sayaka; Nei, Masatoshi (2010)
      MicroRNAs (miRs) regulate gene expression at the posttranscriptional level. To obtain some insights into the origins and evolutionary patterns of miR genes, we have identified miR genes in the genomes of 12 Drosophila species by bioinformatics approaches and examined their evolutionary changes. The results showed that the extant and ancestral Drosophila species had more than 100 miR genes and frequent gains and losses of miR genes have occurred during evolution. Although many miR genes appear to have originated from random hairpin structures in intronic or intergenic regions, duplication of miR genes has also contributed to the generation of new miR genes. Estimating the rate of nucleotide substitution of miR genes, we have found that newly arisen miR genes have a substitution rate similar to that of synonymous nucleotide sites in protein-coding genes and evolve almost neutrally. This suggests that most new miR genes have not acquired any important function and would become inactive. By contrast, old miR genes show a substitution rate much lower than the synonymous rate. Moreover, paired and unpaired nucleotide sites of miR genes tend to remain unchanged during evolution. Therefore, once miR genes acquired their functions, they appear to have evolved very slowly, maintaining essentially the same structures for a long time.
    • Origins and Evolution of MicroRNA Genes in Plant Species

      Nozawa, Masafumi; Miura, Sayaka; Nei, Masatoshi (2012)
      MicroRNAs (miRNAs) are among the most important regulatory elements of gene expression in animals and plants. However, their origin and evolutionary dynamics have not been studied systematically. In this paper, we identified putative miRNA genes in 11 plant species using the bioinformatic technique and examined their evolutionary changes. Our homology search indicated that no miRNA gene is currently shared between green algae and land plants. The number of miRNA genes has increased substantially in the land plant lineage, but after the divergence of eudicots and monocots, the number has changed in a lineage-specific manner. We found that miRNA genes have originated mainly by duplication of preexisting miRNA genes or protein-coding genes. Transposable elements also seem to have contributed to the generation of species-specific miRNA genes. The relative importance of these mechanisms in plants is quite different from that in Drosophila species, where the formation of hairpin structures in the genomes seems to be a major source of miRNA genes. This difference in the origin of miRNA genes between plants and Drosophila may be explained by the difference in the binding to target mRNAs between plants and animals. We also found that young miRNA genes are less conserved than old genes in plants as well as in Drosophila species. Yet, nearly half of the gene families in the ancestor of flowering plants have been lost in at least one species examined. This indicates that the repertoires of miRNA genes have changed more dynamically than previously thought during plant evolution.
    • Origins of shared genetic variation in African cichlids

      Loh, YHE; Bezault, E; Muenzel, FM; Roberts, RB; Swofford, R; Barluenga, M; Kidd, CE; Howe, AE; Di Palma, F; Lindblad-Toh, K; Hey, J; Seehausen, O; Salzburger, W; Kocher, TD; Streelman, JT (2013-04-01)
      Cichlid fishes have evolved tremendous morphological and behavioral diversity in the waters of East Africa. Within each of the Great Lakes Tanganyika, Malawi, and Victoria, the phenomena of hybridization and retention of ancestral polymorphism explain allele sharing across species. Here, we explore the sharing of single nucleotide polymorphisms (SNPs) between the major East African cichlid assemblages. A set of approximately 200 genic and nongenic SNPs was ascertained in five Lake Malawi species and genotyped in a diverse collection of ∼160 species from across Africa. We observed segregating polymorphism outside of the Malawi lineage for more than 50% of these loci; this holds similarly for genic versus nongenic SNPs, as well as for SNPs at putative CpG versus non-CpG sites. Bayesian and principal component analyses of genetic structure in the data demonstrate that the Lake Malawi endemic flock is not monophyletic and that river species have likely contributed significantly to Malawi genomes. Coalescent simulations support the hypothesis that river cichlids have transported polymorphism between lake assemblages. We observed strong genetic differentiation between Malawi lineages for approximately 8% of loci, with contributions from both genic and nongenic SNPs. Notably, more than half of these outlier loci between Malawi groups are polymorphic outside of the lake. Cichlid fishes have evolved diversity in Lake Malawi as new mutations combined with standing genetic variation shared across East Africa. © 2012 The Author(s) 2012. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.