Evolutionary Analysis of Mitogenomes from Parasitic and Free-Living Flatworms

Mitochondrial genomes (mitogenomes) are useful and relatively accessible sources of molecular data to explore and understand the evolutionary history and relationships of eukaryotic organisms across diverse taxonomic levels. The availability of complete mitogenomes from Platyhelminthes is limited; of the 40 or so published most are from parasitic flatworms (Neodermata). Here, we present the mitogenomes of two free-living flatworms (Tricladida): the complete genome of the freshwater species Crenobia alpina (Planariidae) and a nearly complete genome of the land planarian Obama sp. (Geoplanidae). Moreover, we have reanotated the published mitogenome of the species Dugesia japonica (Dugesiidae). This contribution almost doubles the total number of mtDNAs published for Tricladida, a species-rich group including model organisms and economically important invasive species. We took the opportunity to conduct comparative mitogenomic analyses between available free-living and selected parasitic flatworms in order to gain insights into the putative effect of life cycle on nucleotide composition through mutation and natural selection. Unexpectedly, we did not find any molecular hallmark of a selective relaxation in mitogenomes of parasitic flatworms; on the contrary, three out of the four studied free-living triclad mitogenomes exhibit higher A+T content and selective relaxation levels. Additionally, we provide new and valuable molecular data to develop markers for future phylogenetic studies on planariids and geoplanids.     

Carotid Atherosclerotic Disease Predicts Cardiovascular Events in Hemodialysis Patients: A Prospective Study

Background

To evaluate the predictive value of carotid atherosclerotic disease (CAD) and intima-media thickness (IMT) on incident cardiovascular disease and mortality in hemodialysis patients.

Methods

Multicenter, observational, prospective study including 110 patients, followed-up to 6 years. Carotid doppler ultrasonographic findings were classified in 4 degrees of severity: 1) IMT <0.9 mm, 2) IMT >0.9 mm, 3) carotid plaque with stenosis <50% and 4) plaque with stenosis >50%. The associations between IMT and CAD and cardiovascular events, total and cardiovascular mortality were assessed.

Results

83% of the patients had atherosclerotic plaques (CAD degrees 3-4). During follow-up, 29.1% of patients experienced cardiovascular events, and 28.2% died, 38.7% of cardiovascular origin. The presence of plaques was associated with cardiovascular events (p = 0.03) while calcified plaques were associated with both cardiovascular events (p = 0.01), cardiovascular mortality (p = 0.03) and non-significantly with overall mortality (p = 0.08) in the survival analysis. Carotid IMT was not associated with outcomes. Cardiovascular events correlated with CAD severity (HR 2.27, 95% CI 1.13-4.54), age (HR 1.04, 1.01-1.06), previous cardiovascular disease (HR 1.75, 1.05-4.42), dyslipidemia (HR 2.25, 1.11-4.53), lipoprotein (a) (HR 1.01, 1.00-1.02), troponin I (HR 3.89, 1.07-14.18), fibrinogen levels (HR 1.38, 0.98-1.94) and antiplatelet therapy (HR 2.14, 1.04-4.4). In an age-adjusted multivariate model, cardiovascular events were independently associated with previous coronary artery disease (HR 3.29, 1.52-7.15) and lipoprotein (a) (HR 1.01, 1.00-1.02).

Conclusions

The presence of carotid plaques and, especially, calcified plaques, are predictors of new cardiovascular events and cardiovascular mortality in hemodialysis patients, while IMT was not. The prognostic value of calcified plaques should be confirmed in future studies.     

Prevalent HLA Class II Alleles in Mexico City Appear to Confer Resistance to the Development of Amebic Liver Abscess

Amebiasis is an endemic disease and a public health problem throughout Mexico, although the incidence rates of amebic liver abscess (ALA) vary among the geographic regions of the country. Notably, incidence rates are high in the northwestern states (especially Sonora with a rate of 12.57/100,000 inhabitants) compared with the central region (Mexico City with a rate of 0.69/100,000 inhabitants). These data may be related to host genetic factors that are partially responsible for resistance or susceptibility. Therefore, we studied the association of the HLA-DRB1 and HLA-DQB1 alleles with resistance or susceptibility to ALA in two Mexican populations, one each from Mexico City and Sonora. Ninety ALA patients were clinically diagnosed by serology and sonography. Genomic DNA was extracted from peripheral blood mononuclear cells. To establish the genetic identity of both populations, 15 short tandem repeats (STRs) were analyzed with multiplexed PCR, and the allelic frequencies of HLA were studied by PCR-SSO using LUMINEX technology. The allele frequencies obtained were compared to an ethnically matched healthy control group (146 individuals). We observed that both affected populations differed genetically from the control group. We also found interesting trends in the population from Mexico City. HLA-DQB1*02 allele frequencies were higher in ALA patients compared to the control group (0.127 vs 0.047; p= 0.01; pc= NS; OR= 2.9, 95% CI= 1.09-8.3). The less frequent alleles in ALA patients were HLA-DRB1*08 (0.118 vs 0.238 in controls; p= 0.01; pc= NS; OR= 0.42, 95% CI= 0.19-0.87) and HLA-DQB1*04 (0.109 vs 0.214; p= 0.02; pc= NS; OR= 0.40, 95% CI= 0.20-0.94). The haplotype HLA-DRB1*08/-DQB1*04 also demonstrated a protective trend against the development of this disease (0.081 vs. 0.178; p=0.02; pc=NS; OR= 0.40, 95% CI= 0.16-0.93). These trends suggest that the prevalent alleles in the population of Mexico City may be associated with protection against the development of ALA.     

The Effect of Filamentous Turf Algal Removal on the Development of Gametes of the Coral Orbicella annularis

Macroalgae and filamentous turf algae (FTA) are abundant on degraded coral reefs, and the reproductive responses of corals may indicate sub-lethal stress under these conditions. The percentage of gametogenic stages (PGS) and the maximum diameter of eggs (MDE; or egg size) of Orbicella annularis were used to evaluate the effect of long- (7–10 months) and short-term (2.5 months) FTA removal (treatments T1 and T2, respectively) at both the beginning (May) and the end (August) of gametogenesis. Ramets (individual lobes of a colony) surrounded by FTA (T3) or crustose coralline algae (CCA; T4) were used as controls. The removal of FTA enhanced the development of gametes (i.e., a larger and higher percentage of mature gametes (PMG)) of O. annularis for T1 vs. T3 ramets in May and T1 and T2 vs. T3 ramets in August. Similar values of PGS and MDE between gametes from T3 and T4 in both May and August were unexpected because a previous study had shown that the same ramets of T4 (with higher tissue thickness, chlorophyll a cm^-2 and zooxanthellae density and lower mitotic index values) were less stressed than ramets of T3. Evaluating coral stress through reproduction can reveal more sensitive responses than other biological parameters; within reproductive metrics, PGS can be a better stress indicator than egg size. The presence of turf algae strongly impacted the development of gametes and egg size (e.g., PMG in ramets with FTA removal increased almost twofold in comparison with ramets surrounded by FTA in August), most likely exerting negative chronic effects in the long run due to the ubiquity and permanence of turf algae in the Caribbean. These algae can be considered a stressor that affects coral sexual reproduction. Although the effects of turf algae on O. annularis are apparently less severe than those of other stressors, the future of this species is uncertain because of the combined impacts of these effects, the decline of O. annularis populations and the almost complete lack of recruitment.     

Influenza Illness among Case-Patients Hospitalized for Suspected Dengue,El Salvador, 2012

We estimate the proportion of patients hospitalized for suspected dengue that tested positive for influenza virus in El Salvador during the 2012 influenza season. We tested specimens from 321 hospitalized patients: 198 patients with SARI and 123 patients with suspected dengue. Among 121 hospitalized suspected dengue (two co-infected excluded) patients, 28% tested positive for dengue and 19% positive for influenza; among 35 with suspected dengue and respiratory symptoms, 14% were positive for dengue and 39% positive for influenza. One percent presented co-infection between influenza and dengue. Clinicians should consider the diagnosis of influenza among patients with suspected dengue during the influenza season.     

Endemic Viruses of Squirrel Monkeys (Saimiri spp.)

Nonhuman primates are the experimental animals of choice for the study of many human diseases. As such, it is important to understand that endemic viruses of primates can potentially affect the design, methods, and results of biomedical studies designed to model human disease. Here we review the viruses known to be endemic in squirrel monkeys (Saimiri spp.). The pathogenic potential of these viruses in squirrel monkeys that undergo experimental manipulation remains largely unexplored but may have implications regarding the use of squirrel monkeys in biomedical research.Abbreviations: HTLV1, human T-cell leukemia virus type 1; HVS, herpesvirus saimiri; IPF, idiopathic pulmonary fibrosis; SaHV, Saimiriine herpesvirus; SFV, simian foamy virus; SM-CMV, squirrel monkey cytomegalovirus; SMPyV, squirrel monkey polyomavirus; SMRV, squirrel monkey retrovirusThe similarity between the nonhuman primate and human immune systems is a key advantage in the use of nonhuman primates compared with other mammalian models of human disease.^{13,71,88,94,103,113,125} In addition, the diversity of environmental and infectious disease agents encountered by primates is similar to that of humans, providing nonhuman primates a comparable level of biologic complexity.¹ Old World primates, such as macaques and baboons, and New World primates, including squirrel monkeys and marmosets, are commonly used in biomedical research. Squirrel monkeys (Saimiri spp.) are neotropical primates native to the forests of Central and South America. Of the 7 species of squirrel monkey, 3 (S. oerstedii, S. vanzolinii, and S. ustus) are classified as endangered, vulnerable to extinction in the wild, or near threatened, whereas the remaining 4 (S. boliviensis, S. cassiquiarensis, S. macrodon, and S. sciureus) are not endangered, although the S. cassiquiarensis albigena subspecies is near threatened^52,81 (Figure 1). In South America, where squirrel monkeys are indigenous, breeding colonies of S. sciureus have been maintained at the Pasteur Institute in French Guiana and at the Oswaldo Cruz Foundation in Brazil.^7,12 In the United States, the Squirrel Monkey Breeding and Research Resource, an NIH-sponsored national research resource, maintains breeding colonies for S. boliviensis boliviensis, S. sciureus sciureus, and S. boliviensis peruviensis.Open in a separate windowFigure 1.Taxonomy of Saimiri species with associated IUCN designations.^52,81Squirrel monkeys adapt easily to laboratory housing and can be housed in smaller spaces than can Old World primates.¹ Unlike when working with Old World primates, particularly macaques, no additional personnel protective equipment is necessary when working with squirrel monkeys beyond that recommended for working with other New World primates.⁹² Their small size, combined with the reduced need for personnel protective equipment during handling, make squirrel monkeys attractive species for model development and for studies of viral pathogenesis, which cost approximately 30% to 40% less than comparable studies in macaques.¹ The likelihood of zoonotic transmission of infectious pathogens is considerably less than that associated with macaques and the risk of Macacine herpesvirus 1 (B virus) is nonexistent, given that neotropical primates do not harbor this lethal virus.¹ These factors are increasingly important in the current climate of limited grant funding for biomedical research and emphasis on safety for laboratory personnel. The limited availability of immunologic reagents with specificity for neotropical primates has hindered broader use of squirrel monkeys in biomedical research, compared with that of the more commonly used Old World primates. In addition, the small size of neotropical primates limits the volume of blood that can be collected at any one time. To abrogate these limitations, the NIH Nonhuman Primate Reagent Resource (www.nhpreagents.org) provides an increasing repertoire of agents that have been characterized for immunologic studies of neotropical primates.⁸⁹Squirrel monkeys are used in numerous aspects of biomedical research, including studies of viral persistence, neuroendocrinology, infectious diseases, cancer treatments, vaccine development, gene expression, and reproductive physiology.¹¹⁷ The similarity between the squirrel monkey immune system and that of humans means that, as with macaques, there is a high likelihood that research outcomes will recapitulate what occurs in human diseases.^13,71,87,94 This is particularly true for the study of several notable infectious diseases, including malaria, Creutzfeldt–Jakob disease, and human T-cell leukemia virus type 1 (HTLV1) infection.^19,56,128 For these diseases, squirrel monkeys are the model system of choice for studying pathogenesis, experimental treatments, and strategies for prevention.Squirrel monkeys are recognized as some of the most susceptible nonhuman primate species for the experimental transmission of Creutzfeldt–Jakob disease and other transmissible spongiform encephalopathies that cause chronic wasting disease.^11,72,98,130 The experimental infection of squirrel monkeys with HTLV1 has led to their use in vaccine development and chemotherapy research directed against HTLV1.^44,57,58,82 In addition, squirrel monkeys are an important model for studying the immunology of malaria and for testing vaccines against several Plasmodium species.^19,20,68,114 Furthermore, squirrel monkeys have been used in pharmacologic research to raise HDL levels to prevent atherosclerosis and reduce the risk of coronary heart disease.⁶ As the use of squirrel monkeys increases, especially for infectious disease research, accurate information about the endemic viral infections of squirrel monkeys is needed because of the potential for zoonotic transfer of these viruses to humans (and vice versa) and to understand the potential influence these agents may have on research involving other infectious pathogens diseases and immunosuppressive drugs.     

Absolute Leukocyte Telomere Length in HIV-Infected and Uninfected Individuals: Evidence of Accelerated Cell Senescence in HIV-Associated Chronic Obstructive Pulmonary Disease

Combination antiretroviral therapy (cART) has extended the longevity of human immunodeficiency virus (HIV)-infected individuals. However, this has resulted in greater awareness of age-associated diseases such as chronic obstructive pulmonary disease (COPD). Accelerated cellular senescence may be responsible, but its magnitude as measured by leukocyte telomere length is unknown and its relationship to HIV-associated COPD has not yet been established. We measured absolute telomere length (aTL) in peripheral leukocytes from 231 HIV-infected adults. Comparisons were made to 691 HIV-uninfected individuals from a population-based sample. Subject quartiles of aTL were assessed for relationships with measures of HIV disease severity, airflow obstruction, and emphysema severity on computed tomographic (CT) imaging. Multivariable regression models identified factors associated with shortened aTL. Compared to HIV-uninfected subjects, the mean aTL in HIV-infected patients was markedly shorter by 27 kbp/genome (p<0.001); however, the slopes of aTL vs. age were not different (p=0.469). Patients with longer known durations of HIV infection (p=0.019) and lower nadir CD4 cell counts (p=0.023) had shorter aTL. Shorter aTL were also associated with older age (p=0.026), smoking (p=0.005), reduced forced expiratory volume in one second (p=0.030), and worse CT emphysema severity score (p=0.049). HIV-infected subjects demonstrate advanced cellular aging, yet in a cART-treated cohort, the relationship between aTL and age appears no different from that of HIV-uninfected subjects.     

The Impact of Implementing a Test,Treat and Retain HIV Prevention Strategy in Atlanta among Black Men Who Have Sex with Men with a History of Incarceration: A Mathematical Model

Background

Annually, 10 million adults transition through prisons or jails in the United States (US) and the prevalence of HIV among entrants is three times higher than that for the country as a whole. We assessed the potential impact of increasing HIV Testing/Treatment/Retention (HIV-TTR) in the community and within the criminal justice system (CJS) facilities, coupled with sexual risk behavior change, focusing on black men-who-have-sex-with-men, 15–54 years, in Atlanta, USA.

Methods

We modeled the effect of a HIV-TTR strategy on the estimated cumulative number of new (acquired) infections and mortality, and on the HIV prevalence at the end of ten years. We additionally assessed the effect of increasing condom use in all settings.

Results

In the Status Quo scenario, at the end of 10 years, the cumulative number of new infections in the community, jail and prison was, respectively, 9246, 77 and 154 cases; HIV prevalence was 10815, 69 and 152 cases, respectively; and the cumulative number of deaths was 2585, 18 and 34 cases, respectively. By increasing HIV-TTR coverage, the cumulative number of new infections could decrease by 15% in the community, 19% in jail, and 8% in prison; HIV prevalence could decrease by 8%, 9% and 7%, respectively; mortality could decrease by 20%, 39% and 18%, respectively. Based on the model results, we have shown that limited use and access to condoms have contributed to the HIV incidence and prevalence in all settings.

Conclusions

Aggressive implementation of a CJS-focused HIV-TTR strategy has the potential to interrupt HIV transmission and reduce mortality, with benefit to the community at large. To maximize the impact of these interventions, retention in treatment, including during the period after jail and prison release, and increased condom use was vital for decreasing the burden of the HIV epidemic in all settings.     

A Genetic Algorithm for the Bi-Level Topological Design of Local Area Networks

Local access networks (LAN) are commonly used as communication infrastructures which meet the demand of a set of users in the local environment. Usually these networks consist of several LAN segments connected by bridges. The topological LAN design bi-level problem consists on assigning users to clusters and the union of clusters by bridges in order to obtain a minimum response time network with minimum connection cost. Therefore, the decision of optimally assigning users to clusters will be made by the leader and the follower will make the decision of connecting all the clusters while forming a spanning tree. In this paper, we propose a genetic algorithm for solving the bi-level topological design of a Local Access Network. Our solution method considers the Stackelberg equilibrium to solve the bi-level problem. The Stackelberg-Genetic algorithm procedure deals with the fact that the follower’s problem cannot be optimally solved in a straightforward manner. The computational results obtained from two different sets of instances show that the performance of the developed algorithm is efficient and that it is more suitable for solving the bi-level problem than a previous Nash-Genetic approach.