In order to identify Leishmania proteins which may be immunologically relevant or may play a role in interactions between Leishmania and its mammalian host, a Leishmania major genomic DNA library was constructed in the vector λgt11 and screened with antibodies raised to Leishmania major promastigote membranes. Two recombinant DNA clones were identified which encoded repetitive sequences (Clone 20 and Clone 39). Clone 20 encoded a repetitive peptide of 14 amino acids and clone 39 encoded an unrelated repetitive peptide of 10 amino acids. Analysis of one of these clones, Clone 20, indicated that there were two RNA transcripts of 9500 and 5200 nucleotides expressed which corresponded to this clone in Leishmania major and Leishmania donovani and this expression was not stage-specific. The results of genomic DNA analysis and isolation of additional clones encoding Clone 20 sequences indicated that there were two genes which corresponded to Clone 20 in both Leishmania major and Leishmania donovani and that these genes differed from one another with respect to the number of repeats which they contained. Antibodies against the fusion protein produced by Clone 20 recognized a series of Leishmania major proteins of apparent mol wt 250,000. Analysis of Clone 39 indicated that there was a single transcript of 7500 nucleotides expressed which corresponded to this clone in both Leishmania major and Leishmania donovani and that there was a single gene (or two identical genes) which encoded this transcript. The genomes of many protozoan parasites exhibit a high degree of plasticity with respect to chromosome size and number. The presence of highly repetitive regions within their DNA may be involved in maintaining this plasticity, allowing the parasite to evolve rapidly under selective pressure. Repetitive regions have been identified within many Plasmodia antigens and have been implicated in the ability of this parasite to evade the host immune system. The presence of Leishmania genes encoding proteins containing tandemly repeating peptides may indicate that these proteins play a similar role in evading the host immune system during the course of Leishmania infections. The possible evolution and functions of repetitive proteins in protozoan parasites is discussed. / Medicine, Faculty of / Medical Genetics, Department of / Graduate

Orientador: Patrícia Parise Pasquali-Maltempi / Resumo: Os anfíbios anuros correspondem ao segundo grupo de vertebrados com maior número de espécies, perdendo apenas para os peixes. Só no Brasil são mais de 1000 espécies descritas, com novas descrições e revalidações acontecendo todo ano. Esse grupo está envolvido em diversas problemáticas taxonômicas, em parte por ser altamente polimórfico e ao mesmo tempo conter muitas espécies crípticas, em parte por ainda haver muitas lacunas no conhecimento acerca desse grupo, dado o tamanho da sua diversidade. Resolver problemáticas envolvendo esse grupo de vertebrados é fundamental para melhor estimar o tamanho real dessa diversidade, entender os caminhos evolutivos e as relações filogenéticas no grupo e poder auxiliar na conservação das espécies, traçando planos de manejo adequados, já que o declínio de anfíbios devido à perda e fragmentação de habitat, contaminação de ambientes naturais e disseminação de doenças tem aumentado vertiginosamente. Para isso, a taxonomia moderna conta com a soma de diferentes informações a respeito dos grupos, além dos dados morfológicos já tradicionalmente utilizados. Uma das áreas que tem se mostrado promissora como uma ferramenta de auxílio na taxonomia é a citogenética, especialmente depois do advento da citogenômica, além da sua importância para o entendimento da evolução cromossômica dos grupos. No entanto, trabalhos citogenéticos, especialmente aqueles aliados à biologia molecular, são escassos em anuros. Seguindo essa linha, esse trabalho buscou obter ... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Anuran amphibians corresponds to one of the most diverse vertebrate groups, second only to fishes. In Brazil alone there are more than 1000 described species, with new descriptions and revalidations happening every year. This group is involved in several taxonomic issues, partially because it is highly polymorphic and at the same time contains many cryptic species, partially because there are still many gaps in knowledge about this group, given the size of its diversity. To solve these problems is a fundamental step to better estimate its true size, to understand the evolutionary pathways and phylogenetic relationships in the group and also to be able to contribute to the conservation of the species by helping to draw appropriate management plans, as the decline of amphibians due to habitat loss and fragmentation, contamination of natural environments and the spread of disease has increased dramatically. For this, modern taxonomy relies on the sum of different data about the groups, besides the morphological data traditionally used. One of the areas that has shown promise as a taxonomy tool is cytogenetics, especially after the advent of cytogenomics, in addition to its importance for understanding the chromosomal evolution of groups. However, cytogenetic studies, especially those allied to molecular biology, are scarce in anurans. Following this line, this work sought, through the cytogenetic study, using conventional molecular markers, and cytogenomic, with the help of bioi... (Complete abstract click electronic access below) / Doutor

Retrons are genetic elements encoding reverse transcriptase (RT) usually located on the chromosome of a wide variety of mostly Gram-negative bacteria. Here we describe a new retron, designated Ne144, found in the chromosome of the myxobacterium Nannocystis exedens. This element codes for a 515-amino-acid RT that is most closely related to those found in other myxobacterial retrons. The RT is responsible for the production of a small satellite DNA called msDNA. This msDNA is composed of a 144 base, single-stranded DNA that is linked to a 72 base single-stranded RNA. The RNA strand is joined to the 5′ end of the DNA chain via a 2′-5′ linkage that occurs from the 2′ position of an internal guanosine residue in the RNA. In addition to the retron element, the chromosome of N. exedens also contains several partial copies of the msDNA sequence as revealed by DNA hybridization experiments using msDNA as a probe. One of these partial copies was characterized from a chromosome restriction fragment and found to contain a sequence that matches the last 82 bases of the DNA strand and five bases of the RNA strand in msDNA-Ne144. This partial copy of msDNA is very likely a retrotransposed sequence that was generated by reverse transcription using an RNA (the primer-template RNA for msDNA) as a template and the 3′ end of a nick in the chromosome as a primer, followed by incorporation into an open reading frame. The presence of this truncated copy of msDNA is strong evidence of retrotransposition in N. exedens causing an alteration in the bacterial genome.

Among several work-related injuries, low back disorders (LBDs) are the leading cause of lost workdays, and with annual treatment costs in excess of $10 billion in the US. Epidemiological evidence has indicated that prolonged and/or repetitive non-neutral postures, such as trunk flexion, are commonly associated with an increased risk of LBDs. Trunk flexion can result in viscoelastic deformations of soft tissues and subsequent mechanical and neuromuscular alterations of the trunk, and may thereby increase LBD risk. While viscoelastic behaviors of isolated spinal motion segments and muscles have been extensively investigated, in vivo viscoelastic responses of the trunk have not, particularly in response to flexion exposures. Further, most biomechanical efforts at understanding occupational LBDS have not considered the influence of flexion exposures on spine loads. Four studies were completed to characterize viscoelastic deformation of the trunk in response several flexion exposures and to develop and evaluate a computational model of the human trunk that accounts for time-dependent characteristics of soft tissues. Participants were exposed to prolonged flexion at different trunk angles and external moments, and repetitive trunk flexion with different external moments and flexion rates. Viscoelastic properties were quantified using laboratory experiments and viscoelastic models. A multi-segment model of the upper body was developed and evaluated, and then used to estimate muscle forces and spine loads during simulated lifting tasks before and after prolonged trunk flexion at a constant angle and constant external moment. Material properties from the earlier experiments were used to evaluate/calibrate the model. Experimental results indicated important effects of flexion angle, external moment, and flexion rate on trunk viscoelastic behaviors. Material properties from fitted Kelvin-solid models differed with flexion angle and external moment. Nonlinear viscoelastic behavior of the trunk tissues was evident, and predictive performance was enhanced using Kelvin-solid models with ≥2 iii retardation/relaxation time constants. Predictions using the multi-segment model suggested increases in spine loads following prolonged flexion exposures, primarily as a consequence of additional muscle activity. As a whole, these results help to characterize the effects of trunk flexion exposures on trunk biomechanics, contribute to more effective estimates of load distribution among passive and active components, enhance our understanding of LBD etiology, and may facilitate future controls/interventions. / Ph. D.

Study Design: Single group pretest-posttest. Background: There is a lack of consensus concerning the preferred assessment and treatment for radial epicondylalgia. Objectives: Determine whether deficiencies in muscle force, joint range of motion, or painful force threshold are detected when measurements from the involved upper extremity are normalized to values from the uninvolved extremity. Methods and Measures: Ten patients (70% men) 42 ± 7 years in age with unilateral radial epicondylalgia participated. The visual analog pain scale and 6 measurements involving either muscle force, joint range of motion, or painful force threshold were examined. Results: When comparing the initial assessments to final assessments, a significant improvement was found for the visual analog pain scale (5 ± 3 vs 1 ± 3) and for the following normalized scores: grip (78 ± 26% vs 101 ± 20%) and isometric wrist extension forces (68 ± 24% vs 95 ± 35%), painful force threshold over the lateral epicondyle (49 ± 22% vs 94 ± 14%), and active wrist extension range of motion (83 ± 13% vs 96 ± 10%). Conclusions: Normalized force and range of motion measurements following treatment for unilateral radial epicondylalgia are sensitive assessments of patient progress. In comparison with measurements of force and range of motion that are not adjusted to a baseline score, normalized measurements detect changes in patient responses when baseline scores vary.

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The objectives of this thesis are concerned with the peculiar feature of repetitions in the so-called 'Flood-Narrative', Genesis 6-9. The presence of these repetitions has provoked many arguments amongst twentieth century biblical critics as to their origin, their function and even their form. The first objective of the thesis is to review critically a wide spectrum of research done on the repetitive phenomenon, outline the resultant opinions and to weigh the merits or weaknesses of any particular methodology as it relates to how the function of repetitive features is to be understood. The first chapter presents this critical view and finds that up to now, most research done on the text has not been free of methodological bias, with the result that only those repetitions useful to an approach are dealt with, to the exclusion of other repetitive features. The second objective is to catalog and describe the repetitive features of the text in an objective manner, free from methodological or exegetical bias. Chapter II arranges and classifies the repetitions that are evident in Gen. 6-9 and comments on possible patterns or forms suggested by the repetitions. The last objective of the thesis is to look at the repetitions from some perspectives of modern narrative theory to find if this viewpoint can shed any light on the function of repetitive forms. The last chapter of the thesis concludes that explanatory devices from narrative theory which rely on pre-established criteria apart from the text itself, are as well too short-sighted to be useful in corning to grips with repetitive function. However, those approaches which stress certain subjective, exegetical endeavors, or which emphasize a reader's response are found to provide useful insights for the perception of repetitive function. / Thesis / Master of Arts (MA)

Penstemon Mitchell (Plantaginaceae) is one of the largest, most diverse plant genera in North America. Their unique diversity, paired with their drought-tolerance and overall hardiness, give Penstemon a vast amount of potential in the landscaping industry—especially in the more arid western United States where they naturally thrive. In order to develop Penstemon lines for more widespread commercial and private landscaping use, we must improve our understanding of the vast genetic diversity of the genus on a molecular level. In this study we utilize genome reduction and barcoding to optimize 454-pyrosequencing in four target species of Penstemon (P. cyananthus, P. davidsonii, P. dissectus and P. fruticosus). Sequencing and assembly produced contigs representing an average of 0.5% of the Penstemon species. From the sequence, SNP information and microsatellite markers were extracted. One hundred and thirty-three interspecific microsatellite markers were discovered, of which 50 met desired primer parameters, and were of high quality with readable bands on 3% Metaphor gels. Of the microsatellite markers, 82% were polymorphic with an average heterozygosity value of 0.51. An average of one SNP in 2,890 bp per species was found within the individual species assemblies and one SNP in 97 bp were found between any two supposed homologous sequences of the four species. An average of 21.5% of the assembled contigs were associated with putative genes involved in cellular components, biological processes, and molecular functions. On average 19.7% of the assembled contigs were identified as repetitive elements of which LTRs, DNA transposons and other unclassified repeats, were discovered. Our study demonstrates the effectiveness of using the GR-RSC technique to selectively reduce the genome size to putative homologous sequence in different species of Penstemon. It has also enabled us the ability to gain greater insights into microsatellite, SNP, putative gene and repetitive element content in the Penstemon genome which provide essential tools for further genetic work including plant breeding and phylogenetics.

Sleep problems are common among college students and are associated with numerous negative outcomes including anxiety, depression, executive dysfunction, and poor academic performance. When sleep is limited, individuals may suffer impaired cognitive capacities, such as reduced memory and difficulty focusing attention. Difficulty with these cognitive functions can result in difficulty disengaging from negative thoughts, thereby contributing to negative mood. Poor sleep contributes to negative mood states, but few studies have examined in what way poor sleep may exacerbate negative mood. The purpose of this study was to examine cognitive factors as explanatory variables between sleep and state affect. Participants were undergraduate students from a university in the Midwest. Participants (N = 150, completed baseline questionnaires and wore an actigraphy watch for one night. They returned to the lab the following day to complete additional self-report measures and a computerized cognitive control task. Participants were primarily female (66.67%, n = 100) and white (67.33%, n = 101). To test the hypothesis that the relationship between sleep and affect is explained by cognitive factors, a path analytic model was fit to the data. It was hypothesized that cognitive factors (i.e., Posner task performance, repetitive negative thinking, and self-report attention control) would explain the relationship between sleep (as measured by objective total sleep time and self-report sleepiness) and state affect. The hypothesized model yielded poor global and local fit to the data. While several direct effects emerged in the model, no indirect effects were statistically significant. The model was re-specified, adding paths where large magnitude correlational residual statistics coincided with statistically significant standardized residual statistics. The final model yielded good global and local fit to the data, with primary modifications being added covariances among control variables (e.g., GAD-7 and PHQ-8 scores) with cognitive factors. Overall, the results of this study indicate that the relationship between sleep and next-day affect is complex and cannot be simply explained by cognitive factors. However, the current study found several significant relationships among study variables, suggesting that sleep, cognitive functioning, and emotion are highly related constructs that warrant further study. Future research should examine alternative models incorporating these constructs to find a comprehensive model with utility that can explain the relationships among these constructs.

In addition to social communication deficits, restricted repetitive behaviors (RRBs) are a key diagnostic feature of autism spectrum disorder (ASD). Two theories regarding the etiology of RRBs in ASD have been proposed: the hyper-arousal theory, and the hypo-arousal theory. Both of these theories posit the autonomic nervous system (ANS) as being dysfunctional in ASD, resulting in the occurrence of RRBs. Many studies investigating ANS activity in ASD have focused solely on its relation to social functioning. The few that have addressed RRBs have had inconclusive findings. Not only do the current theories and studies simplify ANS activity to a measure of baseline arousal levels through vague measures such as heart rate (HR) and skin conductance response (SCR), but the literature has also framed the theories as mutually exclusive. This study used respiratory sinus arrhythmia (RSA) patterns in children with and without an ASD diagnosis as an indicator of ANS functioning to analyze its relationship to the manifestation of RRBs. Baseline RSA and RSA reactivity were found to predict RRB severity and exploratory analyses revealed that these measures were associated with specific subgroups of RRBs. These results are discussed in regards to the current behavioral literature on RRBs and the benefits of finding biomarkers for these behaviors. / Master of Science