Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds

To assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set (N = 479) from Brown Swiss, Guernsey, Holstein, and Jersey cattle, some of the MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds. This implied that some haplotypes predate modern breed formation and remain in strong linkage disequilibrium. To expand the utility of MS allele imputation across breeds, MS and SNP data from more than 8000 animals representing 39 breeds (Bos taurus and B. indicus) were used to predict 9410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles from 12 MS markers could be accurately be imputed. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds (N = 2 to 36 breeds). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small increase in Mendelian inheritance inconsistancies. Our reported reference haplotypes can be used for any cattle breed and the reported methods can be applied to any species to aid the transition from MS to SNP genetic markers. While ~91% of the animals with imputed alleles for 12 MS markers had ≤1 Mendelian inheritance conflicts with their parents' reported MS genotypes, this figure was 96% for our reference animals, indicating potential errors in the reported MS genotypes. The workflow we suggest autocorrects for genotyping errors and rare haplotypes, by MS genotyping animals whose imputed MS alleles fail parentage verification, and then incorporating those animals into the reference dataset.

Riqueza, abundância e dieta de morcegos (Chiroptera) em floresta de eucaliptos

Os quirópteros apresentam grande diversidade e variação de hábitos alimentares, desempenhando um importante papel ecológico, se destacando pela dispersão de sementes que auxilia na conservação e restauração de ambientes degradados. Em caso de monoculturas, espera-se que reflorestamentos mais antigos com sub-bosque bem desenvolvido abriguem comunidades com maior diversidade de espécies se comparados a reflorestamentos utilizados para fins comerciais. O objetivo deste estudo é conhecer a riqueza, abundância e diversidade de morcegos e a dieta das espécies frugívoras em uma área refloresta por Eucalyptus spp., a Floresta Estadual Edmundo Navarro de Andrade localizada em Rio Claro - SP. As capturas ocorreram entre maio de 2014 e 2015, utilizando redes de neblina e um esforço amostral de 9072 m².h. As fezes encontradas foram coletadas, identificadas usando-se uma coleção de referência em laboratório e associadas às espécies de morcegos. Foi realizado um teste de germinação com Piper amalago para verificar o efeito da passagem de sementes pelo trato digestivo dos morcegos. São apresentados dados de dominância, constância, estimativas de riqueza (Chao1, Jackknife2) e diversidade (Shannon-Wiener) de morcegos, assim como índice de valor de importância de interação (Murray) para plantas e morcegos e a velocidade e a porcentagem germinativa de sementes de Piper amalago. Foram capturados 86 indivíduos de nove espécies de quirópteros pertencentes a duas famílias. As espécies encontradas são, em sua maioria, generalistas, sendo a mais abundante Artibeus lituratus, seguido de Carollia perspicillatta, esta se alimentou de 10 espécies diferentes de plantas, tendo o maior valor no índice de importância, enquanto Piper aduncum foi a planta consumida pelo maior número de morcegos na área de estudo. As espécies de plantas consumidas são principalmente pioneiras como Piperaceae e Solanaceae, que contribuem para a...

Attitudes, Confidence, and Achievement of High-Ability Fifth Grade Math Students

In this action research study of my fifth grade high-ability mathematics class, I investigated student attitudes of mathematics and their confidence in mathematics. Student achievement was compared to two different confidence scales to identify a relationship between confidence and achievement. Six boys and eleven girls gave their consent to the study. I discovered there seems to be a connection between confidence and achievement and that boys are generally more confident than girls. Most students liked math and were comfortable sharing answers and methods of solving problems with other students. As a result of this study I plan to use my survey and interview questions at the beginning of the school year with my new class in order to assess their attitudes and confidence in math. I can use this information to identify potential struggles and better plan for student instruction.

AN OVERVIEW OF DEPREDATING BIRD DAMAGE CONTROL IN CALIFORNIA

To many people, California is synonomous with Disneyland, freeways, Los Angeles smog, Yosemite, the California missions, or for you bird aficionados, the California Condor. But do you think about California when you eat strawberry shortcake? You should -- California leads the nation in strawberry production. How about artichokes? California produces over 98% of the artichokes raised in the United States. Dates? California produces over 99% of the dates in the United States. Yes, California is all of these, and it is much more. California may well be the most diverse state in the United States. Within its 100.2 million acres, California has the lowest place in the U.S. in Death Valley and one of the highest mountains with Mt. Whitney. Because California is such a diverse state and has a wide variety of micro- climates, it supports a uniquely diverse agriculture. Agriculture uses only about 36 million acres of its total 100.2 million acres, and most of the cash return from crops is produced on 8,6 million acres that are irrigated. California produces about 250 crops and livestock commodities (excluding nursery crops) and provides the U.S. with about 25% of its table foods. California leads the nation in the production of 46 commercial crops and livestock commodities; its farmers and ranchers marketed $8.6 billion of crop and livestock products in 1975, and the state’s harvested farm production in 1975 set a new record at 51.1 million tons. HISTORY OF BIRD PROBLEMS Records such as this are not achieved without some risk. Crops growing in Cali- fornia have always had competition from many types of vertebrate pests. The wide variety of crops grown in California and the varied climates and situations in which they are grown has resulted in many different species of birds damaging crops. Birds have compet- ed with man for his crops since the dawn of agriculture. McAtee (1932) cited examples of bird damage that occurred in a wide variety of crops in California during the early 1900s. During the 1920s, many requests for Information and relief from damage caused by a wide variety of birds, culminated in the assignment, in May 1929, of two biologists, S. E. Piper and Johnson Neff, of the former U.S. Bio- logical Survey, to initiate field studies in California. In cooperation with the Cali- fornia Department of Food and Agriculture and County Agricultural Commissioners, the study was to determine the problems and devise control procedures relative to bird depredations. Piper and Neff found such damage as Horned Larks pulling sprouting crops, House Finches disbudding deciduous fruit trees and devouring mature fruit. Blackbirds were a problem in the rice crop. Early controls were varied and, for the most part, lacked effectiveness. Flagging of fields was common to deter Horned Larks. Windmill devices were tried to frighten birds. Shooting to kill birds was common; scarecrows were.used. The six-year study brought forth the basis of most of the depredating bird control techniques still in use in California. At the end of the study, these two biologists compiled a book called “Procedure and Methods in Controlling Birds Injurious to Crops in California.” This was and still is the “Bible” for bird damage control techniques used in California. The thorough investigations conducted by these biologists resulted in techniques that have remained valid in California for over 40 years.

Riqueza, abundância e dieta de morcegos (Chiroptera) em floresta de eucaliptos

Os quirópteros apresentam grande diversidade e variação de hábitos alimentares, desempenhando um importante papel ecológico, se destacando pela dispersão de sementes que auxilia na conservação e restauração de ambientes degradados. Em caso de monoculturas, espera-se que reflorestamentos mais antigos com sub-bosque bem desenvolvido abriguem comunidades com maior diversidade de espécies se comparados a reflorestamentos utilizados para fins comerciais. O objetivo deste estudo é conhecer a riqueza, abundância e diversidade de morcegos e a dieta das espécies frugívoras em uma área refloresta por Eucalyptus spp., a Floresta Estadual Edmundo Navarro de Andrade localizada em Rio Claro - SP. As capturas ocorreram entre maio de 2014 e 2015, utilizando redes de neblina e um esforço amostral de 9072 m².h. As fezes encontradas foram coletadas, identificadas usando-se uma coleção de referência em laboratório e associadas às espécies de morcegos. Foi realizado um teste de germinação com Piper amalago para verificar o efeito da passagem de sementes pelo trato digestivo dos morcegos. São apresentados dados de dominância, constância, estimativas de riqueza (Chao1, Jackknife2) e diversidade (Shannon-Wiener) de morcegos, assim como índice de valor de importância de interação (Murray) para plantas e morcegos e a velocidade e a porcentagem germinativa de sementes de Piper amalago. Foram capturados 86 indivíduos de nove espécies de quirópteros pertencentes a duas famílias. As espécies encontradas são, em sua maioria, generalistas, sendo a mais abundante Artibeus lituratus, seguido de Carollia perspicillatta, esta se alimentou de 10 espécies diferentes de plantas, tendo o maior valor no índice de importância, enquanto Piper aduncum foi a planta consumida pelo maior número de morcegos na área de estudo. As espécies de plantas consumidas são principalmente pioneiras como Piperaceae e Solanaceae, que contribuem para a...

In vitro Metabolism of Grandisin, a Lignan with Anti-chagasic Activity

Tetrahydrofuran lignans represent a well-known group of phenolic compounds capable of acting as antiparasitic agents. In the search for new medicines for the treatment of Chagas disease, one promising compound is grandisin which has shown significant activity on trypomastigote forms of Trypanosoma cruzi. In this work, the in vitro metabolism of grandisin was studied in the pig cecum model and by biomimetic phase I reactions, aiming at an ensuing a preclinical pharmacokinetic investigation. Although grandisin exhibited no metabolization by the pig microbiota, one putative metabolite was formed in a biomimetic model using Jacobsen catalyst. The putative metabolite was tested against T. cruzi revealing loss of activity in comparison to grandisin.

Dillapiole as Antileishmanial Agent: Discovery, Cytotoxic Activity and Preliminary SAR Studies of Dillapiole Analogues

In this paper, the isolation of dillapiole (1) from Piper aduncum was reported as well as the semi-synthesis of two phenylpropanoid derivatives [di-hydrodillapiole (2), isodillapiole (3)], via reduction and isomerization reactions. Also, the compounds' molecular properties (structural, electronic, hydrophobic, and steric) were calculated and investigated to establish some preliminary structureactivity relationships (SAR). Compounds were evaluated for in vitro antileishmanial activity and cytotoxic effects on fibroblast cells. Compound 1 presented inhibitory activity against Leishmania amazonensis (IC50?=?69.3 mu M) and Leishmania brasiliensis (IC50?=?59.4 mu M) and induced cytotoxic effects on fibroblast cells mainly in high concentrations. Compounds 2 (IC50?=?99.9 mu M for L. amazonensis and IC50?=?90.5 mu M for L. braziliensis) and 3 (IC50?=?122.9 mu M for L. amazonensis and IC50?=?109.8 mu M for L. brasiliensis) were less active than dillapiole (1). Regarding the molecular properties, the conformational arrangement of the side chain, electronic features, and the hydrophilic/hydrophobic balance seem to be relevant for explaining the antileishmanial activity of dillapiole and its analogues.

High-throughput sequencing of black pepper root transcriptome

Background: Black pepper (Piper nigrum L.) is one of the most popular spices in the world. It is used in cooking and the preservation of food and even has medicinal properties. Losses in production from disease are a major limitation in the culture of this crop. The major diseases are root rot and foot rot, which are results of root infection by Fusarium solani and Phytophtora capsici, respectively. Understanding the molecular interaction between the pathogens and the host's root region is important for obtaining resistant cultivars by biotechnological breeding. Genetic and molecular data for this species, though, are limited. In this paper, RNA-Seq technology has been employed, for the first time, to describe the root transcriptome of black pepper. Results: The root transcriptome of black pepper was sequenced by the NGS SOLiD platform and assembled using the multiple-k method. Blast2Go and orthoMCL methods were used to annotate 10338 unigenes. The 4472 predicted proteins showed about 52% homology with the Arabidopsis proteome. Two root proteomes identified 615 proteins, which seem to define the plant's root pattern. Simple-sequence repeats were identified that may be useful in studies of genetic diversity and may have applications in biotechnology and ecology. Conclusions: This dataset of 10338 unigenes is crucially important for the biotechnological breeding of black pepper and the ecogenomics of the Magnoliids, a major group of basal angiosperms.

Depression, fatigue, and health-related quality of life in head and neck cancer patients: a prospective pilot study

To assess the prevalence of depression and fatigue symptoms in head and neck cancer patients during radiotherapy treatment and relate them symptoms with these patients' quality of life. This is a prospective study. The Beck Depression Inventory (BDI), Piper Fatigue Scale-revised and Functional Assessment Cancer Therapy Head and Neck (FACT-H&N) were applied to 41 head and neck cancer patients at three times: at the start of treatment (T1), approximately 15 days after the start of treatment (T2) and at the end of treatment (T3), approximately 30 days after the start of the radiotherapy. The mean BDI and PIPER increased during the radiotherapy treatment. BDI scores did not demonstrate the presence of depression, although the number of symptoms increased, and the presence of fatigue rose as treatment advanced. The mean FACT H&N decreased in the middle and at the end of treatment, indicating worsening in these patients' Quality of Life. Depression and fatigue symptoms increased during radiotherapy treatment, while QoL levels decreased. This demonstrates that these symptoms are strongly correlated and that their presence negatively influenced QoL. At the start of treatment, nurses need to advise patients and plan care, offering interventions to decrease these symptoms and improve QoL.

Electrophysiological Responses of the Naupactus bipes Beetle to Essential Oils from Piperaceae Species

Electrophysiological responses based on electroantennographic detection (GC-EAD) and electroantennography (EAG) analysis of Naupactus bipes beetles (Germar, 1824) (Coleoptera: Curculionidae: Brachycerinae) were used to test volatile oils of Piper gaudichaudianum, P. regnellii and P. hispidum. In the EAG experiments, female and male beetles showed significant EAG response to the three volatile oils of Piper species, with the females' responses slightly higher than the males'. The experiments with GC-EAD revealed that some terpenoids (namely, alpha-pinene, beta-pinene, myrcene, alpha-copaene and germacrene) present in the leaf essential oils of the Piper species are perceptible to female and male beetles.

Fatigue in colorectal cancer patients: prevalence and associated factors

This study identified the prevalence and prevalence and predictors of fatigue in colorectal cancer (CRC) patients. Cross-sectional study with 157 adult CRC outpatients (age 60 +/- 11.7 years; 54% male; cancer stage IV 44.8%). The Piper Fatigue Scale-revised was used to assess fatigue scores. Socio-demographic, clinical, depression, performance status, pain and sleep disturbance data were assessed. Associations between fatigue and these data were analyzed through logistic regression models. Fatigue was reported by 26.8% patients. Logistic regression identified three predictors: depression (OR: 4.2; 95%CI 1.68-10.39), performance status (OR: 3.2; 95%CI 1.37-7.51) and sleep disturbance (OR: 3.2; 95%CI 1.30-8.09). When all predictors were present, the probability of fatigue occurrence was 80%; when none were present, the probability was 8%. The model's specificity and sensitivity were 81.9% and 58.6%, respectively. Through the assessment of depression, performance status and sleep disturbance, the probability of fatigue occurrence can be estimated, and preventive and treatment strategies can be rapidly implemented in clinical practice.

Schistosoma mansoni: In vitro schistosomicidal activity and tegumental alterations induced by piplartine on schistosomula

Schistosomiasis is one of the most important parasitic infections in humans that occur in many tropical and subtropical countries. Currently, the control of schistosomiasis rests with a single drug, praziquantel, which is effective against adult worms but not the larval stages. Recent studies have shown that piplartine, an amide isolated from plants of the genus Piper (Piperaceae), reveals interesting antischistosomal properties against Schistosoma mansoni adult worms. Here, we report the in vitro antischistosomal activity of piplartine on S. mansoni schistosomula of different ages (3 h old and 1, 3, 5, and 7 days old), and examine alterations on the tegumental surface of worms by means of confocal laser scanning microscopy. Piplartine at a concentration of 7.5 mu M caused the death of all schistosomula within 120 h. The lethal effect occurred in a dose-dependent manner and was also dependent on the age of the parasite. Microscopy observation revealed extensive tegumental destruction, including blebbing, granularity, and a shorter body length. This report provides the first evidence that piplartine is able to kill schistosomula of different ages and reinforce that piplartine is a promising compound that could be used for the development of new schistosomicidal agent. (c) 2012 Elsevier Inc. All rights reserved.

Composição, diversidade e distribuição geográfica de plantas vasculares de uma Floresta Ombrófila Densa Atlântica do Sudeste do Brasil

In the Montane and Submontane Rain Forest of the Carlos Botelho State Park - PECB (ca. 37,000 ha) the composition, richness and geographical distribution of native, vascular forest species was evaluated. The analysis of 1143 species of 140 families supported the pattern found for other forests of Eastern Brazil, showing high species richness of Myrtaceae (85 species), Orchidaceae (81), Fabaceae (57), Asteraceae, Melastomataceae (54), Lauraceae (53), Rubiaceae (51), Bromeliaceae (43), Piperaceae (30) and Solanaceae (25), besides ferns (123). The most species-rich genera were Eugenia (34), Ocotea (26), Leandra, Myrcia, Vriesea (18), Piper, Solanum (16), Miconia (14), Mollinedia (13), and Peperomia (12). The richness and composition varied greatly among life forms, as well as the number of families represented in each one of them (only Rubiaceae had species in all life forms, except parasites). Trees had the largest contribution of total richness (39.1%), a value that represented more than 20% of the species listed for the whole Atlantic Forest of Southeastern Brazil. Trees were followed by epiphytes (22.4%), herbs (18.4%), shrubs (10.1%), lianas (9.1%), and parasites (0.9%). The overall richness and composition of life forms was quite close to other neotropical forests (e.g. high contribution of ferns among epiphytes), although some life forms remain undersampled in the PECB (mainly herbs, lianas and epiphytes). The occurrence of species endemic to the Atlantic Forest was pronounced (65%), with a predominance of species restricted to the Southern Atlantic Forest (43%). Pantropical species were rare (2%), being more common among ferns. Myrtaceae and Melastomataceae were the families with greater number and proportion of endemic species.

Incapacidade relacionada à dor lombar crônica: prevalência e fatores associados

A incapacidade relacionada à dor lombar crônica (DLC) é um fenômeno complexo e multifatorial. O objetivo desse estudo foi identificar a prevalência e os fatores associados à incapacidade em pacientes com dor lombar crônica. Estudo transversal com amostra composta por 177 pacientes com DLC, de três serviços de saúde; que responderam ao formulário com dados demográficos, ao Inventário de Depressão de Beck, às Escalas Oswestry Disability Index, de autoeficácia para dor crônica, Tampa de Cinesiofobia e de Fadiga de Piper. A prevalência de incapacidade foi de 65% (IC95%: 57,5 - 72,0) e era de moderada a grave em 80,7% dos pacientes. O modelo de regressão múltipla identificou três fatores independentemente associados à incapacidade: ausência de trabalho remunerado, autoeficácia baixa e depressão. Os fatores associados à incapacidade identificados são modificáveis. Intervenções como recolocação no trabalho, tratamento para a depressão e reconceitualização da crença de autoeficácia podem ter um impacto importante na prevenção e redução de incapacidade.

Grandisin caused morphological changes larval and toxicity on Aedes aegypti

Dengue is a tropical disease caused by an arbovirus transmitted by Aedes aegypti. Since no effective vaccine is available for treating dengue, the present study focused on population vector control through investigating the use of the lignan grandisin, isolated from Piper solmsianum C. DC., Piperaceae, against the larvae of A. aegypti. Grandisin caused larval (L3) mortality at LC50 150 µg/mL. Histological analysis on A. aegypti larvae treated with grandisin (LC50 50 µg/mL) showed changes in the anterior-middle midgut, with intense tissue destruction and cell disorganization.