Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal

Background Transcriptomes are powerful resources, providing a window on the expressed portion of the genome that can be generated rapidly and at low cost for virtually any organism. However, because many genes have tissue-specific expression patterns, developing a complete transcriptome usually requires a 'discovery pool' of individuals to be sacrificed in order to harvest mRNA from as many different types of tissue as possible. This hinders transcriptome development in large, charismatic and endangered species, many of which stand the most to gain from such approaches. To circumvent this problem in a model pinniped species, we 454 sequenced cDNA from testis, heart, spleen, intestine, kidney and lung tissues obtained from nine adult male Antarctic fur seals (Arctocephalus gazella) that died of natural causes at Bird Island, South Georgia. Results After applying stringent quality control criteria based on length and annotation, we obtained 12,397 contigs which, in combination with 454 data previously obtained from skin, gave a total of 23,096 unique contigs. Homology was found to 77.0% of dog (Canis lupus familiaris) transcripts, suggesting that the combined assembly represents a substantial proportion of this species' transcriptome. Moreover, only 0.5% of transcripts revealed sequence similarity to bacteria, implying minimal contamination, and the percentage of transcripts involved in cell death was low at 2.6%. Transcripts with immune-related annotations were almost five-fold enriched relative to skin and represented 13.2% of all spleen-specific contigs. By reference to the dog, we also identified transcripts revealing homology to five class I, ten class II and three class III genes of the Major Histocompatibility Complex and derived the putative genomic distribution of 17,121 contigs, 2,119 in silico mined microsatellites and 9,382 single nucleotide polymorphisms. Conclusions Our findings suggest that transcriptome development based on samples collected post mortem may greatly facilitate genomic studies, not only of marine mammals but also more generally of species that are of conservation concern

Integrating livestock in CAADP framework: Policy analysis using a dynamic computable general equilibrium model for Ethiopia

Researchers and policymakers increasingly recognize that the livestock sector supports the livelihoods of a large proportion of rural households in most African countries and may play an important role in rural poverty reduction strategies. To develop this insight, economy-wide models should capture both the biological, dynamic relationships between the stocks and flows of livestock and economic linkages between this sector and the rest of the economy. This study extends an existing dynamic recursive general equilibrium model for the Ethiopian economy so as to better model the livestock sector. A separate herd dynamics module enables researchers to specify stock-flow relationship, distinguishing between the capital role of livestock and the flow of livestock products. The authors also improved the underlying system of economic accounts to better capture draft power and breeding stocks. They used this model to simulate separate, realistic Total Factor Productivity (TFP) shocks to three agricultural subsectors—cereals, cash crops, and livestock—and compared them to a baseline scenario replicating the 1998–2007 productivity trends, following Dorosh and Thurlow (2009), who examined CAADP productivity scenarios. The results revealed the important role of the livestock sector in increasing various measures of GDP and combating food insecurity. Agricultural GDP and overall GDP growth levels achieved in the livestock TFP shock scenario are very similar to those achieved in the cereal TFP shock scenario, contrary to previous assumptions. Importantly, as factors are dynamically re-allocated between agricultural activities, our analysis highlighted the inefficiency of strategies focusing on cereal sector development alone. Moreover, livestock sector productivity growth led to greater factor income growth, particularly labor income, than in the other simulations. Labor is the predominant asset of poor household; hence, a livestock-led scenario realizes large gains in income and food consumption growth

HUBUNGAN ANTARA STATUS MEROKOK DAN PAPARAN ASAP ROKOK DENGAN KUALITAS HIDUP PADA PENDUDUK DI KELURAHAN KOLONGAN KECAMATAN TOMOHON TENGAH KOTA TOMOHON

Kualitas hidup merupakan persepsi atau penilaian subjektif dari individu yang mencakup beberapa aspek sekaligus, yang meliputi kondisi fisik, psikologis, sosial dan lingkungan dalam kehidupan sehari-hari. Perilaku merokok merupakan salah satu faktor resiko penyakit dan masalah kesehatan di dunia. Penelitian ini bertujuan untuk menganalisis hubungan antara status merokok dan paparan asap rokok dengan kualitas hidup pada penduduk di Kelurahan Kolongan Kecamatan Tomohon Tengah Kota Tomohon. Penelitian ini merupakan penelitian survei analitik dengan rancangan cross sectional study dengan jumlah 96 responden yang berusia ≥ 17 tahun. Penelitian ini dilakukan dengan diwawancarai menggunakan kuesioner perilaku merokok untuk tingkat status merokok dan paparan asap rokok, dan kuesioner EQ5D untuk tingkat kualitas hidup. Dalam penelitian ini menggunakan uji hubungan statistik chi-square dengan tingkat kemaknaan 95% (α=0,05). Hasil penelitian menunjukkan paparan asap rokok dengan kualitas hidup (p value = 0,017), sedangkan status merokok dengan kualitas hidup (p value = 0,204). Berdasarkan hasil penelitian yang dilakukan pada penduduk di Kelurahan Kolongan menunjukkan bahwa terdapat hubungan antara paparan asap rokok dengan kualitas hidup dan tidak terdapat hubungan antara status merokok dengan kualitas hidup.Kata Kunci: Status Merokok, Paparan Asap Rokok, Kualitas HidupABSTRACT Quality of life is the perception or subjective assessment of the individual that includes several aspects, such as the physical, psychological, social and environmental conditions in everyday life. Smoking behavior is one of the risk factors of disease and health problems in the world. The purpose of this research is to analyze the relationship between smoking status and exposure of cigarette smoke with the quality of life of the society in Kelurahan Kolongan Kecamatan Tomohon Tengah Kota Tomohon. This research is an analytic survey research with cross sectional study design with 96 respondents aged ≥ 17 years old. Data were collected using questionnaire of smoking behavior for smoking status and cigarette smoke exposure, and EQ5D questionnaires for quality of life. In this study using the statistical test of chi-square with a significance level of 95% (α = 0.05). The results showed exposure to cigarette smoke with quality of life (p value = 0.017), while smoking status with quality of life (p value = 0.204). While the variable that has no relationship is smoking status (p value = 0,204). Based on the results of research conducted on society in Desa Kolongan showed that there is a correlation between exposure of cigarette smoke with quality of life and there is no correlation between smoking status with quality of life.Keywords: Smoking Status, Exposure of Cigarette Smoke, Quality of Lif

Transcriptomic SNP discovery for custom genotyping arrays: impacts of sequence data, SNP calling method and genotyping technology on the probability of validation success

Background Single nucleotide polymorphism (SNP) discovery is an important goal of many studies. However, the number of ‘putative’ SNPs discovered from a sequence resource may not provide a reliable indication of the number that will successfully validate with a given genotyping technology. For this it may be necessary to account for factors such as the method used for SNP discovery and the type of sequence data from which it originates, suitability of the SNP flanking sequences for probe design, and genomic context. To explore the relative importance of these and other factors, we used Illumina sequencing to augment an existing Roche 454 transcriptome assembly for the Antarctic fur seal (Arctocephalus gazella). We then mapped the raw Illumina reads to the new hybrid transcriptome using BWA and BOWTIE2 before calling SNPs with GATK. The resulting markers were pooled with two existing sets of SNPs called from the original 454 assembly using NEWBLER and SWAP454. Finally, we explored the extent to which SNPs discovered using these four methods overlapped and predicted the corresponding validation outcomes for both Illumina Infinium iSelect HD and Affymetrix Axiom arrays. Results Collating markers across all discovery methods resulted in a global list of 34,718 SNPs. However, concordance between the methods was surprisingly poor, with only 51.0 % of SNPs being discovered by more than one method and 13.5 % being called from both the 454 and Illumina datasets. Using a predictive modeling approach, we could also show that SNPs called from the Illumina data were on average more likely to successfully validate, as were SNPs called by more than one method. Above and beyond this pattern, predicted validation outcomes were also consistently better for Affymetrix Axiom arrays. Conclusions Our results suggest that focusing on SNPs called by more than one method could potentially improve validation outcomes. They also highlight possible differences between alternative genotyping technologies that could be explored in future studies of non-model organisms

Hubungan Antara Beban Kerja dan Stres Kerja dengan Perasaan Kelelahan Kerja pada Perawat di Ruang UGD dan Rawat Inap Rumah Sakit Umum Daerah Amurang Kabupaten Minahasa Selatan

Perasaan kelelahahan merupakan suatu keadaan atau kondisi yang muncul karena aktivitas fisik atau mental individu hingga individu menurunnya kinerja saat berkerja dan dalam hal ini disertai dengan munculnya perasaan letih dan lemah. Perawat memiliki beban kerja dan tuntutan yang tinggi dalam memberi pelayanan kepada pasien.Stres kerja pada perawat bisa terjadi apabila dalam tugas dan tuntutan yang dihadapinnya melampui batas kemampuan. Penelitian ini bertujuan untuk mengatahui hubungan beban kerja dan stres kerja dengan perasaan kelelahan kerja pada perawat di ruangan UGD dan Rawat Inap Rumah Sakit Umum Daerah Amurang Minahasa Selatan. Penelitian ini mengunakan metode kuantitatif dengan mengunakan desain survei analitik dengan rancangan studi potong lintang cross-sectional study. waktu dan tempat dilakukan pada bulan Oktober – Desember di RSUD Amurang Minahasa Selatan. Analisis yang digunakan menggunakan analisis bivariat dan univariat. Pengolahan data yang dilakukan menggunakan uji kolerasi spearmen dan didapatkan hubungan beban kerja dan stres kerja dengan perasaan kelelahan kerja pada perawat didapatkan nilai p velue sebesar 0.003 (p < 0,05) dan untuk stres kerja dengan perasaan kelelahan kerja didapatkan nilai p velue sebesar 0.002 (p < 0.05) KataiKuncii : Beban Kerja. Stres Kerja, Perasaan Kelelahan Kerja pada Perawat ABSTRACTikjkFeelings of fatiguei are ai condition or condition that arises due to individual physical or mental activity until the individual decreases in performance at work and in this case is accompanied by the emergence of feelings of fatigue and weakness. Nurses have a high workload and demands in providing services to patients. Work stress on nurses can occur if the tasks and demands they face exceed the ability limit. Thisi study aims itoi determinei the irelationship between workloadI andI worki stress iwithi feelings of worki fatiguei in nurses in thei emergency room and inpatient care at the Amurang South Minahasa Regional General Hospital. This study uses a quantitative method using an analytical survey design with a cross-sectional study design. The time and place was carried out in October – December at the Amurang Hospital, South Minahasa. The analysis used was bivariate and univariate analysis. Data processing was carried out using the Spearmen correlation test and it was found that the relationship between workload and work stress with feelings of work fatigue in nurses obtained a p-value of 0.003 (p <0.05) and for work stress with feelings of work fatigue, a p-value of 0.002 (p-value) was obtained ( p < 0.05) Keywords : Workload. Work Stress, Feelings of Work Fatigue in Nurse

Morphological Characterization, Variability and Traits Association among Accessions of Three Species of Crassocephalum (Moench.) S. Moore from Nigeria

Crassocephalum species have served as vegetables for decades, yet they remain undomesticated and uncultivated. The knowledge of the variability and traits association of these species could enhance the improvement and thus facilitate their domestication and cultivation. Twenty-one accessions of Crassocephalum species were characterized in a Randomized Complete Block Design to determine intra and inter-specifies variability and traits association for their improvement with a view to facilitate their domestication and cultivation. One way Analysis of Variance (ANOVA), Principal Component Analysis (PCA), and correlation coefficients were used to analyze the data. The results revealed significant intra and inter-specifies variability among the accessions characterized. The first three axes of PCA accounted for over 60% of total variation with leaf length, leaf width, days to 50% flowering, days to maturity, number of achenes/head and number of filled achenes/head as discriminants. Positive and significant phenotypic correlations were observed between leaf length and leaf width with petiole length, internode length, peduncle length, and number of days to maturity. High positive correlation was observed for number of capitula/plant with capitulum diameter and number of filled achenes per head. Hence, the principal contributors to total variation which are leaf length, leaf width, days to 50% flowering, days to maturity, number of achenes/head and number of filled achenes/head are hereby suggested to breeders in developing a suitable breeding programme for Crassocephalum crepidioides, C. rubens and C. togoense

Requirement for RAR-mediated gene repression in skeletal progenitor differentiation

Chondrogenesis is a multistep process culminating in the establishment of a precisely patterned template for bone formation. Previously, we identified a loss in retinoid receptor–mediated signaling as being necessary and sufficient for expression of the chondroblast phenotype (Weston et al., 2000. J. Cell Biol. 148:679–690). Here we demonstrate a close association between retinoic acid receptor (RAR) activity and the transcriptional activity of Sox9, a transcription factor required for cartilage formation. Specifically, inhibition of RAR-mediated signaling in primary cultures of mouse limb mesenchyme results in increased Sox9 expression and activity. This induction is attenuated by the histone deacetylase inhibitor, trichostatin A, and by coexpression of a dominant negative nuclear receptor corepressor-1, indicating an unexpected requirement for RAR-mediated repression in skeletal progenitor differentiation

Causality and statistics on the Groenewold-Moyal plane

Quantum theories constructed on the noncommutative spacetime called the Groenewold-Moyal plane exhibit many interesting properties such as Lorentz and CPT noninvariance, causality violation and twisted statistics. We show that such violations lead to many striking features that may be tested experimentally. These theories predict Pauli forbidden transitions due to twisted statistics, anisotropies in the cosmic microwave background radiation due to correlations of observables in spacelike regions and Lorentz and CPT violations in scattering amplitudes.Comment: 12 pages, 1 figure. Based on the talk given by APB at the Workshop "Theoretical and Experimental Aspects of the Spin Statisics Connection and Related Symmetries", Stazione Marittima Conference Center, Trieste, Italy from the 21st to the 25th of October 200