Mapping the sex determination locus in the hāpuku (Polyprion oxygeneios) using ddRAD sequencing

Background  Hāpuku (Polyprion oxygeneios) is a member of the wreckfish family (Polyprionidae) and is highly regarded as a food fish. Although adults grow relatively slowly, juveniles exhibit low feed conversion ratios and can reach market size in 1–2 years, makingP. oxygeneiosa strong candidate for aquaculture. However, they can take over 5years to reach sexual maturity in captivity and are not externally sexually dimorphic, complicating many aspects of broodstock management. Understanding the sex determination system ofP. oxygeneiosand developing accurate assays to assign genetic sex will contribute significantly towards its full-scale commercialisation.  Results  DNA from parents and sexed offspring (n = 57) from a single family of captive bredP. oxygeneioswas used as a template for double digestion Restriction-site Associated DNA (ddRAD) sequencing. Two libraries were constructed usingSbfI–SphI andSbfI –NcoI restriction enzyme combinations, respectively. Two runs on an Illumina MiSeq platform generated 70,266,464 raw reads, identifying 19,669 RAD loci. A combined sex linkage map (1367cM) was constructed based on 1575 Single Nucleotide Polymorphism (SNP) markers that resolved into 35 linkage groups. Sex-specific linkage maps were of similar size (1132 and 1168cM for male and female maps respectively). A single major sex-determining locus, found to be heterogametic in males, was mapped to linkage group 14. Several markers were found to be in strong linkage disequilibrium with the sex-determining locus. Allele-specific PCR assays were developed for two of these markers, SphI6331 and SphI8298, and demonstrated to accurately differentiate sex in progeny within the same pedigree. Comparative genomic analyses indicated that many of the linkage groups within theP. oxygeneiosmap share a relatively high degree of homology with those published for the European seabass (Dicentrarchus labrax).  Conclusion  P. oxygeneioshas an XX/XY sex determination system. Evaluation of allele-specific PCR assays, based on the two SNP markers most closely associated with phenotypic sex, indicates that a simple molecular assay for sexingP. oxygeneiosshould be readily attainable. The high degree of synteny observed withD. labraxshould aid further molecular genetic study and exploitation of hāpuku as a food fish

Application of affymetrix array and massively parallel signature sequencing for identification of genes involved in prostate cancer progression

BACKGROUND: Affymetrix GeneChip Array and Massively Parallel Signature Sequencing (MPSS) are two high throughput methodologies used to profile transcriptomes. Each method has certain strengths and weaknesses; however, no comparison has been made between the data derived from Affymetrix arrays and MPSS. In this study, two lineage-related prostate cancer cell lines, LNCaP and C4-2, were used for transcriptome analysis with the aim of identifying genes associated with prostate cancer progression. METHODS: Affymetrix GeneChip array and MPSS analyses were performed. Data was analyzed with GeneSpring 6.2 and in-house perl scripts. Expression array results were verified with RT-PCR. RESULTS: Comparison of the data revealed that both technologies detected genes the other did not. In LNCaP, 3,180 genes were only detected by Affymetrix and 1,169 genes were only detected by MPSS. Similarly, in C4-2, 4,121 genes were only detected by Affymetrix and 1,014 genes were only detected by MPSS. Analysis of the combined transcriptomes identified 66 genes unique to LNCaP cells and 33 genes unique to C4-2 cells. Expression analysis of these genes in prostate cancer specimens showed CA1 to be highly expressed in bone metastasis but not expressed in primary tumor and EPHA7 to be expressed in normal prostate and primary tumor but not bone metastasis. CONCLUSION: Our data indicates that transcriptome profiling with a single methodology will not fully assess the expression of all genes in a cell line. A combination of transcription profiling technologies such as DNA array and MPSS provides a more robust means to assess the expression profile of an RNA sample. Finally, genes that were differentially expressed in cell lines were also differentially expressed in primary prostate cancer and its metastases

The distinctive gastric fluid proteome in gastric cancer reveals a multi-biomarker diagnostic profile

<p>Abstract</p> <p>Background</p> <p>Overall gastric cancer survival remains poor mainly because there are no reliable methods for identifying highly curable early stage disease. Multi-protein profiling of gastric fluids, obtained from the anatomic site of pathology, could reveal diagnostic proteomic fingerprints.</p> <p>Methods</p> <p>Protein profiles were generated from gastric fluid samples of 19 gastric cancer and 36 benign gastritides patients undergoing elective, clinically-indicated gastroscopy using surface-enhanced laser desorption/ionization time-of-flight mass spectrometry on multiple ProteinChip arrays. Proteomic features were compared by significance analysis of microarray algorithm and two-way hierarchical clustering. A second blinded sample set (24 gastric cancers and 29 clinically benign gastritides) was used for validation.</p> <p>Results</p> <p>By significance analysyis of microarray, 60 proteomic features were up-regulated and 46 were down-regulated in gastric cancer samples (<it>p </it>< 0.01). Multimarker clustering showed two distinctive proteomic profiles independent of age and ethnicity. Eighteen of 19 cancer samples clustered together (sensitivity 95%) while 27/36 of non-cancer samples clustered in a second group. Nine non-cancer samples that clustered with cancer samples included 5 pre-malignant lesions (1 adenomatous polyp and 4 intestinal metaplasia). Validation using a second sample set showed the sensitivity and specificity to be 88% and 93%, respectively. Positive predictive value of the combined data was 0.80. Selected peptide sequencing identified pepsinogen C and pepsin A activation peptide as significantly down-regulated and alpha-defensin as significantly up-regulated.</p> <p>Conclusion</p> <p>This simple and reproducible multimarker proteomic assay could supplement clinical gastroscopic evaluation of symptomatic patients to enhance diagnostic accuracy for gastric cancer and pre-malignant lesions.</p

Behavioral Defects in Chaperone-Deficient Alzheimer's Disease Model Mice

Molecular chaperones protect cells from the deleterious effects of protein misfolding and aggregation. Neurotoxicity of amyloid-beta (Aβ) aggregates and their deposition in senile plaques are hallmarks of Alzheimer's disease (AD). We observed that the overall content of αB-crystallin, a small heat shock protein molecular chaperone, decreased in AD model mice in an age-dependent manner. We hypothesized that αB-crystallin protects cells against Aβ toxicity. To test this, we crossed αB-crystallin/HspB2 deficient (CRYAB-/-HSPB2-/-) mice with AD model transgenic mice expressing mutant human amyloid precursor protein. Transgenic and non-transgenic mice in chaperone-sufficient or deficient backgrounds were examined for representative behavioral paradigms for locomotion and memory network functions: (i) spatial orientation and locomotion was monitored by open field test; (ii) sequential organization and associative learning was monitored by fear conditioning; and (iii) evoked behavioral response was tested by hot plate method. Interestingly, αB-crystallin/HspB2 deficient transgenic mice were severely impaired in locomotion compared to each genetic model separately. Our results highlight a synergistic effect of combining chaperone deficiency in a transgenic mouse model for AD underscoring an important role for chaperones in protein misfolding diseases

A palaeoenvironmental reconstruction of the Middle Jurassic of Sardinia (Italy) based on integrated palaeobotanical, palynological and lithofacies data assessment

During the Jurassic, Sardinia was close to continental Europe. Emerged lands started from a single island forming in time a progressively sinking archipelago. This complex palaeogeographic situation gave origin to a diverse landscape with a variety of habitats. Collection- and literature-based palaeobotanical, palynological and lithofacies studies were carried out on the Genna Selole Formation for palaeoenvironmental interpretations. They evidence a generally warm and humid climate, affected occasionally by drier periods. Several distinct ecosystems can be discerned in this climate, including alluvial fans with braided streams (Laconi-Gadoni lithofacies), paralic swamps and coasts (Nurri-Escalaplano lithofacies), and lagoons and shallow marine environments (Ussassai-Perdasdefogu lithofacies). The non-marine environments were covered by extensive lowland and a reduced coastal and tidally influenced environment. Both the river and the upland/hinterland environments are of limited impact for the reconstruction. The difference between the composition of the palynological and palaeobotanical associations evidence the discrepancies obtained using only one of those proxies. The macroremains reflect the local palaeoenvironments better, although subjected to a transport bias (e.g. missing upland elements and delicate organs), whereas the palynomorphs permit to reconstruct the regional palaeoclimate. Considering that the flora of Sardinia is the southernmost of all Middle Jurassic European floras, this multidisciplinary study increases our understanding of the terrestrial environments during that period of time

Desain Konseptual Kualitas Produk Kopi Menggunakan Metode Importance Performance Analysis (IPA) dan Quality Function Depolyment (QFD)

Saat ini eksistensi kopi semakin berkembang didukung dengan beragamnya olahan produk kopi yang dapat ditemukan pada beberapa gerai salah satunya kedai Kopi Tuju yang berada di kota Malang. Kedai Kopi Tuju menawarkan beragam variasi produk kopi yang disesuaikan dengan kesukaan masing-masing konsumen. Olahan produk kopi memiliki beberapa komponen yang disesuaikan dengan kebutuhan konsumen seperti: aroma khas kopi yang sangat kuat, kopi dominan pahit, cita rasa yang ditinggalkan (aftertaste) serta mampu bertahan lama, tingkat kemanisan atau sweet yang rendah, tingkat keasaman, dan kesan setelah mengkonsumsi kopi yang terasa nikmat. Persaingan bisnis yang semakin luas harus membuat kedai Kopi Tuju meningkatkan strategi bersaingnya, salah satunya peningkatan kualitas produk kopi. Desain konseptual adalah desain teknis yang mengkategorikan atribut penelitian berdasarkan hasil preferensi konsumen dengan tujuan utama yaitu untuk mengetahui kemampuan/kinerja dari masing-masing atribut terhadap penelitian yang dilakukan. Dalam menentukan kualitas produk kopi yang diinginkan konsumen (seperti: rasa, aroma, tekstur, dan warna) dapat dinilai pada produk yang ditawarkan. Kualitas produk kopi tersebut diartikan sebagai peluang untuk memenuhi kepuasan konsumen. Metode yang digunakan yaitu Importance Performance Analysis dan Quality Function Deployment yang digunakan untuk menganalisis kualitas produk kedai Kopi Tuju. Penyebaran kuesioner secara langsung kepada 150 responden dan salah satunya responden ahli yang merupakan salah satu pelayan Kopi Tuju. Atribut yang digunakan dalam penelitian ini sebanyak 9 atribut yang berfungsi untuk mengetahui tingkat kualitas produk Kopi Tuju. Tujuan dari penelitian ini adalah untuk menganalisis atribut kedai Kopi Tuju yang perlu dilakukan perbaikan untuk meningkatkan kualitas produk kopi dengan menggunakan metode IPA dan metode QFD. Hasil yang diperoleh dari metode Importance Performance Analysis (IPA) dapat diketahui perlakuan dari masing-masing kuadran. Pada kuadran 1 terdapat beberapa atribut yang diperlukan perbaikan yaitu harga produk dan tingkat keasamaan. Atribut yang dikategorikan atribut yang perlu dipertahankan tingkat kinerja yaitu tampilan produk. Atribut selanjutnya yang membutuhkan perbaikan terdapat pada kuadran III yaitu tingkat kepahitan. Atribut IV merupakan atribut cenderung rendah tetapi tidak terlalu diharapkan oleh konsumen. Atribut tersebut harus dipertahankan karena dinilai baik oleh pengunjung kedai Kopi Tuju

Pengaruh Letak Baterai Kandang Terhadap Kualitas Telur Burung Puyuh (Coturnix coturnix japonica)

Burung puyuh (Coturnix coturnix japonica) merupakan unggas yang populer dan memiliki potensi di bidang peternakan di Indonesia. Penggunaan kandang bertingkat dapat menghasilkan suhu mikro yang berbeda pada setiap tingkatan. Penelitian ini bertujuan untuk mengetahui pengaruh penempatan battery tier pada kandang burung puyuh (Coturnix coturnix japonica) terhadap kualitas telur yang dihasilkan burung puyuh ditinjau dari bobot telur, indeks bentuk, ketebalan, dan bobot kerabang. Hewan coba yang digunakan dalam penelitian ini adalah 500 ekor puyuh jepang (Coturnix coturnix japonica) yang telah memasuki tahap produksi pada umur 29 minggu. Metode yang akan digunakan dalam penelitian ini adalah percobaan Rancangan Acak Lengkap (RAL) dengan 4 perlakuan dan 5 ulangan. Perlakuan pada penelitian ini adalah dengan baris kandang yang berbeda (baris 1, baris 2, baris 3, dan baris 4). Hasil analisis varians menunjukkan bahwa perbedaan letak deretan kandang baterai tidak berpengaruh nyata (P>0,05) terhadap nilai indeks bobot dan bentuk telur, tetapi berbeda sangat nyata (P<0,01 ) terhadap ketebalan dan berat kerabang telur puyuh. Rata-rata hasil analisis variansi dari P1, P2, P3 dan P4 terhadap bobot telur berturut-turut adalah 11,79 ± 0,626; 11,75 ± 0,356; 12,42 ± 0,764; dan 12,36 ± 0,422; indeks bentuk rata-rata (%) nilai berturut-turut adalah 77,40 ± 0,762; 78,82 ± 1,153; 77,72 ± 1,279; dan 76,71 ± 1,529; nilai rata-rata ketebalan kerabang adalah 0,38 ± 0,0155; 0,32 ± 0,0097; 0,32 ± 0,0097; dan 0,31 ± 0,0077; dan nilai rata-rata berat cangkang telur adalah 1,86 ± 0,443; 1,75 ± 0,086; 1,57 ± 0,133; dan 1,41 ± 0,109. Perbedaan letak barisan kandang baterai berpengaruh sangat nyata terhadap ketebalan dan berat kerabang telur yang dihasilkan burung puyuh tetapi tidak berpengaruh nyata terhadap berat telur dan indeks bentuk telur puyuh

Penggandaan Skala Proses Pretreatment Tandan Kosong Kelapa Sawit (TKKS) Menggunakan Metode Pulsed Electrical Field (PEF) dan Ultrasonik di PT Pertamina (Persero) Research and Technology Innovation

Indonesia merupakan negara yang memiliki potensi sumber daya alam yang sangat tinggi, salah satunya adalah kelapa sawit. Hasil samping yang dihasilkan dalam proses produksi kelapa sawit salah satunya adalah tandan kosong kelapa sawit (TKKS). Limbah TKKS memiliki kandungan biomassa yang cukup tinggi. Kandungan yang ada di dalam TKKS diantaranya adalah selulosa, hemiselulosa, dan lignin. Salah satu kandungan dari TKKS yang dapat dimanfaatkan menjadi produk lain yang bernilai tinggi adalah selulosa. Tujuan penelitian ini adalah mengetahui hasil pretreatment tandan kosong kelapa sawit (TKKS) menggunakan PEF-Ultrasonik di PT Pertamina Research and Technology Innovation setelah penggandaan skala dari skala laboratorium menjadi skala meja ditinjau dari segi kualitas selulosa, alat dan teknologi, neraca massa, serta perhitungan kebutuhan energi dan biaya serta dibandingkan dengan skala laboratoriumnya. Penggandaan skala (scale-up) adalah proses yang dilakukan untuk mendapatkan hasil produksi yang identik (jika memungkinkan) pada skala yang lebih besar berdasarkan pada skala produksi yang telah ditentukan sebelumnya. Tujuan utama dalam penggandaan skala (scale-up) adalah menjaga kualitas produk yang dapat diterima. Hasil yang didapatkan berdasarkan hasil uji chesson yaitu TKKS hasil pretreatment TKKS metode PEF-Ultrasonik skala meja memiliki komposisi HWS, hemiselulosa, selulosa, dan lignin berturut-turut adalah 11,47%, 11,86%, 59,65%, dan 17,02%. Hasil ini tidak identik dan relatif lebih rendah dibandingkan dengan hasil uji chesson untuk hasil pretreatment skala laboratorium namun masih lebih baik daripada penelitian lain. Alat yang digunakan pada pretreatment skala meja merupakan alat yang relatif identik dengan pretreatment skala laboratoriumnya. Sedangkan dalam beberapa penerapan teknologi proses tidak sesuai dengan hasil terbaik pada skala laboratorium. Neraca massa proses pretreatment TKKS metode PEF-Ultrasonik skala meja terjadi kesetimbangan. Energi yang dibutuhkan pretreatment skala meja adalah 0,12 liter BBM berjenis solar dan 9094,4 kJ energi listrik untuk setiap kg serta total biaya yang diperlukan sebesar Rp 4.911,39 untuk setiap kilogram. Kebutuhan energi dan total biaya yang diperlukan pretreatment skala meja lebih besar daripada pretreatment skala laboratoriumnya