bluuebunny/crossref_metadata_2025_split huggingface dataset:
Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E
Authors: Waters Shafagh A , McAteer Sean P , Kudla Grzegorz , Pang Ignatius , Deshpande Nandan P , Amos Timothy G , Leong Kai Wen , Wilkins Marc R , Strugnell Richard , Gally David L , Tollervey David , Tree Jai J 
Published: November 2016

AbstractRNA sequencing studies have identified hundreds of non‐coding RNAs in bacteria, including regulatory small RNA (sRNA). However, our understanding of sRNA function has lagged behind their identification due to a lack of tools for the high‐throughput analysis of RNA–RNA interactions in bacteria. Here we demonstrate that in vivo sRNA–mRNA duplexes can be recovered using UV‐crosslinking, ligation and sequencing of hybrids (CLASH). Many sRNAs recruit the endoribonuclease, RNase E, to facilitate processing of mRNAs. We were able to recover base‐paired sRNA–mRNA duplexes in association with RNase E, allowing proximity‐dependent ligation and sequencing of cognate sRNA–mRNA pairs as chimeric reads. We verified that this approach captures bona fide sRNA–mRNA interactions. Clustering analyses identified novel sRNA seed regions and sets of potentially co‐regulated target mRNAs. We identified multiple mRNA targets for the pathotype‐specific sRNA Esr41, which was shown to regulate colicin sensitivity and iron transport in E. coli. Numerous sRNA interactions were also identified with non‐coding RNAs, including sRNAs and tRNAs, demonstrating the high complexity of the sRNA interactome.
A case of hepatitis C-associated osteosclerosis: accelerated bone turnover controlled by pulse steroid therapy
Authors: Miyamura Nobuhiro , Nishida Shuhei , Itasaka Mina , Matsuda Hirofumi , Ohtou Takeshi , Yamaguchi Yasuhiro , Inaba Daisuke , Tamiya Sadahiro , Nakano Tetsuo 
Published: November 2016

Summary
Hepatitis C-associated osteosclerosis (HCAO), a very rare disorder in which an extremely rapid bone turnover occurs and results in osteosclerosis, was acknowledged in 1990s as a new clinical entity with the unique bone disorder and definite link to chronic type C hepatitis, although the pathogenesis still remains unknown. Affected patients suffer from excruciating deep bone pains. We report the 19th case of HCAO with diagnosis confirmed by bone biopsy, and treated initially with a bisphosphonate, next with corticosteroids and finally with direct acting antivirals (DAA: sofosbuvir and ribavirin) for HCV infection. Risedronate, 17.5 mg/day for 38 days, did not improve the patient’s symptoms or extremely elevated levels of bone markers, which indicated hyper-bone-formation and coexisting hyper-bone-resorption in the patient. Next, intravenous methylprednisolone pulse therapy followed by high-dose oral administration of prednisolone evidently improved them. DAA therapy initiated after steroid therapy successfully achieved sustained virological response, but no additional therapeutic effect on them was observed. Our results strongly suggested that the underlying immunological alteration is the crucial key to clarify the pathogenesis of HCAO. Bone mineral density of lumbar vertebrae of the patient was increased by 14% in four-month period of observation. Clarification of the mechanisms that develop osteosclerosis in HCAO might lead to a new therapeutic perspective for osteoporosis.

Learning points:

HCAO is an extremely rare bone disorder, which occurs exclusively in patients affected with HCV, of which only 18 cases have been reported since 1992 and pathogenesis still remains unclear.

Pathophysiology of HCAO is highly accelerated rates of both bone formation and bone resorption, with higher rate of formation than that of resorption, which occur in general skeletal leading to the diffuse osteosclerosis with severe bone pains.

Steroid therapy including intravenous pulse administration in our patient evidently ameliorated his bone pains and reduced elevated values of bone markers. This was the first successful treatment for HCAO among cases reported so far and seemed to propose a key to solve the question for its pathogenesis.

The speed of increase in the bone mineral content of the patient was very high, suggesting that clarification of the mechanism(s) might lead to the development of a novel therapy for osteoporosis.
Expression of microRNAs that regulate bone turnover in the serum of postmenopausal women with low bone mass and vertebral fractures
Authors: Yavropoulou Maria P , Anastasilakis Athanasios D , Makras Polyzois , Tsalikakis Dimitrios G , Grammatiki Maria , Yovos John G 
Published: November 2016

Background
Circulating microRNAs (miRs) are currently being investigated as novel biomarkers for osteoporosis and osteoporotic fractures.

Aim
The aim of this study was to investigate serum levels of specific microRNAs, known regulators of bone metabolism, in postmenopausal women with low bone mass and with or without vertebral fractures (VFs).

Methods
For the analysis, 14 miRs were isolated from the serum of 35 postmenopausal women with low bone mass and with at least one moderate VF and 35 postmenopausal women with low bone mass without fractures. Thirty postmenopausal women with normal BMD values and no history of fractures served as controls. Main outcome parameters were changes in the expression of selected miRs in the serum of patient population and compared with controls.

Results
From the 14 miRs that were selected, we identified 5 miRs, namely miR-21-5p, miR-23a, miR-29a-3p, miR-124-3p and miR-2861 that were significantly deregulated in the serum of patients with low bone mass compared with controls. Serum miR-124 and miR-2861 were significantly higher, whereas miR-21, miR-23 and miR-29 were lower in patients compared with controls. In a sub-group analysis of the patient population, the expression of miR-21-5p was significantly lower among osteoporotic/osteopenic women with VFs, showing 66% sensitivity and 77% specificity in distinguishing women with a vertebral fracture.

Conclusion
This study identifies a differential expression pattern of miR-21-5p in the serum of women with low BMD and VFs.
Adrenal vein sampling in primary aldosteronism: concordance of simultaneous vs sequential sampling
Authors: Almarzooqi Mohamed-Karji , Chagnon Miguel , Soulez Gilles , Giroux Marie-France , Gilbert Patrick , Oliva Vincent L , Perreault Pierre , Bouchard Louis , Bourdeau Isabelle , Lacroix André , Therasse Eric 
Published: November 2016

Objective
Many investigators believe that basal adrenal venous sampling (AVS) should be done simultaneously, whereas others opt for sequential AVS for simplicity and reduced cost. This study aimed to evaluate the concordance of sequential and simultaneous AVS methods.

Design and methods
Between 1989 and 2015, bilateral simultaneous sets of basal AVS were obtained twice within 5 min, in 188 consecutive patients (59 women and 129 men; mean age: 53.4 years). Selectivity was defined by adrenal-to-peripheral cortisol ratio ≥2, and lateralization was defined as an adrenal aldosterone-to-cortisol ratio ≥2, the contralateral side. Sequential AVS was simulated using right sampling at −5 min (t = −5) and left sampling at 0 min (t = 0).

Results
There was no significant difference in mean selectivity ratio (P = 0.12 and P = 0.42 for the right and left sides respectively) and in mean lateralization ratio (P = 0.93) between t = −5 and t = 0. Kappa for selectivity between 2 simultaneous AVS was 0.71 (95% CI: 0.60–0.82), whereas it was 0.84 (95% CI: 0.76–0.92) and 0.85 (95% CI: 0.77–0.93) between sequential and simultaneous AVS at respectively −5 min and at 0 min. Kappa for lateralization between 2 simultaneous AVS was 0.84 (95% CI: 0.75–0.93), whereas it was 0.86 (95% CI: 0.78–0.94) and 0.80 (95% CI: 0.71–0.90) between sequential AVS and simultaneous AVS at respectively −5 min at 0 min.

Conclusions
Concordance between simultaneous and sequential AVS was not different than that between 2 repeated simultaneous AVS in the same patient. Therefore, a better diagnostic performance is not a good argument to select the AVS method.
Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations
Authors: Montinaro Francesco , Busby George B J , Gonzalez-Santos Miguel , Oosthuitzen Ockie , Oosthuitzen Erika , Anagnostou Paolo , Destro-Bisol Giovanni , Pascali Vincenzo L , Capelli Cristian 
Published: November 2016

AbstractThe characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry and allele frequency based analyses, we identify a tripartite, ancient, Khoesan-related genetic structure. This structure correlates neither with linguistic affiliation nor subsistence strategy, but with geography, revealing the importance of isolation-by-distance dynamics in the area. Fine-mapping of these components in southern African populations reveals admixture and cultural reversion involving several Khoesan groups, and highlights that Bantu speakers and Coloured individuals have different mixtures of these ancient ancestries.
Variation and Evolution of the Meiotic Requirement for Crossing Over in Mammals
Authors: Dumont Beth L 
Published: November 2016

AbstractThe segregation of homologous chromosomes at the first meiotic division is dependent on the presence of at least one well-positioned crossover per chromosome. In some mammalian species, however, the genomic distribution of crossovers is consistent with a more stringent baseline requirement of one crossover per chromosome arm. Given that the meiotic requirement for crossing over defines the minimum frequency of recombination necessary for the production of viable gametes, determining the chromosomal scale of this constraint is essential for defining crossover profiles predisposed to aneuploidy and understanding the parameters that shape patterns of recombination rate evolution across species. Here, I use cytogenetic methods for in situ imaging of crossovers in karyotypically diverse house mice (Mus musculus domesticus) and voles (genus Microtus) to test how chromosome number and configuration constrain the distribution of crossovers in a genome. I show that the global distribution of crossovers in house mice is thresholded by a minimum of one crossover per chromosome arm, whereas the crossover landscape in voles is defined by a more relaxed requirement of one crossover per chromosome. I extend these findings in an evolutionary metaanalysis of published recombination and karyotype data for 112 mammalian species and demonstrate that the physical scale of the genomic crossover distribution has undergone multiple independent shifts from one crossover per chromosome arm to one per chromosome during mammalian evolution. Together, these results indicate that the chromosomal scale constraint on crossover rates is itself a trait that evolves among species, a finding that casts light on an important source of crossover rate variation in mammals.
INTERAKSI GENOTIPE DENGAN LINGKUNGAN, ADAPTABILITAS, DAN STABILITAS PENAMPILAN FENOTIPIK EMPAT VARIETAS UNGGUL IKAN NILA (Oreochromis niloticus)
Authors: Ariyanto Didik , Listiyowati Nunuk 
Published: November 2016

Penampilan fenotipik suatu organisme ditentukan oleh faktor genetik dan dipengaruhi oleh faktor lingkungan tempat organisme tersebut hidup. Dalam beberapa kasus, interaksi antara faktor genetik dengan lingkungan juga berpengaruh terhadap penampilan fenotipik yang dihasilkan. Penelitian ini bertujuan untuk mempelajari interaksi antara faktor genetik dengan lingkungan, daya adaptabilitas dan stabilitas penampilan fenotipik khususnya bobot individu pada empat varietas unggul ikan nila yang dipelihara di tiga lokasi berbeda. Ikan nila varietas GMT, merah NIFI, NIRWANA dan BEST dipelihara di tambak payau di Indramayu, kolam air tenang di Sukamandi dan karamba jaring apung di Waduk Cirata, Kabupaten Cianjur, selama empat bulan pemeliharaan. Benih ikan nila diberi pakan pelet komersial dengan kandungan protein kasar 28%-30%, sebanyak 10%; 7,5%; 5%; dan 2,5% dari biomassa ikan masing-masing pada bulan pertama, kedua, ketiga, dan keempat. Pakan diberikan dengan frekuensi dua kali setiap hari. Hasil penelitian menunjukkan bahwa bobot ikan nila secara nyata dipengaruhi oleh faktor genetik, lingkungan, serta interaksi antara kedua faktor tersebut. Selain ikan nila GMT, tiga varietas ikan nila yang diuji mempunyai adaptabilitas lingkungan relatif sempit, serta stabilitas penampilan fenotipik karakter bobot individu relatif rendah. Hal ini mengindikasikan bahwa pengembangan budidaya ikan nila GMT dapat dilakukan di semua lokasi, sedangkan ikan nila merah NIFI, NIRWANA, dan BEST akan optimal jika dilakukan di lokasi tertentu saja.Phenotypic performance was determined by genetic and environment factors and their interaction. This study was conducted to examinethe present of interaction both of genetic and environment factors, adaptability, and stability of phenotypic performance of four varieties of tilapia which maintained in three different location. GMT, red NIFI, NIRWANA, and BEST tilapia strains were reared for four months in net cages in Cirata reservoir in Cianjur, in earthen ponds in Sukamandi and in brackish water ponds in Indramayu. All fish were fed with commercial pelleted feed contained of crude protein 28%-30%, about 10%, 7.5%, 5%, and 2.5% each day in 1st, 2nd, 3rd, and 4th month, respectively. The results showed that tilapia’s phenotipic performance especially the average body weight was significantly affected by genetic factor, environment factor, and interaction both of them factors. Except the GMT, all tilapia strains used in this study have narrow phenotypic adaptability and stability, especially in average body weight. This results indicated that GMT tilapia strain can be farmed in various areas, but red NIFI, NIRWANA, and BEST tilapia strains are most likely in a specific location.
PEMAPARAN INSEKTISIDA ENDOSULFAN PADA KONSENTRASI SUBLETAL TERHADAP KONDISI HEMATOLOGIS DAN HISTOLOGIS IKAN MAS (Cyprinus carpio)
Authors: Taufik Imam , Setiadi Eri 
Published: November 2016

Endosulfan merupakan insektisida golongan organoklorin non-sistemik yang banyak digunakan di bidang pertanian, khususnya di negara-negara berkembang termasuk di Indonesia. Insektisida ini bersifat sangat toksik terhadap organisme akuatik termasuk ikan. Penelitian bertujuan untuk mengetahui kondisi hematologis dan histologis insang dan hati ikan mas (Cyprinus carpio) yang terpapar insektisida endosulfan. Sebagai perlakuan digunakan konsentrasi subletal endosulfan, yaitu: A) 0,00 μg/L; B) 0,24 μg/L; C) 0,73 μg/L; dan D) 1,21 μg/L. Hewan uji adalah ikan mas dengan bobot rata-rata 0,81±0,098 g/ekor. Wadah uji berupa akuarium kaca 70 cm x 50 cm x 60 cm berisi 150 liter air. Waktu pemaparan selama 12 minggu. Hasil penelitian menunjukkan bahwa endosulfan berpengaruh nyata terhadap kondisi hematologis seperti hematokrit, hemoglobin, eritrosit, dan leukosit pada setiap perlakuan (P<0,05). Hematokrit dan hemoglobin semakin meningkat sejalan dengan peningkatan konsentrasi endosulfan, sedangkan eritrosit dan leukosit mengalami penurunan. Hasil histologi insang menunjukkan bahwa semakin tinggi konsentrasi endosulfanmaka kerusakan insang semakin meningkat, seperti hiperflasia lamella epithelium, degenerasi sel epithelium, pendarahan, vakuolasi, nekrosis, dan ploriferasi sel tulang rawan. Kerusakan pada hati yang dijumpai, yaitu dilatasi sinusoid, vakuolasi, degenerasi hepatosit, piknosis, ploriferasi hepatosit, dan nekrosis. Kerusakan jaringan hati semakin meningkat seiring dengan peningkatan konsentrasi endosulfan dalam air. Berdasarkan hasil penelitian sekarang insektisida endosulfan menyebabkan kerusakan jaringan organ filamen insang dan hati, serta ikan menjadi tidak sehat dengan aktivitas berenang menjadi abnormal dan kehilangan keseimbangan.
OPSI PENGELOLAAN TANAH UNTUK TEKNOLOGI TRADISIONAL BERDASARKAN KARAKTERISTIK TANAH TAMBAK DI KECAMATAN TAYU KABUPATEN PATI PROVINSI JAWA TENGAH
Authors: Mustafa Akhmad , Suhaimi Rezki Antoni , Hasnawi Hasnawi 
Published: November 2016

Kecamatan Tayu Kabupaten Pati Provinsi Jawa Tengah memiliki lahan tambak, namun produksi tambaknya belum optimum yang diduga disebabkan oleh pengelolaan tanahnya yang belum tepat. Penelitian ini bertujuan untuk mengetahui karakteristik tanah sebagai dasar dalam menentukan opsi pengelolaan tanahnya agar produktivitas tambak dapat meningkat dan berkelanjutan. Penelitian dilaksanakan di Desa Keboromo, Jepat Lor, dan Tunggulsari Kecamatan Tayu dengan metode survai pada bulan Juni dan Agustus-September 2014. Pengambilan contoh tanah dilakukan di 90 titik pada kedalaman 0-0,2 m. Sebanyak 17 peubah kualitas tanah diukur dan dianalisis. Statistik deskriptif digunakan untuk mendapatkan gambaran umum dari data kualitas tanah yang ada. Kebutuhan kapur didasarkan pada pH dan tekstur tanah dengan mempertimbangkan kualitas kapur (nilai netralisasi dan nilai efisiensi), sedangkan kebutuhan unsur hara didasarkan juga pada kualitas tanah dan kebutuhan optimum untuk budidaya tambak teknologi tradisional. Hasil penelitian menunjukkan bahwa tanah tambak di Kecamatan Tayu tergolong tanah aluvial nonsulfat masam yang dicirikan secara umum dengan pH yang tergolong netral namun masam pada daerah tertentu, konsentrasi karbon, nitrogen, besi, aluminium, dan sulfur yang relatif rendah, konsentrasi fosfat yang relatif tinggi serta tekstur yang tergolong kasar. Opsi pengelolaan tanah yang ditawarkan berupa pengapuran yang berkisar dari 0-5.119 kg/ha dengan rata-rata 141 kg/ha jika menggunakan dolomit atau 0-4.159 kg/ha dengan rata-rata 116 kg/ha jika menggunakan kaptan. Pupuk urea yang mengandung 46,0% nitrogen dapat diaplikasikan dengan dosis antara 0 dan 191 kg/ha dengan rata-rata 117 kg/ha dan pupuk organik yang mengandung 26,51% karbon dapat diaplikasikan dengan dosis 0 sampai dengan 3.361 kg/ha dengan rata-rata 1.781 kg/ha.
INDEKS KUALITAS AIR DAN SEBARAN NUTRIEN SEKITAR BUDIDAYA LAUT TERINTEGRASI DI PERAIRAN TELUK EKAS, NUSA TENGGARA BARAT: ASPEK PENTING BUDIDAYA RUMPUT LAUT
Authors: Radiarta I Nyoman , Erlania Erlania 
Published: November 2016

Kualitas perairan merupakan salah satu aspek penting dalam perikanan budidaya. Perubahan yang terjadi pada kondisi kimia atau fisik perairan dapat menyebabkan dampak negatif terhadap pertumbuhan biota budidaya. Data kualitas air hasil program pemantauan selama enam bulan di lokasi penelitian telah dianalisis untuk melihat kisaran indeks kualitas air dan sebaran nutrien yang terjadi di sekitar unit budidaya laut terintegrasi berbasis integrated multi-trophic aquaculture (IMTA) di Teluk Ekas Provinsi Nusa Tenggara Barat. Pengamatan dilakukan pada bulan Juni-November 2014, sebanyak 13 titik pengamatan yang disebar secara diagonal dengan pusat keramba jaring apung ikan laut. Seluruh data dianalisis secara spasial dan temporal. Hasil penelitian menunjukkan bahwa nilai indeks kualitas air di lokasi penelitian tergolong kategori sedang-baik. Bulan Juli merupakan bulan dengan nilai indeks yang baik dengan kategori sedang-sangat baik (50-83); sedangkan bulan September memiliki nilai indeks yang relatif rendah dengan kategori buruk sedang (33-60). Berdasarkan sebaran nutrien (amonium, nitrat, dan orto-fosfat) menunjukkan fluktuasi secara spasial dan temporal. Konsentrasi nutrien umumnya tersedia dengan baik pada jarak 60 m dari KJA. Hasil penelitian ini dapat memberikan gambaran tentang kondisi kualitas perairan dan ketersediaan nutrien untuk mendukung pertumbuhan dan produktivitas budidaya rumput laut dengan sistem IMTA.
PATOGENESIS KO-INFEKSI PENYAKIT FISH TUBERCULOSIS DAN MOTILE AEROMONAS SEPTICEMIA PADA IKAN GURAME (Osphronemus gouramy)
Authors: Purwaningsih Uni , Indrawati Agustin , Lusiastuti Angela Mariana 
Published: November 2016

Penyakit fish tuberculosis dan Motile Aeromonas Septicemia (MAS) merupakan penyakit potensial pada budidaya ikan gurame. Infeksi kedua penyakit tersebut dimungkinkan terjadi dalam waktu yang bersamaan walaupun etiologi kedua jenis penyakit tersebut memiliki karakteristik yang berbeda. Penelitian ini bertujuan untuk mengetahui perjalanan kedua penyakit tersebut dalam waktu yang bersamaan ketika menginfeksi gurame uji dengan melihat perubahan parameter hematologi, pola kematian, dan histopatologi. Gurame uji yangdigunakan berukuran 25-30 g dengan dosis infeksi berdasarkan dosis LD50 bakteri A. hydrophila 108 cfu dan LD50 M. fortuitum 107 cfu. Gejala klinis akibat infeksi M. fortuitum mulai terlihat pada hari ke-14 ditandai dengan penurunan nafsu makan dan hari ke-18 mulai terlihat nodul dalam ukuran 0,1-0,2 mm pada permukaan tubuh. Sedangkan infeksi A. hydrophila menunjukkan gejala klinis luka pada bekas injeksi dan terlihat pembengkakan pada rongga perut mulai 24-48 jam pascainfeksi. Respons fisiologis tubuh ikan gurame terhadap adanya ko-infeksi ditunjukkan dengan nilai hemoglobin, hematokrit, persentase komponen sel darah putih yang berbeda (P<0,05) dengan kontrol. Perubahan histopatologi pada perlakuan koinfeksi menunjukkan adanya kongesti, peradangan, nekrosis, melano macrofag center, dan gramuloma yangbersifat multifocal pada organ hati, ginjal, dan limpa.
PERTUMBUHAN DAN SIGOSITAS IKAN LELE AFRIKA (Clarias gariepinus) TRANSGENIK F-2 YANG MEMBAWA GEN HORMON PERTUMBUHAN IKAN PATIN SIAM (Pangasianodon hypophthalmus)
Authors: Marnis Huria , Iswanto Bambang , Suprapto Rommy , Imron Imron , Dewi Raden Roro Sri Pudji Sinarni 
Published: November 2016

Teknologi transgenesis telah banyak digunakan untuk memperbaiki karakter pertumbuhan pada ikan budidaya. Pada penelitian sebelumnya, telah dihasilkan ikan lele transgenik F-1 yang memiliki pertumbuhan lebih cepat. Penelitian ini bertujuan untuk menguji performa pertumbuhan, dan mengidentifikasi sigositasikan lele transgenik F-2. Ikan lele transgenik F-2 dihasilkan dari persilangan antar ikan lele transgenik F-1. Sigositas ikan F-2 dievaluasi menggunakan uji progeni dengan menyilangkan antara ikan transgenik F-2 dan non-transgenik. Parameter digunakan untuk mengevaluasi performa ikan lele transgenik F-2 meliputi:derajat pembuahan, derajat penetasan, sintasan larva, pertumbuhan, dan efisiensi pakan. Analisis sigositas ikan lele transgenik F-2 dilakukan dengan menggunakan uji progeni. Hasil penelitian menunjukkan bahwa transgen (PhGH) yang ada pada ikan transgenik tidak memengaruhi derajat pembuahan dan derajat penetasan embrio, serta sintasan larva. Populasi ikan lele transgenik F-2 memiliki laju pertumbuhan 75,3% lebih tinggi dibandingkan populasi ikan non-transgenik (P<0,05). Efisiensi pakan ikan transgenik adalah 51,95% lebih tinggi dari ikan non-transgenik (P<0,05). Hasil analisis sigositas ikan lele transgenik F-2 dari 56 ekor yang diuji, hanya 16 ekor ikan lele membawa gen PhGH, emuanya heterozigot.