scholarly journals A phased, diploid assembly of the Cascade hop (Humulus lupulus) genome reveals patterns of selection and haplotype variation

2019 ◽  
Author(s):  
Lillian K. Padgitt-Cobb ◽  
Sarah B. Kingan ◽  
Jackson Wells ◽  
Justin Elser ◽  
Brent Kronmiller ◽  
...  
Keyword(s):  
Large Scale ◽  
Humulus Lupulus ◽  
Plant Genome ◽  
Repeat Content ◽  
Haplotype Variation ◽  
Genomic Landscape ◽  
Cannabidiolic Acid ◽  
Long Read ◽  
History Of ◽  
Insight Into

AbstractHop (Humulus lupulus L. var Lupulus) is a diploid, dioecious plant with a history of cultivation spanning more than one thousand years. Hop cones are valued for their use in brewing, and around the world, hop has been used in traditional medicine to treat a variety of ailments. Efforts to determine how biochemical pathways responsible for desirable traits are regulated have been challenged by the large, repetitive, and heterozygous genome of hop. We present the first report of a haplotype-phased assembly of a large plant genome. Our assembly and annotation of the Cascade cultivar genome is the most extensive to date. PacBio long-read sequences from hop were assembled with FALCON and phased with FALCON-Unzip. Using the diploid assembly to assess haplotype variation, we discovered genes under positive selection enriched for stress-response, growth, and flowering functions. Comparative analysis of haplotypes provides insight into large-scale structural variation and the selective pressures that have driven hop evolution. Previous studies estimated repeat content at around 60%. With improved resolution of long terminal retrotransposons (LTRs) due to long-read sequencing, we found that hop is nearly 78% repetitive. Our quantification of repeat content provides context for the size of the hop genome, and supports the hypothesis of whole genome duplication (WGD), rather than expansion due to LTRs. With our more complete assembly, we have identified a homolog of cannabidiolic acid synthase (CBDAS) that is expressed in multiple tissues. The approaches we developed to analyze a phased, diploid assembly serve to deepen our understanding of the genomic landscape of hop and may have broader applicability to the study of other large, complex genomes.

scholarly journals The history of settlement and agrarian land use in a boreal forest in Värmland, Sweden, new evidence from pollen analysis

2021 ◽  
Author(s):  
Sigrún Dögg Eddudóttir ◽  
Eva Svensson ◽  
Stefan Nilsson ◽  
Anneli Ekblom ◽  
Karl-Johan Lindholm ◽  
...  
Keyword(s):  
Land Use ◽  
Pollen Analysis ◽  
Large Scale ◽  
Pollen Grains ◽  
Ice Age ◽  
Valuable Insight ◽  
Archaeological Survey ◽  
History Of ◽  
New Evidence ◽  
Insight Into

AbstractShielings are the historically known form of transhumance in Scandinavia, where livestock were moved from the farmstead to sites in the outlands for summer grazing. Pollen analysis has provided a valuable insight into the history of shielings. This paper presents a vegetation reconstruction and archaeological survey from the shieling Kårebolssätern in northern Värmland, western Sweden, a renovated shieling that is still operating today. The first evidence of human activities in the area near Kårebolssätern are Hordeum- and Cannabis-type pollen grains occurring from ca. 100 bc. Further signs of human impact are charcoal and sporadic occurrences of apophyte pollen from ca. ad 250 and pollen indicating opening of the canopy ca. ad 570, probably a result of modification of the forest for grazing. A decrease in land use is seen between ad 1000 and 1250, possibly in response to a shift in emphasis towards large scale commodity production in the outlands. Emphasis on bloomery iron production and pitfall hunting may have caused a shift from agrarian shieling activity. The clearest changes in the pollen assemblage indicating grazing and cultivation occur from the mid-thirteenth century, coinciding with wetter climate at the beginning of the Little Ice Age. The earliest occurrences of anthropochores in the record predate those of other shieling sites in Sweden. The pollen analysis reveals evidence of land use that predates the results of the archaeological survey. The study highlights how pollen analysis can reveal vegetation changes where early archaeological remains are obscure.

scholarly journals Chronic Myelomonocytic Leukemia—Hematopathology Perspective

2021 ◽  
Author(s):  
Siba El Hussein ◽  
Sa A. Wang ◽  
Naveen Pemmaraju ◽  
Joseph D. Khoury ◽  
Sanam Loghavi
Keyword(s):  
Risk Stratification ◽  
Large Scale ◽  
Chronic Myelomonocytic Leukemia ◽  
Clinical Implications ◽  
The Past ◽  
Genomic Landscape ◽  
Sequencing Studies ◽  
Myelomonocytic Leukemia ◽  
Insight Into

ABSTRACT Our understanding of chronic myelomonocytic leukemia (CMML) has evolved tremendously over the past decade. Large-scale sequencing studies have led to increased insight into the genomic landscape of CMML and clinical implications of these changes. This in turn has resulted in refined and improved risk stratification models, which to date remain versatile and subject to remodeling, as new and evolving studies continue to refine our understanding of this disease. In this article, we present an up-to-date review of CMML from a hematopathology perspective, while providing a clinically practical summary that sheds light on the constant evolution of our understanding of this disease.

Interference fold patterns of the early Precambrian Rock Groups in the Songshan area, China

1982 ◽  
Vol 119 (5) ◽  
pp. 433-461 ◽  
Author(s):  
Shutian Suo ◽  
Ruqi Liu ◽  
Xingyuan Ma
Keyword(s):  
Large Scale ◽  
North China ◽  
Small Scale ◽  
Deformation History ◽  
North China Platform ◽  
Early Proterozoic ◽  
The North ◽  
Regional Deformation ◽  
History Of ◽  
Insight Into

SummaryThe Songshan area is located in the southern part of the North China platform, which is one of the most completely cratonized tectonic units of China. Its basement has experienced a complex evolutionary history and was eventually consolidated at the end of early Proterozoic time about 1.7 Ga ago.A systematic study has been made of the deformation history of the lower Proterozoic Songshan Group and the Archean Dengfeng Group. At least two widespread episodes of deformation can be recognised in the early Proterozoic Zhongyue tectonic cycle and three in the Archean Songyang cycle. Large scale and small scale interference patterns of the superimposed folding are investigated with the aim of recognizing possible regularities in their occurrence and of gaining an insight into the regional deformation history. Two important aspects of superimposition relationships are illustrated: the control of earlier structures upon later ones and the reform of the former by thelatter; their geometrical regularities are also dealt with respectively.

scholarly journals Nauka na usługach polityki? Przypadek Józefa Obrębskiego

2019 ◽  
Author(s):  
Anna Engelking
Keyword(s):  
Large Scale ◽  
Field Research ◽  
Master Narrative ◽  
Efficient Tool ◽  
Political Views ◽  
History Of ◽  
Scientific Project ◽  
Polish Government ◽  
Insight Into

Research in the service of politics? The case of Józef ObrębskiThe paper concentrates on the circumstances of the production of anthropological knowledge, created in a dynamic tension between its cognitive goal and the way it is used for political purposes. It provides an insight into a complex network of conditions (intelectual, institutional, financial, personal, political) which determined the production of knowledge in interwar Poland within the then emerging disciplines of ethnology and sociology, in the scope of what today we would call social anthropology.This case study takes a closer look at Polish anthropologist Józef Obrębski (1905-1967), a close student of Malinowski, whose outstanding achievements remained mostly unpublished and thus never came into existence in the master narrative of the history of our discipline. In the 1930s Obrębski conducted ethnosociological field research in the Polesie region in eastern Poland (nowadays, part of Belarus and Ukraine), which was part of a large scale scientific project of the Commission for Scientific Research of the Eastern Territories. This project, financed by the Polish government and headed by a politician, general Kasprzycki, was supposed to be an efficient tool in the politics of the so called state and national assimilation of the Slavic-speaking ethnic minorities. Obrębski’s political views, which were democratic and liberal in character, were opposed to the official political line whereas his functionalist anthropological stance was unacceptable for the mainstream Polish ethnology of the era, still rooted in the positivist paradigm.Anthropological knowledge produced by Obrębski, which we would call today a postcolonial and constructivist approach, began to find recognition only after his death. The biography of this scholar and the story of his “unknown” work, a great example of a non-mainstream phenomenon in a provincial country, makes it easier to reveal undisclosed mechanisms of the system and the thought-collectives of science. Nauka na usługach polityki? Przypadek Józefa ObrębskiegoArtykuł dotyczy uwarunkowań produkcji wiedzy antropologicznej w dynamicznym napięciu między jej celem poznawczym a zastosowaniem do celów politycznych. Przynosi wgląd w złożoną sieć uwarunkowań (intelektualnych, instytucjonalnych, finansowych, personalnych, politycznych) produkcji wiedzy w międzywojennej Polsce, na polu młodych dyscyplin, jakimi były wówczas etnologia i socjologia, polu, które dzisiaj nazywamy antropologią społeczno-kulturową.Bohaterem tego studium przypadku jest polski antropolog Józef Obrębski (1905-1967), bliski uczeń Malinowskiego, którego wybitne prace w większości pozostały nieopublikowane, nie funkcjonują zatem w wielkiej opowieści o historii dyscypliny. W latach 1930. Obrębski prowadził etnosocjologiczne badania terenowe na Polesiu we wschodniej Polsce (region ten dziś należy do Białorusi i Ukrainy), w ramach wdrażanego tam na szeroką skalę programu naukowego Komisji Naukowych Badań Ziem Wschodnich. Projekt ten, finansowany przez polski rząd i kierowany przez polityka, gen. Kasprzyckiego, miał być skutecznym narzędziem polityki asymilacji państwowej i narodowej słowiańskojęzycznych mniejszości etnicznych. Demokratyczne i liberalne poglądy polityczne Obrębskiego były opozycyjne wobec linii politycznej jego mocodawców, zaś stanowisko teoretyczno-metodologiczne, związane z funkcjonalizmem, było z kolei nie do przyjęcia przez polskich etnologów głównego nurtu, przywiązanych do paradygmatu pozytywistycznego.Antropologiczne osiągnięcia Obrębskiego, które dziś sytuujemy w obrębie podejścia postkolonialnego i konstruktywistycznego, zaczęły zyskiwać uznanie dopiero po jego śmierci. Biografia uczonego i dzieje jego „nieznanych” prac, ważny przykład pozamainstreamowego fenomenu w prowincjonalnym kraju, przyczyniają się do poznania nieujawnionych mechanizmów systemu i kolektywów myślowych w nauce.

scholarly journals The peripheral blood proteome signature of idiopathic pulmonary fibrosis is distinct from normal and is associated with novel immunological processes

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
David N. O’Dwyer ◽  
Katy C. Norman ◽  
Meng Xia ◽  
Yong Huang ◽  
Stephen J. Gurczynski ◽  
...  
Keyword(s):  
Idiopathic Pulmonary Fibrosis ◽  
Pulmonary Fibrosis ◽  
Peripheral Blood ◽  
Large Scale ◽  
Biological Processes ◽  
Protein Levels ◽  
Disease Biology ◽  
History Of ◽  
Protein Discovery ◽  
Insight Into

Abstract Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal interstitial pneumonia. The disease pathophysiology is poorly understood and the etiology remains unclear. Recent advances have generated new therapies and improved knowledge of the natural history of IPF. These gains have been brokered by advances in technology and improved insight into the role of various genes in mediating disease, but gene expression and protein levels do not always correlate. Thus, in this paper we apply a novel large scale high throughput aptamer approach to identify more than 1100 proteins in the peripheral blood of well-characterized IPF patients and normal volunteers. We use systems biology approaches to identify a unique IPF proteome signature and give insight into biological processes driving IPF. We found IPF plasma to be altered and enriched for proteins involved in defense response, wound healing and protein phosphorylation when compared to normal human plasma. Analysis also revealed a minimal protein signature that differentiated IPF patients from normal controls, which may allow for accurate diagnosis of IPF based on easily-accessible peripheral blood. This report introduces large scale unbiased protein discovery analysis to IPF and describes distinct biological processes that further inform disease biology.

scholarly journals DEVELOPMENT OF SPATIAL AND MASS ON KERATON KASEPUHAN CIREBON

2019 ◽  
Vol 3 (04) ◽  
pp. 345-362
Author(s):  
Deby Sinantya Purbodewi ; Rahadian P. Herwindo
Keyword(s):  
Spatial Pattern ◽  
Large Scale ◽  
Residential Buildings ◽  
Cultural Influences ◽  
Spatial Development ◽  
Long Time ◽  
History Of ◽  
Relationship Of ◽  
The Relationship ◽  
Insight Into

Abstract- Keraton Kasepuhan Cirebon is one of the oldest palace that built during the transition era of Hindu Buddhism and Islam. Therefore. Keraton Kasepuhan has many periods of cultural period, where each period of time has its own distinctive culture, especially from special activities and daily activities that can affect the needs that create a spatial pattern. In terms of architecture, the existence of cultural influences resulted in the development of spatial and mass patterns, so that Kasepuhan Palace has elements of the culture in the spatial pattern and mass. According to the results of previous research, the culture is: Hindu-Buddhist, Islam, and also Colonial.  Using linear analytical methods, the data were analyzed by discussing according to the history of spatial development from the influence of each culture. The data were analyzed based on the composition of the HinduBuddhist, Islamic, Chinese, and Colonial spatial layout with the spatial development in the history of the Kasepuhan Palace, which was divided into four ages of leadership namely Ketemenggungan, Kesunanan, Panembahan and Kasultanan, in the focus of large-scale contexts, sacred building contexts, residential buildings.  This study aims to tell the architectural pattern that form Keraton Kasepuhan. The benefits of the completion of this research are to add to the architectural treasury of spatial and mass principles by various cultures in Indonesia, and add insight into the principles of spatial and mass arrangement based on theory and culture.  The conclusion of this research is the development of spatial and mass on Keraton Kasepuhan is most influenced by local culture, Hindu and Javanese Islam, while the outside culture does not much influence especially on spatial and mass Keraton Kasepuhan. In this case also found that the spatial and mass of a building can survive in a long time, while the form elements in the building can whenever changed and can be adopted or inspired from any culture. Spatial and mass is very crucial, it is the key to the relationship of architecture with humans.  Key Words: Acculturation, Spatial and Mass, History, Keraton, Keraton Kasepuhan Cirebon

scholarly journals The first draft genome of feather grasses using SMRT sequencing and its implications in molecular studies of Stipa

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Evgenii Baiakhmetov ◽  
Cervin Guyomar ◽  
Ekaterina Shelest ◽  
Marcin Nobis ◽  
Polina D. Gudkova
Keyword(s):  
Single Molecule ◽  
Large Scale ◽  
Draft Genome ◽  
Molecular Data ◽  
Protein Coding ◽  
Widespread Species ◽  
Chloroplast Genomes ◽  
The Pacific ◽  
Long Read ◽  
History Of

AbstractThe Eurasian plant Stipa capillata is the most widespread species within feather grasses. Many taxa of the genus are dominants in steppe plant communities and can be used for their classification and in studies related to climate change. Moreover, some species are of economic importance mainly as fodder plants and can be used for soil remediation processes. Although large-scale molecular data has begun to appear, there is still no complete or draft genome for any Stipa species. Thus, here we present a single-molecule long-read sequencing dataset generated using the Pacific Biosciences Sequel System. A draft genome of about 1004 Mb was obtained with a contig N50 length of 351 kb. Importantly, here we report 81,224 annotated protein-coding genes, present 77,614 perfect and 58 unique imperfect SSRs, reveal the putative allopolyploid nature of S. capillata, investigate the evolutionary history of the genus, demonstrate structural heteroplasmy of the chloroplast genome and announce for the first time the mitochondrial genome in Stipa. The assembled nuclear, mitochondrial and chloroplast genomes provide a significant source of genetic data for further works on phylogeny, hybridisation and population studies within Stipa and the grass family Poaceae.

Materials for the history of the gospel-Baptist movement in Ukraine

1996 ◽  
pp. 4-15
Author(s):  
S. Golovaschenko ◽  
Petro Kosuha
Keyword(s):  
Large Scale ◽  
Religious Studies ◽  
Theological Seminary ◽  
National Academy Of Sciences ◽  
Evangelical Christians ◽  
Evangelical Christian ◽  
First Results ◽  
History Of ◽  
Fruitful Cooperation ◽  
Academy Of Sciences

The report is based on the first results of the study "The History of the Evangelical Christians-Baptists in Ukraine", carried out in 1994-1996 by the joint efforts of the Department of Religious Studies at the Institute of Philosophy of the National Academy of Sciences of Ukraine and the Odessa Theological Seminary of Evangelical Christian Baptists. A large-scale description and research of archival sources on the history of evangelical movements in our country gave the first experience of fruitful cooperation between secular and church researchers.

The Subaltern Speak- A Study On The Culture Of The Arunachalis With Special Reference To Mamang Dai’s The Legends Of Pensam

2019 ◽  
Vol 5 (4) ◽  
pp. 14-20
Author(s):  
Ms. Cheryl Antonette Dumenil ◽  
Dr. Cheryl Davis
Keyword(s):  
Special Reference ◽  
Small World ◽  
Natural World ◽  
Arunachal Pradesh ◽  
North East India ◽  
North East ◽  
Shared History ◽  
History Of ◽  
And Gender ◽  
Insight Into

North- East India is an under veiled region with an awe-inspiring landscape, different groups of ethnic people, their culture and heritage. Contemporary writers from this region aspire towards a vision outside the tapered ethnic channel, and they represent a shared history. In their writings, the cultural memory is showcased, and the intensity of feeling overflows the labour of technique and craft. Mamang Dai presents a rare glimpse into the ecology, culture, life of the tribal people and history of the land of the dawn-lit mountains, Arunachal Pradesh, through her novel The Legends of Pensam. The word ‘Pensam’ in the title means ‘in-between’,  but it may also be interpreted as ‘the hidden spaces of the heart’. This is a small world where anything can happen. Being adherents of the animistic faith, the tribes here believe in co-existence with the natural world along with the presence of spirits in their forests and rivers. This paper attempts to draw an insight into the culture and gender of the Arunachalis with special reference to The Legends of Pensam by Mamang Dai.

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