scholarly journals Sequence dependence of transient Hoogsteen base-pairing in DNA

2021 ◽  
Author(s):  
Alberto Pérez de Alba Ortíz ◽  
Jocelyne Vreede ◽  
Bernd Ensing
Keyword(s):  
Dynamic Equilibrium ◽  
Double Helix ◽  
Free Energy Calculations ◽  
Dominant Factor ◽  
Base Pairing ◽  
Sequence Dependence ◽  
Purine Base ◽  
Sequence Variations ◽  
Hoogsteen Base Pairing

Hoogsteen (HG) base-pairing is characterized by a 180° rotation of the purine base with respect to the Watson-Crick-Franklin (WCF) motif. Recently, it has been found that both conformations coexist in a dynamical equilibrium and that several biological functions require HG pairs. This relevance has motivated experimental and computational investigations of the base-pairing transition. However, a systematic simulation of sequence variations has remained out of reach. Here, we employ advanced path-based methods to perform unprecedented free-energy calculations. Our methodology enables us to study the different mechanisms of purine rotation, either remaining inside or after flipping outside of the double helix. We study seven different sequences, which are neighbor variations of a well-studied A·T pair in A6-DNA. We observe the known effect of A·T steps favoring HG stability, and find evidence of triple-hydrogen-bonded neighbors hindering the inside transition. More importantly, we identify a dominant factor: the direction of the A rotation, with the 6-ring pointing either towards the longer or shorter segment of the chain, respectively relating to a lower or higher barrier. This highlights the role of DNA's relative flexibility as a modulator of the WCF/HG dynamic equilibrium. Additionally, we provide a robust methodology for future HG proclivity studies.

scholarly journals The role of G-quadruplex/i-motif secondary structures as cis-acting regulatory elements

2010 ◽  
Vol 82 (8) ◽  
pp. 1609-1621 ◽  
Author(s):  
Samantha Kendrick ◽  
Laurence H. Hurley
Keyword(s):  
Secondary Structure ◽  
Small Molecules ◽  
Dynamic Equilibrium ◽  
Double Helix ◽  
Regulatory Elements ◽  
Cis Acting ◽  
Secondary Structure Formation ◽  
G Quadruplex ◽  
Intracellular Proteins

The nature of DNA has captivated scientists for more than 50 years. The discovery of the double-helix model of DNA by Watson and Crick in 1953 not only established the primary structure of DNA, but also provided the mechanism behind DNA function. Since then, researchers have continued to further the understanding of DNA structure and its pivotal role in transcription. The demonstration of DNA secondary structure formation has allowed for the proposal that the dynamics of DNA itself can function to modulate transcription. This review presents evidence that DNA can exist in a dynamic equilibrium between duplex and secondary conformations. In addition, data demonstrating that intracellular proteins as well as small molecules can shift this equilibrium in either direction to alter gene transcription will be discussed, with a focus on the modulation of proto-oncogene expression.

scholarly journals Base pairing structure in the poly d(G-T) double helix: wobble base pairs

1978 ◽  
Vol 5 (6) ◽  
pp. 1955-1970 ◽  
Author(s):  
Thomas A. Early ◽  
John Olmsted ◽  
David R. Kearns ◽  
Axel G. Lezius
Keyword(s):  
Double Helix ◽  
Base Pairing ◽  
Base Pairs

A critical appraisal of the role of respiratory supercomplexes in mitochondria

2013 ◽  
Vol 394 (5) ◽  
pp. 631-639 ◽  
Author(s):  
Maria Luisa Genova ◽  
Giorgio Lenaz
Keyword(s):  
Critical Appraisal ◽  
Dynamic Equilibrium ◽  
Coenzyme Q ◽  
Mitochondrial Respiratory Chain ◽  
Substantial Evidence ◽  
Mammalian Mitochondria ◽  
Respiratory Supercomplexes ◽  
Functional Relevance ◽  
The Individual

Abstract Substantial evidence exists that the mitochondrial respiratory chain is organized in supramolecular units called supercomplexes or respirasomes. While the structural evidence of the supercomplexes is overwhelming, fewer studies have focused on their functional relevance. Although the presence of coenzyme Q channeling between complexes I and III has been ascertained, no such clear demonstration has been carried out for cytochrome c between complexes III and IV, at least in mammalian mitochondria. This review also discusses the implications concerning the number of respiratory complexes organized in supercomplexes and the possibility that they represent associations in dynamic equilibrium with the individual complexes.

scholarly journals SUATU PENDEKATAN ANALISIS MULTIVARIAT TENTANG TINGKAT KELAHIRAN PADA BEBERAPA KELOMPOK DAN ETNIS WANITA PERNAH KAWIN DI IRIAN JAYA

Populasi ◽  
2016 ◽  
Vol 3 (1) ◽  
Author(s):  
Pieter J. Soumokil
Keyword(s):  
Rural Women ◽  
Rural Areas ◽  
Urban Women ◽  
Developed Countries ◽  
Low Fertility ◽  
Dominant Factor ◽  
High Fertility ◽  
Irian Jaya ◽  
Lower Fertility

It has been argued by many demographers that socio economic development with its associated fundamental changes in the role of women and the value of children is the dominant factor in the transition from high to low fertility. Research in less developed countries has found lower fertility levels in urban population compared to rural population. It was therefore assumed that the modernizing role of urbanlife helped bring about a decline infertility levels.This study in Irian Jaya, however, convincingly shows that fertility of urban women in Irian Jaya is higher than that of rural women. This differential infertility in favour of urban women in Irian Jaya appears to be real and not a result of underreporting of total live births in rural areas.The reasons for lower fertility in the rural areas in IrianJaya remain unknown, and more research is therefore needed. However, this study strongly suggests that the traditional system of swidden agricultyure in Irian Jaya, which places a highvalue on the labour input of women, may play a major role in constraining fertility in rural area of this province. On the other hand, high fertility in urban areas takes place because urbanwomen have their first birth earlier thanwomen inthe rural areas.

scholarly journals Long-term persistence of crAss-like phage crAss001 is associated with phase variation in Bacteroides intestinalis

2020 ◽  
Author(s):  
Andrey N Shkoporov ◽  
Ekaterina V Khokhlova ◽  
Niamh Stephens ◽  
Cara Hueston ◽  
Samuel Seymour ◽  
...  
Keyword(s):  
Dynamic Equilibrium ◽  
Phase Variation ◽  
Carrier State ◽  
Human Gut ◽  
Rapid Phase ◽  
Host Interaction ◽  
Infected Cells ◽  
Phage Sensitivity

The crAss-like phages are ubiquitous and highly abundant members of the human gut virome that infect commensal bacteria of the order Bacteroidales. Although incapable of classical lysogeny, these viruses demonstrate unexplained long-term persistence in the human gut microbiome, dominating the virome in some individuals. Here we demonstrate that rapid phase variation of alternate capsular polysaccharides plays an important role in dynamic equilibrium between phage sensitivity and resistance in B. intestinalis cultures, allowing phage and bacteria to multiply in parallel. The data also suggests the role of concomitant phage persistence mechanisms associated with delayed lysis of infected cells, such as carrier state infection. From an ecological and evolutionary standpoint this type of phage-host interaction is consistent with the Piggyback-the-Winner model, which suggests a preference towards lysogenic or other 'benign' forms of phage infection when the host is stably present at high abundance.

scholarly journals FAKTOR-FAKTOR YANG BERHUBUNGAN DENGAN KONSUMSI TABLET TAMBAH DARAH PADA IBU NIFAS DI WILAYAH KERJA PUSKESMAS MUTIARA BARAT TAHUN 2019

2020 ◽  
Vol 4 (2) ◽  
pp. 321
Author(s):  
Fatmini Fatmini ◽  
Heru Santoso ◽  
Kesaktian Manurung ◽  
Rosdiana Rosdiana
Keyword(s):  
Nutritional Status ◽  
Pregnant Women ◽  
Health Center ◽  
Health Workers ◽  
Post Partum ◽  
Dominant Factor ◽  
Chi Square ◽  
Cross Sectional ◽  
Work Area

Anemia is still a problem in the world, especially in developing countries. This condition can have a detrimental impact on every age group including pregnant women. In pregnant women, anemia can cause complications for the mother and the baby she is carrying, such as life-threatening bleeding, miscarriage, low birth weight and premature birth. The purpose of this study was to determine the relationship between parity, anemia, ANC visits, nutritional status and the role of health workers with the consumption of blood-added tablets in post-partum mothers in the work area of the Mutiara Barat Health Center in 2019. This type of research is a correlation analytic study with cross-sectional method. The population in this study were all pregnant women in the third trimester who were recorded at the Mutiara Barat Health Center in January 2019 as many as 139 people and the sample was the total population of 139 respondents. Data were analyzed using the chi square statistical test which includes univariate, bivariate and multivariate analysis. The results obtained: there is a relationship between parity (p = 0.000), anemia (p = 0.016), ANC visits (p = 0.015), nutritional status (p = 0.021) and the role of officers (p = 0.000) with the consumption of tablets with blood added at postpartum mother. The dominant factor related to the consumption of blood-added tablets is the role of the officer. From the research results obtained, it is hoped that the Puskesmas can increase the knowledge of mothers about blood supplemented tablets through counseling so that it can influence the attitude of pregnant women to consume blood supplemented tablets. Keywords: ANC visit; anemia; consumption of blood added tablets; nutritional status; parity; role of officers ABSTRAKAnemia masih menjadi permasalahan di dunia terutama di negara-negara berkembang. Kondisi ini dapat memberikan dampak merugikan di setiap kelompok umur termasuk ibu hamil. Pada ibu hamil, kejadian anemia dapat menyebabkan penyulit pada ibu maupun bayi yang dikandungnya seperti perdarahan yang mengancam jiwa, keguguran, berat badan bayi lahir rendah dan kelahiran prematur. Tujuan dari penelitian ini adalah untuk mengetahui hubungan faktor paritas, anemia, kunjugan ANC, status gizi dan peran petugas kesehatan dengankonsumsi tablet tambah darah pada ibu nifas di wilayah kerja Puskesmas Mutiara Barat tahun 2019. Jenis penelitian ini adalah penelitian analitik korelasi dengan metode cross sectional. Populasi dalam penelitian ini adalah seluruh ibu hamil trimester III yang terdata di Puskesmas Mutiara Barat pada bulan Januari 2019 sebanyak 139 orang dan sampel merupakan total populasi yaitu 139 responden. Data dianalisis menggunakan uji statistik chi square yang meliputi analisis univariat, bivariat dan multivariat. Hasil penelitian diperoleh: ada hubungan antara paritas (p=0,000), anemia (p=0,016), kunjungan ANC (p=0,015), status gizi (p=0,021) dan peran petugas(p=0,000) dengan konsumsi tablet tambah darah pada ibu nifas. Faktor yang dominan berhubungan dengan konsumsi tablet tambah darah adalah peran petugas. Dari hasil penelitian yang diperoleh diharapkan Puskesmas dapat meningkatkan pengetahuan ibu tentang tablet tambah darah melalui penyuluhan sehingga dapat mempengaruhi sikap para ibu hamil untuk berperilaku mengkonsumsi tablet tambah darah. 

scholarly journals Masjid Kuno di Pulau Haruku Propinsi Maluku (Kajian Sejarah, Bentuk dan Fungsi)

2016 ◽  
Vol 14 (1) ◽  
pp. 1
Author(s):  
Alfan Firmanto
Keyword(s):  
Indigenous People ◽  
Customary Law ◽  
Dominant Factor ◽  
Floor Plan ◽  
Sharia Law ◽  
Culture Influence ◽  
On This Island ◽  
History Of

The history of Islamic development on the Haruku island, cannot be separated from the role of Muslim leaders or scholars who came from the Java. Evidence of the influence of Islam in Java can be seen from the architecture of the mosque on this island which takes the form of mosques of Wali in Java. This influence can also be seen from the shape of the terraced roof and floor plan of the mosque is square, which suggests a very strong Javanese mosque architecture. Nevertheless Javanese culture influence on the structure of society in Haruku is not always visible. The mosque on the island Haruku, not only serves as a place of worship, but also has other functions, namely as a symbol of communion between state and customs , as well as a symbol of the existence of an indigenous people. Customary law is a stronger influence than the main sharia law in Rohomoni. This study concludes that the Mosque has developed a more dominant factor as a customary symbol than a religious building. Keywords : Ancient Mosque, Haruku, Ambon, Islam, Indonesia. Sejarah perkembangan agama Islam di pulau Haruku Ambon tidak bisa dilepaskan dari para tokoh ataupun ulama yang berasal dari pulau Jawa. Bukti pengaruh Islam dari Jawa dapat dilihat dari bentuk arsitektur masjid di pulau tersebut yang mengambil bentuk dari masjid-masjid Wali di Jawa. Terlihat dari bentuk Atapnya yang bertumpang dan denah masjid yang berbentuk bujur sangkar, dari segi ini pengaruh arsitektur masjid Jawa sangat kuat. Meskipun demikian secara adat dan budaya tidak terlihat pengaruh budaya Jawa pada struktur masyarakat di Haruku. Masjid di pulau Haruku, tidak sekedar berfungsi sebagai tempat ibadah, tetapi mempunyai fungsi lain yaitu sebagai simbol persekutuan antar negeri dan adat, juga sebagai simbol eksistensi sebuah masyarakat adat. Pengaruh hukum Adat lebih kuat daripada hukum syariat utamanya di negeri Rohomoni. Sehingga terkesan Masjid lebih dominan digunakan sebagai simbol adat daripada bangunan ibadah. Kata Kunci : Masjid Kuno, Haruku, Ambon, Islam, Indonesia.

scholarly journals Analisis Faktor yang Berhubungan dengan Kinerja Bidan dalam Memberikan Pelayanan Antenatal Berkualitas Diwilayah Kerja Puskesmas Kota Bukittinggi Tahun 2018

2019 ◽  
Vol 19 (1) ◽  
pp. 53
Author(s):  
Khairan Nisa ◽  
Joserizal Serudji ◽  
Delmi Sulastri
Keyword(s):  
Data Analysis ◽  
Antenatal Care ◽  
Pregnant Women ◽  
Monitoring And Evaluation ◽  
Dominant Factor ◽  
The Public ◽  
Depth Interview ◽  
Quantitative Data Analysis

Quality antenatal care has a major role in reducing maternal mortality. Every effort to improve quality must also be accompanied by efforts to pay attention to factors that contribute to improving the performance of midwives in providing services. The study used a combination of quantitative approaches in 67 midwives in the Bukittinggi and qualitatively in 15 informants, of which 9 people included in-depth interview informants to coordinator midwives, head of the Public health center and staffing and 6 FGD informants to midwives on duty at the health center.The results of quantitative data analysis, factors related to the performance of midwives are incentives, motivation and workload. Motivation is the most dominant factor related to the performance of midwives. The results of qualitative data analysis, the leadership plays an important role in increasing motivation to work midwives and optimizing the role of midwives in overcoming problems related to overlapping workloads. Midwives also need to increase their participation efforts and empower pregnant women so that programs can run well and provide positive feedback for improving the health status of pregnant women. Basically antenatal services provided by midwives are in accordance with standards, but the paradigm of antenatal care for pregnant women must shift from achieving quantity to focus on quality. To improve the performance of midwives in providing antenatal care, several efforts are needed: monitoring and evaluation of the quality of antenatal care by midwives, leadership involvement in efforts to increase midwife motivation both from supervision and reward management in non-material forms. Providing equal opportunities for midwives to improve competence through training, especially training related to quality antenatal care. In addition, the provision of infrastructure at the polindes needs attention. 

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