2,263 results match your criteria tad

SARS-CoV-2 Restructures the Host Chromatin Architecture.

bioRxiv 2021 Jul 21. Epub 2021 Jul 21.

SARS-CoV-2 has made >190-million infections worldwide, thus it is pivotal to understand the viral impacts on host cells. Many viruses can significantly alter host chromatin , but such roles of SARS-CoV-2 are largely unknown. Here, we characterized the three-dimensional (3D) genome architecture and epigenome landscapes in human cells after SARS-CoV-2 infection, revealing remarkable restructuring of host chromatin architecture. Read More

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Improved Implant Positioning of Cephalomedullary Nail for Trochanteric Fractures Using the Stryker ADAPT Navigation System.

Injury 2021 Jul 15. Epub 2021 Jul 15.

Department of Orthopedic Surgery, NYU Langone - Long Island Hospital, NYU Langone Health, Mineola, New York, USA.

Background: Tip-apex distance (TAD) of greater than 25 mm increases the risk of cephalomedullary nail (CMN) cutout for trochanteric hip fractures. The Stryker ADAPT navigation system provides intraoperative feedback to guide implant positioning. This study compares lag screw positioning using the ADAPT to conventional methods and investigates if the use of ADAPT impacts operating room efficiency. Read More

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DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell.

Genome Biol 2021 Jul 27;22(1):217. Epub 2021 Jul 27.

CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, and China National Center for Bioinformation, Beijing, 100101, China.

Topologically associating domains (TAD) are a key structure of the 3D mammalian genomes. However, the prevalence and dynamics of TAD-like domains in single cells remain elusive. Here we develop a new algorithm, named deTOKI, to decode TAD-like domains with single-cell Hi-C data. Read More

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Disruption of topologically associating domains by structural variations in tetraploid cottons.

Genomics 2021 Jul 23. Epub 2021 Jul 23.

National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, Hubei, China. Electronic address:

Structural variations (SVs) are recognized to have an important role in transcriptional regulation, especially in the light of resolved 3D genome structure using high-throughput chromosome conformation capture (Hi-C) technology in mammals. However, the effect of SVs on 3D genome organization in plants remains rarely understood. In this study, we identified 295,496 SVs and 5251 topologically associating domains (TADs) in two diploid and two tetraploid cottons. Read More

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Feasibility and validation of the targeted axillary dissection technique in the axillary staging of breast cancer after neoadjuvant therapy: Definitive results.

Surg Oncol 2021 Jul 21;38:101636. Epub 2021 Jul 21.

General Surgery Department, Morales Meseguer University Hospital, Murcia, Spain; University of Murcia, Faculty of Medicine, IMIB-Arrixaca, "Mare Nostrum" International Excellence Campus, Murcia, Spain.

Aim: to study the feasibility and value of "Targeted Axillary Dissection" (TAD) in cN1 breast cancer (BC) patients undergoing neoadjuvant chemotherapy (NACT), in order to avoid unnecessary axillary lymph node dissection (ALND).

Materials And Methods: Design: Prospective observational study.

Inclusion Criteria: Patients with histologically confirmed cN1 staging BC and treated with NACT between January 2016 and August 2019 who accomplished clinical response. Read More

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Induction of a chromatin boundary in vivo upon insertion of a tad border.

PLoS Genet 2021 Jul 22;17(7):e1009691. Epub 2021 Jul 22.

Department of Genetics and Evolution, Faculty of Science, University of Geneva, Geneva, Switzerland.

Mammalian genomes are partitioned into sub-megabase to megabase-sized units of preferential interactions called topologically associating domains or TADs, which are likely important for the proper implementation of gene regulatory processes. These domains provide structural scaffolds for distant cis regulatory elements to interact with their target genes within the three-dimensional nuclear space and architectural proteins such as CTCF as well as the cohesin complex participate in the formation of the boundaries between them. However, the importance of the genomic context in providing a given DNA sequence the capacity to act as a boundary element remains to be fully investigated. Read More

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Reactivation of a developmentally silenced embryonic globin gene.

Nat Commun 2021 07 21;12(1):4439. Epub 2021 Jul 21.

MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.

The α- and β-globin loci harbor developmentally expressed genes, which are silenced throughout post-natal life. Reactivation of these genes may offer therapeutic approaches for the hemoglobinopathies, the most common single gene disorders. Here, we address mechanisms regulating the embryonically expressed α-like globin, termed ζ-globin. Read More

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WNT2 activation through proximal germline deletion predisposes to small intestinal neuroendocrine tumors and intestinal adenocarcinomas.

Hum Mol Genet 2021 Jul 19. Epub 2021 Jul 19.

Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, FI-00014 Helsinki, Finland.

Many hereditary cancer syndromes are associated with an increased risk of small and large intestinal adenocarcinomas. However, conditions bearing a high risk to both adenocarcinomas and neuroendocrine tumors are yet to be described. We studied a family with 16 individuals in four generations affected by a wide spectrum of intestinal tumors, including hyperplastic polyps, adenomas, small intestinal neuroendocrine tumors, and colorectal and small intestinal adenocarcinomas. Read More

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Impaired visual search in posterior cortical atrophy vs. typical Alzheimer's disease.

J Neurol Sci 2021 Jul 12;428:117574. Epub 2021 Jul 12.

Department of Neurology, Lahey Hospital and Medical Center, USA. Electronic address:

Background: Posterior cortical atrophy (PCA) is a neurocognitive disorder characterized by difficulty localizing in space. Recognizing PCA is important because it is usually missed early in its course and may result from a number of neurological disorders other than Alzheimer's disease (AD).

Objective: This study aimed to clarify whether impaired visual search tasks of spatial localization distinguished patients with PCA from those with other more typical dementias as well as from healthy control (HC) subjects. Read More

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The Impact of COVID-19 on Hospitalised COPD Exacerbations in Malta.

Pulm Med 2021 23;2021:5533123. Epub 2021 Jun 23.

Mater Dei Hospital, Triq id-Donaturi tad-Demm, Msida MSD2090, Malta.

Method: Data was collected retrospectively from electronic hospital records during the periods 1st March until 10th May in 2019 and 2020.

Results: There was a marked decrease in AECOPD admissions in 2020, with a 54.2% drop in admissions ( = 119 in 2020 vs. Read More

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Transcription-coupled structural dynamics of topologically associating domains regulate replication origin efficiency.

Genome Biol 2021 Jul 12;22(1):206. Epub 2021 Jul 12.

State Key Laboratory of Membrane Biology, Biomedical Pioneer Innovation Center (BIOPIC), School of Life Sciences, Peking University, Beijing, 100871, China.

Background: Metazoan cells only utilize a small subset of the potential DNA replication origins to duplicate the whole genome in each cell cycle. Origin choice is linked to cell growth, differentiation, and replication stress. Although various genetic and epigenetic signatures have been linked to the replication efficiency of origins, there is no consensus on how the selection of origins is determined. Read More

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Multiple CTCF sites cooperate with each other to maintain a TAD for enhancer-promoter interaction in the β-globin locus.

FASEB J 2021 08;35(8):e21768

Department of Molecular Biology, College of Natural Sciences, Pusan National University, Busan, Korea.

Insulators are cis-regulatory elements that block enhancer activity and prevent heterochromatin spreading. The binding of CCCTC-binding factor (CTCF) protein is essential for insulators to play the roles in a chromatin context. The β-globin locus, consisting of multiple genes and enhancers, is flanked by two insulators 3'HS1 and HS5. Read More

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How subtle changes in 3D structure can create large changes in transcription.

Elife 2021 Jul 9;10. Epub 2021 Jul 9.

Department of Developmental Biology, Stanford University, Stanford, United States.

Animal genomes are organized into topologically associated domains (TADs). TADs are thought to contribute to gene regulation by facilitating enhancer-promoter (E-P) contacts within a TAD preventing these contacts across TAD borders. However, the absolute difference in contact frequency across TAD boundaries is usually less than two-fold, even though disruptions of TAD borders can change gene expression by ten-fold. Read More

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M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity.

Nat Commun 2021 07 7;12(1):4170. Epub 2021 Jul 7.

Nuclear Organization and Gene Expression Section, Bethesda, MD, USA.

Genome organization is driven by forces affecting transcriptional state, but the relationship between transcription and genome architecture remains unclear. Here, we identified the Drosophila transcription factor Motif 1 Binding Protein (M1BP) in physical association with the gypsy chromatin insulator core complex, including the universal insulator protein CP190. M1BP is required for enhancer-blocking and barrier activities of the gypsy insulator as well as its proper nuclear localization. Read More

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Position effects of 22q13 rearrangements on candidate genes in Phelan-McDermid syndrome.

PLoS One 2021 6;16(7):e0253859. Epub 2021 Jul 6.

Greenwood Genetic Center, Greenwood, SC, United States of America.

Phelan-McDermid syndrome (PMS) is a multi-system disorder characterized by significant variability in clinical presentation. The genetic etiology is also variable with differing sizes of deletions in the chromosome 22q13 region and types of genetic abnormalities (e.g. Read More

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Significance of Tip Apex Distance in Intertrochanteric Fracture femur managed with Proximal femoral nailing.

Orthop Traumatol Surg Res 2021 Jul 1:103009. Epub 2021 Jul 1.

Department of Orthopaedics, National Institute of Medical Sciences, Jaipur, India.

Introduction: Tip Apex distance (TAD) is well established method of prediction of outcome in intertrochanteric fractures managed by Dynamic Hip Screw. This retrospective study was done to assess the significance of Tip Apex Distance in the management of the intertrochanteric fractures by Proximal femoral nail.

Material And Methods: The study was done in a tertiary care centre where 174 follow-up patients operated for intertrochanteric fractures with proximal femoral nail were included in the study. Read More

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TAD cliques predict key features of chromatin organization.

BMC Genomics 2021 Jul 3;22(1):499. Epub 2021 Jul 3.

Institute of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.

Background: Mechanisms underlying genome 3D organization and domain formation in the mammalian nucleus are not completely understood. Multiple processes such as transcriptional compartmentalization, DNA loop extrusion and interactions with the nuclear lamina dynamically act on chromatin at multiple levels. Here, we explore long-range interaction patterns between topologically associated domains (TADs) in several cell types. Read More

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Trochanteric fractures treated by internal fixation using short intramedullary nails: Does the visual intraoperative estimation of the Tip-Apex Distance (TAD) concur with its digital postoperative measurement?

Orthop Traumatol Surg Res 2021 Jun 30:103001. Epub 2021 Jun 30.

Service de chirurgie orthopédique et traumatologique, CHU Dupuytren, 2, avenue Martin Luther King, 87042 Limoges cedex, France. Electronic address:

Introduction: The tip-apex distance (TAD) is the only predictor for mechanical failure after internal fixation of trochanteric fractures. The main objective of our study was to assess whether the intraoperative visual estimation of the TAD concurred with the measurement taken on postoperative digital X-rays. We hypothesized that there was a good concordance between these 2 different methods of measurement. Read More

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Functional and structural investigation of N-terminal domain of the SpTad2/3 heterodimeric tRNA deaminase.

Comput Struct Biotechnol J 2021 5;19:3384-3393. Epub 2021 Jun 5.

MOE Key Laboratory of Gene Function and Regulation, State Key Laboratory for Biocontrol, School of Life Sciences, The Sun Yat-Sen University, Guangzhou, Guangdong 510006, People's Republic of China.

Editing is a post-transcriptional process that changes the content of nucleic acids occurring on both DNA and RNA levels. Inosine at position 34 in tRNA is one such example, commonly produced via the deamination of A34, catalyzed by adenosine deaminase acting on tRNA (ADAT or Tad). The formation of inosine is essential for cell viability. Read More

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Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome.

Genome Res 2021 Jun 29. Epub 2021 Jun 29.

Department of Biology, Penn State University, University Park, Pennsylvania 16802, USA.

Approximately 1% of the human genome has the ability to fold into G-quadruplexes (G4s)-noncanonical strand-specific DNA structures forming at G-rich motifs. G4s regulate several key cellular processes (e.g. Read More

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Impacts of chromatin dynamics and compartmentalization on DNA repair.

DNA Repair (Amst) 2021 Jun 19;105:103162. Epub 2021 Jun 19.

Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, 02129, USA. Electronic address:

The proper spatial organization of DNA, RNA, and proteins is critical for a variety of cellular processes. The genome is organized into numerous functional units, such as topologically associating domains (TADs), the formation of which is regulated by both proteins and RNA. In addition, a group of chromatin-bound proteins with the ability to undergo liquid-liquid phase separation (LLPS) can affect the spatial organization and compartmentalization of chromatin, RNA, and proteins by forming condensates, conferring unique properties to specific chromosomal regions. Read More

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Development of a predictive score of axillary lymph node dissection based on targeted axillary dissection in patients with breast cancer diagnosis, affected lymph nodes, and neoadjuvant treatment.

Surg Oncol 2021 Jun 18;38:101629. Epub 2021 Jun 18.

General Surgery Department, Morales Meseguer University Hospital, Murcia, Spain.

Aim: To determine predictive factors of axillary lymph node dissection (ALND) results in breast cancer (BC) patients undergoing neoadjuvant chemotherapy (NACT), and subsequent staging using Targeted Axillary Dissection (TAD).

Material And Method: Case-control study between January 2016 and August 2019. Patients with BC, cN1 staging, marked with a metallic clip prior to NACT, and subsequently staged with TAD and ALND were included. Read More

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TFNA Implant Failure with Helical Blade Cut-out.

J Orthop Case Rep 2020 Dec;10(9):61-64

Department of Orthopedics, PD Hinduja Hospital and Medical Research Centre, Mumbai. Maharashtra. India.

Introduction: Trochanteric femoral nail-advanced (TFNA) was introduced in the market with better nail design, better alloy (titanium molybdenum) and both sliding and static locking options of the helical blade. Although, it was devised to overcome the shortcomings of roximal Femoral Nail Anti-rotation (PFNA), it still can have complications, if the principles of fracture management are not met. Here, we report a case of a TFNA implant failure with helical blade cut-out in an elderly osteoporotic patient treated for inter-trochanteric femur fracture. Read More

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December 2020

A perspective on the molecular simulation of DNA from structural and functional aspects.

Chem Sci 2021 Mar 15;12(15):5390-5409. Epub 2021 Mar 15.

Institute of Systems and Physical Biology, Shenzhen Bay Laboratory 518055 Shenzhen China

As genetic material, DNA not only carries genetic information by sequence, but also affects biological functions ranging from base modification to replication, transcription and gene regulation through its structural and dynamic properties and variations. The motion and structural properties of DNA involved in related biological processes are also multi-scale, ranging from single base flipping to local DNA deformation, TF binding, G-quadruplex and i-motif formation, TAD establishment, compartmentalization and even chromosome territory formation, just to name a few. The sequence-dependent physical properties of DNA play vital role in all these events, and thus it is interesting to examine how simple sequence information affects DNA and the formation of the chromatin structure in these different hierarchical orders. Read More

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Light-fueled dynamic covalent crosslinking of single polymer chains in non-equilibrium states.

Chem Sci 2020 Nov 17;12(4):1302-1310. Epub 2020 Nov 17.

School of Chemistry and Physics, Queensland University of Technology (QUT) 2 George Street Brisbane QLD 4000 Australia

While polymer synthesis proceeds predominantly towards the thermodynamic minimum, living systems operate on the reverse principle - consuming fuel to maintain a non-equilibrium state. Herein, we report the controlled formation of 3D macromolecular architectures based on light-fueled covalent non-equilibrium chemistry. In the presence of green light (525 nm) and a bivalent triazolinedione (TAD) crosslinker, naphthalene-containing polymers can be folded into single chain nanoparticles (SCNPs). Read More

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November 2020

Phase separation of p53 precedes aggregation and is affected by oncogenic mutations and ligands.

Chem Sci 2021 Apr 26;12(21):7334-7349. Epub 2021 Apr 26.

Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro Rio de Janeiro RJ 21941-902 Brazil

Mutant p53 tends to form aggregates with amyloid properties, especially amyloid oligomers inside the nucleus, which are believed to cause oncogenic gain-of-function (GoF). The mechanism of the formation of the aggregates in the nucleus remains uncertain. The present study demonstrated that the DNA-binding domain of p53 (p53C) underwent phase separation (PS) on the pathway to aggregation under various conditions. Read More

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SBTD: A Novel Method for Detecting Topological Associated Domains from Hi-C Data.

Interdiscip Sci 2021 Jun 23. Epub 2021 Jun 23.

College of Chemistry, Sichuan University, Chengdu, 610064, China.

The development of Hi-C technology has generated terabytes of chromatin interaction data, which bring possibilities for insight study of chromatin structure. Several studies revealed that mammalian chromosomes are folded into topological associated domains (TADs), which are conserved across cell types. Accurate detection of topological associated domains is now a vital process for revealing the relationship between the structure and function of genome organization. Read More

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Tip-neck distance ratio as a novel predictor for failure in cephalomedullary nailing of unstable trochanteric fractures (UTF).

Arch Orthop Trauma Surg 2021 Jun 19. Epub 2021 Jun 19.

Department of Orthopaedics, Ankara Bilkent City Hospital, Bilkent Bulvarı No: 1 Bilkent, Ankara, Turkey.

Objectives: Intertrochanteric femur fractures (ITFF) are frequently fixed with proximal femoral nailing (PFN), and a common cause of fixation failure is cut-out of the lag screws. In the literature, many factors have been defined to determine the failure risk, including the tip-apex distance (TAD), calcar-referenced tip-apex distance (CalTAD), the Cleveland zone and Parker's ratio. In this study, a novel technique is described which favors infero-posterior placement of the lag screw and predicts failure risk for PFN. Read More

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Evaluation of sonographic detectability of different markers within an in vitro simulation model of the axilla.

Arch Gynecol Obstet 2021 Jun 17. Epub 2021 Jun 17.

Department for Women's Health, University of Tübingen, Calwerstraße 7, 72076, Tübingen, Germany.

Purpose: Clip-marking of axillary lymph nodes with initial biopsy-confirmed metastasis is required for targeted axillary dissection (TAD), which includes sentinel lymph node dissection (SLND) and selective localization and removal of the clipped targeted lymph node. There have been several studies which examined the feasibility of TAD in routine clinical use. In this context, the optimal clip visualisation was noted as one of the crucial limiting factors. Read More

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