High-Resolution in Vivo Footprinting of a Protein−DNA Complex Using γ-Radiation

2000 ◽  
Vol 122 (24) ◽  
pp. 5901-5902 ◽  
Author(s):  
Lori M. Ottinger ◽  
Thomas D. Tullius
Keyword(s):  
High Resolution ◽  
Γ Radiation ◽  
In Vivo Footprinting ◽  
Dna Complex

scholarly journals In vivo footprinting and high-resolution methylation analysis of the mouse hypoxanthine phosphoribosyltransferase gene 5' region on the active and inactive X chromosomes.

1996 ◽  
Vol 16 (11) ◽  
pp. 6190-6199 ◽  
Author(s):  
M D Litt ◽  
I K Hornstra ◽  
T P Yang
Keyword(s):  
High Resolution ◽  
X Chromosome ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Genomic Sequencing ◽  
Hypoxanthine Phosphoribosyltransferase ◽  
Hprt Gene ◽  
Methylation Analysis ◽  
In Vivo Footprinting

To investigate potential mechanisms regulating the hypoxanthine phosphoribosyltransferase (HPRT) gene by X-chromosome inactivation, we performed in vivo footprinting and high-resolution DNA methylation analysis on the 5' region of the active and inactive mouse HPRT alleles and compared these results with those from the human HPRT gene. We found multiple footprinted sites on the active mouse HPRT allele and no footprints on the inactive allele. Comparison of the footprint patterns of the mouse and human HPRT genes demonstrated that the in vivo binding of regulatory proteins between these species is generally conserved but not identical. Detailed nucleotide sequence comparison of footprinted regions in the mouse and human genes revealed a novel 9-bp sequence associated with transcription factor binding near the transcription sites of both genes, suggesting the identification of a new conserved initiator element. Ligation-mediated PCR genomic sequencing showed that all CpG dinucleotides examined on the active allele are unmethylated, while the majority of CpGs on the inactive allele are methylated and interspersed with a few hypomethylated sites. This pattern of methylation on the inactive mouse allele is notably different from the unusual methylation pattern of the inactive human gene, which exhibited strong hypomethylation specifically at GC boxes. These studies, in conjunction with other genomic sequencing studies of X-linked genes, demonstrate that (i) the active alleles are essentially unmethylated, (ii) the inactive alleles are hypermethylated, and (iii) the high-resolution methylation patterns of the hypermethylated inactive alleles are not strictly conserved. There is no obvious correlation between the pattern of methylated sites on the inactive alleles and the pattern of binding sites for transcription factors on the active alleles. These results are discussed in relationship to potential mechanisms of transcriptional regulation by X-chromosome inactivation.

scholarly journals High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

2010 ◽  
Vol 21 (3) ◽  
pp. 456-464 ◽  
Author(s):  
A. P. Boyle ◽  
L. Song ◽  
B.-K. Lee ◽  
D. London ◽  
D. Keefe ◽  
...  
Keyword(s):  
Transcription Factors ◽  
High Resolution ◽  
Human Cells ◽  
Genome Wide ◽  
In Vivo Footprinting

scholarly journals Optimization of spectral-domain optical coherence tomography with a supercontinuum source for in vivo motion detection of low reflective outer hair cells in guinea pig cochleae

2021 ◽  
Author(s):  
Fumiaki Nin ◽  
Samuel Choi ◽  
Takeru Ota ◽  
Zhang Qi ◽  
Hiroshi Hibino
Keyword(s):  
Optical Coherence Tomography ◽  
High Resolution ◽  
Guinea Pig ◽  
Hair Cells ◽  
Sensory Epithelium ◽  
Outer Hair Cells ◽  
Acquisition Time ◽  
Total Acquisition Time ◽  
Sd Oct

AbstractSound evokes sub-nanoscale vibration within the sensory epithelium. The epithelium contains not only immotile cells but also contractile outer hair cells (OHCs) that actively shrink and elongate synchronously with the sound. However, the in vivo motion of OHCs has remained undetermined. The aim of this work is to perform high-resolution and -accuracy vibrometry in live guinea pigs with an SC-introduced spectral-domain optical coherence tomography system (SD-OCT). In this study, to reveal the effective contribution of SC source in the recording of the low reflective materials with the short total acquisition time, we compare the performances of the SC-introduced SD-OCT (SCSD-OCT) to that of the conventional SD-OCT. As inanimate comparison objects, we record a mirror, a piezo actuator, and glass windows. For the measurements in biological materials, we use in/ex vivo guinea pig cochleae. Our study achieved the optimization of a SD-OCT system for high-resolution in vivo vibrometry in the cochlear sensory epithelium, termed the organ of Corti, in mammalian cochlea. By introducing a supercontinuum (SC) light source and reducing the total acquisition time, we improve the axial resolution and overcome the difficulty in recording the low reflective material in the presence of biological noise. The high power of the SC source enables the system to achieve a spatial resolution of 1.72 ± 0.00 μm on a mirror and reducing the total acquisition time contributes to the high spatial accuracy of sub-nanoscale vibrometry. Our findings reveal the vibrations at the apical/basal region of OHCs and the extracellular matrix, basilar membrane.

scholarly journals Iron accumulation in the oculomotor nerve of the progressive supranuclear palsy brain

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hansol Lee ◽  
Myung Jun Lee ◽  
Eun-Joo Kim ◽  
Gi Yeong Huh ◽  
Jae-Hyeok Lee ◽  
...  
Keyword(s):  
High Resolution ◽  
Progressive Supranuclear Palsy ◽  
Oculomotor Nerve ◽  
Iron Accumulation ◽  
Blue Staining ◽  
Normal Brain ◽  
Myelinated Fiber ◽  
Healthy Controls ◽  
Icp Ms

AbstractAbnormal iron accumulation around the substantia nigra (SN) is a diagnostic indicator of Parkinsonism. This study aimed to identify iron-related microarchitectural changes around the SN of brains with progressive supranuclear palsy (PSP) via postmortem validations and in vivo magnetic resonance imaging (MRI). 7 T high-resolution MRI was applied to two postmortem brain tissues, from one normal brain and one PSP brain. Histopathological examinations were performed to demonstrate the molecular origin of the high-resolution postmortem MRI findings, by using ferric iron staining, myelin staining, and two-dimensional laser ablation-inductively coupled plasma-mass spectrometry (LA-ICP-MS) imaging. In vivo iron-related MRI was performed on five healthy controls, five patients with Parkinson’s disease (PD), and five patients with PSP. In the postmortem examination, excessive iron deposition along the myelinated fiber at the anterior SN and third cranial nerve (oculomotor nerve) fascicles of the PSP brain was verified by LA-ICP-MS. This region corresponded to those with high R2* values and positive susceptibility from quantitative susceptibility mapping (QSM), but was less sensitive in Perls’ Prussian blue staining. In in vivo susceptibility-weighted imaging, hypointense pixels were observed in the region between the SN and red nucleus (RN) in patients with PSP, but not in healthy controls and patients with PD. R2* and QSM values of such region were significantly higher in patients with PSP compared to those in healthy controls and patients with PD as well (vs. healthy control: p = 0.008; vs. PD: p = 0.008). Thus, excessive iron accumulation along the myelinated fibers at the anterior SN and oculomotor nerve fascicles may be a pathological characteristic and crucial MR biomarker in a brain with PSP.

scholarly journals High-resolution in vivo imaging of rhesus cerebral cortex with ultrafast portable photoacoustic microscopy

NeuroImage ◽  
2021 ◽  
pp. 118260
Author(s):  
Wei Qin ◽  
Qi Gan ◽  
Lei Yang ◽  
Yongchao Wang ◽  
Weizhi Qi ◽  
...  
Keyword(s):  
Cerebral Cortex ◽  
High Resolution ◽  
In Vivo Imaging ◽  
Photoacoustic Microscopy

scholarly journals Polymorphisms in Plasmodium falciparum dihydropteroate synthetase and dihydrofolate reductase genes in Nigerian children with uncomplicated malaria using high-resolution melting technique

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Adeyemi T. Kayode ◽  
Fehintola V. Ajogbasile ◽  
Kazeem Akano ◽  
Jessica N. Uwanibe ◽  
Paul E. Oluniyi ◽  
...  
Keyword(s):  
High Resolution ◽  
Dihydrofolate Reductase ◽  
Uncomplicated Malaria ◽  
High Resolution Melting ◽  
Intermittent Preventive Treatment ◽  
Preventive Treatment ◽  
Triple Mutant ◽  
Seasonal Malaria Chemoprevention

AbstractIn 2005, the Nigerian Federal Ministry of Health revised the treatment policy for uncomplicated malaria with the introduction of artemisinin-based combination therapies (ACTs). This policy change discouraged the use of Sulphadoxine-pyrimethamine (SP) as the second-line treatment of uncomplicated falciparum malaria. However, SP is used as an intermittent preventive treatment of malaria in pregnancy (IPTp) and seasonal malaria chemoprevention (SMC) in children aged 3–59 months. There have been increasing reports of SP resistance especially in the non-pregnant population in Nigeria, thus, the need to continually monitor the efficacy of SP as IPTp and SMC by estimating polymorphisms in dihydropteroate synthetase (dhps) and dihydrofolate reductase (dhfr) genes associated with SP resistance. The high resolution-melting (HRM) assay was used to investigate polymorphisms in codons 51, 59, 108 and 164 of the dhfr gene and codons 437, 540, 581 and 613 of the dhps gene. DNA was extracted from 271 dried bloodspot filter paper samples obtained from children (< 5 years old) with uncomplicated malaria. The dhfr triple mutant I51R59N108, dhps double mutant G437G581 and quadruple dhfr I51R59N108 + dhps G437 mutant haplotypes were observed in 80.8%, 13.7% and 52.8% parasites, respectively. Although the quintuple dhfr I51R59N108 + dhps G437E540 and sextuple dhfr I51R59N108 + dhps G437E540G581 mutant haplotypes linked with in-vivo and in-vitro SP resistance were not detected, constant surveillance of these haplotypes should be done in the country to detect any change in prevalence.

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