Chromosomal Inversions between Human and Chimpanzee Lineages Caused by Retrotransposons

The long interspersed element-1 (LINE-1 or L1) and Alu elements are the most abundant mobile elements comprising 21% and 11% of the human genome, respectively. Since the divergence of human and chimpanzee lineages, these elements have vigorously created chromosomal rearrangements causing genomic difference between humans and chimpanzees by either increasing or decreasing the size of genome. Here, we report an exotic mechanism, retrotransposon recombination-mediated inversion (RRMI), that usually does not alter the amount of genomic material present. Through the comparison of the human and chimpanzee draft genome sequences, we identified 252 inversions whose respective inversion junctions can clearly be characterized. Our results suggest that L1 and Alu elements cause chromosomal inversions by either forming a secondary structure or providing a fragile site for double-strand breaks. The detailed analysis of the inversion breakpoints showed that L1 and Alu elements are responsible for at least 44% of the 252 inversion loci between human and chimpanzee lineages, including 49 RRMI loci. Among them, three RRMI loci inverted exonic regions in known genes, which implicates this mechanism in generating the genomic and phenotypic differences between human and chimpanzee lineages. This study is the first comprehensive analysis of mobile element bases inversion breakpoints between human and chimpanzee lineages, and highlights their role in primate genome evolution

Comparison of central corneal thickness: ultrasound pachymetry versus slit-lamp optical coherence tomography, specular microscopy, and Orbscan

Wassia A Khaja, Sandeep Grover, Amy T Kelmenson, Lee R Ferguson, Kumar Sambhav, Kakarla V Chalam Department of Ophthalmology, University of Florida, College of Medicine, Jacksonville, FL, USA Background: Central corneal thickness (CCT) can be measured by using contact and non-contact methods. Ultrasound pachymetry (US pachymetry) is a contact method for measuring CCT and is perhaps the most commonly used method. However, non-contact methods like scanning slit topography (Orbscan II), slit-lamp optical coherence tomography (SL-OCT), and specular microscopy are also used. Not many studies have correlated the measurement of CCT with all four modalities. The purpose of this study was to compare and correlate the CCT measurements obtained by US pachymetry with SL-OCT, specular microscopy, and Orbscan. Method: This is a prospective, comparative study done in an institutional setting. Thirty-two eyes of 32 subjects with no known ocular disease and best-corrected visual acuity of 20/20 were enrolled. CCT measurements were obtained using SL-OCT, specular microscopy, scanning slit topography (Orbscan), and US pachymetry. Three measurements were made with each instrument by the same operator. Mean, standard deviation, and coefficient of variation were calculated for CCT measurements acquired by the four measurement devices. Bland–Altman plot was constructed to determine the agreements between the CCT measurements obtained by different equipment. Results: The mean CCT was 548.16±48.68 µm by US pachymetry. In comparison, CCT averaged 546.36±44.17 µm by SL-OCT, 557.61±49.92 µm by specular microscopy, and 551.03±48.96 µm by Orbscan for all subjects. Measurements by the various modalities were strongly correlated. Correlations (r2) of CCT, as measured by US pachymetry compared with other modalities, were: SL-OCT (r2=0.98, P<0.0001), specular microscopy (r2=0.98, P<0.0001), and Orbscan (r2=0.96, P<0.0001). All modalities had a linear correlation with US pachymetry measurements. Conclusion: In subjects with healthy corneas, SL-OCT, specular microscopy, and Orbscan (with correction factor) can be used interchangeably with US pachymetry in certain clinical settings. The four modalities showed significant linear correlations with one another. Keywords: central corneal thickness, pachymetry, slit-lamp optical coherence tomography, specular microscopy, Orbsca

Inter-optometrist variability of IOP measurement for modern tonometers and their agreement with Goldmann Applanation Tonometry

Background: This study investigates: agreement in intraocular pressure measurements between three tonometers and Goldmann applanation tonometry (GAT); inter-optometrist agreement for each tonometer; intra-optometrist agreement for GAT; association between central corneal thickness (CCT) and IOP measurements with each tonometer. Methods: IOP was measured using: CT-1P Non-Contact Tonometer (NCT) (Topcon Corporation, Tokyo, Japan), Pulsair IntelliPuff (Keeler Ltd., Windsor, UK) and Icare rebound tonometer (Icare, Helsinki, Finland) by two optometrists in a random order. Two GAT readings were obtained by each optometrist in a randomised masked manner. Mean differences, and 95% limits of agreement (LoA) for each measurement were calculated. CCT was measured by CT-1P pachymeter. Results: Forty-one participants’ IOPs were measured. Mean differences (95% LoA) between NCT, Pulsair, Icare compared to GAT for one optometrist were: 0.8 (−5.4 to 6.9) mmHg, −1.7 (−8.2 to 4.8) mmHg, −1.6 (−9.0 to 5.9) mmHg. Mean differences (95% LoA) in inter-optometrist agreement for GAT, NCT, Pulsair and Icare were: 0.3 (−6.7 to 7.3) mmHg, 0.4 (−2.1 to 2.9) mmHg, −0.9 (−3.6 to 1.9) mmHg and −0.2 (−4.9 to 4.5) mmHg, respectively. Mean differences (95% LoA) for intra-optometrist agreement for GAT were 0.2 (4.3 to −4.7) mmHg and 0.1 (3.6 to −3.9) mmHg for each optometrist, respectively. There was a weak positive association between CCT and both GAT (r2 = 0.11) and NCT (r2 = 0.12). Conclusion: Pulsair and Icare may measure IOP lower than GAT. Mean differences for inter-optometrist agreement for all tonometers were < 1 mmHg; Pulsair showed a statistically significant difference. Intra-optometrist agreement for GAT was good. IOP measurements taken by two community optometrists are comparable using tonometers used in community practice

In vivo cross-sectional imaging of the phonating larynx using long-range Doppler optical coherence tomography

Diagnosis and treatment of vocal fold lesions has been a long-evolving science for the otolaryngologist. Contemporary practice requires biopsy of a glottal lesion in the operating room under general anesthesia for diagnosis. Current in-office technology is limited to visualizing the surface of the vocal folds with fiber-optic or rigid endoscopy and using stroboscopic or high-speed video to infer information about submucosal processes. Previous efforts using optical coherence tomography (OCT) have been limited by small working distances and imaging ranges. Here we report the first full field, high-speed, and long-range OCT images of awake patients’ vocal folds as well as cross-sectional video and Doppler analysis of their vocal fold motions during phonation. These vertical-cavity surface-emitting laser source (VCSEL) OCT images offer depth resolved, high-resolution, high-speed, and panoramic images of both the true and false vocal folds. This technology has the potential to revolutionize in-office imaging of the larynx