Publications by authors named "Jeffrey Palmer"

174 Publications

Annular Flow in the Upper Esophageal Sphincter Demonstrated with Dynamic 320-row Area Detector Computed Tomography.

Dysphagia 2021 Jan 28. Epub 2021 Jan 28.

Department of Physical Medicine and Rehabilitation, Johns Hopkins University, Baltimore, MD, USA.

Understanding bolus flow patterns in swallowing (rheology, the study of flow) is fundamental to assessment and treatment of dysphagia. These patterns are complex and poorly understood. A liquid swallow is typically biphasic, including air, so the actual bolus has both liquid and gas phases. We report a novel observation of annular two-phase flow (a ring of liquid around a core of air) as thin liquids passed through the upper esophageal sphincter (UES). Dynamic CT was performed on 27 healthy asymptomatic volunteers swallowing liquid barium in a semi-reclining position. Each subject swallowed 3, 10, and 20 ml of either thin (14 subjects) or thick liquid (13 subjects). Sagittal and axial images were analyzed. Flow patterns in the UES were assessed on cross-sectional images. Annular flow was seen in the majority of subjects with thin liquid but few with thick liquid swallows. The percentage of Annular flow during UES opening was 3 ml 58%, 10 ml 58%, 20 ml 56% in thin and 3 ml 0%, 10 ml 4%, 20 ml 1% in thick. Annular flow was usually observed from the second or third frames after onset of UES opening. The other pattern, Plug flow was seldom seen with thin but was typical with thick liquid swallows. Annular flow was the most common pattern for thin liquids (but not thick liquids) passing through the UES. Annular flow has been defined as a liquid continuum adjacent to the channel wall with a gas continuum (core) in the center of the channel. The two regions are demarcated by a gas-liquid interface. Annular flow is typical for two-phase gas-liquid flow in a vertical or inclined channel. It results from the interaction of viscosity with cohesive and adhesive forces in the two phases. We infer that the difference in flow pattern between thin liquid-air and thick liquid-air boluses resulted from the differing magnitudes of viscous forces.
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http://dx.doi.org/10.1007/s00455-020-10241-9DOI Listing
January 2021

Life After College: Employment, Social, and Community Outcomes for Young Deaf Adults.

Am Ann Deaf 2020 ;165(4):401-417

While most research on transition outcomes focuses on education and employment, the transition to adulthood also includes social outcomes, such as group involvement and community service. The present study examined a broader set of outcomes for young deaf adults after postsecondary education. A secondary analysis of a large-scale data set, the National Longitudinal Transition Study (NLTS2), was conducted to compare the employment, income assistance, and social/community outcomes of three postsecondary education cohorts: graduates, noncompleters, and nonattendees. The findings indicate that young deaf adults with more postsecondary education have more positive outcomes, e.g., higher employment rates, higher wages, and greater civic and social participation. These findings further demonstrate the importance of postsecondary education for young deaf adults and can be used to inform transition planning for deaf students, supporting the need to consider exploration of various career pathways available through college or postsecondary career/technical education.
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http://dx.doi.org/10.1353/aad.2020.0027DOI Listing
January 2020

Horizontal gene transfers dominate the functional mitochondrial gene space of a holoparasitic plant.

New Phytol 2021 02 15;229(3):1701-1714. Epub 2020 Oct 15.

IBAM, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Agrarias, Almirante Brown 500, Chacras de Coria, M5528AHB, Argentina.

Although horizontal gene transfer (HGT) is common in angiosperm mitochondrial DNAs (mtDNAs), few cases of functional foreign genes have been identified. The one outstanding candidate for large-scale functional HGT is the holoparasite Lophophytum mirabile, whose mtDNA has lost most native genes but contains intact foreign homologs acquired from legume host plants. To investigate the extent to which this situation results from functional replacement of native by foreign genes, functional mitochondrial gene transfer to the nucleus, and/or loss of mitochondrial biochemical function in the context of extreme parasitism, we examined the Lophophytum mitochondrial and nuclear transcriptomes by deep paired-end RNA sequencing. Most foreign mitochondrial genes in Lophophytum are highly transcribed, accurately spliced, and efficiently RNA edited. By contrast, we found no evidence for functional gene transfer to the nucleus or loss of mitochondrial functions in Lophophytum. Many functional replacements occurred via the physical replacement of native genes by foreign genes. Some of these events probably occurred as the final act of HGT itself. Lophophytum mtDNA has experienced an unprecedented level of functional replacement of native genes by foreign copies. This raises important questions concerning population-genetic and molecular regimes that underlie such a high level of foreign gene takeover.
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http://dx.doi.org/10.1111/nph.16926DOI Listing
February 2021

Sensorimotor conflict tests in an immersive virtual environment reveal subclinical impairments in mild traumatic brain injury.

Sci Rep 2020 09 8;10(1):14773. Epub 2020 Sep 8.

Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA.

Current clinical tests lack the sensitivity needed for detecting subtle balance impairments associated with mild traumatic brain injury (mTBI). Patient-reported symptoms can be significant and have a huge impact on daily life, but impairments may remain undetected or poorly quantified using clinical measures. Our central hypothesis was that provocative sensorimotor perturbations, delivered in a highly instrumented, immersive virtual environment, would challenge sensory subsystems recruited for balance through conflicting multi-sensory evidence, and therefore reveal that not all subsystems are performing optimally. The results show that, as compared to standard clinical tests, the provocative perturbations illuminate balance impairments in subjects who have had mild traumatic brain injuries. Perturbations delivered while subjects were walking provided greater discriminability (average accuracy ≈ 0.90) than those delivered during standing (average accuracy ≈ 0.65) between mTBI subjects and healthy controls. Of the categories of features extracted to characterize balance, the lower limb accelerometry-based metrics proved to be most informative. Further, in response to perturbations, subjects with an mTBI utilized hip strategies more than ankle strategies to prevent loss of balance and also showed less variability in gait patterns. We have shown that sensorimotor conflicts illuminate otherwise-hidden balance impairments, which can be used to increase the sensitivity of current clinical procedures. This augmentation is vital in order to robustly detect the presence of balance impairments after mTBI and potentially define a phenotype of balance dysfunction that enhances risk of injury.
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http://dx.doi.org/10.1038/s41598-020-71611-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7479615PMC
September 2020

The effect of bolus consistency on pharyngeal volume during swallowing: Kinematic analysis in three dimensions using dynamic Area Detector CT.

J Oral Rehabil 2020 Oct 26;47(10):1287-1296. Epub 2020 Aug 26.

Department of Physical Medicine and Rehabilitation, Johns Hopkins University, Baltimore, USA.

Objective: This study investigated the effects of bolus consistency on pharyngeal volume during swallowing using three-dimensional kinematic analysis.

Methods: Eight subjects (2 males and 6 females, mean ± SD 44 ± 10 years old) underwent a 320-row area detector scan during swallows of 10 mL of honey-thick liquid and thin liquid. Critical event timing (hyoid, soft palate, UES) and volume of pharyngeal cavity and bolus were measured and compared between two swallows.

Results: The pharynx is almost completely obliterated by pharyngeal constriction against the tongue base for both consistencies. There were no significant differences in maximum volume, minimum volume and pharyngeal volume constriction ratio values between thick and thin liquids. However, the pattern of pharyngeal volume change (decrease) was different. For thick liquids, the air volume started to decrease before the onset of hyoid anterosuperior movement and decreased rapidly after onset of hyoid anterosuperior movement. During thin liquid swallowing, air volume remained relatively large throughout the swallow and started to decrease later when compared to swallowing thick liquids. At onset of UES opening, the bolus volume was not significantly different between thin and thick liquids; however, air volume was significantly larger when swallowing thin liquids, which made the total volume of the pharyngeal cavity larger.

Conclusion: This difference between the two consistencies is associated with differences in tongue motion to propel the bolus and clear the pharynx from possible residue.
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http://dx.doi.org/10.1111/joor.13062DOI Listing
October 2020

The use of Alloderm® for correction of severe chordee in children: An initial experience.

J Pediatr Urol 2020 Aug 14;16(4):446.e1-446.e5. Epub 2020 Jun 14.

Division Pediatric Urology, Cohen Children's Medical Center of New York, Zucker School of Medicine at Hofstra/Northwell, Long Island, NY, USA.

Introduction: Correction of chordee remains a prerequisite prior to urethroplasty in children with severe hypospadias. The use of an interposition graft is indicated when significant chordee (>30) persists after division of the urethral plate. The use of free dermis or tunica vaginalis are most often used, but the use of a pre-packaged graft material is attractive with regards to efficiency. The success with small intestine submucosa (SIS) has been variable and experience with Alloderm® has not been published.

Objective: To determine if Alloderm®, an acellular dermal matrix with regenerative properties, can effectively, safely, and efficiently be used for corporal grafting in cases of severe chordee in children associated with hypospadias or intersex STUDY DESIGN: All boys underwent planned staged repair of severe hypospadias (penoscrotal or more proximal). If artificial erection (AE) demonstrated chordee >45 after penile degloving and removal of fibrotic tissue, and again after urethral plate division, the ventral tunica albuginea was incised 180 transversely and the oval defect measured in both axes. Alloderm® was trimmed to size and sewn into the defect. AE confirmed chordee correction. At the second stage repair (>6 months later), AE was performed to confirm continued absence of chordee.

Conclusion: Alloderm®is safe, effective and simple to use graft material for correcting severe chordee. The benefits include performance efficiency without need for separate harvesting and donor site closure, and redundancy of material, if needed. Additional series and longer follow up must confirm these results and better assess durability.

Results:
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http://dx.doi.org/10.1016/j.jpurol.2020.06.007DOI Listing
August 2020

Randomized phase 2 trial and open-label extension of domagrozumab in Duchenne muscular dystrophy.

Neuromuscul Disord 2020 06 19;30(6):492-502. Epub 2020 May 19.

University of Massachusetts Medical School, Worcester, MA, USA.

We report results from a phase 2, randomized, double-blind, 2-period trial (48 weeks each) of domagrozumab and its open-label extension in patients with Duchenne muscular dystrophy (DMD). Of 120 ambulatory boys (aged 6 to <16 years) with DMD, 80 were treated with multiple ascending doses (5, 20, and 40 mg/kg) of domagrozumab and 40 treated with placebo. The primary endpoints were safety and mean change in 4-stair climb (4SC) time at week 49. Secondary endpoints included other functional tests, pharmacokinetics, and pharmacodynamics. Mean (SD) age was 8.4 (1.7) and 9.3 (2.3) years in domagrozumab- and placebo-treated patients, respectively. Difference in mean (95% CI) change from baseline in 4SC at week 49 for domagrozumab vs placebo was 0.27 (-7.4 to 7.9) seconds (p = 0.94). There were no significant between-group differences in any secondary clinical endpoints. Most patients had ≥1 adverse event in the first 48 weeks; most were mild and not treatment-related. Median serum concentrations of domagrozumab increased with administered dose within each dose level. Non-significant increases in muscle volume were observed in domagrozumab- vs placebo-treated patients. Domagrozumab was generally safe and well tolerated in patients with DMD. Efficacy measures did not support a significant treatment effect. Clinicaltrials.gov identifiers: NCT02310763 and NCT02907619.
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http://dx.doi.org/10.1016/j.nmd.2020.05.002DOI Listing
June 2020

Organellomic data sets confirm a cryptic consensus on (unrooted) land-plant relationships and provide new insights into bryophyte molecular evolution.

Am J Bot 2020 01 8;107(1):91-115. Epub 2019 Dec 8.

Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, British Columbia, V6T 1Z4, Canada.

Premise: Phylogenetic trees of bryophytes provide important evolutionary context for land plants. However, published inferences of overall embryophyte relationships vary considerably. We performed phylogenomic analyses of bryophytes and relatives using both mitochondrial and plastid gene sets, and investigated bryophyte plastome evolution.

Methods: We employed diverse likelihood-based analyses to infer large-scale bryophyte phylogeny for mitochondrial and plastid data sets. We tested for changes in purifying selection in plastid genes of a mycoheterotrophic liverwort (Aneura mirabilis) and a putatively mycoheterotrophic moss (Buxbaumia), and compared 15 bryophyte plastomes for major structural rearrangements.

Results: Overall land-plant relationships conflict across analyses, generally weakly. However, an underlying (unrooted) four-taxon tree is consistent across most analyses and published studies. Despite gene coverage patchiness, relationships within mosses, liverworts, and hornworts are largely congruent with previous studies, with plastid results generally better supported. Exclusion of RNA edit sites restores cases of unexpected non-monophyly to monophyly for Takakia and two hornwort genera. Relaxed purifying selection affects multiple plastid genes in mycoheterotrophic Aneura but not Buxbaumia. Plastid genome structure is nearly invariant across bryophytes, but the tufA locus, presumed lost in embryophytes, is unexpectedly retained in several mosses.

Conclusions: A common unrooted tree underlies embryophyte phylogeny, [(liverworts, mosses), (hornworts, vascular plants)]; rooting inconsistency across studies likely reflects substantial distance to algal outgroups. Analyses combining genomic and transcriptomic data may be misled locally for heavily RNA-edited taxa. The Buxbaumia plastome lacks hallmarks of relaxed selection found in mycoheterotrophic Aneura. Autotrophic bryophyte plastomes, including Buxbaumia, hardly vary in overall structure.
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http://dx.doi.org/10.1002/ajb2.1397DOI Listing
January 2020

Dysphagia in Myositis: A Study of the Structural and Physiologic Changes Resulting in Disordered Swallowing.

Am J Phys Med Rehabil 2020 05;99(5):404-408

From the Department of Physical Medicine and Rehabilitation, Johns Hopkins University School of Medicine, Baltimore, Maryland (AA, RM, JP, THC); Department of Psychological Sciences, Case Western Reserve University, Cleveland, Ohio (RM); Rehabilitation Department, Johns Hopkins Bayview Medical Center, Baltimore, Maryland (GM); Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland (TL, THC); and Department of Rheumatology, Johns Hopkins University School of Medicine, Baltimore, Maryland (LC-S).

Objectives: Dysphagia in patients with myositis is associated with an increased risk of aspiration pneumonia. However, the pathophysiology of dysphagia is poorly understood. The aim of this study was to understand how myositis affects swallowing physiology on videofluoroscopic swallow study.

Design: This is a retrospective review of video fluoroscopic swallowing studies on 23 myositis patients with dysphagia from 2011 to 2016. Swallow studies were analyzed by timing of swallowing events and duration of swallowing events, diameter of upper esophageal sphincter opening, Modified Barium Swallow Impairment Profile, and Penetration-Aspiration Scale. The outcome measures for patients were compared with an archived videofluoroscopic swallow study from healthy, age-matched participants by Wilcoxon rank-sum tests.

Results: Patients with myositis had a shorter duration of upper esophageal sphincter opening (P < 0.0001) and laryngeal vestibule closure (P < 0.0001) than healthy subjects. The diameter of upper esophageal sphincter opening did not differ between groups. Patients with myositis presented with higher scores on the MBSIMP than healthy subjects, indicating great impairment particularly during the pharyngeal phase of swallowing, and a higher frequency of penetration and aspiration.

Conclusions: Dysphagia in patients with myositis may be attributed to reduced endurance of swallowing musculature rather than mechanical obstruction of the upper esophageal sphincter.
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http://dx.doi.org/10.1097/PHM.0000000000001354DOI Listing
May 2020

The Association of 3-D Volume and 2-D Area of Post-swallow Pharyngeal Residue on CT Imaging.

Dysphagia 2019 10 14;34(5):665-672. Epub 2019 Jan 14.

Department of Physical Medicine and Rehabilitation, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA.

Pharyngeal residue, the material that remains in the pharynx after swallowing, is an important marker of impairments in swallowing and prandial aspiration risk. The goals of this study were to determine whether the 2D area of post-swallow residue accurately represents its 3D volume, and if the laterality of residue would affect this association. Thirteen patients with dysphagia due to brainstem stroke completed dynamic 320-detector row computed tomography while swallowing a trial of 10 ml honey-thick barium. 3D volumes of pharyngeal residue were compared to 2D lateral and anterior-posterior areas, and a laterality index for residue location was computed. Although the anteroposterior area of residue was larger than the lateral area, the two measures were positively correlated with one another and with residue volume. On separate bivariate regression analyses, residue volume was accurately predicted by both lateral (R = 0.91) and anteroposterior (R = 0.88) residue areas, with limited incidence of high residuals. Half of the sample demonstrated a majority of pharyngeal residue lateralized to one side of the pharynx, with no effect of laterality on the association between areas and volume. In conclusion, the area of post-swallow pharyngeal residue was associated with volume, with limitations in specific cases. Direct measurement of pharyngeal residue volume and swallowing physiology with 3D-CT can be used to validate results from standard 2D instrumentation.
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http://dx.doi.org/10.1007/s00455-018-09968-3DOI Listing
October 2019

Novel genetic code and record-setting AT-richness in the highly reduced plastid genome of the holoparasitic plant .

Proc Natl Acad Sci U S A 2019 01 31;116(3):934-943. Epub 2018 Dec 31.

Department of Biology, Pennsylvania State University, University Park, PA 16802;

Plastid genomes (plastomes) vary enormously in size and gene content among the many lineages of nonphotosynthetic plants, but key lineages remain unexplored. We therefore investigated plastome sequence and expression in the holoparasitic and morphologically bizarre Balanophoraceae. The two plastomes examined are remarkable, exhibiting features rarely if ever seen before in plastomes or in any other genomes. At 15.5 kb in size and with only 19 genes, they are among the most reduced plastomes known. They have no tRNA genes for protein synthesis, a trait found in only three other plastid lineages, and thus plastids must import all tRNAs needed for translation. plastomes are exceptionally compact, with numerous overlapping genes, highly reduced spacers, loss of all -spliced introns, and shrunken protein genes. With A+T contents of 87.8% and 88.4%, the genomes are the most AT-rich genomes known save for a single mitochondrial genome that is merely bloated with AT-rich spacer DNA. Most plastid protein genes in consist of ≥90% AT, with several between 95% and 98% AT, resulting in the most biased codon usage in any genome described to date. A potential consequence of its radical compositional evolution is the novel genetic code used by plastids, in which TAG has been reassigned from stop to tryptophan. Despite its many exceptional properties, the plastome must be functional because all examined genes are transcribed, its only intron is correctly -spliced, and its protein genes, although highly divergent, are evolving under various degrees of selective constraint.
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http://dx.doi.org/10.1073/pnas.1816822116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6338844PMC
January 2019

High and Variable Rates of Repeat-Mediated Mitochondrial Genome Rearrangement in a Genus of Plants.

Mol Biol Evol 2018 11;35(11):2773-2785

Department of Biology, Indiana University, Bloomington, IN.

For 30 years, it has been clear that angiosperm mitochondrial genomes evolve rapidly in sequence arrangement (i.e., synteny), yet absolute rates of rearrangement have not been measured in any plant group, nor is it known how much these rates vary. To investigate these issues, we sequenced and reconstructed the rearrangement history of seven mitochondrial genomes in Monsonia (Geraniaceae). We show that rearrangements (occurring mostly as inversions) not only take place at generally high rates in these genomes but also uncover significant variation in rearrangement rates. For example, the hyperactive mitochondrial genome of Monsonia ciliata has accumulated at least 30 rearrangements over the last million years, whereas the branch leading to M. ciliata and its sister species has sustained rearrangement at a rate that is at least ten times lower. Furthermore, our analysis of published data shows that rates of mitochondrial genome rearrangement in seed plants vary by at least 600-fold. We find that sites of rearrangement are highly preferentially located in very close proximity to repeated sequences in Monsonia. This provides strong support for the hypothesis that rearrangement in angiosperm mitochondrial genomes occurs largely through repeat-mediated recombination. Because there is little variation in the amount of repeat sequence among Monsonia genomes, the variable rates of rearrangement in Monsonia probably reflect variable rates of mitochondrial recombination itself. Finally, we show that mitochondrial synonymous substitutions occur in a clock-like manner in Monsonia; rates of mitochondrial substitutions and rearrangements are therefore highly uncoupled in this group.
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http://dx.doi.org/10.1093/molbev/msy176DOI Listing
November 2018

Pharyngeal swallowing in older adults: Kinematic analysis using three-dimensional dynamic computed tomography.

J Oral Rehabil 2018 Dec 14;45(12):959-966. Epub 2018 Sep 14.

Department of Physical Medicine and Rehabilitation, Johns Hopkins University, Baltimore, Maryland.

Objectives: To assess the effect of age on swallowing with a focus on structural movement, timing and duration of physiologic events.

Design: Cross-sectional study.

Setting: Tertiary University Medical Center.

Participants: Community-dwelling adults (3 age groups): younger 20 to 39 (n = 23; mean 32 ± 5), middle-aged 40 to 59 (n = 29; mean 49 ± 5) and older adults 60 to 74 (n = 15; mean 67 ± 5).

Intervention: One 10-mL honey-thick liquid (1700 mPa) swallow was studied using 320-row area detector computed tomography scanning.

Measurements: Kinematic analysis was performed for each swallow including temporal characteristics and structural movements.

Results: The duration of velopharyngeal closure and laryngeal closure (including epiglottis inversion, laryngeal vestibule closure, true vocal cord closure) was significantly different by age group (P = 0.002, P < 0.001, P = 0.017, P = 0.041, respectively). Events were prolonged in older adults compared with middle-aged and younger adults. The pharyngeal phase was longer for older adults. Velopharyngeal closure started earlier and continued until after complete UES opening. In younger adults, velopharyngeal and laryngeal opening occurred before complete UES opening. No differences were found in bolus movement through the oropharynx by group.

Conclusion: During swallowing, older adults had a longer pharyngeal phase characterised by prolonged velopharyngeal and laryngeal closure. This difference may be a protective mechanism to compensate for age-related weakness. A better understanding of the mechanism by which this adaptation occurs is needed to tailor rehabilitation strategies and to maintain swallowing function during the lifespan.
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http://dx.doi.org/10.1111/joor.12703DOI Listing
December 2018

Swallowing Changes in Community-Dwelling Older Adults.

Dysphagia 2018 12 8;33(6):848-856. Epub 2018 Jun 8.

Department of Physical Medicine and Rehabilitation, Johns Hopkins University School of Medicine, 600N. Wolfe Street, Baltimore, MD, 21287, USA.

Older adults may evidence changes in swallowing physiology. Our goals were to identify dysphagia risk in community-dwelling older adults with no history of dysphagia, and to compare swallowing physiology and safety between older and younger adults. Thirty-two older adults with no history of dysphagia were prospectively recruited and completed the Dysphagia Handicap Index (DHI), two trials of a 3 oz. swallow screen, and videofluoroscopy (VFSS). Self-ratings of swallowing function were compared to published norms by paired t tests, and multivariate logistic regression models were generated to determine whether these ratings and VFSS analysis of swallowing function were associated with failure of one or both swallow screen trials. Archived VFSS of 33 younger adults were compared to older adults with Wilcoxon rank-sum tests. The DHI scores of older adults were higher than published non-dysphagic adults but lower than dysphagic adults. Older participants with greater Oral Residue scores were more likely to fail both swallow screen trials. Older adults received higher median MBSImP™© scores for select pharyngeal components than younger adults. The two age groups did not differ on Penetration-Aspiration Scale scores, and no aspiration was observed. Measures of swallowing in older individuals may reflect age-related sensory and motor changes in the context of functional swallowing and adequate airway protection.
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http://dx.doi.org/10.1007/s00455-018-9911-xDOI Listing
December 2018

Coordination of Pharyngeal and Laryngeal Swallowing Events During Single Liquid Swallows After Oral Endotracheal Intubation for Patients with Acute Respiratory Distress Syndrome.

Dysphagia 2018 12 30;33(6):768-777. Epub 2018 Apr 30.

Department of Physical Medicine and Rehabilitation, Johns Hopkins University, 600 N. Wolfe St. - Phipps 181, Baltimore, MD, 21287, USA.

To evaluate timing and duration differences in airway protection and esophageal opening after oral intubation and mechanical ventilation for acute respiratory distress syndrome (ARDS) survivors versus age-matched healthy volunteers. Orally intubated adult (≥ 18 years old) patients receiving mechanical ventilation for ARDS were evaluated for swallowing impairments via a videofluoroscopic swallow study (VFSS) during usual care. Exclusion criteria were tracheostomy, neurological impairment, and head and neck cancer. Previously recruited healthy volunteers (n = 56) served as age-matched controls. All subjects were evaluated using 5-ml thin liquid barium boluses. VFSS recordings were reviewed frame-by-frame for the onsets of 9 pharyngeal and laryngeal events during swallowing. Eleven patients met inclusion criteria, with a median (interquartile range [IQR]) intubation duration of 14 (9, 16) days, and VFSSs completed a median of 5 (4, 13) days post-extubation. After arrival of the bolus in the pharynx, ARDS patients achieved maximum laryngeal closure a median (IQR) of 184 (158, 351) ms later than age-matched, healthy volunteers (p < 0.001) and it took longer to achieve laryngeal closure with a median (IQR) difference of 151 (103, 217) ms (p < 0.001), although there was no significant difference in duration of laryngeal closure. Pharyngoesophageal segment opening was a median (IQR) of - 116 (- 183, 1) ms (p = 0.004) shorter than in age-matched, healthy controls. Evaluation of swallowing physiology after oral endotracheal intubation in ARDS patients demonstrates slowed pharyngeal and laryngeal swallowing timing, suggesting swallow-related muscle weakness. These findings may highlight specific areas for further evaluation and potential therapeutic intervention to reduce post-extubation aspiration.
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http://dx.doi.org/10.1007/s00455-018-9901-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6207471PMC
December 2018

The Mendelsohn Maneuver and its Effects on Swallowing: Kinematic Analysis in Three Dimensions Using Dynamic Area Detector CT.

Dysphagia 2018 08 26;33(4):419-430. Epub 2017 Dec 26.

Department of Physical Medicine and Rehabilitation, Johns Hopkins University, Baltimore, USA.

This study investigated the effects of Mendelsohn maneuver with three-dimensional kinematic analysis. Nine female speech-language pathologists (nine females, mean ± SD 27.1 ± 3.5 years old) underwent 320-row area detector scan during swallows of 4-ml nectar-thick liquid using with no maneuvers (control) and with Mendelsohn maneuver (MM). Critical event timing (hyoid, soft palate, epiglottis, laryngeal vestibule, true vocal cords (TVC), UES), hyoid and laryngeal excursion, cross-sectional area of UES, and volume of pharyngeal cavity and bolus were measured and compared between two swallows. In MM, all the events were significantly prolonged with delayed termination time (p < 0.05) except UES opening. The onset, termination, and duration of UES opening were not significantly affected by MM nor was timing of bolus transport. The hyoid bone was positioned significantly higher at maximum displacement (p = 0.011). Pharyngeal constriction ratio was 95.1% in control and 100% of all subjects in MM. Duration of minimum pharyngeal volume was significantly longer in MM than in control (p = 0.007). The MM produces several distinct changes in the kinematics of swallowing in healthy subjects with no dysphagia. The changes in the timing and magnitude of hyoid displacements and prolonged closure of the pharynx during swallowing suggest the utility of MM for improving the safety and efficiency of swallowing in selected cases.
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http://dx.doi.org/10.1007/s00455-017-9870-7DOI Listing
August 2018

The physiology of oral whistling: a combined radiographic and MRI analysis.

J Appl Physiol (1985) 2018 01 24;124(1):34-39. Epub 2017 Aug 24.

Department of Cognitive Biology, University of Vienna , Vienna , Austria.

The fluid mechanics of whistling involve the instability of an air jet, resultant vortex rings, and the interaction of these rings with rigid boundaries (see http://www.canal-u.tv/video/cerimes/etude_radiocinematographique_d_un_siffleur_turc_de_kuskoy.13056 and Meyer J. Whistled Languages. Berlin, Germany: Springer, 2015, p. 74-774). Experimental models support the hypothesis that the sound in human whistling is generated by a Helmholtz resonator, suggesting that the oral cavity acts as a resonant chamber bounded by two orifices, posteriorly by raising the tongue to the hard palate, and anteriorly by pursed lips (Henrywood RH, Agarwal A. Phys Fluids 25: 107101, 2013). However, the detailed anatomical changes in the vocal tract and their relation to the frequencies generated have not been described in the literature. In this study, videofluoroscopic and simultaneous audio recordings were made of subjects whistling with the bilabial (i.e., "puckered lip") technique. One whistling subject was also recorded, using magnetic resonance imaging. As predicted by theory, the frequency of sound generated decreased as the size of the resonant cavity increased; this relationship was preserved throughout various whistling tasks and was consistent across subjects. Changes in the size of the resonant cavity were primarily modulated by tongue position rather than jaw opening and closing. Additionally, when high-frequency notes were produced, lateral chambers formed in the buccal space. These results provide the first dynamic anatomical evidence concerning the acoustic production of human whistling. NEW & NOTEWORTHY We establish a new and much firmer quantitative and physiological footing to current theoretical models on human whistling. We also document a novel lateral airflow mechanism used by both of our participants to produce high-frequency notes.
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http://dx.doi.org/10.1152/japplphysiol.00902.2016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6048461PMC
January 2018

Food transit duration is associated with the number of stage II transport cycles when eating solid food.

Arch Oral Biol 2017 Sep 20;81:186-191. Epub 2017 May 20.

Department of Rehabilitation Medicine, Kawasaki Medical School, Kurashiki, Okayama, Japan. Electronic address:

Objective: When eating solids, stage II transport (St2Tr) propels triturated food into the pharynx for bolus formation and storage before swallowing. Although the existence of St2Tr is acknowledged, the reason for its existence remains unclear. Understanding it may facilitate development of food appropriate for individuals with dysphagia. The purpose of this study was to explore how measures of duration of eating and swallowing affect the number of St2Tr cycles.

Design: Videofluorography was performed on 13 healthy subjects eating 6-g squares of banana, tofu, and cookies. Measurements included the number of St2Tr cycles, duration of processing (from food entering the mouth to onset of swallowing), pre-upper esophageal sphincter (UES) transit duration (from onset of swallowing to onset of UES transit), UES transit duration (leading edge to trailing edge passing the UES), and total sequence duration (from onset of swallowing to terminal swallow). Principal component (PC) analysis was used to identify factors affecting the number of St2Tr cycles. Analysis of covariance was performed using the 1st PC as an independent variable for predicting the number of St2Tr cycles.

Results: All four duration measures were significantly positively correlated with the number of St2Tr cycles. Analysis revealed two orthogonal PCs with variable loading. The 1st PC was a function of the timing variables. The 2nd PC was a function of the number of swallows.

Conclusions: The number of St2Tr cycles was associated with measures of food transit duration and was greater with harder foods before processing and more viscous foods just before swallowing.
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http://dx.doi.org/10.1016/j.archoralbio.2017.05.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5536103PMC
September 2017

Mitochondrial Retroprocessing Promoted Functional Transfers of rpl5 to the Nucleus in Grasses.

Mol Biol Evol 2017 09;34(9):2340-2354

Department of Biology, King University, Bristol, TN.

Functional gene transfers from the mitochondrion to the nucleus are ongoing in angiosperms and have occurred repeatedly for all 15 ribosomal protein genes, but it is not clear why some of these genes are transferred more often than others nor what the balance is between DNA- and RNA-mediated transfers. Although direct insertion of mitochondrial DNA into the nucleus occurs frequently in angiosperms, case studies of functional mitochondrial gene transfer have implicated an RNA-mediated mechanism that eliminates introns and RNA editing sites, which would otherwise impede proper expression of mitochondrial genes in the nucleus. To elucidate the mechanisms that facilitate functional gene transfers and the evolutionary dynamics of the coexisting nuclear and mitochondrial gene copies that are established during these transfers, we have analyzed rpl5 genes from 90 grasses (Poaceae) and related monocots. Multiple lines of evidence indicate that rpl5 has been functionally transferred to the nucleus at least three separate times in the grass family and that at least seven species have intact and transcribed (but not necessarily functional) copies in both the mitochondrion and nucleus. In two grasses, likely functional nuclear copies of rpl5 have been subject to recent gene conversion events via secondarily transferred mitochondrial copies in what we believe are the first described cases of mitochondrial-to-nuclear gene conversion. We show that rpl5 underwent a retroprocessing event within the mitochondrial genome early in the evolution of the grass family, which we argue predisposed the gene towards successful, DNA-mediated functional transfer by generating a "pre-edited" sequence.
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http://dx.doi.org/10.1093/molbev/msx170DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850859PMC
September 2017

Comparative mitogenomics indicates respiratory competence in parasitic Viscum despite loss of complex I and extreme sequence divergence, and reveals horizontal gene transfer and remarkable variation in genome size.

BMC Plant Biol 2017 02 21;17(1):49. Epub 2017 Feb 21.

Department of Biology, Indiana University, Bloomington, IN, 47405, USA.

Background: Aerobically respiring eukaryotes usually contain four respiratory-chain complexes (complexes I-IV) and an ATP synthase (complex V). In several lineages of aerobic microbial eukaryotes, complex I has been lost, with an alternative, nuclear-encoded NADH dehydrogenase shown in certain cases to bypass complex I and oxidize NADH without proton translocation. The first loss of complex I in any multicellular eukaryote was recently reported in two studies; one sequenced the complete mitogenome of the hemiparasitic aerial mistletoe, Viscum scurruloideum, and the other sequenced the V. album mitogenome. The V. scurruloideum study reported no significant additional loss of mitochondrial genes or genetic function, but the V. album study postulated that mitochondrial genes encoding all ribosomal RNAs and proteins of all respiratory complexes are either absent or pseudogenes, thus raising questions as to whether the mitogenome and oxidative respiration are functional in this plant.

Results: To determine whether these opposing conclusions about the two Viscum mitogenomes reflect a greater degree of reductive/degenerative evolution in V. album or instead result from interpretative and analytical differences, we reannotated and reanalyzed the V. album mitogenome and compared it with the V. scurruloideum mitogenome. We find that the two genomes share a complete complement of mitochondrial rRNA genes and a typical complement of genes encoding respiratory complexes II-V. Most Viscum mitochondrial protein genes exhibit very high levels of divergence yet are evolving under purifying, albeit relaxed selection. We discover two cases of horizontal gene transfer in V. album and show that the two Viscum mitogenomes differ by 8.6-fold in size (66 kb in V. scurruloideum; 565 kb in V. album).

Conclusions: Viscum mitogenomes are extraordinary compared to other plant mitogenomes in terms of their wide size range, high rates of synonymous substitutions, degree of relaxed selection, and unprecedented loss of respiratory complex I. However, contrary to the initial conclusions regarding V. album, both Viscum mitogenomes possess conventional sets of rRNA and, excepting complex I, respiratory genes. Both plants should therefore be able to carry out aerobic respiration. Moreover, with respect to size, the V. scurruloideum mitogenome has experienced a greater level of reductive evolution.
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http://dx.doi.org/10.1186/s12870-017-0992-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319169PMC
February 2017

Recovery from Dysphagia Symptoms after Oral Endotracheal Intubation in Acute Respiratory Distress Syndrome Survivors. A 5-Year Longitudinal Study.

Ann Am Thorac Soc 2017 Mar;14(3):376-383

1 Department of Physical Medicine and Rehabilitation.

Rationale: Nearly 60% of patients who are intubated in intensive care units (ICUs) experience dysphagia after extubation, and approximately 50% of them aspirate. Little is known about dysphagia recovery time after patients are discharged from the hospital.

Objectives: To determine factors associated with recovery from dysphagia symptoms after hospital discharge for acute respiratory distress syndrome (ARDS) survivors who received oral intubation with mechanical ventilation.

Methods: This is a prospective, 5-year longitudinal cohort study involving 13 ICUs at four teaching hospitals in Baltimore, Maryland. The Sydney Swallowing Questionnaire (SSQ), a 17-item visual analog scale (range, 0-1,700), was used to quantify patient-perceived dysphagia symptoms at hospital discharge, and at 3, 6, 12, 24, 36, 48, and 60 months after ARDS. An SSQ score greater than or equal to 200 was used to indicate clinically important dysphagia symptoms at the time of hospital discharge. Recovery was defined as an SSQ score less than 200, with a decrease from hospital discharge greater than or equal to 119, the reliable change index for SSQ score. Fine and Gray proportional subdistribution hazards regression analysis was used to evaluate patient and ICU variables associated with time to recovery accounting for the competing risk of death.

Measurements And Main Results: Thirty-seven (32%) of 115 patients had an SSQ score greater than or equal to 200 at hospital discharge; 3 died before recovery. All 34 remaining survivors recovered from dysphagia symptoms by 5-year follow-up, 7 (23%) after 6 months. ICU length of stay was independently associated with time to recovery, with a hazard ratio (95% confidence interval) of 0.96 (0.93-1.00) per day.

Conclusions: One-third of orally intubated ARDS survivors have dysphagia symptoms that persist beyond hospital discharge. Patients with a longer ICU length of stay have slower recovery from dysphagia symptoms and should be carefully considered for swallowing assessment to help prevent complications related to dysphagia.
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http://dx.doi.org/10.1513/AnnalsATS.201606-455OCDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5427721PMC
March 2017

Video fluoroscopic techniques for the study of Oral Food Processing.

Curr Opin Food Sci 2016 Jun;9:1-10

Department of Physical Medicine and Rehabilitation, Johns Hopkins University, Baltimore, MD 21287; Department of Otolaryngology - Head and Neck Surgery, Johns Hopkins University, Baltimore, MD 21287; Center for Functional Anatomy and Evolution, Johns Hopkins University, Baltimore, MD 21287.

Food oral processing and pharyngeal food passage cannot be observed directly from the outside of the body without instrumental methods. Videofluoroscopy (x-ray video recording) reveals the movement of oropharyngeal anatomical structures in two dimensions. By adding a radiopaque contrast medium, the motion and shape of the food bolus can be also visualized, providing critical information about the mechanisms of eating, drinking, and swallowing. For quantitative analysis of the kinematics of oral food processing, radiopaque markers are attached to the teeth, tongue or soft palate. This approach permits kinematic analysis with a variety of textures and consistencies, both solid and liquid. Fundamental mechanisms of food oral processing are clearly observed with videofluoroscopy in lateral and anteroposterior projections.
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http://dx.doi.org/10.1016/j.cofs.2016.03.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4871608PMC
June 2016

Alemtuzumab improves neurological functional systems in treatment-naive relapsing-remitting multiple sclerosis patients.

J Neurol Sci 2016 Apr 12;363:188-94. Epub 2016 Feb 12.

Sanofi Genzyme, Cambridge, MA, USA. Electronic address:

Background: Individual functional system scores (FSS) of the Expanded Disability Status Scale (EDSS) play a central role in determining the overall EDSS score in patients with early-stage multiple sclerosis (MS). Alemtuzumab treatment improves preexisting disability for many patients; however, it is unknown whether improvement is specific to certain functional systems.

Objective: We assessed the effect of alemtuzumab on individual FSS of the EDSS.

Methods: CAMMS223 was a 36-month, rater-blinded, phase 2 trial; treatment-naive patients with active relapsing-remitting MS, EDSS ≤3, and symptom onset within 3 years were randomized to annual courses of alemtuzumab or subcutaneous interferon beta-1a (SC IFNB-1a) 44 μg three times weekly.

Results: Alemtuzumab-treated patients had improved outcomes versus SC IFNB-1a patients on most FSS at Month 36; the greatest effect occurred for sensory, pyramidal, and cerebellar FSS. Among patients who experienced 6-month sustained accumulation of disability, clinical worsening occurred most frequently in the brainstem and sensory systems. For patients with 6-month sustained reduction in preexisting disability, pyramidal and sensory systems contributed most frequently to clinical improvement.

Conclusions: Alemtuzumab demonstrated a broad treatment effect in improving preexisting disability. These findings may influence treatment decisions in patients with early, active relapsing-remitting MS displaying neurological deficits. ClinicalTrials.gov Identifier NCT00050778.
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http://dx.doi.org/10.1016/j.jns.2016.02.025DOI Listing
April 2016

Ginkgo and Welwitschia Mitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution.

Mol Biol Evol 2016 06 1;33(6):1448-60. Epub 2016 Feb 1.

Center for Plant Science Innovation, University of Nebraska, Lincoln Department of Agronomy and Horticulture, University of Nebraska, Lincoln

Mitochondrial genomes (mitogenomes) of flowering plants are well known for their extreme diversity in size, structure, gene content, and rates of sequence evolution and recombination. In contrast, little is known about mitogenomic diversity and evolution within gymnosperms. Only a single complete genome sequence is available, from the cycad Cycas taitungensis, while limited information is available for the one draft sequence, from Norway spruce (Picea abies). To examine mitogenomic evolution in gymnosperms, we generated complete genome sequences for the ginkgo tree (Ginkgo biloba) and a gnetophyte (Welwitschia mirabilis). There is great disparity in size, sequence conservation, levels of shared DNA, and functional content among gymnosperm mitogenomes. The Cycas and Ginkgo mitogenomes are relatively small, have low substitution rates, and possess numerous genes, introns, and edit sites; we infer that these properties were present in the ancestral seed plant. By contrast, the Welwitschia mitogenome has an expanded size coupled with accelerated substitution rates and extensive loss of these functional features. The Picea genome has expanded further, to more than 4 Mb. With regard to structural evolution, the Cycas and Ginkgo mitogenomes share a remarkable amount of intergenic DNA, which may be related to the limited recombinational activity detected at repeats in Ginkgo Conversely, the Welwitschia mitogenome shares almost no intergenic DNA with any other seed plant. By conducting the first measurements of rates of DNA turnover in seed plant mitogenomes, we discovered that turnover rates vary by orders of magnitude among species.
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http://dx.doi.org/10.1093/molbev/msw024DOI Listing
June 2016

The Complete Moss Mitochondrial Genome in the Angiosperm Amborella Is a Chimera Derived from Two Moss Whole-Genome Transfers.

PLoS One 2015 30;10(11):e0137532. Epub 2015 Nov 30.

Department of Biology, Indiana University, Bloomington, Indiana, United States of America.

Sequencing of the 4-Mb mitochondrial genome of the angiosperm Amborella trichopoda has shown that it contains unprecedented amounts of foreign mitochondrial DNA, including four blocks of sequences that together correspond almost perfectly to one entire moss mitochondrial genome. This implies whole-genome transfer from a single moss donor but conflicts with phylogenetic results from an earlier, PCR-based study that suggested three different moss donors to Amborella. To resolve this conflict, we conducted an expanded set of phylogenetic analyses with respect to both moss lineages and mitochondrial loci. The moss DNA in Amborella was consistently placed in either of two positions, depending on the locus analyzed, as sister to the Ptychomniales or within the Hookeriales. This agrees with two of the three previously suggested donors, whereas the third is no longer supported. These results, combined with synteny analyses and other considerations, lead us to favor a model involving two successive moss-to-Amborella whole-genome transfers, followed by recombination that produced a single intact and chimeric moss mitochondrial genome integrated in the Amborella mitochondrial genome. Eight subsequent recombination events account for the state of fragmentation, rearrangement, duplication, and deletion of this chimeric moss mitochondrial genome as it currently exists in Amborella. Five of these events are associated with short-to-intermediate sized repeats. Two of the five probably occurred by reciprocal homologous recombination, whereas the other three probably occurred in a non-reciprocal manner via microhomology-mediated break-induced replication (MMBIR). These findings reinforce and extend recent evidence for an important role of MMBIR in plant mitochondrial DNA evolution.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0137532PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664403PMC
June 2016

Poststroke Communication Disorders and Dysphagia.

Phys Med Rehabil Clin N Am 2015 Nov;26(4):657-70

Department of Physical Medicine and Rehabilitation, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

Communication and swallowing disorders are common after stroke. Targeted surveillance followed by prompt evaluation and treatment is of paramount importance. The overall goals of rehabilitation for impaired swallowing and communication and swallowing deficits may differ based on the specific deficits caused by the stroke but the main goal is always to improve the patient's everyday interpersonal interactions and optimize participation in society. Fortunately, therapeutic or compensatory interventions can decrease the effects that communication and swallowing deficits have on the quality of life of stroke survivors.
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http://dx.doi.org/10.1016/j.pmr.2015.06.005DOI Listing
November 2015

Electromyography of Swallowing with Fine Wire Intramuscular Electrodes in Healthy Human: Amplitude Difference of Selected Hyoid Muscles.

Dysphagia 2016 Feb 20;31(1):33-40. Epub 2015 Oct 20.

Department of Physical Medicine and Rehabilitation, Johns Hopkins University School of Medicine, Baltimore, MD, USA.

Few studies have examined the intensity of muscle activity during swallowing in healthy humans. We examined selected hyoid muscles using fine wire intramuscular electromyography (EMG) during swallowing of four food consistencies. Thirteen healthy adults were studied using videofluorography and EMG of the anterior belly of digastric (ABD), geniohyoid (GH), sternohyoid (SH), and masseter (MA; surface electrodes) while ingesting thin liquid (three trials) and solid food of three consistencies (banana, tofu, and cookie, three trials each). After rectification, integration, and normalization, peak EMG amplitudes for each muscle in each trial were measured. Hyoid displacements were measured in two dimensions. Data were analyzed using repeated measures ANOVA with Bonferroni correction. GH had the highest adjusted amplitude for both solids and liquid. For MA and ABD, amplitude was highest with triturated cookie. For ABD, amplitude was lowest with liquid. There were no significant food consistency effects for GH or SH. Hyoid displacements were greatest for cookie and the lowest for liquid. EMG amplitude varied with initial food consistency. The high peak EMG amplitude of GH is consistent with its essential role in opening the upper esophageal sphincter. High MA amplitude with hard solid foods is likely due to the higher tongue-palate pressure with triturated solids. The higher ABD amplitude with solid food is associated with greater hyoid displacement. These findings support the existence of a central pattern generator that modifies the level of muscle activity during pharyngeal swallowing in response to input from mechanoreceptors in the oral cavity.
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http://dx.doi.org/10.1007/s00455-015-9655-9DOI Listing
February 2016

Miniaturized mitogenome of the parasitic plant Viscum scurruloideum is extremely divergent and dynamic and has lost all nad genes.

Proc Natl Acad Sci U S A 2015 Jul 22;112(27):E3515-24. Epub 2015 Jun 22.

Department of Biology, Indiana University, Bloomington, IN 47405;

Despite the enormous diversity among parasitic angiosperms in form and structure, life-history strategies, and plastid genomes, little is known about the diversity of their mitogenomes. We report the sequence of the wonderfully bizarre mitogenome of the hemiparasitic aerial mistletoe Viscum scurruloideum. This genome is only 66 kb in size, making it the smallest known angiosperm mitogenome by a factor of more than three and the smallest land plant mitogenome. Accompanying this size reduction is exceptional reduction of gene content. Much of this reduction arises from the unexpected loss of respiratory complex I (NADH dehydrogenase), universally present in all 300+ other angiosperms examined, where it is encoded by nine mitochondrial and many nuclear nad genes. Loss of complex I in a multicellular organism is unprecedented. We explore the potential relationship between this loss in Viscum and its parasitic lifestyle. Despite its small size, the Viscum mitogenome is unusually rich in recombinationally active repeats, possessing unparalleled levels of predicted sublimons resulting from recombination across short repeats. Many mitochondrial gene products exhibit extraordinary levels of divergence in Viscum, indicative of highly relaxed if not positive selection. In addition, all Viscum mitochondrial protein genes have experienced a dramatic acceleration in synonymous substitution rates, consistent with the hypothesis of genomic streamlining in response to a high mutation rate but completely opposite to the pattern seen for the high-rate but enormous mitogenomes of Silene. In sum, the Viscum mitogenome possesses a unique constellation of extremely unusual features, a subset of which may be related to its parasitic lifestyle.
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http://dx.doi.org/10.1073/pnas.1504491112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4500244PMC
July 2015