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

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 Balanophora 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 Balanophora plastids must import all tRNAs needed for translation. Balanophora plastomes are exceptionally compact, with numerous overlapping genes, highly reduced spacers, loss of all cis-spliced introns, and shrunken protein genes. With A+T contents of 87.8% and 88.4%, the Balanophora 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 Balanophora 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 Balanophora plastids, in which TAG has been reassigned from stop to tryptophan. Despite its many exceptional properties, the Balanophora plastome must be functional because all examined genes are transcribed, its only intron is correctly trans-spliced, and its protein genes, although highly divergent, are evolving under various degrees of selective constraint.

The Self-Determination Inventory: Student Report American Sign Language Translation.

Research literature and community narratives both emphasize the importance of self-determination in the lives of deaf youth. This paper describes the development, initial validation, and potential applications of a translated measure of self-determination for deaf youth, the SDI:SR ASL Translation (SDI:SR ASL). A sample of 3,309 young people who completed the SDI:SR, of whom 392 were deaf, was used in this validation study. Results provide preliminary support for the use of SDI:SR ASL with deaf youth. Findings also indicate that deaf youth who take the SDI:SR ASL score more similarly to youth without disabilities taking the SDI:SR than youth with disabilities. The SDI:SR ASL can be an important tool for researchers and practitioners to better understand self-determination among deaf youth and facilitate continued development of self-determination skills.

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

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.

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

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.

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

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.

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

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.

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

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.

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

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 (R2 = 0.91) and anteroposterior (R2 = 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.

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

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.

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

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.

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

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.

Swallowing Changes in Community-Dwelling Older Adults.

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.

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

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.

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

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.

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

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.

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.

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.

Unique role for translation initiation factor 3 in the light color regulation of photosynthetic gene expression.

Light-harvesting antennae are critical for collecting energy from sunlight and providing it to photosynthetic reaction centers. Their abundance and composition are tightly regulated to maintain efficient photosynthesis in changing light conditions. Many cyanobacteria alter their light-harvesting antennae in response to changes in ambient light-color conditions through the process of chromatic acclimation. The control of green light induction (Cgi) pathway is a light-color-sensing system that controls the expression of photosynthetic genes during chromatic acclimation, and while some evidence suggests that it operates via transcription attenuation, the components of this pathway have not been identified. We provide evidence that translation initiation factor 3 (IF3), an essential component of the prokaryotic translation initiation machinery that binds the 30S subunit and blocks premature association with the 50S subunit, is part of the control of green light induction pathway. Light regulation of gene expression has not been previously described for any translation initiation factor. Surprisingly, deletion of the IF3-encoding gene infCa was not lethal in the filamentous cyanobacterium Fremyella diplosiphon, and its genome was found to contain a second, redundant, highly divergent infC gene which, when deleted, had no effect on photosynthetic gene expression. Either gene could complement an Escherichia coli infC mutant and thus both encode bona fide IF3s. Analysis of prokaryotic and eukaryotic genome databases established that multiple infC genes are present in the genomes of diverse groups of bacteria and land plants, most of which do not undergo chromatic acclimation. This suggests that IF3 may have repeatedly evolved important roles in the regulation of gene expression in both prokaryotes and eukaryotes.

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

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.

Homologous recombination and retention of a single form of most genes shape the highly chimeric mitochondrial genome of a cybrid plant.

The structure and evolution of angiosperm mitochondrial genomes are driven by extremely high rates of recombination and rearrangement. An excellent experimental system for studying these events is offered by cybrid plants, in which parental mitochondria usually fuse and their genomes recombine. Little is known about the extent, nature and consequences of mitochondrial recombination in these plants. We conducted the first study in which the organellar genomes of a cybrid - between Nicotiana tabacum and Hyoscyamus niger - were sequenced and compared to those of its parents. This cybrid mitochondrial genome is highly recombinant, reflecting at least 30 crossovers and five gene conversions between its parental genomes. It is also surprisingly large (41% and 64% larger than the parental genomes), yet contains single alleles for 90% of mitochondrial genes. Recombination produced a remarkably chimeric cybrid mitochondrial genome and occurred entirely via homologous mechanisms involving the double-strand break repair and/or break-induced replication pathways. Retention of a single form of most genes could be advantageous to minimize intracellular incompatibilities and/or reflect neutral forces that preferentially eliminate duplicated regions. We discuss the relevance of these findings to the surprisingly frequent occurrence of horizontal gene - and genome - transfer in angiosperm mitochondrial DNAs.

Rapid evolution of enormous, multichromosomal genomes in flowering plant mitochondria with exceptionally high mutation rates.

Genome size and complexity vary tremendously among eukaryotic species and their organelles. Comparisons across deeply divergent eukaryotic lineages have suggested that variation in mutation rates may explain this diversity, with increased mutational burdens favoring reduced genome size and complexity. The discovery that mitochondrial mutation rates can differ by orders of magnitude among closely related angiosperm species presents a unique opportunity to test this hypothesis. We sequenced the mitochondrial genomes from two species in the angiosperm genus Silene with recent and dramatic accelerations in their mitochondrial mutation rates. Contrary to theoretical predictions, these genomes have experienced a massive proliferation of noncoding content. At 6.7 and 11.3 Mb, they are by far the largest known mitochondrial genomes, larger than most bacterial genomes and even some nuclear genomes. In contrast, two slowly evolving Silene mitochondrial genomes are smaller than average for angiosperms. Consequently, this genus captures approximately 98% of known variation in organelle genome size. The expanded genomes reveal several architectural changes, including the evolution of complex multichromosomal structures (with 59 and 128 circular-mapping chromosomes, ranging in size from 44 to 192 kb). They also exhibit a substantial reduction in recombination and gene conversion activity as measured by the relative frequency of alternative genome conformations and the level of sequence divergence between repeat copies. The evolution of mutation rate, genome size, and chromosome structure can therefore be extremely rapid and interrelated in ways not predicted by current evolutionary theories. Our results raise the hypothesis that changes in recombinational processes, including gene conversion, may be a central force driving the evolution of both mutation rate and genome structure.