Community and shotgun metagenomic analysis of Alligator mississippiensis oral cavity and GI tracts reveal complex ecosystems and potential reservoirs of antibiotic resistance.

We report here the community structure and functional analysis of the microbiome of the Alligator mississippiensis GI tract from the oral cavity through the entirety of the digestive tract. Although many vertebrate microbiomes have been studied in recent years, the archosaur microbiome has only been given cursory attention. In the oral cavity we used amplicon-based community analysis to examine the structure of the oral microbiome during alligator development. We found a community that diversified over time and showed many of the hallmarks we would expect of a stable oral community. This is a bit surprising given the rapid turnover of alligator teeth but suggests that the stable gumline microbes are able to rapidly colonize the emerging teeth. As we move down the digestive tract, we were able to use both long and short read sequencing approaches to evaluate the community using a shotgun metagenomics approach. Long read sequencing was applied to samples from the stomach/duodenum, and the colorectal region, revealing a fairly uniform and low complexity community made up primarily of proteobacteria at the top of the gut and much more diversity in the colon. We used deep short read sequencing to further interrogate this colorectal community. The two sequencing approaches were concordant with respect to community structure but substantially more detail was available in the short read data, in spite of high levels of host DNA contamination. Using both approaches we were able to show that the colorectal community is a potential reservoir for antibiotic resistance, human pathogens such as Clostridiodes difficile and a possible source of novel antimicrobials or other useful secondary metabolites.

Defibrillate You Later, Alligator: Q10 Scaling and Refractoriness Keeps Alligators from Fibrillation.

Effective cardiac contraction during each heartbeat relies on the coordination of an electrical wave of excitation propagating across the heart. Dynamically induced heterogeneous wave propagation may fracture and initiate reentry-based cardiac arrhythmias, during which fast-rotating electrical waves lead to repeated self-excitation that compromises cardiac function and potentially results in sudden cardiac death. Species which function effectively over a large range of heart temperatures must balance the many interacting, temperature-sensitive biochemical processes to maintain normal wave propagation at all temperatures. To investigate how these species avoid dangerous states across temperatures, we optically mapped the electrical activity across the surfaces of alligator (Alligator mississippiensis) hearts at 23°C and 38°C over a range of physiological heart rates and compare them with that of rabbits (Oryctolagus cuniculus). We find that unlike rabbits, alligators show minimal changes in wave parameters (action potential duration and conduction velocity) which complement each other to retain similar electrophysiological wavelengths across temperatures and pacing frequencies. The cardiac electrophysiology of rabbits accommodates the high heart rates necessary to sustain an active and endothermic metabolism at the cost of increased risk of cardiac arrhythmia and critical vulnerability to temperature changes, whereas that of alligators allows for effective function over a range of heart temperatures without risk of cardiac electrical arrhythmias such as fibrillation, but is restricted to low heart rates. Synopsis La contracción cardíaca efectiva durante cada latido del corazón depende de la coordinación de una onda eléctrica de excitación que se propaga a través del corazón. Heterogéidades inducidas dinámicamente por ondas de propagación pueden resultar en fracturas de las ondas e iniciar arritmias cardíacas basadas en ondas de reingreso, durante las cuales ondas espirales eléctricas de rotación rápida producen una autoexcitación repetida que afecta la función cardíaca y pude resultar en muerte súbita cardíaca. Las especies que funcionan eficazmente en una amplia gama de temperaturas cardíacas deben equilibrar los varios procesos bioquímicos que interactúan, sensibles a la temperatura para mantener la propagación normal de ondas a todas las temperaturas. Para investigar cómo estas especies evitan los estados peligrosos a través de las temperaturas, mapeamos ópticamente la actividad eléctrica a través de las superficies de los corazones de caimanes (Alligator mississippiensis) a 23°C and 38°C sobre un rango de frecuencias fisiológicas del corazón y comparamos con el de los conejos (Oryctolagus cuniculus). Encontramos que a diferencia de los conejos, los caimanes muestran cambios mínimos en los parámetros de onda (duración potencial de acción y velocidad de conducción) que se complementan entre sí para retener longitudes de onda electrofisiológicas similares a través de los rangos de temperaturas y frecuencias de ritmo. La electrofisiología cardíaca de los conejos acomoda las altas frecuencias cardíacas necesarias para mantener un metabolismo activo y endotérmico a costa de un mayor riesgo de arritmia cardíaca y vulnerabilidad crítica a los cambios de temperatura, mientras que la de los caimanes permite un funcionamiento eficaz en una serie de temperaturas cardíacas sin riesgo de arritmias eléctricas cardíacas como la fibrilación, pero está restringida a bajas frecuencias cardíacas.

Regulation of myosin heavy chain antisense long noncoding RNA in human vastus lateralis in response to exercise training.

Alterations to muscle activity or loading state can induce changes in expression of myosin heavy chain (MHC). For example, sedentary individuals that initiate exercise training can induce a pronounced shift from IIx to IIa MHC. We sought to examine the regulatory response of MHC RNA in human subjects in response to exercise training. In particular, we examined how natural antisense RNA transcripts (NATs) are regulated throughout the MHC gene locus that includes MYH2 (IIa), MYH1 (IIx), MYH4 (IIb), and MYH8 (Neonatal) in vastus lateralis before and after a 5-wk training regime that consisted of a combination of aerobic and resistance types of exercise. The exercise program induced a IIx to IIa MHC shift that was associated with a corresponding increase in transcription on the antisense strand of the IIx MHC gene and a decrease in antisense transcription of the IIa MHC gene, suggesting an inhibitory mechanism mediated by NATs. We also report that the absence of expression of IIb MHC in human limb muscle is associated with the abundant expression of antisense transcript overlapping the IIb MHC coding gene, which is the opposite expression pattern as compared with that previously observed in rats. The NAT provides a possible regulatory mechanism for the suppressed expression of IIb MHC in humans. These data indicate that NATs may play a regulatory role with regard to the coordinated shifts in MHC gene expression that occur in human muscle in response to exercise training.

Exercise Responses to Gravity-Independent Flywheel Aerobic and Resistance Training.

BACKGROUND: Although several exercise systems have been developed to mitigate the physiological deconditioning that occurs in microgravity, few have the capacity to positively impact multiple physiological systems and still meet the volume/mass requirements needed for missions beyond low Earth orbit. The purpose of this study was to test the gravity-independent Multi-Mode Exercise Device (M-MED) for both resistance (RE) and aerobic (AE) training stimuli. METHODS: Eight men and nine women (mean age 22.0 ± 0.4 yr) completed 5 wk of training on the M-MED: RE 4 × 7 squats 2 d/wk, and AE 4 × 4-min rowing bouts at ∼90% Vo2max 3 d/wk. Pre- and post-training data collection included an aerobic capacity test, MR imaging, strength testing, and vastus lateralis muscle biopsy. RESULTS: Vo2max increased 8%, 3RM strength 18%, and quadriceps femoris cross-sectional area (CSA) 10%. Knee extensor strength increased at all isokinetic speeds tested. Subjects also demonstrated improved fatigue resistance in knee extension. At the cellular and molecular level, the biopsy revealed increases in mixed myofiber CSA (13%), citrate synthase activity (26%), total RNA concentration (24%), IGF-I mRNA (77%), and Type IIa myosin heavy chain (MHC) mRNA (8%), and a concomitant decrease in Type IIx MHC mRNA (-23%). None of the changes were gender-specific. DISCUSSION: Both the functional outcomes and biomarker changes indicate that a very low volume of M-MED exercise results in robust adaptation in the cardiovascular and musculoskeletal systems. The M-MED has the potential to provide a wide range of countermeasure exercises and should be considered for testing in ground-based spaceflight simulation.

The accessory role of the diaphragmaticus muscle in lung ventilation in the estuarine crocodile Crocodylus porosus.

Crocodilians use a combination of three muscular mechanisms to effect lung ventilation: the intercostal muscles producing thoracic movement, the abdominal muscles producing pelvic rotation and gastralial translation, and the diaphragmaticus muscle producing visceral displacement. Earlier studies suggested that the diaphragmaticus is a primary muscle of inspiration in crocodilians, but direct measurements of the diaphragmatic contribution to lung ventilation and gas exchange have not been made to date. In this study, ventilation, metabolic rate and arterial blood gases were measured from juvenile estuarine crocodiles under three conditions: (i) while resting at 30°C and 20°C; (ii) while breathing hypercapnic gases; and (iii) during immediate recovery from treadmill exercise. The relative contribution of the diaphragmaticus was then determined by obtaining measurements before and after transection of the muscle. The diaphragmaticus was found to make only a limited contribution to lung ventilation while crocodiles were resting at 30°C and 20°C, and during increased respiratory drive induced by hypercapnic gas. However, the diaphragmaticus muscle was found to play a significant role in facilitating a higher rate of inspiratory airflow in response to exercise. Transection of the diaphragmaticus decreased the exercise-induced increase in the rate of inspiration (with no compensatory increases in the duration of inspiration), thus compromising the exercise-induced increases in tidal volume and minute ventilation. These results suggest that, in C. porosus, costal ventilation alone is able to support metabolic demands at rest, and the diaphragmaticus is largely an accessory muscle used at times of elevated metabolic demand.

Masticatory motor pattern in the koala (Phascolarctos cinereus): a comparison of jaw movements in marsupial and placental herbivores.

Do closely related marsupial herbivores (Diprotodontia) conserve a common masticatory motor pattern or are motor patterns linked to the structure and function of the masticatory apparatus? We recorded the sequence and duration of activity of the individual jaw closing muscles during rhythmic chewing in koalas and then compared their motor pattern with that of their closest extant relatives, wombats, and their more distant marsupial relatives, macropodoids. These three lineages prove to have fundamentally different motor patterns and jaw movements during mastication. Each motor pattern represents independent modifications of an earlier motor pattern that was probably present in an ancestral diprotodontian. We show that koalas evolved a motor program that is in many aspects similar to that of placental herbivores with a fused mandibular symphysis (artiodactyls, perissodactyls, and higher primates) and almost identical to one artiodactyl, viz. alpacas. Anatomically, koalas are convergent on placental herbivores because they lost the inflected mandibular angle and large external part of the medial pterygoid muscle characteristic of other marsupials. We support the view that many different motor programs evolved for the control of transverse jaw movements, but identical motor programs for the control of transverse jaw movements can evolve independently in distantly related taxa.

Turning crocodilian hearts into bird hearts: growth rates are similar for alligators with and without right-to-left cardiac shunt.

The functional and possible adaptive significance of non-avian reptiles' dual aortic arch system and the ability of all non-avian reptiles to perform central vascular cardiac shunts have been of great interest to comparative physiologists. The unique cardiac anatomy of crocodilians - a four-chambered heart with the dual aortic arch system - allows for only right-to-left (R-L; pulmonary bypass) cardiac shunt and for surgical elimination of this shunt. Surgical removal of the R-L shunt, by occluding the left aorta (LAo) upstream and downstream of the foramen of Panizza, results in a crocodilian with an obligatory, avian/mammalian central circulation. In this study, R-L cardiac shunt was eliminated in age-matched, female American alligators (Alligator mississippiensis; 5-7 months of age). We tested the hypothesis that surgical elimination of R-L cardiac shunt would impair growth (a readily measured proxy for fitness) compared with sham-operated, age-matched controls, especially in animals subjected to exhaustive exercise. While regular exercise caused a decrease in size (snout-to-vent length, head length and body mass), elimination of the capacity for R-L cardiac shunt did not greatly reduce animal growth, despite a chronic ventricular enlargement in surgically altered juvenile alligators. We speculate that, despite being slightly smaller, alligators with an occluded LAo would have reached sexual maturity in the same breeding season as control alligators. This study suggests that crocodilian R-L cardiac shunt does not provide an adaptive advantage for juvenile alligator growth and supports the logic that cardiac shunts persist in crocodilians because they have not been selected against.

Surgical removal of right-to-left cardiac shunt in the American alligator (Alligator mississippiensis) causes ventricular enlargement but does not alter apnoea or metabolism during diving.

Crocodilians have complete anatomical separation between the ventricles, similar to birds and mammals, but retain the dual aortic arch system found in all non-avian reptiles. This cardiac anatomy allows surgical modification that prevents right-to-left (R-L) cardiac shunt. A R-L shunt is a bypass of the pulmonary circulation and recirculation of oxygen-poor blood back to the systemic circulation and has often been observed during the frequent apnoeic periods of non-avian reptiles, particularly during diving in aquatic species. We eliminated R-L shunt in American alligators (Alligator mississippiensis) by surgically occluding the left aorta (LAo; arising from right ventricle) upstream and downstream of the foramen of Panizza (FoP), and we tested the hypotheses that this removal of R-L shunt would cause afterload-induced cardiac remodelling and adversely affect diving performance. Occlusion of the LAo both upstream and downstream of the FoP for approximately 21 months caused a doubling of RV pressure and significant ventricular enlargement (average approximately 65%) compared with age-matched, sham-operated animals. In a separate group of recovered, surgically altered alligators allowed to dive freely in a dive chamber at 23 degrees C, occlusion of the LAo did not alter oxygen consumption or voluntary apnoeic periods relative to sham animals. While surgical removal of R-L shunt causes considerable changes in cardiac morphology similar to aortic banding in mammals, its removal does not affect the respiratory pattern or metabolism of alligators. It appears probable that the low metabolic rate of reptiles, rather than pulmonary circulatory bypass, allows for normal aerobic dives.

Phylogeny of the telencephalic subventricular zone in sauropsids: evidence for the sequential evolution of pallial and subpallial subventricular zones.

The telencephalon of birds and placental mammals harbors a proliferative subventricular zone (SVZ) in the subpallium as well as the pallium. Turtles, which are phylogenetically intermediate between bird, and mammals, exhibit at best a rudimentary SVZ. This suggests that SVZs evolved independently in mammals and birds, but it is not clear whether subpallial and pallial SVZs evolved with the origin of birds or in some earlier, non-avian sauropsid ancestor. To answer this question, we examined the brains of embryonic alligators (Ferguson stages 15-22) because crocodilians are the closest extant sister group to birds. To visualize the SVZ we labeled mitotic cells with antibodies against phosphorylated histone-3 (pH3) and proliferating cells with antibodies against proliferating cell nuclear antigen (PCNA). We found that the telencephalon of alligators contains an SVZ only in the subpallium. Because turtles, lizards and amphibians seem to lack SVZs, our finding suggests that a subpallial SVZ evolved in the last common ancestor of birds and crocodilians. Given that placental mammals and birds, but not marsupial mammals or reptiles, possess an SVZ within their pallium, we conclude that a pallial SVZ probably evolved independently in birds and placental mammals.

Exhaustive exercise training enhances aerobic capacity in American alligator (Alligator mississippiensis).

The oxygen transport system in mammals is extensively remodelled in response to repeated bouts of activity, but many reptiles appear to be 'metabolically inflexible' in response to exercise training. A recent report showed that estuarine crocodiles (Crocodylus porosus) increase their maximum metabolic rate in response to exhaustive treadmill training, and in the present study, we confirm this response in another crocodilian, American alligator (Alligator mississippiensis). We further specify the nature of the crocodilian training response by analysing effects of training on aerobic [citrate synthase (CS)] and anaerobic [lactate dehydrogenase (LDH)] enzyme activities in selected skeletal muscles, ventricular and skeletal muscle masses and haematocrit. Compared to sedentary control animals, alligators regularly trained for 15 months on a treadmill (run group) or in a flume (swim group) exhibited peak oxygen consumption rates higher by 27 and 16%, respectively. Run and swim exercise training significantly increased ventricular mass (~11%) and haematocrit (~11%), but not the mass of skeletal muscles. However, exercise training did not alter CS or LDH activities of skeletal muscles. Similar to mammals, alligators respond to exercise training by increasing convective oxygen transport mechanisms, specifically heart size (potentially greater stroke volume) and haematocrit (increased oxygen carrying-capacity of the blood). Unlike mammals, but similar to squamate reptiles, alligators do not also increase citrate synthase activity of the skeletal muscles in response to exercise.

Atmospheric oxygen level affects growth trajectory, cardiopulmonary allometry and metabolic rate in the American alligator (Alligator mississippiensis).

Recent palaeoatmospheric models suggest large-scale fluctuations in ambient oxygen level over the past 550 million years. To better understand how global hypoxia and hyperoxia might have affected the growth and physiology of contemporary vertebrates, we incubated eggs and raised hatchlings of the American alligator. Crocodilians are one of few vertebrate taxa that survived these global changes with distinctly conservative morphology. We maintained animals at 30 degrees C under chronic hypoxia (12% O(2)), normoxia (21% O(2)) or hyperoxia (30% O(2)). At hatching, hypoxic animals were significantly smaller than their normoxic and hyperoxic siblings. Over the course of 3 months, post-hatching growth was fastest under hyperoxia and slowest under hypoxia. Hypoxia, but not hyperoxia, caused distinct scaling of major visceral organs-reduction of liver mass, enlargement of the heart and accelerated growth of lungs. When absorptive and post-absorptive metabolic rates were measured in juvenile alligators, the increase in oxygen consumption rate due to digestion/absorption of food was greatest in hyperoxic alligators and smallest in hypoxic ones. Hyperoxic alligators exhibited the lowest breathing rate and highest oxygen consumption per breath. We suggest that, despite compensatory cardiopulmonary remodelling, growth of hypoxic alligators is constrained by low atmospheric oxygen supply, which may limit their food utilisation capacity. Conversely, the combination of elevated metabolism and low cost of breathing in hyperoxic alligators allows for a greater proportion of metabolised energy to be available for growth. This suggests that growth and metabolic patterns of extinct vertebrates would have been significantly affected by changes in the atmospheric oxygen level.

Impact of rhythmic oral activity on the timing of muscle activation in the swallow of the decerebrate pig.

The pharyngeal swallow can be elicited as an isolated event but, in normal animals, it occurs within the context of rhythmic tongue and jaw movement (RTJM). The response includes activation of the multifunctional geniohyoid muscle, which can either protract the hyoid or assist jaw opening; in conscious nonprimate mammals, two bursts of geniohyoid EMG activity (GHemg) occur in swallow cycles at times consistent with these two actions. However, during experimentally elicited pharyngeal swallows, GHemg classically occurs at the same time as hyoglossus and mylohyoid activity (short latency response) but, when the swallow is elicited in the decerebrate in the absence of RTJM, GHemg occurs later in the swallow (long latency response). We tested the hypothesis that it was not influences from higher centers but a brain stem mechanism, associated with RTJM, which caused GHemg to occur earlier in the swallow. In 38 decerebrate piglets, RTJM occurred sporadically in seven animals. Before RTJM, GHemg had a long latency, but, during RTJM, swallow related GHemg occurred synchronously with activity in hyoglossus and mylohyoid, early in the swallow. Both early and late responses were present during the changeover period. During this changeover period, duplicate electrodes in the geniohyoid could individually detect either the early or the late burst in the same swallow. This suggested that two sets of geniohyoid task units existed that were potentially active in the swallow and that they were differentially facilitated or inhibited depending on the presence or absence of rhythmic activity originating in the brain stem.

Exercise training enhances aerobic capacity in juvenile estuarine crocodiles (Crocodylus porosus).

Aerobic capacity (VO2max) of endothermic vertebrates is known to increase with exercise training, but this effect has not been found to-date in non-avian reptiles. We exercised juvenile estuarine crocodiles (Crocodylus porosus) to walk at 0.75-0.88 km/h on a treadmill for up to 20 min a day over 16 weeks, and compared their aerobic performance with that of unexercised crocodiles. In the exercised group, VO2max increased from 6.9 to 8.5 mLO2/kg/min (+28%), and locomotor endurance increased from 3.8 to 6.9 min (+82%). Neither VO2max nor endurance changed significantly in the sedentary group. This finding extends the exercise training effect onto another vertebrate clade, and demonstrates that ectothermic amniotes are capable of elevating their aerobic capacity in response to exercise training. We propose that differences in cardiopulmonary structure and function in non-avian reptiles may be responsible for the absence (in squamates) or presence (in crocodilians) of a strong training effect on aerobic capacity.

Function of intracoelomic septa in lung ventilation of amniotes: lessons from lizards.

Aspiration breathing is the dominant mechanism of lung inflation among extant amniotes. However, aspiration has two fundamental problems associated with it: paradoxical visceral translation and partial lung collapse. These can constrain the inspiratory tidal volume, reduce the effective lung ventilation, and ultimately curtail the aerobic capacity of an animal. Separation of the pleural and peritoneal cavities by an intracoelomic septum can restrict the cranial shift of abdominal viscera and provide structural support to the caudal lung surface. A muscular septum, such as the diaphragm of mammals or the diaphragmaticus of crocodilians, can exert active control over visceral translation and the degree of lung inflation. To a lesser degree, a nonmuscular septum can also function as a passive barrier when stretched taut by rib rotation. Studies of the posthepatic septum in teiid lizards and the postpulmonary septum in varanid lizards underscore the importance of nonmuscular septa in aspiration. These septa provide plausible functional models that help us infer the evolution of mammalian and avian lung ventilatory systems, respectively.

Functional morphology and evolution of aspiration breathing in tetrapods.

In the evolution of aspiration breathing, the responsibility for lung ventilation gradually shifted from the hyobranchial to the axial musculoskeletal system, with axial muscles taking over exhalation first, at the base of Tetrapoda, and then inhalation as well at the base of Amniota. This shift from hyobranchial to axial breathing freed the tongue and head to adapt to more diverse feeding styles, but generated a mechanical conflict between costal ventilation and high-speed locomotion. Some "lizards" (non-serpentine squamates) have been shown to circumvent this speed-dependent axial constraint with accessory gular pumping during locomotion, and here we present a new survey of gular pumping behavior in the tuatara and 40 lizard species. We observed gular pumping behavior in 32 of the 40 lizards and in the tuatara, indicating that the ability to inflate the lungs by gular pumping is a shared-derived character for Lepidosauria. Gular pump breathing in lepidosaurs may be homologous with buccal pumping in amphibians, but non-ventilatory buccal oscillation and gular flutter have persisted throughout amniote evolution and gular pumping may have evolved independently by modification of buccal oscillation. In addition to gular pumping in some lizards, three other innovations have evolved repeatedly in the major amniote clades to circumvent the speed-dependent axial constraint: accessory inspiratory muscles (mammals, crocodylians and turtles), changing locomotor posture (mammals and birds) and respiratory-locomotor phase coupling to reduce the mechanical conflict between aspiration breathing and locomotion (mammals and birds).

Volume and rate of milk delivery as determinants of swallowing in an infant model animal (Sus scrofia).

The volume transported into the valleculae by the rhythmic tongue movements of suckling is considered the prime factor for initiating pharyngeal swallowing (the movement of milk out of the valleculae and through the pharynx to the esophagus). This study addressed the impact of variation in two factors on sucking (oral phase) and on swallowing (pharyngeal phase) in infant pigs, as a model for mammalian function: (1) the delivery of different-volume aliquots of milk and (2) the delivery of equal-sized aliquots at different frequencies. The number of sucks per second remained constant with change in both aliquot volume and change in the frequency of milk delivery. However, while the number of swallows per second remained constant as delivery volume increased, it increased as delivery frequency increased. Conversely, swallow volume increased with both increase in aliquot volume and in the frequency of delivery. Piglets consequently initiated pharyngeal swallows with a highly variable amount of milk in the valleculae. We conclude that volume is only one factor initiating the pharyngeal swallow. The sensory stimulation of milk delivery to the anterior oral cavity is also a factor in determining the frequency of swallows and the volume of milk per swallow.