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Biomedical subjects

Xiang Ji

Publications and source records attributed to Xiang Ji.

At least 19 recordsLinked to original sources

TreeFlow: Probabilistic Modelling and Automatic Differentiation for Phylogenetics.

Probabilistic modelling frameworks are powerful tools for statistical modelling and inference. They are not immediately generalizable to phylogenetic problems due to the particular computational properties of the phylogenetic tree object. TreeFlow is a software library for probabilistic modelling and automatic differentiation with phylogenetic trees. It embeds phylogenetic trees in the TensorFlow Probability framework, and implements inference algorithms for phylogenetic models given a fixed tree topology. We demonstrate how TreeFlow can be used to quickly implement and assess new models. We also show that it provides reasonable performance for gradient-based inference algorithms compared to specialized computational libraries for phylogenetics.

Bayesian inference↗

Parallel algorithms for phylogenetic inference under a structured coalescent approximation.

While advances in molecular epidemiology and computational modeling have enhanced our capacity to track pathogen evolution, the accurate reconstruction of spatiotemporal transmission dynamics remains essential for developing epidemic preparedness frameworks and implementing outbreak response measures. Structured coalescent models offer a phylogeographic framework by restricting lineage coalescence events to geographically proximate host populations. Although the Bayesian structured coalescent approximation (BASTA) provides a tractable approach, contemporary phylogeographic analyses involving dozens of geographic localities and hundreds to thousands of viral genomes substantially exceed the computational capacity of existing implementations. The BASTA likelihood scales cubically with deme count and quadratically with sequence count due to matrix exponentiation and pairwise coalescent probability calculations. Here, we introduce a comprehensive algorithmic restructuring of the structured coalescent likelihood that eliminates redundancies, optimizes memory access, and exposes parallelization opportunities. Our approach reorganizes computations along three dimensions: (i) independent calculation of deme-transition probability matrices across time intervals; (ii) simultaneous evaluation of partial likelihood vectors within temporal slices; and (iii) concurrent aggregation of coalescent probabilities. Algorithmic restructuring cuts average coalescent likelihood computation by 7-8 fold, and parallelization further boosts performance to 10-26 fold, enabling joint phylogeographic analyses of dengue virus across 10 South American countries and H5N1 avian influenza across 20 Eurasian regions to finish in a fraction of prior time. This computational efficiency also enables comparison between backward-in-time structured coalescent approximations and forward-in-time phylogeographic methods, revealing that the former provides appropriately conservative posterior estimates, particularly at intermediate phylogenetic depths. We integrate our implementation into the popular BEAST X and BEAGLE software packages, with an accompanying interface in BEAUti X to easily set up the analyses, providing researchers with an accessible and scalable tool for real-time phylogeographic surveillance of rapidly evolving pathogens.

Journal Article↗

Sexual dimorphism, female reproduction and egg incubation in the oriental leaf-toed gecko (Hemidactylus bowringii) from southern China.

We studied sexual dimorphism, female reproduction and egg incubation of the oriental leaf-toed gecko (Hemidactylus bowringii) from a population in southern China. The largest male and female in our sample were 60 and 57 mm snout-vent length (SVL), respectively. Males are the larger sex; sexual dimorphism in head size and tail length (TL) is evident in juveniles and adults, with males having larger heads as well as longer tails than females. Oviposition occurred between late May and late July. Females switched from laying two eggs early in the breeding season to 1-2 eggs later in the season. Clutch mass and egg mass were both independent of female SVL, whereas relative clutch mass was negatively correlated with female SVL. The previous conclusion that female H. bowringii lay a single clutch of eggs per breeding season is unlikely to be true. Thermal environments experienced by H. bowringii eggs affect incubation length as well as morphological and locomotor phenotypes of hatchlings. Hatchlings from eggs incubated at 30 degrees C were larger (SVL, tail length and body mass) and performed better in the racetrack than their counterparts from eggs incubated at 24 degrees C. Temperatures suitable for embryonic development are relatively high in H. bowringii, primarily as a consequence of the adaptive response to warm environments in southern China.

Animals↗

Experimentally reducing clutch size reveals a fixed upper limit to egg size in snakes, evidence from the king ratsnake, Elaphe carinata.

Snakes are free of the pelvic girdle's constraint on maximum offspring size, and therefore present an opportunity to investigate the upper limit to offspring size without the limit imposed by the pelvic girdle dimension. We used the king ratsnake (Elaphe carinata) as a model animal to examine whether follicle ablation may result in enlargement of egg size in snakes and, if so, whether there is a fixed upper limit to egg size. Females with small sized yolking follicles were assigned to three manipulated, one sham-manipulated and one control treatments in mid-May, and two, four or six yolking follicles in the manipulated females were then ablated. Females undergoing follicle ablation produced fewer, but larger as well as more elongated, eggs than control females primarily by increasing egg length. This finding suggests that follicle ablation may result in enlargement of egg size in E. carinata. Mean values for egg width remained almost unchanged across the five treatments, suggesting that egg width is more likely to be shaped by the morphological feature of the oviduct. Clutch mass dropped dramatically in four- and six-follicle ablated females. The function describing the relationship between size and number of eggs reveals that egg size increases with decreasing clutch size at an ever-decreasing rate, with the tangent slope of the function for the six-follicle ablation treatment being -0.04. According to the function describing instantaneous variation in tangent slope, the maximum value of tangent slope should converge towards zero. This result provides evidence that there is a fixed upper limit to egg size in E. carinata.

Animals↗

Does follicle excision always result in enlargement of offspring size in lizards?

An experimental reduction of offspring number has been reported to result in enlargement of offspring size in lizards. We applied the "follicle excision" technique to a lacertid lizard (Takydromus septentrionalis) to examine whether this effect is generalisable to lizards. Of the 82 females that produced 3 successive clutches in the laboratory, 23 females underwent follicle excision after they oviposited the first clutch. Follicle excision reduced clutch size, but did not alter egg size. This result indicates that egg size is not altered during vitellogenesis in T. septentrionalis. Females undergoing follicle excision produced a third clutch (a second post-surgical clutch) as normally as did control females. Females switched from producing more but smaller eggs early in the breeding season to fewer but larger eggs later in the season. Our results indicate that female T. septentrionalis maximize reproductive success by diverting an optimal, rather than a higher, fraction of the available energy to individual offspring. This optimized allocation of the available energy to offspring production explains why follicle excision does not result in enlargement of egg size in this species. Our study provides evidence that an experimental reduction of offspring number does not always result in enlargement of offspring size in lizards.

Animals↗

Energetic and locomotor costs of tail loss in the Chinese skink, Eumeces chinensis.

Caudal autotomy is a defense mechanism used by numerous lizards to evade predators, but this entails costs. We collected 294 adult Chinese skinks (Eumeces chinensis) from a population in Lishui (eastern China) to evaluate energetic and locomotor costs of tail loss. Of the 294 skinks, 214 (c. 73%) had previously experienced caudal autotomy. Neither the proportion of individuals with regenerated tails nor the frequency distribution of locations of the tail break differed between sexes. We successively removed four tail segments from each of the 20 experimental skinks (adult males) initially having intact tails. Lipid content in each removed tail segment was measured, and locomotor performance (sprint speed, the maximal length traveled without stopping and the number of stops in the racetrack) was measured for each skink before and after each tail-removing treatment. Another independent sample of 20 adult males with intact tails was measured for locomotor performance to serve as controls for successive measurements taken for the experimental lizards. Caudal lipids were disproportionately stored along the length of the tail, with most lipids being aggregated in its proximal portion. Tail loss significantly affected sprint speed, but not the maximal length of, or the number of stops during the sprint. However, the adverse influence of tail loss on sprint speed was not significant until more than 51% of the tail (in length) was lost. Our data show that partial tail loss due to predatory encounters or other factors may not severely affect energy stores or locomotor performance in E. chinensis. As tail breaks occurred more frequently in the proximal portion of the tail in skinks collected from the field, we conclude that caudal autotomy occurring in nature often incurs substantial energetic and locomotor costs in E. chinensis.

Animals↗

Effects of constant and fluctuating temperatures on egg survival and hatchling traits in the northern grass lizard (Takydromus septentrionalis, Lacertidae).

To understand how nest temperatures influence phenotypic traits of reptilian hatchlings, the effects of fluctuating temperature on hatchling traits must be known. Most investigations, however, have only considered the effects of constant temperatures. We incubated eggs of Takydromus septentrionalis (Lacertidae) at constant (24 degrees C, 27 degrees C, 30 degrees C and 33 degrees C) and fluctuating temperatures to determine the effects of these thermal regimes on incubation duration, hatching success and hatchling traits (morphology and locomotor performance). Hatching success at 24 degrees C and 27 degrees C was higher, and hatchlings derived from these two temperatures were larger and performed better than their counterparts from 30 degrees C and 33 degrees C. Eggs incubated at fluctuating temperatures exhibited surprisingly high hatching success and also produced large and well-performed hatchlings in spite of the extremely wide range of temperatures (11.6-36.2 degrees C) they experienced. This means that exposure of eggs to adversely low or high temperatures for short periods does not increase embryonic mortality. The variance of fluctuating temperatures affected hatchling morphology and locomotor performance more evidently than did the mean of the temperatures in this case. The head size and sprint speed of the hatchlings increased with increasing variances of fluctuating temperatures. These results suggest that thermal variances significantly affect embryonic development and phenotypic traits of hatchling reptiles and are therefore ecologically meaningful.

Adaptation, Physiological↗

Ontogenetic shifts in thermal tolerance, selected body temperature and thermal dependence of food assimilation and locomotor performance in a lacertid lizard, Eremias brenchleyi.

We used Eremias brenchleyi as a model animal to examine differences in thermal tolerance, selected body temperature, and the thermal dependence of food assimilation and locomotor performance between juvenile and adult lizards. Adults selected higher body temperatures (33.5 vs. 31.7 degrees C) and were able to tolerate a wider range of body temperatures (3.4-43.6 vs. 5.1-40.8 degrees C) than juveniles. Within the body temperature range of 26-38 degrees C, adults overall ate more than juveniles, and food passage rate was faster in adults than juveniles. Apparent digestive coefficient (ADC) and assimilation efficiency (AE) varied among temperature treatments but no clear temperature associated patterns could be discerned for these two variables. At each test temperature ADC and AE were both higher in adults than in juveniles. Sprint speed increased with increase in body temperature at lower body temperatures, but decreased at higher body temperatures. At each test temperature adults ran faster than did juveniles, and the range of body temperatures where lizards maintained 90% of maximum speed differed between adults (27-34 degrees C) and juveniles (29-37 degrees C). Optimal temperatures and thermal sensitivities differed between food assimilation and sprint speed. Our results not only show strong patterns of ontogenetic variation in thermal tolerance, selected body temperature and thermal dependence of food assimilation and locomotor performance in E. brenchleyi, but also add support for the multiple optima hypothesis for the thermal dependence of behavioral and physiological variables in reptiles.

Adaptation, Physiological↗

Partial tail loss has no severe effects on energy stores and locomotor performance in a lacertid lizard, Takydromus septentrionalis.

Many species of lizards use caudal autotomy as a defense strategy to avoid predation, but tail loss entails costs. These topics were studied experimentally in the northern grass lizard, Takydromus septentrionalis. We measured lipids in the three-tail segments removed from each of the 20 experimental lizards (adult females) initially having intact tails to evaluate the effect of tail loss on energy stores; we obtained data on locomotor performance (sprint speed, the maximal length traveled without stopping and the number of stops in the racetrack) for these lizards before and after the tail-removing treatments to evaluate the effect of tail loss on locomotor performance. An independent sample of 20 adult females that retained intact tails was measured for locomotor performance to serve as controls for successive measurements taken for the experimental lizards. The lipids stored in the removed tail was positively correlated with tailbase width when holding the tail length constant, indicating that thicker tails contained more lipids than did thinner tails of the same overall length. Most of the lipids stored in the tail were concentrated in the proximal portion of the tail. Locomotor performance was almost unaffected by tail loss until at least more than 71% of the tail (in length) was lost. Our data show that partial tail loss due to predatory encounters or other factors may not severely affect energy stores and locomotor performance in T. septentrionalis.

Animals↗

Does body volume constrain reproductive output in lizards?

The numbers and sizes of eggs produced by adult females ultimately determine the viability of populations, as well as the evolutionary fitness of the females themselves. Despite an enormous amount of literature on the adaptive significance of fecundity variation within and among populations, simpler questions--such as the proximate mechanisms by which a female determines her clutch size--have attracted less attention. Our surgical manipulations show that the amount of space available to hold eggs within a female's abdomen influences her total reproductive allocation, enabling her to flexibly modify her reproductive output as she grows larger.

Animals↗

Influence of food type on specific dynamic action of the Chinese skink Eumeces chinensis.

We used the Chinese skink (Eumeces chinensis) as an experimental model to study influence of food type on specific dynamic action (SDA) of feeding. Thirty-three adult males collected from a natural population were divided equally into three (one control and two experimental) groups. We starved all skinks at 30 degrees C for 3 days and then provided the experimental skinks with a single meal consisting of either mealworms or meat [the flesh of the bullfrog (Rana catesbeiana)]. Food ingested by skinks of the two experimental groups differed in lipid content and lean dry mass but not in total dry mass and energy. Defecation following feeding occurred slightly earlier in skinks ingesting mealworms (mean=41.7 h) than in those ingesting meat (mean=47.7 h), but the difference was not significant. Analyses of variance (ANOVAs) with repeated measures showed that temporal variation in oxygen consumption over 72 h after feeding was evident in the experimental skinks but not in the control ones. Oxygen consumption was higher in the experimental skinks than in the control ones during the time interval between 4.5 and 36 h after feeding. The peak metabolic rate was greater but occurred later in skinks ingesting meat than in those ingesting mealworms. The estimated amounts of oxygen consumed by mealworm-fed, meat-fed and unfed skinks at 30 degrees C over 72 h after feeding were 356.5, 393.8 and 295.2 mL, respectively. Our results provide a support for the previous prediction that SDA is affected by types of food ingested by animals as skinks ingesting mealworms and meat differed in the time to reach a peak metabolic rate, the level of the peak metabolic rate and the magnitude of the SDA effect.

Animal Feed↗

Metabolic response to feeding in the Chinese striped-necked turtle, Ocadia sinensis.

We measured oxygen consumption in juvenile Chinese striped-necked turtles (Ocadia sinensis) after they ingested food, either as a single meal or as double meals, to examine the influence of meal type and feeding frequency on specific dynamic action (SDA). Temporal variation in oxygen consumption after feeding was evident in the ingesting turtles but not in the unfed control turtles. In the single-meal experiment, the peak metabolic rate and the integrated SDA response (the whole energetic cost for the processes of digestion) both did not differ between turtles ingesting mealworms and shrimps when the influence of variation in ingested energy was removed, and the time to reach peak metabolic rate was not affected by meal type and the amount of food ingested. Turtles in the double-meal experiment ingested more energy and hence had a prolonged duration of SDA response than did those in the single-meal experiment, but the integrated SDA response did not differ between both experimental treatments when the influence of variation in ingested energy was removed. Our results show that meal type and feeding frequency have important consequences on the SDA response of juvenile O. sinensis. As the integrated SDA response remained remarkably constant either between turtles ingesting different food or between turtles ingesting the same food but at different frequencies when the influence of variation in ingested energy was removed, we therefore conclude that the energetic cost associated with ingestion is primarily determined by energy content of food ingested in juvenile O. sinensis.

Animal Nutritional Physiological Phenomena↗

Nuclear matrices and matrix attachment regions from Green alga: Dunaliella salina.

Nuclear DNA of eukaryotic organism attaches to the proteinaceous nuclear matrices via specific matrix attachment regions (MARs). In order to investigate the interactions between chromosomal DNA and nuclear matrices,we isolated the MARs from unicellular alga Dunaliella salina. As the first step,a random MAR library was set up and then the binding affinity of the selected clones to nuclear matrices was tested in this study. Three DNA fragments were found to bind specifically to the nuclear matrices in vitro,of which two were strong binders and all contained known consensus motifs and a hairpin loop structure of MAR.

Base Sequence↗

Propyl paraben inhibits voltage-dependent sodium channels and protects cardiomyocytes from ischemia-reperfusion injury.

The effects of propyl paraben, an antimicrobial preservative, on voltage-dependent sodium current and myocardial ischemia-reperfusion injury were investigated in isolated adult rat cardiomyocytes. Whole cell voltage-clamp recording showed that propyl paraben reversibly blocked the voltage-gated sodium channel both in concentration- and voltage-dependent manners. Propyl paraben (500 microM but not 100 microM) significantly shifted the steady-state inactivation of the sodium channel toward the hyperpolarizing direction at the V(1/2) point. Consistent with the above result, the propidium iodide (PI) uptake test revealed that pretreatment with 500 microM but not 100 microM of propyl paraben significantly reduced cell death induced by 45 min of sustained ischemia followed by 15 h of reperfusion (42.37 +/- 7.01% of cell viability in control and 71.05 +/- 7.06% in the propyl paraben group), suggesting that propyl paraben can protect myocytes from ischemia-reperfusion injury. These results indicate a possible correlation between the inhibition of sodium current and cardioprotection against ischemia-reperfusion injury.

Animals↗

[Pattern of plasma sex steroid hormone levels during the breeding season of male and female skink: Eumeces chinensis].

Changes in gonadal activity and plasma sex steroid hormone levels in male and female Eumece chinensis during the breeding season were described. The results showed that: The vitellogensis of follicles of female Eumeces chinensis needed the stimulation of 17beta-estradiol (E2). As ovary masses reached peak values between late April and mid-May, E2 levels rose to the top value by late March, and then sharply declined but went up again before preovulation; The physiological functions of plasma progesterone (P) consisted in its oviductal egg retention, embryo development, and eggshell formation. P levels fluctuated near the basic value between mid-March and late April. In mid-May, with the onset of ovulation, plasma P levels rose rapidly, reached peak value by late May and declined sharply after ovulation. Plasma E2 levels declined as plasma P levels rose, showing an inverse relationship between them; In males, plasma Testosterone (T) levels were closely correlated with the maintenance of spermatogenesis activities, male and male combat, sexual display, and mating. Plasma T levels tended to rise after the termination of hibernation, and reached peak value by mid-April. After mid-May, with the testis aggressing, plasma T levels gradually went down and reached bottom value by late June.

Animals↗

Exogenous nitric oxide generates ROS and induces cardioprotection: involvement of PKG, mitochondrial KATP channels, and ERK.

We examined whether cGMP-dependent protein kinase (PKG) and mitochondrial ATP-sensitive potassium (K(ATP)) channels are involved in S-nitroso-N-acetyl penicillamine (SNAP)-induced reactive oxygen species (ROS) generation. SNAP significantly increased ROS generation in cardiomyocytes. This increase was suppressed by both 5-hydroxydecanoate (5-HD) and glibenclamide. Direct opening of mitochondrial K(ATP) channels with diazoxide led to ROS generation. The increased ROS generation was reversed by N-(2-mercaptopropionyl)glycine (MPG), a scavenger of ROS. Myxothiazol partially suppressed the ROS generation. KT-5823, an inhibitor of PKG, prevented ROS generation, indicating that PKG is required for ROS generation. In addition, 8-bromoguanosine 3',5'-cyclic monophosphate (8-BrcGMP), an activator of PKG, induced ROS generation. The effect of 8-BrcGMP was reversed by either 5-HD or MPG. YC-1, an activator of guanylyl cyclase, also increased ROS production, which was reversed by 5-HD. Neither LY-294002 nor wortmannin, the inhibitors of phosphatidylinositol 3-kinase (PI3-kinase), affected SNAP's action. In a whole heart study, SNAP significantly reduced infarct size. The anti-infarct effect of SNAP was abrogated by either MPG or 5-HD. This effect was also blocked by PD-98059, an ERK inhibitor, but not by LY-294002. A Western blotting study showed that SNAP significantly enhanced phosphorylation of ERK, which was reversed by MPG. These results suggest that SNAP-induced ROS generation is mediated by activation of PKG and mitochondrial K(ATP) channels and that opening of mitochondrial K(ATP) channels is the downstream event of PKG activation. ROS and mitochondrial K(ATP) channels participate in the anti-infarct effect of SNAP. Moreover, phosphorylation of ERK is the downstream signaling event of ROS and plays a role in the cardioprotection of SNAP.

Animals↗

Signaling mechanisms that mediate nitric oxide production induced by acetylcholine exposure and withdrawal in cat atrial myocytes.

Fluorescence microscopy and the NO-sensitive indicator 4,5-diaminofluorescein were used to determine the effects of acetylcholine (ACh) on intracellular NO (NOi) in cat atrial myocytes. Field stimulation (1 Hz) of cells or exposure of quiescent cells to ACh (1 to 10 micromol/L) had no effect on NOi. However, in field-stimulated cells, ACh exposure increased NOi, and ACh withdrawal elicited an additional, prominent increase in NOi production. During ACh exposure, addition of 1 micromol/L atropine increased NOi production similar to ACh withdrawal. ACh-induced increases in NOi were reduced by prior exposure to 1 mmol/L extracellular Ca2+ ([Ca2+]o) and prevented by 0.5 mmol/L [Ca2+]o, 1 micromol/L verapamil, 1 micromol/L atropine, 10 micromol/L L-N5-(1-iminoethyl)ornithine, 10 micromol/L W-7, or incubating cells in pertussis toxin or 10 micromol/L LY294002 (inhibits phosphatidylinositol 3-kinase). Switching to 0.5 mmol/L [Ca2+]o during ACh withdrawal prevented the additional increase in NOi. ACh exposure increased phosphorylation (Ser473) of protein kinase B (Akt), and this effect was blocked by LY294002 and unaffected in low (0.5 mmol/L) [Ca2+]o. Confocal microscopy revealed that ACh exposure increased NOi at local subsarcolemmal sites, and ACh withdrawal additionally increased NOi by recruiting additional subsarcolemmal release sites. Disruption of caveolae by 2 mmol/L methyl-beta-cyclodextrin abolished ACh-induced NOi production. We conclude that in cat atrial myocytes, ACh stimulates NOi release from local subsarcolemmal sites. ACh-induced increases in NOi requires both muscarinic receptor-mediated Gi protein/phosphatidylinositol 3-kinase/Akt signaling and voltage-activated Ca2+ influx for stimulation of calmodulin-dependent endothelial NO synthase activity. Increases in NOi elicited by ACh withdrawal result from the recovery of Ca2+ influx after ACh inhibition. NO signaling elicited by ACh withdrawal stimulates rapid recovery from cholinergic atrial inhibition.

Acetylcholine↗

Mitochondrial calcium uptake stimulates nitric oxide production in mitochondria of bovine vascular endothelial cells.

Although nitric oxide (NO) is a known modulator of cell respiration in vascular endothelium, the presence of a mitochondria-specific nitric oxide synthase (mtNOS) in these cells is still a controversial issue. We have used laser scanning confocal microscopy in combination with the NO-sensitive fluorescent dye DAF-2 to monitor changes in NO production by mitochondria of calf vascular endothelial (CPAE) cells. Cells were loaded with the membrane-permeant NO-sensitive dye 4,5-diaminofluorescein (DAF-2) diacetate and subsequently permeabilized with digitonin to remove cytosolic DAF-2 to allow measurements of NO production in mitochondria ([NO]mt). Stimulation of mitochondrial Ca2+ uptake by exposure to different cytoplasmic Ca2+ concentrations (1, 2, and 5 microM) resulted in a dose-dependent increase of NO production by mitochondria. This increase of [NO]mt was sensitive to the NOS antagonist l-N5-(1-iminoethyl)ornithine and the calmodulin antagonist calmidazolium (R-24571), demonstrating the endogenous origin of NO synthesis and its calmodulin dependence. Collapsing the mitochondrial membrane potential with the protonophore FCCP or blocking the mitochondrial Ca2+ uniporter with ruthenium red, as well as blocking the respiratory chain with antimycin A in combination with oligomycin, inhibited mitochondrial NO production. Addition of the NO donor spermine NONOate caused a profound increase in DAF-2 fluorescence that was not affected by either of these treatments. The mitochondrial origin of the DAF-2 signals was confirmed by colocalization with the mitochondrial marker MitoTracker Red and by the observation that disruption of caveolae (where cytoplasmic NOS is localized) formation with methyl-beta-cyclodextrin did not prevent the increase of DAF-2 fluorescence. The activation of mitochondrial calcium uptake stimulates mtNOS phosphorylation (at Ser-1177) which was prevented by FCCP. The data demonstrate that stimulation of mitochondrial Ca2+ uptake activates NO production in mitochondria of CPAE cells. This indicates the presence of a mitochondria-specific NOS that can provide a fast local modulatory effect of NO on cell respiration, membrane potential, and apoptosis.

Animals↗