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Drug Clearance in Neonates: A Combination of Population Pharmacokinetic Modelling and Machine Learning Approaches to Improve Individual Prediction

Tang BH, Guan Z, Allegaert K, Wu YE, Manolis E, Leroux S, et al.

Clin Pharmacokinet, 2021 11;60(11):1435-1448.
PMID: 34041714 DOI: 10.1007/s40262-021-01033-x

BACKGROUND: Population pharmacokinetic evaluations have been widely used in neonatal pharmacokinetic studies, while machine learning has become a popular approach to solving complex problems in the current era of big data.
OBJECTIVE: The aim of this proof-of-concept study was to evaluate whether combining population pharmacokinetic and machine learning approaches could provide a more accurate prediction of the clearance of renally eliminated drugs in individual neonates.
METHODS: Six drugs that are primarily eliminated by the kidneys were selected (vancomycin, latamoxef, cefepime, azlocillin, ceftazidime, and amoxicillin) as 'proof of concept' compounds. Individual estimates of clearance obtained from population pharmacokinetic models were used as reference clearances, and diverse machine learning methods and nested cross-validation were adopted and evaluated against these reference clearances. The predictive performance of these combined methods was compared with the performance of two other predictive methods: a covariate-based maturation model and a postmenstrual age and body weight scaling model. Relative error was used to evaluate the different methods.
RESULTS: The extra tree regressor was selected as the best-fit machine learning method. Using the combined method, more than 95% of predictions for all six drugs had a relative error of < 50% and the mean relative error was reduced by an average of 44.3% and 71.3% compared with the other two predictive methods.
CONCLUSION: A combined population pharmacokinetic and machine learning approach provided improved predictions of individual clearances of renally cleared drugs in neonates. For a new patient treated in clinical practice, individual clearance can be predicted a priori using our model code combined with demographic data.

Matched MeSH terms: Models, Biological*
Effects of Environmental Stresses and in Vitro Digestion on the Release of Tocotrienols Encapsulated Within Chitosan-Alginate Microcapsules

Tan PY, Tan TB, Chang HW, Tey BT, Chan ES, Lai OM, et al.

J Agric Food Chem, 2017 Dec 06;65(48):10651-10657.
PMID: 29124932 DOI: 10.1021/acs.jafc.7b03521

Considering the health benefits of tocotrienols, continuous works have been done on the encapsulation and delivery of these compounds. In this study, we encapsulated tocotrienols in chitosan-alginate microcapsules and evaluated their release profile. Generally, these tocotrienols microcapsules (TM) displayed high thermal stability. When subjected to pH adjustments (pH 1-9), we observed that the release of tocotrienols was the highest (33.78 ± 0.18%) under basic conditions. The TM were also unstable against the effect of ionic strength, with a high release (70.73 ± 0.04%) of tocotrienols even at a low sodium chloride concentration (50 mM). As for the individual isomers, δ-tocotrienol was the most sensitive to pH and ionic strength. In contrast, β-/γ-tocotrienols were the most ionic-stable isomers but more responsive toward thermal treatment. Simulated gastrointestinal model showed that the chitosan-alginate-based TM could be used to retain tocotrienols in the gastric and subsequently release them in the intestines for possible absorption.

Matched MeSH terms: Models, Biological
Sonication reduces the attachment of Salmonella Typhimurium ATCC 14028 cells to bacterial cellulose-based plant cell wall models and cut plant material

Tan MSF, Rahman S, Dykes GA

Food Microbiol, 2017 Apr;62:62-67.
PMID: 27889167 DOI: 10.1016/j.fm.2016.10.009

This study investigated the removal of bacterial surface structures, particularly flagella, using sonication, and examined its effect on the attachment of Salmonella Typhimurium ATCC 14028 cells to plant cell walls. S. Typhimurium ATCC 14028 cells were subjected to sonication at 20 kHz to remove surface structures without affecting cell viability. Effective removal of flagella was determined by staining flagella of sonicated cells with Ryu's stain and enumerating the flagella remaining by direct microscopic counting. The attachment of sonicated S. Typhimurium cells to bacterial cellulose-based plant cell wall models and cut plant material (potato, apple, lettuce) was then evaluated. Varying concentrations of pectin and/or xyloglucan were used to produce a range of bacterial cellulose-based plant cell wall models. As compared to the non-sonicated controls, sonicated S. Typhimurium cells attached in significantly lower numbers (between 0.5 and 1.0 log CFU/cm2) to all surfaces except to the bacterial cellulose-only composite without pectin and xyloglucan. Since attachment of S. Typhimurium to the bacterial cellulose-only composite was not affected by sonication, this suggests that bacterial surface structures, particularly flagella, could have specific interactions with pectin and xyloglucan. This study indicates that sonication may have potential applications for reducing Salmonella attachment during the processing of fresh produce.

Matched MeSH terms: Models, Biological
Attachment of bacterial pathogens to a bacterial cellulose-derived plant cell wall model: a proof of concept

Tan MS, Wang Y, Dykes GA

Foodborne Pathog Dis, 2013 Nov;10(11):992-4.
PMID: 23941519 DOI: 10.1089/fpd.2013.1536

This study aimed to establish, as a proof of concept, whether bacterial cellulose (BC)-derived plant cell wall models could be used to investigate foodborne bacterial pathogen attachment. Attachment of two strains each of Salmonella enterica and Listeria monocytogenes to four BC-derived plant cell wall models (namely, BC, BC-pectin [BCP], BC-xyloglucan [BCX], and BC-pectin-xyloglucan [BCPX]) was investigated. Chemical analysis indicated that the BCPX composite (31% cellulose, 45.6% pectin, 23.4% xyloglucan) had a composition typical of plant cell walls. The Salmonella strains attached in significantly (p<0.05) higher numbers (~6 log colony-forming units [CFU]/cm(2)) to the composites than the Listeria strains (~5 log CFU/cm(2)). Strain-specific differences were also apparent with one Salmonella strain, for example, attaching in significantly (p<0.05) higher numbers to the BCX composite than to the other composites. This study highlights the potential usefulness of these composites to understand attachment of foodborne bacteria to fresh produce.

Matched MeSH terms: Models, Biological
Fulltext Attachment of Salmonella strains to a plant cell wall model is modulated by surface characteristics and not by specific carbohydrate interactions

Tan MS, Moore SC, Tabor RF, Fegan N, Rahman S, Dykes GA

BMC Microbiol, 2016 09 15;16:212.
PMID: 27629769 DOI: 10.1186/s12866-016-0832-2

BACKGROUND: Processing of fresh produce exposes cut surfaces of plant cell walls that then become vulnerable to human foodborne pathogen attachment and contamination, particularly by Salmonella enterica. Plant cell walls are mainly composed of the polysaccharides cellulose, pectin and hemicelluloses (predominantly xyloglucan). Our previous work used bacterial cellulose-based plant cell wall models to study the interaction between Salmonella and the various plant cell wall components. We demonstrated that Salmonella attachment was favoured in the presence of pectin while xyloglucan had no effect on its attachment. Xyloglucan significantly increased the attachment of Salmonella cells to the plant cell wall model only when it was in association with pectin. In this study, we investigate whether the plant cell wall polysaccharides mediate Salmonella attachment to the bacterial cellulose-based plant cell wall models through specific carbohydrate interactions or through the effects of carbohydrates on the physical characteristics of the attachment surface.
RESULTS: We found that none of the monosaccharides that make up the plant cell wall polysaccharides specifically inhibit Salmonella attachment to the bacterial cellulose-based plant cell wall models. Confocal laser scanning microscopy showed that Salmonella cells can penetrate and attach within the tightly arranged bacterial cellulose network. Analysis of images obtained from atomic force microscopy revealed that the bacterial cellulose-pectin-xyloglucan composite with 0.3 % (w/v) xyloglucan, previously shown to have the highest number of Salmonella cells attached to it, had significantly thicker cellulose fibrils compared to other composites. Scanning electron microscopy images also showed that the bacterial cellulose and bacterial cellulose-xyloglucan composites were more porous when compared to the other composites containing pectin.
CONCLUSIONS: Our study found that the attachment of Salmonella cells to cut plant cell walls was not mediated by specific carbohydrate interactions. This suggests that the attachment of Salmonella strains to the plant cell wall models were more dependent on the structural characteristics of the attachment surface. Pectin reduces the porosity and space between cellulose fibrils, which then forms a matrix that is able to retain Salmonella cells within the bacterial cellulose network. When present with pectin, xyloglucan provides a greater surface for Salmonella cells to attach through the thickening of cellulose fibrils.

Matched MeSH terms: Models, Biological
Fulltext Pectin and Xyloglucan Influence the Attachment of Salmonella enterica and Listeria monocytogenes to Bacterial Cellulose-Derived Plant Cell Wall Models

Tan MS, Rahman S, Dykes GA

Appl Environ Microbiol, 2016 01 15;82(2):680-8.
PMID: 26567310 DOI: 10.1128/AEM.02609-15

Minimally processed fresh produce has been implicated as a major source of foodborne microbial pathogens globally. These pathogens must attach to the produce in order to be transmitted. Cut surfaces of produce that expose cell walls are particularly vulnerable. Little is known about the roles that different structural components (cellulose, pectin, and xyloglucan) of plant cell walls play in the attachment of foodborne bacterial pathogens. Using bacterial cellulose-derived plant cell wall models, we showed that the presence of pectin alone or xyloglucan alone affected the attachment of three Salmonella enterica strains (Salmonella enterica subsp. enterica serovar Enteritidis ATCC 13076, Salmonella enterica subsp. enterica serovar Typhimurium ATCC 14028, and Salmonella enterica subsp. indica M4) and Listeria monocytogenes ATCC 7644. In addition, we showed that this effect was modulated in the presence of both polysaccharides. Assays using pairwise combinations of S. Typhimurium ATCC 14028 and L. monocytogenes ATCC 7644 showed that bacterial attachment to all plant cell wall models was dependent on the characteristics of the individual bacterial strains and was not directly proportional to the initial concentration of the bacterial inoculum. This work showed that bacterial attachment was not determined directly by the plant cell wall model or bacterial physicochemical properties. We suggest that attachment of the Salmonella strains may be influenced by the effects of these polysaccharides on physical and structural properties of the plant cell wall model. Our findings improve the understanding of how Salmonella enterica and Listeria monocytogenes attach to plant cell walls, which may facilitate the development of better ways to prevent the attachment of these pathogens to such surfaces.

Matched MeSH terms: Models, Biological
In Vitro Biodegradation of Hepatotoxic Indospicine in Indigofera spicata and Its Degradation Derivatives by Camel Foregut and Cattle Rumen Fluids

Tan ETT, Al Jassim R, D'Arcy BR, Fletcher MT

J Agric Food Chem, 2017 Aug 30;65(34):7528-7534.
PMID: 28787565 DOI: 10.1021/acs.jafc.7b02492

The known accumulation of the hepatotoxin indospicine in tissues of camels and cattle grazing Indigofera pasture plants is unusual in that free amino acids would normally be expected to be degraded during the fermentation processes in these foregut fermenters. In this study, in vitro experiments were carried out to examine the degradability of indospicine of Indigofera spicata by camel and cattle foregut microbiota. In the first experiment, a 48 h in vitro incubation was carried out using foregut fluid samples that were collected from 15 feral camels and also a fistulated cow. Degradability of indospicine ranged between 97% and 99%, with the higher value of 99% for camels. A pooled sample of foregut fluids from three camels that were on a roughage diet was used in a second experiment to examine the time-dependent degradation of indospicine present in the plant materials. Results indicated that camels' foregut fluids have the ability to biodegrade ∼99% of the indospicine in I. spicata within 48 h of incubation and produced 2-aminopimelamic acid and 2-aminopimelic acid. The time-dependent degradation analysis showed rapid indospicine degradation (65 nmol/h) during the first 8-18 h of incubation followed by a slower degradation rate (12 nmol/h) between 18 and 48 h. Indospicine degradation products were also degraded toward the end of the experiment. The results of these in vitro degradation studies suggest that dietary indospicine may undergo extensive degradation in the foregut of the camel, resulting in trace levels after 48 h. The retention time for plant material in the camel foregut varies depending on feed quality, and the results of this study together with the observed accumulation of indospicine in camel tissues suggest that, although indospicine can be degraded by foregut fermentation, this degradation is not complete before the passage of the digesta into the intestine.

Matched MeSH terms: Models, Biological
Insertional torque and pullout strength of pedicle screws with or without repositioning: a porcine study

Tan CE, Fok MW, Luk KD, Cheung KM

J Orthop Surg (Hong Kong), 2014 Aug;22(2):224-7.
PMID: 25163961

PURPOSE. To evaluate the insertion torque and pullout strength of pedicle screws with or without repositioning. METHODS. 20 fresh porcine lumbar vertebrae of similar size were used. The entry point was at the site just lateral and distal to the superior facet joint of the vertebra, and to a depth of 35 mm. A 6.2-mm-diameter, 35-mm-long pedicle screw was inserted parallel to the superior end plate on one side as control. On the other side, an identical screw was first inserted 10º caudal to the superior end plate, and then repositioned parallel to the superior end plate. The insertional torque and pullout strength were measured. RESULTS. Three of the specimens were excluded owing to pedicle fractures during the pullout test. Repositioned pedicle screws were significantly weaker than controls in terms of the maximum insertional torque (3.20 ± 0.28 vs. 2.04 ± 0.28 Nm, 36% difference, p<0.01) and pullout strength (1664 ± 378 vs.1391 ± 295 N, p<0.01). CONCLUSION. Repositioning pedicle screws should be avoided, especially when the pedicle wall is breached. If repositioning is deemed necessary, augmentation with polymethyl methacrylate or a screw with a larger diameter should be considered.

Matched MeSH terms: Models, Biological
Fulltext In vitro and in silico Approaches to Study Cytochrome P450-Mediated Interactions

Tan BH, Pan Y, Dong AN, Ong CE

J Pharm Pharm Sci, 2017;20(1):319-328.
PMID: 29145931 DOI: 10.18433/J3434R

In vitro and in silico models of drug metabolism are utilized regularly in the drug research and development as tools for assessing pharmacokinetic variability and drug-drug interaction risk. The use of in vitro and in silico predictive approaches offers advantages including guiding rational design of clinical drug-drug interaction studies, minimization of human risk in the clinical trials, as well as cost and time savings due to lesser attrition during compound development process. This article gives a review of some of the current in vitro and in silico methods used to characterize cytochrome P450(CYP)-mediated drug metabolism for estimating pharmacokinetic variability and the magnitude of drug-drug interactions. Examples demonstrating the predictive applicability of specific in vitro and in silico approaches are described. Commonly encountered confounding factors and sources of bias and error in these approaches are presented. With the advent of technological advancement in high throughput screening and computer power, the in vitro and in silico methods are becoming more efficient and reliable and will continue to contribute to the process of drug discovery, development and ultimately safer and more effective pharmacotherapy. This article is open to POST-PUBLICATION REVIEW. Registered readers (see "For Readers") may comment by clicking on ABSTRACT on the issue's contents page.

Matched MeSH terms: Models, Biological*
Patchy stomatal behavior in broad-leaved trees grown in different habitats

Takanashi S, Kosugi Y, Matsuo N, Tani M, Ohte N

Tree Physiol, 2006 Dec;26(12):1565-78.
PMID: 17169896

Effects of heterogeneity in stomatal behavior on gas-exchange characteristics of leaves from four tree species growing in different climates, including temperate, tropical monsoon and tropical rain forest, were investigated by combining gas-exchange measurements and the pressure-infiltration method. Field observations indicated linear relationships between whole-leaf conductance and the ratio of infiltrated to non-infiltrated leaf area (open stomata area) in Dipterocarpus sublamellatus Foxw. and Neobalanocarpus heimii (King) Ashton in a tropical rain forest in Peninsular Malaysia, whereas the ratio of infiltrated to non-infiltrated area rapidly increased up to the whole-leaf conductance at which the entire leaf was infiltrated in Cinnamomum camphora Sieb. in a temperate evergreen forest in Japan and in Azadirachta indica Juss. in a tropical monsoon area in Thailand. These results strongly suggest small ranges in bell-shaped stomatal conductance distributions in C. camphora and A. indica and bimodal stomatal conductance distributions in D. sublamellatus and N. heimii. The values of normalized maximum carboxylation rate at 25 degrees C (V(cmax25)) derived from gas-exchange measurements were not constant, but decreased with decreasing whole-leaf conductance in D. sublamellatus and N. heimii. A gas-exchange model analysis revealed a linear relationship between whole-leaf conductance and the ratio of infiltrated to non-infiltrated leaf area for bimodal stomatal conductance distributions, whereas for bell-shaped distributions, the relationships were nonlinear. Midday depression of apparent V(cmax25) in these species was mainly caused by bimodal stomatal closure. The bimodal stomatal distribution model could also explain diurnal changes in photosynthetic assimilation and transpiration rates in these species.

Matched MeSH terms: Models, Biological
Fulltext Synthesis of diindolylmethane (DIM) bearing thiadiazole derivatives as a potent urease inhibitor

Taha M, Rahim F, Khan AA, Anouar EH, Ahmed N, Shah SAA, et al.

Sci Rep, 2020 05 14;10(1):7969.
PMID: 32409737 DOI: 10.1038/s41598-020-64729-3

The current study describes synthesis of diindolylmethane (DIM) derivatives based-thiadiazole as a new class of urease inhibitors. Diindolylmethane is natural product alkaloid reported to use in medicinal chemistry extensively. Diindolylmethane-based-thiadiazole analogs (1-18) were synthesized and characterized by various spectroscopic techniques 1HNMR, 13C-NMR, EI-MS and evaluated for urease (jack bean urease) inhibitory potential. All compounds showed excellent to moderate inhibitory potential having IC50 value within the range of 0.50 ± 0.01 to 33.20 ± 1.20 µM compared with the standard thiourea (21.60 ± 0.70 µM). Compound 8 (IC50 = 0.50 ± 0.01 µM) was the most potent inhibitor amongst all derivatives. Structure-activity relationships have been established for all compounds. The key binding interactions of most active compounds with enzyme were confirmed through molecular docking studies.

Matched MeSH terms: Models, Biological
Scopoletin, an active principle of tree tobacco (Nicotiana glauca) inhibits human tumor vascularization in xenograft models and modulates ERK1, VEGF-A, and FGF-2 in computer model

Tabana YM, Hassan LE, Ahamed MB, Dahham SS, Iqbal MA, Saeed MA, et al.

Microvasc Res, 2016 09;107:17-33.
PMID: 27133199 DOI: 10.1016/j.mvr.2016.04.009

We recently reported the antineovascularization effect of scopoletin on rat aorta and identified its potential anti-angiogenic activity. Scopoletin could be useful as a systemic chemotherapeutic agent against angiogenesis-dependent malignancies if its antitumorigenic activity is investigated and scientifically proven using a suitable human tumor xenograft model. In the present study, bioassay-guided (anti-angiogenesis) phytochemical investigation was conducted on Nicotiana glauca extract which led to the isolation of scopoletin. Further, anti-angiogenic activity of scopoletin was characterized using ex vivo, in vivo and in silico angiogenesis models. Finally, the antitumorigenic efficacy of scopoletin was studied in human colorectal tumor xenograft model using athymic nude mice. For the first time, an in vivo anticancer activity of scopoletin was reported and characterized using xenograft models. Scopoletin caused significant suppression of sprouting of microvessels in rat aortic explants with IC50 (median inhibitory concentration) 0.06μM. Scopoletin (100 and 200mg/kg) strongly inhibited (59.72 and 89.4%, respectively) vascularization in matrigel plugs implanted in nude mice. In the tumor xenograft model, scopoletin showed remarkable inhibition on tumor growth (34.2 and 94.7% at 100 and 200mg/kg, respectively). Tumor histology revealed drastic reduction of the extent of vascularization. Further, immunostaining of CD31 and NG2 receptors in the histological sections confirmed the antivascular effect of scopoletin in tumor vasculature. In computer modeling, scopoletin showed strong ligand affinity and binding energies toward the following angiogenic factors: protein kinase (ERK1), vascular endothelial growth factor A (VEGF-A), and fibroblast growth factor 2 (FGF-2). These results suggest that the antitumor activity of scopoletin may be due to its strong anti-angiogenic effect, which may be mediated by its effective inhibition of ERK1, VEGF-A, and FGF-2.

Matched MeSH terms: Models, Biological*
Permeability study of cancellous bone and its idealised structures

Syahrom A, Abdul Kadir MR, Harun MN, Öchsner A

Med Eng Phys, 2015 Jan;37(1):77-86.
PMID: 25523865 DOI: 10.1016/j.medengphy.2014.11.001

Artificial bone is a suitable alternative to autografts and allografts, however their use is still limited. Though there were numerous reports on their structural properties, permeability studies of artificial bones were comparably scarce. This study focused on the development of idealised, structured models of artificial cancellous bone and compared their permeability values with bone surface area and porosity. Cancellous bones from fresh bovine femur were extracted and cleaned following an established protocol. The samples were scanned using micro-computed tomography (μCT) and three-dimensional models of the cancellous bones were reconstructed for morphology study. Seven idealised and structured cancellous bone models were then developed and fabricated via rapid prototyping technique. A test-rig was developed and permeability tests were performed on the artificial and real cancellous bones. The results showed a linear correlation between the permeability and the porosity as well as the bone surface area. The plate-like idealised structure showed a similar value of permeability to the real cancellous bones.

Matched MeSH terms: Models, Biological*
Fulltext TRPC3-Nox2 axis mediates nutritional deficiency-induced cardiomyocyte atrophy

Sudi SB, Tanaka T, Oda S, Nishiyama K, Nishimura A, Sunggip C, et al.

Sci Rep, 2019 07 05;9(1):9785.
PMID: 31278358 DOI: 10.1038/s41598-019-46252-2

Myocardial atrophy, characterized by the decreases in size and contractility of cardiomyocytes, is caused by severe malnutrition and/or mechanical unloading. Extracellular adenosine 5'-triphosphate (ATP), known as a danger signal, is recognized to negatively regulate cell volume. However, it is obscure whether extracellular ATP contributes to cardiomyocyte atrophy. Here, we report that ATP induces atrophy of neonatal rat cardiomyocytes (NRCMs) without cell death through P2Y2 receptors. ATP led to overproduction of reactive oxygen species (ROS) through increased amount of NADPH oxidase (Nox) 2 proteins, due to increased physical interaction between Nox2 and canonical transient receptor potential 3 (TRPC3). This ATP-mediated formation of TRPC3-Nox2 complex was also pathophysiologically involved in nutritional deficiency-induced NRCM atrophy. Strikingly, knockdown of either TRPC3 or Nox2 suppressed nutritional deficiency-induced ATP release, as well as ROS production and NRCM atrophy. Taken together, we propose that TRPC3-Nox2 axis, activated by extracellular ATP, is the key component that mediates nutritional deficiency-induced cardiomyocyte atrophy.

Matched MeSH terms: Models, Biological
Fulltext The possible potential therapeutic targets for drug induced gingival overgrowth

Subramani T, Rathnavelu V, Alitheen NB

Mediators Inflamm, 2013;2013:639468.
PMID: 23690667 DOI: 10.1155/2013/639468

Gingival overgrowth is a side effect of certain medications. The most fibrotic drug-induced lesions develop in response to therapy with phenytoin, the least fibrotic lesions are caused by cyclosporin A, and the intermediate fibrosis occurs in nifedipine-induced gingival overgrowth. Fibrosis is one of the largest groups of diseases for which there is no therapy but is believed to occur because of a persistent tissue repair program. During connective tissue repair, activated gingival fibroblasts synthesize and remodel newly created extracellular matrix. Proteins such as transforming growth factor (TGF), endothelin-1 (ET-1), angiotensin II (Ang II), connective tissue growth factor (CCN2/CTGF), insulin-like growth factor (IGF), and platelet-derived growth factor (PDGF) appear to act in a network that contributes to the development of gingival fibrosis. Since inflammation is the prerequisite for gingival overgrowth, mast cells and its protease enzymes also play a vital role in the pathogenesis of gingival fibrosis. Drugs targeting these proteins are currently under consideration as antifibrotic treatments. This review summarizes recent observations concerning the contribution of TGF-β, CTGF, IGF, PDGF, ET-1, Ang II, and mast cell chymase and tryptase enzymes to fibroblast activation in gingival fibrosis and the potential utility of agents blocking these proteins in affecting the outcome of drug-induced gingival overgrowth.

Matched MeSH terms: Models, Biological
Rate of tree carbon accumulation increases continuously with tree size

Stephenson NL, Das AJ, Condit R, Russo SE, Baker PJ, Beckman NG, et al.

Nature, 2014 Mar 6;507(7490):90-3.
PMID: 24429523 DOI: 10.1038/nature12914

Forests are major components of the global carbon cycle, providing substantial feedback to atmospheric greenhouse gas concentrations. Our ability to understand and predict changes in the forest carbon cycle--particularly net primary productivity and carbon storage--increasingly relies on models that represent biological processes across several scales of biological organization, from tree leaves to forest stands. Yet, despite advances in our understanding of productivity at the scales of leaves and stands, no consensus exists about the nature of productivity at the scale of the individual tree, in part because we lack a broad empirical assessment of whether rates of absolute tree mass growth (and thus carbon accumulation) decrease, remain constant, or increase as trees increase in size and age. Here we present a global analysis of 403 tropical and temperate tree species, showing that for most species mass growth rate increases continuously with tree size. Thus, large, old trees do not act simply as senescent carbon reservoirs but actively fix large amounts of carbon compared to smaller trees; at the extreme, a single big tree can add the same amount of carbon to the forest within a year as is contained in an entire mid-sized tree. The apparent paradoxes of individual tree growth increasing with tree size despite declining leaf-level and stand-level productivity can be explained, respectively, by increases in a tree's total leaf area that outpace declines in productivity per unit of leaf area and, among other factors, age-related reductions in population density. Our results resolve conflicting assumptions about the nature of tree growth, inform efforts to undertand and model forest carbon dynamics, and have additional implications for theories of resource allocation and plant senescence.

Matched MeSH terms: Models, Biological
Demography and the canonical ensemble

Smith JD

Math Biosci, 1998 Nov;153(2):151-61.
PMID: 9825637

The Gibbs canonical ensemble of statistical mechanics is used to describe the probability distribution of the age classes of mothers of new-borns in an age-structured population. The Malthusian parameter emerges as a Lagrange multiplier corresponding to a generation time constraint, while a new perturbation parameter appears as the Lagrange multiplier corresponding to a maternity constraint. Classical Lotka stability reduces to the unperturbed case of the more general canonical ensemble model. The model is used in a case study of the female (peninsular) Malaysian population of 1970. The Malthusian parameter and perturbation are calculated easily by linear regression. Use of the model identifies an anomaly in the population due to the effects of World War II.

Matched MeSH terms: Models, Biological*
Fulltext Soils on exposed Sunda shelf shaped biogeographic patterns in the equatorial forests of Southeast Asia

Slik JW, Aiba S, Bastian M, Brearley FQ, Cannon CH, Eichhorn KA, et al.

Proc Natl Acad Sci U S A, 2011 Jul 26;108(30):12343-7.
PMID: 21746913 DOI: 10.1073/pnas.1103353108

The marked biogeographic difference between western (Malay Peninsula and Sumatra) and eastern (Borneo) Sundaland is surprising given the long time that these areas have formed a single landmass. A dispersal barrier in the form of a dry savanna corridor during glacial maxima has been proposed to explain this disparity. However, the short duration of these dry savanna conditions make it an unlikely sole cause for the biogeographic pattern. An additional explanation might be related to the coarse sandy soils of central Sundaland. To test these two nonexclusive hypotheses, we performed a floristic cluster analysis based on 111 tree inventories from Peninsular Malaysia, Sumatra, and Borneo. We then identified the indicator genera for clusters that crossed the central Sundaland biogeographic boundary and those that did not cross and tested whether drought and coarse-soil tolerance of the indicator genera differed between them. We found 11 terminal floristic clusters, 10 occurring in Borneo, 5 in Sumatra, and 3 in Peninsular Malaysia. Indicator taxa of clusters that occurred across Sundaland had significantly higher coarse-soil tolerance than did those from clusters that occurred east or west of central Sundaland. For drought tolerance, no such pattern was detected. These results strongly suggest that exposed sandy sea-bed soils acted as a dispersal barrier in central Sundaland. However, we could not confirm the presence of a savanna corridor. This finding makes it clear that proposed biogeographic explanations for plant and animal distributions within Sundaland, including possible migration routes for early humans, need to be reevaluated.

Matched MeSH terms: Models, Biological
Can we predict ectotherm responses to climate change using thermal performance curves and body temperatures?

Sinclair BJ, Marshall KE, Sewell MA, Levesque DL, Willett CS, Slotsbo S, et al.

Ecol Lett, 2016 11;19(11):1372-1385.
PMID: 27667778 DOI: 10.1111/ele.12686

Thermal performance curves (TPCs), which quantify how an ectotherm's body temperature (Tb ) affects its performance or fitness, are often used in an attempt to predict organismal responses to climate change. Here, we examine the key - but often biologically unreasonable - assumptions underlying this approach; for example, that physiology and thermal regimes are invariant over ontogeny, space and time, and also that TPCs are independent of previously experienced Tb. We show how a critical consideration of these assumptions can lead to biologically useful hypotheses and experimental designs. For example, rather than assuming that TPCs are fixed during ontogeny, one can measure TPCs for each major life stage and incorporate these into stage-specific ecological models to reveal the life stage most likely to be vulnerable to climate change. Our overall goal is to explicitly examine the assumptions underlying the integration of TPCs with Tb , to develop a framework within which empiricists can place their work within these limitations, and to facilitate the application of thermal physiology to understanding the biological implications of climate change.

Matched MeSH terms: Models, Biological
Fulltext The Protective Effects of a Synthetic Geranyl Acetophenone in a Cellular Model of TNF-α-Induced Pulmonary Epithelial Barrier Dysfunction

Sim TY, Harith HH, Tham CL, Md Hashim NF, Shaari K, Sulaiman MR, et al.

Molecules, 2018 Jun 05;23(6).
PMID: 29874809 DOI: 10.3390/molecules23061355

Alveolar epithelial barrier dysfunction contributes to lung edema and can lead to acute lung injury (ALI). The features include increased epithelial permeability, upregulation of inflammatory mediators and downregulation of junctional complex molecules; these changes are often induced by inflammation. tHGA is an acetophenone analogue with therapeutic potential in asthma. Its therapeutic potential in ALI is presently unknown. Herein, the effects of tHGA on epithelial barrier dysfunction were determined in TNF-α-induced human alveolar epithelial cells. The anti-inflammatory properties of tHGA were assessed by monocyte adhesion assay and analysis of MCP-1 and ICAM-1 expression. The epithelial barrier function was assessed by paracellular permeability and transepithelial electrical resistance (TEER) assays, and analysis of junctional complex molecules expression. To elucidate the mechanism of action, the effects of tHGA on the NF-κB and MAPK pathways were determined. Gene and protein expression were analyzed by RT-PCR and Western blotting or ELISA, respectively. tHGA suppressed leukocyte adhesion to TNF-α-induced epithelium and reduced MCP-1 and ICAM-1 gene expression and secretion. tHGA also increased TEER readings, reduced epithelial permeability and enhanced expression of junctional complex molecules (zona occludens-1, occludin and E-cadherin) in TNF-α-induced cells. Correspondingly, the NF-κB, ERK and p38 MAPK pathways were also inhibited by tHGA. These findings suggest that tHGA is able to preserve alveolar epithelial barrier function in response to acute inflammation, via its anti-inflammatory activity and stabilization of epithelial barrier integrity, mediated by NF-κB, ERK and p38 MAPK signaling.

Matched MeSH terms: Models, Biological*

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