Noise Analysis in Biochemical Complex Formation

AbstractSeveral biological functions are carried out via complexes that are formed via multimerization of either a single species (homomers) or multiple species (heteromers). Given functional relevance of these complexes, it is arguably desired to maintain their level at a set point and minimize fluctuations around it. Here we consider two simple models of complex formation – one for homomer and another for heteromer of two species – and analyze how important model parameters affect the noise in complex level. In particular, we study effects of (i) sensitivity of the complex formation rate with respect to constituting species’ abundance, and (ii) relative stability of the complex as compared with that of the constituents. By employing an approximate moment analysis, we find that for a given steady state level, there is an optimal sensitivity that minimizes noise (quantified by fano-factor; variance/mean) in the complex level. Furthermore, the noise becomes smaller if the complex is less stable than its constituents. Finally, for the heteromer case, our findings show that noise is enhanced if the complex is comparatively more sensitive to one constituent. We briefly discuss implications of our result for general complex formation processes.

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Toxicokinetics of U-47700, tramadol, and their main metabolites in pigs following intravenous administration: is a multiple species allometric scaling approach useful for the extrapolation of toxicokinetic parameters to humans?

Archives of Toxicology ◽

10.1007/s00204-021-03169-y ◽

2021 ◽

Author(s):

Frederike Nordmeier ◽

Iryna Sihinevich ◽

Adrian A. Doerr ◽

Nadja Walle ◽

Matthias W. Laschke ◽

...

Keyword(s):

Allometric Scaling ◽

Solid Phase ◽

Safety Data ◽

Single Species ◽

Health Concern ◽

New Psychoactive Substances ◽

Model Parameters ◽

Time Profiles ◽

Concentration Time ◽

Multiple Species

AbstractNew synthetic opioids (NSOs) pose a public health concern since their emergence on the illicit drug market and are gaining increasing importance in forensic toxicology. Like many other new psychoactive substances, NSOs are consumed without any preclinical safety data or any knowledge on toxicokinetic (TK) data. Due to ethical reasons, controlled human TK studies cannot be performed for the assessment of these relevant data. As an alternative animal experimental approach, six pigs per drug received a single intravenous dose of 100 µg/kg body weight (BW) of U-47700 or 1000 µg/kg BW of tramadol to evaluate whether this species is suitable to assess the TK of NSOs. The drugs were determined in serum and whole blood using a fully validated method based on solid-phase extraction and LC–MS/MS. The concentration–time profiles and a population (pop) TK analysis revealed that a three-compartment model best described the TK data of both opioids. Central volumes of distribution were 0.94 L/kg for U-47700 and 1.25 L/kg for tramadol and central (metabolic) clearances were estimated at 1.57 L/h/kg and 1.85 L/h/kg for U-47700 and tramadol, respectively. The final popTK model parameters for pigs were upscaled via allometric scaling techniques. In comparison to published human data, concentration–time profiles for tramadol could successfully be predicted with single species allometric scaling. Furthermore, possible profiles for U-47700 in humans were simulated. The findings of this study indicate that unlike a multiple species scaling approach, pigs in conjunction with TK modeling are a suitable tool for the assessment of TK data of NSOs and the prediction of human TK data.

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Best practices on the differential expression analysis of multi-species RNA-seq

Genome Biology ◽

10.1186/s13059-021-02337-8 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Matthew Chung ◽

Vincent M. Bruno ◽

David A. Rasko ◽

Christina A. Cuomo ◽

José F. Muñoz ◽

...

Keyword(s):

Best Practices ◽

Differential Expression ◽

Expression Analysis ◽

Differential Expression Analysis ◽

Single Species ◽

Rna Seq ◽

Species Analysis ◽

Differential Gene ◽

Multiple Species ◽

Downstream Analysis

AbstractAdvances in transcriptome sequencing allow for simultaneous interrogation of differentially expressed genes from multiple species originating from a single RNA sample, termed dual or multi-species transcriptomics. Compared to single-species differential expression analysis, the design of multi-species differential expression experiments must account for the relative abundances of each organism of interest within the sample, often requiring enrichment methods and yielding differences in total read counts across samples. The analysis of multi-species transcriptomics datasets requires modifications to the alignment, quantification, and downstream analysis steps compared to the single-species analysis pipelines. We describe best practices for multi-species transcriptomics and differential gene expression.

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Evaluating Coexistence of Fish Species with Coastal Cutthroat Trout in Low Order Streams of Western Oregon and Washington, USA

Fishes ◽

10.3390/fishes6010004 ◽

2021 ◽

Vol 6 (1) ◽

pp. 4

Author(s):

Kyle D. Martens ◽

Jason Dunham

Keyword(s):

Pacific Northwest ◽

Species Interactions ◽

Coho Salmon ◽

Cutthroat Trout ◽

Single Species ◽

The Pacific ◽

Small Streams ◽

Coastal Cutthroat Trout ◽

Multiple Species ◽

Low Order

When multiple species of fish coexist there are a host of potential ways through which they may interact, yet there is often a strong focus on studies of single species without considering these interactions. For example, many studies of forestry–stream interactions in the Pacific Northwest have focused solely on the most prevalent species: Coastal cutthroat trout. To examine the potential for interactions of other fishes with coastal cutthroat trout, we conducted an analysis of 281 sites in low order streams located on Washington’s Olympic Peninsula and along the central Oregon coast. Coastal cutthroat trout and juvenile coho salmon were the most commonly found salmonid species within these streams and exhibited positive associations with each other for both presence and density. Steelhead were negatively associated with the presence of coastal cutthroat trout as well as with coho salmon and sculpins (Cottidae). Coastal cutthroat trout most frequently shared streams with juvenile coho salmon. For densities of these co-occurring species, associations between these two species were relatively weak compared to the strong influences of physical stream conditions (size and gradient), suggesting that physical conditions may have more of an influence on density than species interactions. Collectively, our analysis, along with a review of findings from prior field and laboratory studies, suggests that the net effect of interactions between coastal cutthroat trout and coho salmon do not appear to inhibit their presence or densities in small streams along the Pacific Northwest.

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Recurrence time distribution and temporal clustering properties of a cellular automaton modelling landslide events

Nonlinear Processes in Geophysics ◽

10.5194/npg-20-1071-2013 ◽

2013 ◽

Vol 20 (6) ◽

pp. 1071-1078 ◽

Cited By ~ 1

Author(s):

E. Piegari ◽

R. Di Maio ◽

A. Avella

Keyword(s):

Time Series ◽

Probability Distribution ◽

Cellular Automaton ◽

Time Window ◽

Fano Factor ◽

Recent Analysis ◽

Recurrence Time ◽

Model Parameters ◽

Reasonable Prediction ◽

First Time

Abstract. Reasonable prediction of landslide occurrences in a given area requires the choice of an appropriate probability distribution of recurrence time intervals. Although landslides are widespread and frequent in many parts of the world, complete databases of landslide occurrences over large periods are missing and often such natural disasters are treated as processes uncorrelated in time and, therefore, Poisson distributed. In this paper, we examine the recurrence time statistics of landslide events simulated by a cellular automaton model that reproduces well the actual frequency-size statistics of landslide catalogues. The complex time series are analysed by varying both the threshold above which the time between events is recorded and the values of the key model parameters. The synthetic recurrence time probability distribution is shown to be strongly dependent on the rate at which instability is approached, providing a smooth crossover from a power-law regime to a Weibull regime. Moreover, a Fano factor analysis shows a clear indication of different degrees of correlation in landslide time series. Such a finding supports, at least in part, a recent analysis performed for the first time of an historical landslide time series over a time window of fifty years.

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Estimation of the relative abundance of species in artificial mixtures of insects using low-coverage shotgun metagenomics

Metabarcoding and Metagenomics ◽

10.3897/mbmg.4.48281 ◽

2020 ◽

Vol 4 ◽

Cited By ~ 3

Author(s):

Lidia Garrido-Sanz ◽

Miquel Àngel Senar ◽

Josep Piñol

Keyword(s):

Relative Abundance ◽

Species Abundance ◽

Single Species ◽

Insect Species ◽

Individual Species ◽

Advanced Degree ◽

Mixed Species ◽

Species List ◽

Shotgun Metagenomics ◽

Low Coverage

Amplicon metabarcoding is an established technique to analyse the taxonomic composition of communities of organisms using high-throughput DNA sequencing, but there are doubts about its ability to quantify the relative proportions of the species, as opposed to the species list. Here, we bypass the enrichment step and avoid the PCR-bias, by directly sequencing the extracted DNA using shotgun metagenomics. This approach is common practice in prokaryotes, but not in eukaryotes, because of the low number of sequenced genomes of eukaryotic species. We tested the metagenomics approach using insect species whose genome is already sequenced and assembled to an advanced degree. We shotgun-sequenced, at low-coverage, 18 species of insects in 22 single-species and 6 mixed-species libraries and mapped the reads against 110 reference genomes of insects. We used the single-species libraries to calibrate the process of assignation of reads to species and the libraries created from species mixtures to evaluate the ability of the method to quantify the relative species abundance. Our results showed that the shotgun metagenomic method is easily able to set apart closely-related insect species, like four species of Drosophila included in the artificial libraries. However, to avoid the counting of rare misclassified reads in samples, it was necessary to use a rather stringent detection limit of 0.001, so species with a lower relative abundance are ignored. We also identified that approximately half the raw reads were informative for taxonomic purposes. Finally, using the mixed-species libraries, we showed that it was feasible to quantify with confidence the relative abundance of individual species in the mixtures.

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Labour sharing promotes coexistence in atrazine degrading bacterial communities

Scientific Reports ◽

10.1038/s41598-019-54978-2 ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 5

Author(s):

Loren Billet ◽

Marion Devers ◽

Nadine Rouard ◽

Fabrice Martin-Laurent ◽

Aymé Spor

Keyword(s):

Bacterial Communities ◽

Gene Loss ◽

Bacterial Species ◽

Single Species ◽

Microbial Consortia ◽

The Public ◽

Herbicide Atrazine ◽

Set Up ◽

Multiple Species ◽

Isolated Species

AbstractMicrobial communities are pivotal in the biodegradation of xenobiotics including pesticides. In the case of atrazine, multiple studies have shown that its degradation involved a consortia rather than a single species, but little is known about how interdependency between the species composing the consortium is set up. The Black Queen Hypothesis (BQH) formalized theoretically the conditions leading to the evolution of dependency between species: members of the community called ‘helpers’ provide publicly common goods obtained from the costly degradation of a compound, while others called ‘beneficiaries’ take advantage of the public goods, but lose access to the primary resource through adaptive degrading gene loss. Here, we test whether liquid media supplemented with the herbicide atrazine could support coexistence of bacterial species through BQH mechanisms. We observed the establishment of dependencies between species through atrazine degrading gene loss. Labour sharing between members of the consortium led to coexistence of multiple species on a single resource and improved atrazine degradation potential. Until now, pesticide degradation has not been approached from an evolutionary perspective under the BQH framework. We provide here an evolutionary explanation that might invite researchers to consider microbial consortia, rather than single isolated species, as an optimal strategy for isolation of xenobiotics degraders.

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Two new frog species (Microhylidae: Cophixalus) from the Australian Wet Tropics region, and redescription of Cophixalus ornatus

Zootaxa ◽

10.11646/zootaxa.3271.1.1 ◽

2012 ◽

Vol 3271 (1) ◽

pp. 1 ◽

Cited By ~ 1

Author(s):

CONRAD J. HOSKIN

Keyword(s):

Single Species ◽

Biological Species ◽

Tropical Rainforests ◽

Genetic Lineages ◽

North East ◽

The North ◽

Mating Call ◽

The Family ◽

Wet Tropics ◽

Multiple Species

In Australia the frog family Microhylidae is largely restricted to tropical rainforests of the Wet Tropics region in the north-east of the country, but in that region the family is diverse. Only one species, Cophixalus ornatus, is widespread in the WetTropics but there has been suspicion that it may comprise multiple species. A recent study (Hoskin et al. 2011) assessedgenetic and phenotypic variation across the range of C. ornatus, finding three deeply divergent genetic lineages that differin mating call and some aspects of morphology. Two of these lineages abutt in the central Wet Tropics and in that areahybridization was found to be very limited despite sympatry at high densities. Based on multiple lines of data, Hoskin etal. (2011) concluded that the three genetic lineages represent biological species. The taxonomy of these three lineages isresolved here. I describe two new species, Cophixalus australis sp. nov. and Cophixalus hinchinbrookensis sp. nov., andredescribe C. ornatus. The three species are not distinguishable based on any single morphological or call trait and arebest identified by genetics or locality. The distributions of the three species are largely allopatric. Cophixalus ornatus isfound in rainforest in the northern Wet Tropics, C. australis sp. nov. occurs in rainforest and adjacent wet sclerophyllforests in the central and southern Wet Tropics, and C. hinchinbrookensis sp. nov. inhabits rainforest and montane heathon Hinchinbrook Island. All three species are common. Cophixalus australis sp. nov. contains three genetic subgroupsthat are considered a single species based on phenotypic similarity and high levels of hybridization at contact zones. Thedescription of Cophixalus australis sp. nov. and Cophixalus hinchinbrookensis sp. nov. brings the number of Australian Cophixalus species to 18, 15 of which are restricted to the Wet Tropics region.

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Semi-analytic forecasts for JWST – II. Physical properties and scaling relations for galaxies at z = 4–10

Monthly Notices of the Royal Astronomical Society ◽

10.1093/mnras/stz2755 ◽

2019 ◽

Vol 490 (2) ◽

pp. 2855-2879 ◽

Cited By ~ 14

Author(s):

L Y Aaron Yung ◽

Rachel S Somerville ◽

Gergö Popping ◽

Steven L Finkelstein ◽

Harry C Ferguson ◽

...

Keyword(s):

Star Formation ◽

Physical Properties ◽

High Redshift ◽

Formation Rate ◽

Distribution Functions ◽

Scaling Relations ◽

Physical Parameters ◽

Model Parameters ◽

Galaxy Populations ◽

The Impact

ABSTRACT The long anticipated James Webb Space Telescope (JWST) will be able to directly detect large samples of galaxies at very high redshift. Using the well-established, computationally efficient Santa Cruz semi-analytic model, with recently implemented multiphase gas partitioning, and H2-based star formation recipes, we make predictions for a wide variety of galaxy properties for galaxy populations at z = 4–10. In this work, we provide forecasts for the physical properties of high-redshift galaxies and links to their photometric properties. With physical parameters calibrated only to z ∼ 0 observations, our model predictions are in good agreement with current observational constraints on stellar mass and star formation rate distribution functions up to z ∼ 8. We also provide predictions representing wide, deep, and lensed JWST survey configurations. We study the redshift evolution of key galaxy properties and the scaling relations among them. Taking advantage of our models’ high computational efficiency, we study the impact of systematically varying the model parameters. All distribution functions and scaling relations presented in this work are available at https://www.simonsfoundation.org/semi-analytic-forecasts-for-jwst/.

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Three new species of leaflitter frogs from the upper Amazon forests: cryptic diversity within Pristimantis "ockendeni" (Anura: Strabomantidae) in Ecuador

Zootaxa ◽

10.11646/zootaxa.1784.1.2 ◽

2008 ◽

Vol 1784 (1) ◽

pp. 11 ◽

Cited By ~ 19

Author(s):

KATHRYN R. ELMER ◽

DAVID C. CANNATELLA

Keyword(s):

New Species ◽

Dna Sequences ◽

Amazon Basin ◽

Single Species ◽

Cryptic Diversity ◽

Morphological Differences ◽

Three New Species ◽

Multiple Species

We describe three new species of Pristimantis leaflitter frogs from the upper Amazon basin of Ecuador: Pristimantis achuar, Pristimantis altamnis, and Pristimantis kichwarum. Each of these new species was previously considered to be part of a single species, formerly known as Eleutherodactylus ockendeni (Boulenger) morph B. However, analysis of DNA sequences together with examination of the morphology of more than 600 specimens from Ecuador reveals that multiple species were confused under the same name. The morphological differences among the three new species are subtle but consistent: presence or absence of a black canthal stripe and/or supratympanic ridge, snout-vent length, and ventral colouration. The three species are generally allopatric and geographically restricted, although at some localities two of the species occur sympatrically.Describimos tres especies nuevas de ranas del sotobosque de la cuenca Amazónica Ecuatoriana: Pristimantis achuar, Pristimantis altamnis y Pristimantis kichwarum. Estas especies fueron consideradas antes como una sola especie bajo el nombre Eleutherodactylus ockendeni (Boulenger) morfo B. Sin embargo, el análisis de secuencias de ADN y la examinación de la morfología de más que 600 especímenes Ecuatorianos indican que en realidad existen tres especies. Sus diferencias morfológicas son sutiles pero constantes: presencia o ausencia de una raya cantal negra y/o de un pliegue supratimpánico y su coloración ventral. Las tres especies tienen distribuciones alopátricas y distintas aunque en algunas localidades se puede encontrar dos de las tres especies juntas.

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A MODEL OF DYNAMIC REWIRING AND KNOWLEDGE EXCHANGE IN R&D NETWORKS

Advances in Complex Systems ◽

10.1142/s0219525916500041 ◽

2016 ◽

Vol 19 (01n02) ◽

pp. 1650004 ◽

Cited By ~ 8

Author(s):

MARIO V. TOMASELLO ◽

CLAUDIO J. TESSONE ◽

FRANK SCHWEITZER

Keyword(s):

Network Performance ◽

Formation Rate ◽

Knowledge Exchange ◽

Model Parameters ◽

Agent Based Model ◽

Knowledge Space ◽

Interaction Radius ◽

Agent Based ◽

Knowledge Stocks ◽

Alliance Partners

This paper investigates the process of knowledge exchange in inter-firm Research and Development (R&D) alliances by means of an agent-based model. Extant research has pointed out that firms select alliance partners considering both network-related and network-unrelated features (e.g., social capital versus complementary knowledge stocks). In our agent-based model, firms are located in a metric knowledge space. The interaction rules incorporate an exploration phase and a knowledge transfer phase, during which firms search for a new partner and then evaluate whether they can establish an alliance to exchange their knowledge stocks. The model parameters determining the overall system properties are the rate at which alliances form and dissolve and the agents’ interaction radius. Next, we define a novel indicator of performance, based on the distance traveled by the firms in the knowledge space. Remarkably, we find that — depending on the alliance formation rate and the interaction radius — firms tend to cluster around one or more attractors in the knowledge space, whose position is an emergent property of the system. And, more importantly, we find that there exists an inverted U-shaped dependence of the network performance on both model parameters.

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