New observations of fluorescent organisms in the Banda Sea and in the Red Sea.

Fluorescence is a widespread phenomenon found in animals, bacteria, fungi, and plants. In marine environments fluorescence has been proposed to play a role in physiological and behavioral responses. Many fluorescent proteins and other molecules have been described in jellyfish, corals, and fish. Here we describe fluorescence in marine species, which we observed and photographed during night dives in the Banda Sea, Indonesia, and in the Red Sea, Egypt. Among various phyla we found fluorescence in sponges, molluscs, tunicates, and fish. Our study extends the knowledge on how many different organisms fluoresce in marine environments. We describe the occurrence of fluorescence in 27 species, in which fluorescence has not been described yet in peer-reviewed literature. It especially extends the knowledge beyond Scleractinia, the so far best described taxon regarding diversity in fluorescent proteins.

Diversity and function of fluorescent molecules in marine animals.

Fluorescence in marine animals has mainly been studied in Cnidaria but is found in many different phyla such as Annelida, Crustacea, Mollusca, and Chordata. While many fluorescent proteins and molecules have been identified, very little information is available about the biological functions of fluorescence. In this review, we focus on describing the occurrence of fluorescence in marine animals and the behavioural and physiological functions of fluorescent molecules based on experimental approaches. These biological functions of fluorescence range from prey and symbiont attraction, photoprotection, photoenhancement, stress mitigation, mimicry, and aposematism to inter- and intraspecific communication. We provide a comprehensive list of marine taxa that utilise fluorescence, including demonstrated effects on behavioural or physiological responses. We describe the numerous known functions of fluorescence in anthozoans and their underlying molecular mechanisms. We also highlight that other marine taxa should be studied regarding the functions of fluorescence. We suggest that an increase in research effort in this field could contribute to understanding the capacity of marine animals to respond to negative effects of climate change, such as rising sea temperatures and increasing intensities of solar irradiation.

Amendment to: populations in environments with a soft carrying capacity are eventually extinct.

This sharpens the result in the paper Jagers and Zuyev (J Math Biol 81:845-851, 2020): consider a population changing at discrete (but arbitrary and possibly random) time points, the conditional expected change, given the complete past population history being negative, whenever population size exceeds a carrying capacity. Further assume that there is an [Formula: see text] such that the conditional probability of a population decrease at the next step, given the past, always exceeds [Formula: see text] if the population is not extinct but smaller than the carrying capacity. Then the population must die out.

Social signaling via bioluminescent blinks determines nearest neighbor distance in schools of flashlight fish Anomalops katoptron.

The schooling flashlight fish Anomalops katoptron can be found at dark nights at the water surface in the Indo-Pacific. Schools are characterized by bioluminescent blink patterns of sub-ocular light organs densely-packed with bioluminescent, symbiotic bacteria. Here we analyzed how blink patterns of A. katoptron are used in social interactions. We demonstrate that isolated specimen of A. katoptron showed a high motivation to align with fixed or moving artificial light organs in an experimental tank. This intraspecific recognition of A. katoptron is mediated by blinking light and not the body shape. In addition, A. katoptron adjusts its blinking frequencies according to the light intensities. LED pulse frequencies determine the swimming speed and the blink frequency response of A. katoptron, which is modified by light organ occlusion and not exposure. In the natural environment A. katoptron is changing its blink frequencies and nearest neighbor distance in a context specific manner. Blink frequencies are also modified by changes in the occlusion time and are increased from day to night and during avoidance behavior, while group cohesion is higher with increasing blink frequencies. Our results suggest that specific blink patterns in schooling flashlight fish A. katoptron define nearest neighbor distance and determine intraspecific communication.

Populations in environments with a soft carrying capacity are eventually extinct.

Consider a population whose size changes stepwise by its members reproducing or dying (disappearing), but is otherwise quite general. Denote the initial (non-random) size by [Formula: see text] and the size of the nth change by [Formula: see text], [Formula: see text]. Population sizes hence develop successively as [Formula: see text] and so on, indefinitely or until there are no further size changes, due to extinction. Extinction is thus assumed final, so that [Formula: see text] implies that [Formula: see text], without there being any other finite absorbing class of population sizes. We make no assumptions about the time durations between the successive changes. In the real world, or more specific models, those may be of varying length, depending upon individual life span distributions and their interdependencies, the age-distribution at hand and intervening circumstances. We could consider toy models of Galton-Watson type generation counting or of the birth-and-death type, with one individual acting per change, until extinction, or the most general multitype CMJ branching processes with, say, population size dependence of reproduction. Changes may have quite varying distributions. The basic assumption is that there is a carrying capacity, i.e. a non-negative number K such that the conditional expectation of the change, given the complete past history, is non-positive whenever the population exceeds the carrying capacity. Further, to avoid unnecessary technicalities, we assume that the change [Formula: see text] equals -1 (one individual dying) with a conditional (given the past) probability uniformly bounded away from 0. It is a simple and not very restrictive way to avoid parity phenomena, it is related to irreducibility in Markov settings. The straightforward, but in contents and implications far-reaching, consequence is that all such populations must die out. Mathematically, it follows by a supermartingale convergence property and positive probability of reaching the absorbing extinction state.

On the establishment of a mutant.

How long does it take for an initially advantageous mutant to establish itself in a resident population, and what does the population composition look like then? We approach these questions in the framework of the so called Bare Bones evolution model (Klebaner et al. in J Biol Dyn 5(2):147-162, 2011. https://doi.org/10.1080/17513758.2010.506041) that provides a simplified approach to the adaptive population dynamics of binary splitting cells. As the mutant population grows, cell division becomes less probable, and it may in fact turn less likely than that of residents. Our analysis rests on the assumption of the process starting from resident populations, with sizes proportional to a large carrying capacity K. Actually, we assume carrying capacities to be [Formula: see text] and [Formula: see text] for the resident and the mutant populations, respectively, and study the dynamics for [Formula: see text]. We find conditions for the mutant to be successful in establishing itself alongside the resident. The time it takes turns out to be proportional to [Formula: see text]. We introduce the time of establishment through the asymptotic behaviour of the stochastic nonlinear dynamics describing the evolution, and show that it is indeed [Formula: see text], where [Formula: see text] is twice the probability of successful division of the mutant at its appearance. Looking at the composition of the population, at times [Formula: see text], we find that the densities (i.e. sizes relative to carrying capacities) of both populations follow closely the corresponding two dimensional nonlinear deterministic dynamics that starts at a random point. We characterise this random initial condition in terms of the scaling limit of the corresponding dynamics, and the limit of the properly scaled initial binary splitting process of the mutant. The deterministic approximation with random initial condition is in fact valid asymptotically at all times [Formula: see text] with [Formula: see text].

What can be observed in real time PCR and when does it show?

Real time, or quantitative, PCR typically starts from a very low concentration of initial DNA strands. During iterations the numbers increase, first essentially by doubling, later predominantly in a linear way. Observation of the number of DNA molecules in the experiment becomes possible only when it is substantially larger than initial numbers, and then possibly affected by the randomness in individual replication. Can the initial copy number still be determined? This is a classical problem and, indeed, a concrete special case of the general problem of determining the number of ancestors, mutants or invaders, of a population observed only later. We approach it through a generalised version of the branching process model introduced in Jagers and Klebaner (J Theor Biol 224(3):299-304, 2003. doi: 10.1016/S0022-5193(03)00166-8 ), and based on Michaelis-Menten type enzyme kinetical considerations from Schnell and Mendoza (J Theor Biol 184(4):433-440, 1997). A crucial role is played by the Michaelis-Menten constant being large, as compared to initial copy numbers. In a strange way, determination of the initial number turns out to be completely possible if the initial rate v is one, i.e all DNA strands replicate, but only partly so when [Formula: see text], and thus the initial rate or probability of succesful replication is lower than one. Then, the starting molecule number becomes hidden behind a "veil of uncertainty". This is a special case, of a hitherto unobserved general phenomenon in population growth processes, which will be adressed elsewhere.

Activation of odorant receptor in colorectal cancer cells leads to inhibition of cell proliferation and apoptosis.

The analysis and functional characterization of ectopically expressed human olfactory receptors (ORs) is becoming increasingly important, as many ORs have been identified in several healthy and cancerous tissues. OR activation has been demonstrated to have influence on cancer cell growth and progression. Here, ORs were identified using RNA-Seq analyses and RT-PCR. We demonstrated the OR protein localization in HCT116 cells using immunocytochemistry (IHC). In order to analyze the physiological role of OR51B4, we deorphanized the receptor by the use of CRE-Luciferase assays, conducted calcium imaging experiments as well as scratch- and proliferation assays. Furthermore, western blot analyses revealed the involvement of different protein kinases in the ligand-dependent signaling pathway. Receptor knockdown via shRNA was used to analyze the involvement of OR51B4. We identified OR51B4, which is highly expressed in the colon cancer cell line HCT116 and in native human colon cancer tissues. We deorphanized the receptor and identified Troenan as an effective ligand. Troenan stimulation of HCT116 cells has anti-proliferative, anti-migratory and pro-apoptotic effects, mediated by changes in the intracellular calcium level upon PLC activation. These effects cause changes in the phosphorylation levels of p38, mTor and Akt kinases. Knockdown of the receptor via shRNA confirmed the involvement of OR51B4. This study emphasizes the importance of ectopically expressed ORs in the therapy for several diseases. The findings provide the basis for alternative treatments of colorectal cancer.

The Flashlight Fish Anomalops katoptron Uses Bioluminescent Light to Detect Prey in the Dark.

Bioluminescence is a fascinating phenomenon occurring in numerous animal taxa in the ocean. The reef dwelling splitfin flashlight fish (Anomalops katoptron) can be found in large schools during moonless nights in the shallow water of coral reefs and in the open surrounding water. Anomalops katoptron produce striking blink patterns with symbiotic bacteria in their sub-ocular light organs. We examined the blink frequency in A. katoptron under various laboratory conditions. During the night A. katoptron swims in schools roughly parallel to their conspecifics and display high blink frequencies of approximately 90 blinks/minute with equal on and off times. However, when planktonic prey was detected in the experimental tank, the open time increased compared to open times in the absence of prey and the frequency decreased to 20% compared to blink frequency at night in the absence of planktonic prey. During the day when the school is in a cave in the reef tank the blink frequency decreases to approximately 9 blinks/minute with increasing off-times of the light organ. Surprisingly the non-luminescent A. katoptron with non-functional light organs displayed the same blink frequencies and light organ open/closed times during the night and day as their luminescent conspecifics. In the presence of plankton non-luminescent specimens showed no change in the blink frequency and open/closed times compared to luminescent A. katoptron. Our experiments performed in a coral reef tank show that A. katoptron use bioluminescent illumination to detect planktonic prey and that the blink frequency of A. katoptron light organs follow an exogenous control by the ambient light.

On the establishment, persistence, and inevitable extinction of populations.

Comprehensive models of stochastic, clonally reproducing populations are defined in terms of general branching processes, allowing birth during maternal life, as for higher organisms, or by splitting, as in cell division. The populations are assumed to start small, by mutation or immigration, reproduce supercritically while smaller than the habitat carrying capacity but subcritically above it. Such populations establish themselves with a probability wellknown from branching process theory. Once established, they grow up to a band around the carrying capacity in a time that is logarithmic in the latter, assumed large. There they prevail during a time period whose duration is exponential in the carrying capacity. Even populations whose life style is sustainble in the sense that the habitat carrying capacity is not eroded but remains the same, ultimately enter an extinction phase, which again lasts for a time logarithmic in the carrying capacity. However, if the habitat can carry a population which is large, say millions of individuals, and it manages to avoid early extinction, time in generations to extinction will be exorbitantly long, and during it, population composition over ages, types, lineage etc. will have time to stabilise. This paper aims at an exhaustive description of the life cycle of such populations, from inception to extinction, extending and overviewing earlier results. We shall also say some words on persistence times of populations with smaller carrying capacities and short life cycles, where the population may indeed be in danger in spite of not eroding its environment.

Stochasticity in the adaptive dynamics of evolution: the bare bones.

First a population model with one single type of individuals is considered. Individuals reproduce asexually by splitting into two, with a population-size-dependent probability. Population extinction, growth and persistence are studied. Subsequently the results are extended to such a population with two competing morphs and are applied to a simple model, where morphs arise through mutation. The movement in the trait space of a monomorphic population and its possible branching into polymorphism are discussed. This is a first report. It purports to display the basic conceptual structure of a simple exact probabilistic formulation of adaptive dynamics.

Nuclear energy.

Nuclear energy can play a role in carbon free production of electrical energy, thus making it interesting for tomorrow's energy mix. However, several issues have to be addressed. In fission technology, the design of so-called fourth generation reactors show great promise, in particular in addressing materials efficiency and safety issues. If successfully developed, such reactors may have an important and sustainable part in future energy production. Working fusion reactors may be even more materials efficient and environmental friendly, but also need more development and research. The roadmap for development of fourth generation fission and fusion reactors, therefore, asks for attention and research in these fields must be strengthened.

A plea for stochastic population dynamics.

It is argued that biological populations are finite and consisting of individuals with varying life span and reproduction, and that they should be thus modelled. Modern probability theory provides tools for this.

On the path to extinction.

Populations can die out in many ways. We investigate one basic form of extinction, stable or intrinsic extinction, caused by individuals on the average not being able to replace themselves through reproduction. The archetypical such population is a subcritical branching process, i.e., a population of independent, asexually reproducing individuals, for which the expected number of progeny per individual is less than one. The main purpose is to uncover a fundamental pattern of nature. Mathematically, this emerges in large systems, in our case subcritical populations, starting from a large number, x, of individuals. First we describe the behavior of the time to extinction T: as x grows to infinity, it behaves like the logarithm of x, divided by r, where r is the absolute value of the Malthusian parameter. We give a more precise description in terms of extreme value distributions. Then we study population size partway (or u-way) to extinction, i.e., at times uT, for 0 < u < 1, e.g., u = 1/2 gives halfway to extinction. (Note that mathematically this is no stopping time.) If the population starts from x individuals, then for large x, the proper scaling for the population size at time uT is x into the power u - 1. Normed by this factor, the population u-way to extinction approaches a process, which involves constants that are determined by life span and reproduction distributions, and a random variable that follows the classical Gumbel distribution in the continuous time case. In the Markov case, where an explicit representation can be deduced, we also find a description of the behavior immediately before extinction.

Random variation and concentration effects in PCR.

Even though the efficiency of the polymerase chain reaction (PCR) reaction decreases, analyses are made in terms of Galton-Watson processes, or simple deterministic models with constant replication probability (efficiency). Recently, Schnell and Mendoza have suggested that the form of the efficiency, can be derived from enzyme kinetics. This results in the sequence of molecules numbers forming a stochastic process with the properties of a branching process with population size dependence, which is supercritical, but has a mean reproduction number that approaches one. Such processes display ultimate linear growth, after an initial exponential phase, as is the case in PCR. It is also shown that the resulting stochastic process for a large Michaelis-Menten constant behaves like the deterministic sequence x(n) arising by iterations of the function f(x)=x+x/(1+x).