Can calmodulin function without binding calcium?

Calmodulin is a small Ca(2+)-binding protein proposed to act as the intracellular Ca2+ receptor that translates Ca2+ signals into cellular responses. We have constructed mutant yeast calmodulins in which the Ca(2+)-binding loops have been altered by site-directed mutagenesis. Each of the mutant proteins has a dramatically reduced affinity for Ca2+; one does not bind detectable levels of 45Ca2+ either during gel filtration or when bound to a solid support. Furthermore, none of the mutant proteins change conformation even in the presence of high Ca2+ concentrations. Surprisingly, yeast strains relying on any of the mutant calmodulins not only survive but grow well. In contrast, yeast strains deleted for the calmodulin gene are not viable. Thus, calmodulin is required for growth, but it can perform its essential function without the apparent ability to bind Ca2+.     

Do calcium and calmodulin trigger maturation in amphibian oocytes?

In contrast to earlier reports (J. L. Maller and E. G. Krebs, 1980, Curr. Top. Cell. Regul. 16, 271-311; M. Moreau, J. P. Vilian, and P. Guerrier, 1980, Dev. Biol. 78, 201-214; W. J. Wasserman and L. D. Smith, 1981, J. Cell Biol. 89, 389-394; D. Huchon, R. Ozon, E. H. Fischer, and J. G. Demaille, 1981, Mol. Cell. Endocrinol. 22, 211-222) calmodulin preparations isolated from Xenopus laevis ovaries or obtained commercially rarely induced maturation upon microinjection into individual oocytes. Calmodulin injections did result in significant cases of maturation when oocytes were first pretreated (primed) with calcium-free (EGTA) OR-2 and then injected in regular OR-2 medium. However, under these conditions the injected buffer solution alone was sometimes found to induce maturation. Under more optimal priming conditions, cases were found where as high as 100% of the oocytes matured simply by returning them to regular OR-2 medium. To determine which divalent cations could be involved in the priming effects of EGTA pretreatment we repeated the earlier ionophore work of W. J. Wasserman and Y. Masui (1975, J. Exp. Zool. 193, 369-375), looking not just at calcium and magnesium but other divalent cations as well. Several divalent cations (10 mM) were found to induce germinal vesicle breakdown with the following tentative order of efficacy, Co2+ greater than or equal to Zn2+ greater than or equal to Mn2+ greater than Ca2+ greater than Mg2+ greater than Ba2+, regardless of whether or not ionophore A23187 was present. These results, along with other reports in the literature, are discussed with respect to the theory that a rise in free calcium and calmodulin is involved in triggering oocyte maturation; we conclude that neither is involved.     

Do protein motifs read the histone code?

The existence of different patterns of chemical modifications (acetylation, methylation, phosphorylation, ubiquitination and ADP-ribosylation) of the histone tails led, some years ago, to the histone code hypothesis. According to this hypothesis, these modifications would provide binding sites for proteins that can change the chromatin state to either active or repressed. Interestingly, some protein domains present in histone-modifying enzymes are known to interact with these covalent marks in the histone tails. This was first shown for the bromodomain, which was found to interact selectively with acetylated lysines at the histone tails. More recently, it has been described that the chromodomain can be targeted to methylation marks in histone N-terminal domains. Finally, the interaction between the SANT domain and histones is also well documented. Overall, experimental evidence suggests that these domains could be involved in the recruitment of histone-modifying enzymes to discrete chromosomal locations, and/or in the regulation their enzymatic activity. Within this context, we review the distribution of bromodomains, chromodomains and SANT domains among chromatin-modifying enzymes and discuss how they can contribute to the translation of the histone code.     

Do you have a probiotic in your future?

The possibility of using microbes to maintain health, and to prevent or treat disease is a topic as old as microbiology. However, one factor impeding the introduction of effective probiotics has been our very limited understanding of the composition of the human microbiome, as well as the biological requirements for these organisms. With advances in understanding the microbiome and its metagenome in humans and other mammals, we now can build a more robust scientific basis to develop probiotic strategies. Increasing knowledge of intramicrobial competition and cooperation, as well as host-microbe cross-signaling, will facilitate design of new probiotics and the modeling of their deployment, leading to eventual clinical trials.     

Do individual allocyclic chromosomes in metaphase reflect their interphase domains?

Summary Individual S phase allocyclic chromosomes have been analyzed in Bloom syndrome lymphocytes, in cells with an r(9), and in hypotetraploid Ehrlich mouse ascites cells treated with 1-methyl-2-benzyl hydrazine. On the basis of the following observations, we conclude that such chromosomes more or less reflect their domains in interphase: (1) The S phase allocyclic chromosomes have the same structure as S phase prematurely condensed chromatin (PCC) in fused cells; in other words they form limited areas of chromatin dots; (2) the allocyclic chromosome is the only chromosome in a metaphase plate which synthesizes DNA simultanneously with interphase nuclei; (3) the size of the allocyclic chromosomes is related to the size of the corresponding metaphase chromosome; and (4) the S phase allocyclic chromosomes resemble closely the chromosome domains in interphase made visible with biotinylated human DNA. A variety of evidence shows that most allocyclic chromosomes are simply left behind in their cycle, which presumably is caused by a deletion or inactivation of a hypothetical coiling center situated on each chromosome arm.     

Do bacteria have sex?

Do bacteria have genes for genetic exchange? The idea that the bacterial processes that cause genetic exchange exist because of natural selection for this process is shared by almost all microbiologists and population geneticists. However, this assumption has been perpetuated by generations of biology, microbiology and genetics textbooks without ever being critically examined.     

Do electrostatic interactions destabilize protein–nucleic acid binding?

The negatively charged phosphates of nucleic acids are often paired with positively charged residues upon binding proteins. It was thus counter-intuitive when previous Poisson-Boltzmann (PB) calculations gave positive energies from electrostatic interactions, meaning that they destabilize protein-nucleic acid binding. Our own PB calculations on protein-protein binding have shown that the sign and the magnitude of the electrostatic component are sensitive to the specification of the dielectric boundary in PB calculations. A popular choice for the boundary between the solute low dielectric and the solvent high dielectric is the molecular surface; an alternative is the van der Waals (vdW) surface. In line with results for protein-protein binding, in this article, we found that PB calculations with the molecular surface gave positive electrostatic interaction energies for two protein-RNA complexes, but the signs are reversed when the vdW surface was used. Therefore, whether destabilizing or stabilizing effects are predicted depends on the choice of the dielectric boundary. The two calculation protocols, however, yielded similar salt effects on the binding affinity. Effects of charge mutations differentiated the two calculation protocols; PB calculations with the vdW surface had smaller deviations overall from experimental data.     

LAST motifs and SMART domains in gene 32 protein: an unfolding story of autoregulation?

Bacteriophage T4 gene 32 protein is a classical single strand-specific DNA binding protein. It is a single polypeptide chain of 301 amino acid residues that consists of three structural domains, each of which has a binding function. The N-terminal domain is involved in homotypic protein-protein interaction (the basis of binding cooperativity), the core domain binds single strands directly, and the C-terminal domain has a role in heterotypic protein-protein association. The three domains have traditionally been thought to be independent of each other. However, the observation of a striking repetition of a basic, polar sequence (the "LAST" Motif), seen in both the N-terminal and core domains, suggests a linkage between these domains. Moreover, the C-domain and adjoining portion (flap) of the core are highly acidic, and are potential mimics of single-stranded DNA. With these observations, I construct a model in which this flap is associated with the ssDNA binding site in the absence of DNA, and upon cooperative protein binding to DNA, the flap now associates with the N-terminal domain of the adjacent DNA-bound protein. The flap thus acts as a gate, which might slow the binding of the protein to DNA. This could lead to the regulation of the protein's various interactions with other proteins, as well as affect its ability to lower DNA melting temperature.     

Pricklier with the proper predator? Predator‐induced small‐scale changes of spinescence in Daphnia

Phenotypic plasticity in defensive traits is a common response of prey organisms to variable and unpredictable predation regimes and risks. Cladocerans of the genus Daphnia are keystone species in the food web of lentic freshwater bodies and are well known for their ability to express a large variety of inducible morphological defenses in response to invertebrate and vertebrate predator kairomones. The developed defenses render the daphnids less susceptible to predation. So far, primarily large‐scale morphological defenses, like helmets, crests, and tail‐spines, have been documented. However, less is known on whether the tiny spinules, rather inconspicuous traits which cover many Daphnia’s dorsal and ventral carapace margins, respond to predator kairomones, as well. For this reason, we investigated two Daphnia species (D. magna and D. longicephala) concerning their predator kairomone‐induced changes in dorsal and ventral spinules. Since these small, inconspicuous traits may only act as a defense against predatory invertebrates, with fine‐structured catching apparatuses, and not against vertebrate predators, we exposed them to both, an invertebrate (Triops cancriformis or Notontecta maculata) and a vertebrate predator (Leucaspius delineatus). Our results show that the length of these spinules as well as spinules‐covered areas vary, likely depending on the predator the prey is exposed to. We further present first indications of a Daphnia species‐specific elongation of the spinules and an increase of the spinules‐bearing areas. Although we cannot exclude that spinescence is altered because it is developmentally connected to changes in body shape in general, our results suggest that the inducible alterations to the spinule length and spinules‐covered areas disclose another level of predator‐induced changes in two common Daphnia species. The predator‐induced changes on this level together with the large‐scale and ultrastructural defensive traits may act as the overall morphological defense, adjusted to specific predator regimes in nature.     

Do tastants have a smell?

The stimuli used in taste research are usually considered to be odourless. This was tested in two experiments with aqueous solutions of two representative compounds for each of the five taste qualities including umami. In the first experiment elderly and young subjects rated the intensity and pleasantness of three concentrations of the stimuli, while wearing or not wearing a noseclip. Saliva production was also measured. Blocking olfaction only influenced salivation for umami. It reduced taste intensity ratings, but as in an earlier experiment with the same compounds in food products, this effect was stronger in the young, who also liked the stimuli better wearing the noseclip. In the second experiment, another group of young people tried to detect the odours of the tastants dissolved in demineralized, double-distilled or Evian water. A considerable number of subjects could regularly detect seven of the ten tastants by olfaction and the extent to which they did correlated significantly with the reduction in taste intensity ratings for the different tastants found in the first experiment. We suggest that most tastants can be smelled and that this smell contributes to taste intensity ratings.     

Do the eyes have it?

Since Btt last examined the iris and retina markets, demand has grown, the technology has improved, new players have entered the arena and new products have been developed. For the first time ever, Btt is devoting a complete survey to these two very different methods of recognising an individual by the unique patterns within parts of their eye.     

Do hornets have zombie workers?

Colonies of the European hornet, Vespa crabro, are typically founded by a single queen mated to a single male. From the resulting colony relatedness pattern we predicted strong worker-queen conflict over male production where both the workers and the queen attempt to produce the colony's males. To test for this conflict, male production was studied in 15 hornet nests using a combination of DNA microsatellite analysis (282 males), worker ovary dissections (500 workers from eight nests) and 50 h of observation (four nests). In contrast to our prediction, the data show that hornet males are queens' sons, that workers never attempt to lay eggs, rarely have activated ovaries, and that there is no direct aggression between the queen and the workers. This contrasts with other data for vespine wasps, which support relatedness predictions. Dolichovespula arenaria has the same kin structure as V. crabro and workers produce males in many colonies. The similarity between these two species makes it difficult to explain why workers do not reproduce in V. crabro. Self-restraint is expected if worker reproduction significantly reduces colony productivity but there is no obvious reason why this should be important to V. crabro but not to D. arenaria. Alternatively, queen control may be important. The absence of expressed queen-worker conflict rules out physical control. Indirect pheromonal control is a possibility and is supported by the occurrence of royal courts and queen pheromone in Vespa but not Dolichovespula. Pheromonal queen control is considered evolutionarily unstable, but could result from a queen-worker arms race over reproductive control in which the queen is ahead. The genetic data also revealed diploid males in one colony, the first example in the vespine wasps, and two colonies with double matrilines, suggesting that occasional usurpation by spring queens occurs.     

PhosphoSerine/threonine binding domains: you can't pSERious?

The fundamental biological importance of protein phosphorylation is underlined by the existence of more than 500 protein kinase genes within the human genome. In many cases, phosphorylation on serine, threonine, and tyrosine residues creates binding surfaces for a variety of phospho-amino acid binding proteins/modules. Here, we review the insights into serine/threonine phosphorylation-dependent signal transduction processes provided by structures of several of these proteins and their complexes.     

Is negative density‐dependent reproduction regulated by density‐induced stress in root voles? Two field experiments

Density dependence in reproduction plays an important role in stabilizing population dynamics via immediate negative feedback from population density to reproductive output. Although previous studies have shown that negative density‐dependent reproduction is associated with strong spacing behavior and social interaction between individuals, the proximal mechanism for generating negative density‐dependent reproduction remains unclear. In this study, we investigated the effects of density‐induced stress on reproduction in root voles. Enclosed founder populations were established by introducing 6 (low density) and 30 (high density) adults per sex into per enclosure (four enclosures per density in total) during the breeding season from April to July 2012 and from May to August 2015. Fecal corticosterone metabolite (FCM) levels, reproductive traits (recruitment rate and the proportion of reproductively active individuals), and founder population numbers were measured following repeated live trapping in both years. The number of founders was negatively associated with recruitment rates and the proportion of reproductively active individuals, displaying a negative density‐dependent reproduction. FCM level was positively associated with the number of founders. The number of founder females directly affected the proportion of reproductive females, and directly and indirectly through their FCM levels affected the recruitment rate; the effect of the number of male founders on the proportion of reproductive males was mediated by their FCM level. Our results showed that density‐induced stress negatively affected reproductive traits and that density‐induced stress is one ecological factor generating negative density‐dependent reproduction.     

How many animals are used for SARS‐CoV‐2 research?: An overview on animal experimentation in pre‐clinical and basic research

Non‐technical summaries of research projects allow tracking the numbers and purpose of animal experiments related to SARS‐CoV2 research so as to provide greater transparency on animal use. Subject Categories: Economics, Law & Politics, Pharmacology & Drug Discovery, Science Policy & Publishing

The COVID‐19 pandemic has accelerated biomedical research and drug development to an unprecedented pace. Governments worldwide released emergency funding for biomedical research that allowed scientists to focus on COVID‐19 and related drug and vaccine development. As a result, a flood of scientific articles on SARS‐CoV‐2 and COVID‐19 was published since early 2020. More importantly though, within less than 2 years, scientists in academia and industry developed vaccines against the virus from scratch: Several vaccines have now received regulatory approval and are being mass produced to immunize the human population worldwide.This colossal success of science rests in large part on the shoulders of animals that were used in basic and pre‐clinical research and regulatory testing. Notwithstanding, animal experimentation has remained a highly controversial and heated topic between advocates for research and animal rights activists. During the past decades, European policymakers responded to the debate by enacting stricter regulations, which inevitably has increased the bureaucratic hurdles for experimentation on animals. Scientists have for long spoken out against this additional burden, arguing that both basic and translational researches to improve human health crucially relies on animal experimentation—as the COVID‐19 pandemic aptly demonstrated (Genzel et al, 2020).