How long would it take to become a giant squid?

Laboratory and field studies suggest that cephalopod growth occurs rapidly and is linked to temperature throughout a short life span. For giant squid such as Architeuthis, a paucity of size-at-age data means that growth is only inferred from isolated field specimens, based on either statoliths or isotopic analyses of tissue. In this study we apply simple growth models to obtain projections of the life span required to achieve the Architeuthis average body mass in scenarios which include an energy balance between rates of food intake and expenditure on growth and metabolism. Although the analysis shows that a wide range for the estimated life span is possible, energy conservation suggests that achievement of a larger size would be assisted by slower exponential growth early on. The results are compared with a sparse set of size-at-age data obtained from male and female Architeuthis wild specimens and possibly hint at some behavioural differences between males and females.     

How long does it take to equilibrate the unfolded state of a protein?

How long does it take to equilibrate the unfolded state of a protein? The answer to this question has important implications for our understanding of why many small proteins fold with two state kinetics. When the equilibration within the unfolded state U is much faster than the folding, the folding kinetics will be two state even if there are many folding pathways with different barriers. Yet the mean first passage times (MFPTs) between different regions of the unfolded state can be much longer than the folding time. This seems to imply that the equilibration within U is much slower than the folding. In this communication we resolve this paradox. We present a formula for estimating the time to equilibrate the unfolded state of a protein. We also present a formula for the MFPT to any state within U, which is proportional to the average lifetime of that state divided by the state population. This relation is valid when the equilibration within U is very fast as compared with folding as it often is for small proteins. To illustrate the concepts, we apply the formulas to estimate the time to equilibrate the unfolded state of Trp-cage and MFPTs within the unfolded state based on a Markov State Model using an ultra-long 208 microsecond trajectory of the miniprotein to parameterize the model. The time to equilibrate the unfolded state of Trp-cage is ∼100 ns while the typical MFPTs within U are tens of microseconds or longer.     

How long did it take for life to begin and evolve to cyanobacteria?

There is convincing paleontological evidence showing that stromatolite-building phototactic prokaryotes were already in existence 3.5 × 10⁹ years ago. Late accretion impacts may have killed off life on our planet as late as 3.8 × 10⁹ years ago. This leaves only 300 million years to go from the prebiotic soup to the RNA world and to cyanobacteria. However, 300 million years should be more than sufficient time. All known prebiotic reactions take place in geologically rapid time scales, and very slow prebiotic reactions are not feasible because the intermediate compounds would have been destroyed due to the passage of the entire ocean through deep-sea vents every 10⁷ years or in even less time. Therefore, it is likely that self-replicating systems capable of undergoing Darwinian evolution emerged in a period shorter than the destruction rates of its components (<5 million years). The time for evolution from the first DNA/protein organisms to cyanobacteria is usually thought to be very long. However, the similarities of many enzymatic reactions, together with the analysis of the available sequence data, suggest that a significant number of the components involved in basic biological processes are the result of ancient gene duplication events. Assuming that the rate of gene duplication of ancient prokaryotes was comparable to today's present values, the development of a filamentous cyanobacterial-like genome would require approximately 7 × 10⁶ years—or perhaps much less. Thus, in spite of the many uncertainties involved in the estimates of time for life to arise and evolve to cyanobacteria, we see no compelling reason to assume that this process, from the beginning of the primitive soup to cyanobacteria, took more than 10 million years.Correspondence to: A. Lazcano     

Subfunctionalization: How often does it occur? How long does it take?

The mechanisms responsible for the preservation of duplicate genes have been debated for more than 70 years. Recently, Lynch and Force have proposed a new explanation: subfunctionalization--after duplication the two gene copies specialize to perform complementary functions. We investigate the probability that subfunctionalization occurs, the amount of time after duplication that it takes for the outcome to be resolved, and the relationship of these quantities to the population size and mutation rates.     

How many polymorphic marker genes will it take to span the human genome?

It is desirable to know how many polymorphic marker loci will be required so that every human genetic locus can be mapped by classical pedigree methods to a specific region of a specific chromosome. Assuming a total autosomal map length of 33 morgans, it would take only about 33/(2d) evenly spaced markers for every locus to be within d morgans of a marker. Taking into account that the markers will fall randomly along the genome, we show that a much larger number of such loci will have to be isolated and tested before the goal of a saturated gene map is reached.     

What does it take to make a heart?

Ever increasing advances are being made in our quest to understand what it takes to direct pluripotent precursor cells to adopt a specific developmental fate. Eventually, the obvious goal is that targeted manipulation of these precursor cells will result in an efficient and reliable production of tissue‐specific cells, which can be safely employed for therapeutic purposes. We have gained an incredible insight as to which molecular pathways are involved in governing neural, skeletal and cardiac muscle fate decisions. However, we still face the challenge of how to direct, for example, a cardiac fate in stem cells in the amounts needed to be employed for regenerative means. Equally importantly, we need to resolve critical questions such as: can the in vitro generated cardiomyocytes actually functionally replace damaged heart tissue? Here I will provide an overview of the molecules and signalling pathways that have first been demonstrated in embryological studies to function in cardiogenesis, and summarize how this knowledge is being applied to differentiate mouse and human embryonic stem cells into cardiomyocytes.     

What does it take to get the job done?

I am extremely honored to be the recipient of the 2015 Women in Cell Biology Junior Award. When I reflect on my journey in science, many great people and memorable experiences come to mind. Some of these encounters were truly career-defining moments. Others provided priceless lessons. In this essay, I recount some of the moments and experiences that influenced my scientific trajectory with the hope that they may inspire others.     

How does life adapt to a gravitational environment? The outline of the terrestrial gastropod shell

How do several characteristics adapt to gravity while mutually influencing each other? Our study addresses this issue by focusing on the terrestrial gastropod shell. The geometric relationship between the spire index (shell height/diameter) and outline (cylindricality) is theoretically estimated. When the shell grows isometrically, a high-spired shell becomes conical in shape and a low-spired shell becomes cylindrical in shape. A physical model shows that the lowest- and highest-spired shells are the most balanced. In addition, a cone shape is the most balanced for a low-spired shell, and a column shape is the most balanced for a high-spired shell. Spire index and cylindricality measured for freshwater gastropods follow the relationship estimated by the model, whereas those for terrestrial gastropods deviate from this relationship. This translates to a high shell being more cylindrical than a flat shell, except in the case of extremely high or low shells. This suggests that the shape of the most balanced shells (lowest and highest shell heights) is constrained by coiling geometry but that relatively unbalanced shells (intermediate shell heights) do not follow a coiling geometry, as a result of adaptation to enable the snail to carry its shell more effectively.     

Recognition and the evolution of distinctive signatures: when does it pay to reveal identity?

A simple evolutionarily stable strategy (ESS) model of identity advertisement is presented, which is applicable to many different situations, ranging from parental recognition of young to recognition of kin by workers in social insect colonies that comprise several genetically distinct lineages. The model assumes that the receiver may respond favourably or unfavourably to the signaller, but that it cannot immediately determine which type of response is appropriate. The signaller, who always benefits by eliciting a favourable response (but is unaware of which type of response is appropriate for the receiver), may choose to reveal or conceal its identity, making the task of discrimination easier or harder for the receiver. The evolutionarily stable outcome of the model depends on the probability that an unfavourable response is appropriate, the relative costs to the receiver of acceptance and rejection errors, and the relative benefits to the signaller of eliciting a favourable response when this is appropriate and when it is inappropriate for the receiver. High costs of acceptance errors to the receiver, and high benefits of appropriate favourable responses to the signaller, favour provision of distinctive identity cues: so, paradoxically, does a high probability that an unfavourable response is appropriate. However, under a wide range of conditions, selection favours the withholding of signature cues, which prevents discrimination by the receiver. Finally, if the signaller must provide some information to elicit a favourable response, but stands to gain more from such a response when it is undesirable, it may do best to provide partial but incomplete information about its identity.     

Does one subgenome become dominant in the formation and evolution of a polyploid?

BackgroundPolyploids are common in flowering plants and they tend to have more expanded ranges of distributions than their diploid progenitors. Possible mechanisms underlying polyploid success have been intensively investigated. Previous studies showed that polyploidy generates novel changes and that subgenomes in allopolyploid species often differ in gene number, gene expression levels and levels of epigenetic alteration. It is widely believed that such differences are the results of conflicts among the subgenomes. These differences have been treated by some as subgenome dominance, and it is claimed that the magnitude of subgenome dominance increases in polyploid evolution.ScopeIn addition to changes which occurred during evolution, differences between subgenomes of a polyploid species may also be affected by differences between the diploid donors and changes which occurred during polyploidization. The variable genome components in many plant species are extensive, which would result in exaggerated differences between a subgenome and its progenitor when a single genotype or a small number of genotypes are used to represent a polyploid or its donors. When artificially resynthesized polyploids are used as surrogates for newly formed genotypes which have not been exposed to evolutionary selection, differences between diploid genotypes available today and those involved in the formation of the natural polyploid genotypes must also be considered.ConclusionsContrary to the now widely held views that subgenome biases in polyploids are the results of conflicts among the subgenomes and that one of the parental subgenomes generally retains more genes which are more highly expressed, available results show that subgenome biases mainly reflect legacy from the progenitors and that they can be detected before the completion of polyploidization events. Further, there is no convincing evidence that the magnitudes of subgenome biases have significantly changed during evolution for any of the allopolyploid species assessed.     

HLA-DQ system and insulin-dependent diabetes mellitus in Japanese: does it contribute to the development of IDDM as it does in Caucasians?

Fifty-six unrelated Japanese patients with insulin-dependent diabetes mellitus (IDDM) were HLA-typed, and restriction fragment length polymorphism (RFLP) analysis was performed after enzyme digestion with Bam HI and Taq I by using both DR and DQ probes. As previously reported, increased frequencies of Bw54, Cw1, DR4, and DRw53, which are in strong linkage disequilibrium in the Japanese population and make the characteristic Japanese haplotype, were confirmed. DQw4, a new allele of the DQ system recognized by the monoclonal antibody HU-46 and in linkage disequilibrium with this haplotype, presented the highest IDDM association. The RFLP analysis also showed the strongest correlation to IDDM when the DQ probe was applied. These results indicate that HLA-DQ might play the most important role in the development of IDDM in Japanese as well as in Caucasians. The correlation of DQ amino acid sequences strongly associated with IDDM in Japanese are discussed in this study, and contrasting results were found when such sequences were compared with those of Caucasians.Abbreviations used in this paper IDDM insulin-dependent diabetes mellitus - RFLP restriction fragment length polymorphism - Asp aspartic acid - Asp-57 aspartic acid at the 57th residue of the DQ chain - non-Asp-57 nonaspartic acid at the 57th residue of the DQ chain - R.R. relative risk of Woolf and Haldane     

How does transferrin overcome the in vitro block to development of the mouse preimplantation embryo?

Transferrin promotes development of mouse embryos through the two-cell block in vitro. Uptake of transferrin into blastocysts was shown to occur by both receptor-mediated and nonspecific pathways, but neither pathway was used to a detectable extent by embryos before the eight-cell stage. Conversely, the dialysis of culture medium, non-permissive for development through the two-cell block, against a solution of transferrin rendered it capable of supporting development. It was therefore concluded that transferrin exerts its supportive effect on development in vitro via its chelating effects.     

When does it pay to invest in a patch? The evolution of intentional niche construction

Humans modify their environments in ways that significantly transform the earth's ecosystems. 1 - 3 Recent research suggests that such niche‐constructing behaviors are not passive human responses to environmental variation, but instead should be seen as active and intentional management of the environment. 4 - 10 Although such research is useful in highlighting the interactive dynamics between humans and their natural world, the niche‐construction framework, as currently applied, fails to explain why people would decide to modify their environments in the first place. 11 - 13 To help resolve this problem, we use a model of technological intensification 14 , 15 to analyze the cost‐benefit trade‐offs associated with niche construction as a form of patch investment. We use this model to assess the costs and benefits of three paradigmatic cases of intentional niche construction in Western North America: the application of fire in acorn groves, the manufacture of fishing weirs, and the adoption of maize agriculture. Intensification models predict that investing in patch modification (niche construction) only provides a net benefit when the amount of resources needed crosses a critical threshold that makes the initial investment worthwhile. From this, it follows that low‐cost investments, such as burning in oak groves, should be quite common, while more costly investments, such as maize agriculture, should be less common and depend on the alternatives available in the local environment. We examine how patterns of mobility, 16 risk management, 17 territoriality, 12 and private property 18 also co‐evolve with the costs and benefits of niche construction. This approach illustrates that explaining niche‐constructing behavior requires understanding the economic trade‐offs involved in patch investment. Integrating concepts from niche construction and technological intensification models within a behavioral ecological framework provides insights into the coevolution and active feedback between adaptive behaviors and environmental change across human history.     

Immunosensing during colonization by Candida albicans: does it take a village to colonize the intestine?

Candida albicans, an opportunistic fungal pathogen and a component of the normal flora of the gastrointestinal tract, is a frequent colonizer of humans. Is C. albicans capable of sensing the immune status of its host, a process we term immunosensing, and, if so, how? C. albicans causes serious disease only in immunocompromised hosts and therefore the ability to immunosense would be advantageous to an organism. We propose a speculative model whereby, during colonization, C. albicans produces phenotypic variants that vary in relative concentration depending on host status. One variant is optimized for persistence as a commensal, whereas the other variant has higher capacity to initiate pathogenic interactions. When the ratio of the two variants changes, the pathogenic potential of the population changes. The critical element of this model is that the C. albicans colonizing population is not uniform but is composed of subpopulations of phenotypic variants that are advantageous under different host conditions.