Breaking Lander-Waterman’s Coverage Bound

Lander-Waterman’s coverage bound establishes the total number of reads required to cover the whole genome of size G bases. In fact, their bound is a direct consequence of the well-known solution to the coupon collector’s problem which proves that for such genome, the total number of bases to be sequenced should be O(G ln G). Although the result leads to a tight bound, it is based on a tacit assumption that the set of reads are first collected through a sequencing process and then are processed through a computation process, i.e., there are two different machines: one for sequencing and one for processing. In this paper, we present a significant improvement compared to Lander-Waterman’s result and prove that by combining the sequencing and computing processes, one can re-sequence the whole genome with as low as O(G) sequenced bases in total. Our approach also dramatically reduces the required computational power for the combined process. Simulation results are performed on real genomes with different sequencing error rates. The results support our theory predicting the log G improvement on coverage bound and corresponding reduction in the total number of bases required to be sequenced.     

Astrobiological Phase Transition: Towards Resolution of Fermi’s Paradox

Can astrophysics explain Fermi’s paradox or the “Great Silence” problem? If available, such explanation would be advantageous over most of those suggested in literature which rely on unverifiable cultural and/or sociological assumptions. We suggest, instead, a general astrobiological paradigm which might offer a physical and empirically testable paradox resolution. Based on the idea of James Annis, we develop a model of an astrobiological phase transition of the Milky Way, based on the concept of the global regulation mechanism(s). The dominant regulation mechanisms, arguably, are γ-ray bursts, whose properties and cosmological evolution are becoming well-understood. Secular evolution of regulation mechanisms leads to the brief epoch of phase transition: from an essentially dead place, with pockets of low-complexity life restricted to planetary surfaces, it will, on a short (Fermi–Hart) timescale, become filled with high-complexity life. An observation selection effect explains why we are not, in spite of the very small prior probability, to be surprised at being located in that brief phase of disequilibrium. In addition, we show that, although the phase-transition model may explain the “Great Silence”, it is not supportive of the “contact pessimist” position. To the contrary, the phase-transition model offers a rational motivation for continuation and extension of our present-day Search for ExtraTerrestrial Intelligence (SETI) endeavours. Some of the unequivocal and testable predictions of our model include the decrease of extinction risk in the history of terrestrial life, the absence of any traces of Galactic societies significantly older than human society, complete lack of any extragalactic intelligent signals or phenomena, and the presence of ubiquitous low-complexity life in the Milky Way.     

Charisma and conservation: charismatic megafauna’s influence on safari and zoo tourists’ pro-conservation behaviors

Annually, millions of tourists go on safari and visit zoos primarily to view large charismatic wildlife. These venues rely on the inherent appeal of these animals to increase visitation and anchor conservation efforts. In conservation campaigns, flagship species are used to stimulate a connection to a species and promote pro-conservation behaviors. However, empirical support for behavioral outcomes associated with flagships is lacking. Nor is it known how a connection to a species influences behaviors. This study explored (a) how tourists connect to wildlife, how this relationship is influenced by the on-site experience, and how these factors interact to influence behavior, and (b) how the experiences between safari and zoo venues differed. A model was developed using interactional theory and analyzed with structural equation modeling. Data were obtained from 416 tourists to Tanzanian parks and protected areas and 452 tourists to two U.S. zoos and one aquarium. An existing connection to wildlife and experiential factors directly influenced tourists’ connection to a species, but not behaviors. Tourists’ connection to a species had a significant positive influence on pro-conservation behaviors for individual species and general biodiversity. The influence of the experience was equivalent across safari and zoo venues. Results support the ability of safari and zoo wildlife tourism to produce conservation outcomes.     

A Quasistationary Analysis of a Stochastic Chemical Reaction: Keizer’s Paradox

For a system of biochemical reactions, it is known from the work of T.G. Kurtz [J. Appl. Prob. 8, 344 (1971)] that the chemical master equation model based on a stochastic formulation approaches the deterministic model based on the Law of Mass Action in the infinite system-size limit in finite time. The two models, however, often show distinctly different steady-state behavior. To further investigate this “paradox,” a comparative study of the deterministic and stochastic models of a simple autocatalytic biochemical reaction, taken from a text by the late J. Keizer, is carried out. We compute the expected time to extinction, the true stochastic steady state, and a quasistationary probability distribution in the stochastic model. We show that the stochastic model predicts the deterministic behavior on a reasonable time scale, which can be consistently obtained from both models. The transition time to the extinction, however, grows exponentially with the system size. Mathematically, we identify that exchanging the limits of infinite system size and infinite time is problematic. The appropriate system size that can be considered sufficiently large, an important parameter in numerical computation, is also discussed.     

Breaking down to build up: Neuroligin’s C-terminal domain strengthens the synapse

The mechanisms by which neuroligin adhesion molecules modulate synaptic plasticity remain unclear. In this issue, Liu et al. (2016. J. Cell Biol. http://dx.doi.org/10.1083/jcb.201509023) demonstrate that neuroligin 1 promotes actin assembly associated with synaptic strengthening independent of adhesion, suggesting additional ways for neuroligins to contribute to neuronal development and disease pathology.Spines are actin-enriched dendritic protrusions that serve as the major site of excitatory neurotransmission, underlying learning and memory formation (Lynch et al., 2007). Spines associate with presynaptic axon terminals through diverse adhesion molecules to form synapses (Siddiqui and Craig, 2011). Dynamic rearrangements of these synaptic adhesions and of the underlying actin cytoskeleton lead to either strengthening or weakening of particular synaptic connections. Synaptic strengthening, or long-term potentiation (LTP), is initiated by excitation of glutamate N-methyl-d-aspartate (NMDA) receptors, which promotes cleavage of synaptic adhesion molecules and disassembly of actin filaments (Lynch et al., 2007). Actin disassembly is mediated in part by recruitment of the actin-severing protein cofilin into the spine (Bosch et al., 2014). After the breakdown of the existing synaptic architecture, the actin cytoskeleton is stabilized again via Rac1-driven actin polymerization (Rex et al., 2009) and phosphorylation-mediated cofilin inactivation (Bosch et al., 2014). In parallel, recruitment and anchoring of synaptic adhesion molecules, including neuroligin 1 (NLG1; Schapitz et al., 2010) and glutamate receptors, increases the size of the postsynaptic signaling scaffold (PSD) across from the presynaptic terminal. In the final stage of LTP, the changes in synaptic morphology are consolidated by stabilization of actin filaments through actin capping and cross-linking together with the insertion of newly synthesized synaptic proteins (Lynch et al., 2007). Although the different steps of LTP shaping spine morphology and stability are generally understood, the signaling events that coordinate the initial disassembly of the existing synaptic architecture with reassembly of a stronger synaptic connection remain unclear.Neuroligins (NLGs) are a family of four transmembrane postsynaptic adhesion molecules (NLGs 1–4) that form heterotypic adhesions with presynaptic neurexins via an extracellular acetylcholinesterase-like domain (Südhof, 2008). Of the four NLG family members, NLG1 localizes predominantly to excitatory glutamatergic synapses (Song et al., 1999). Both in vitro and in vivo evidence demonstrate that the NLG–neurexin binding interaction is sufficient to promote synapse formation (Südhof, 2008; Chen et al., 2010). However, NLG knockout mice exhibit normal spine density but impaired synaptic transmission, suggesting that NLGs may regulate synaptic function independent of adhesion (Südhof, 2008). In addition to trans-synaptic adhesion mediated by the extracellular domain of NLGs, their short intracellular C-terminal domain (CTD) contains a PDZ binding domain (PBD) that facilitates binding and recruitment of postsynaptic density scaffold proteins, such as PSD95 (Irie et al., 1997; Dresbach et al., 2004). NLG1 is cleaved in an activity-dependent manner, leading to the release of an extracellular fragment that destabilizes synaptic adhesion and of the intracellular CTD (Suzuki et al., 2012).In this issue, Liu et al. focused on how activity-dependent cleavage of NLG1 and the subsequent release of its CTD affect actin organization and spine stability at excitatory synapses. They first observed that NLG1 knockout mouse brains, as well as cultured neurons infected with an shRNA targeting NLG1, exhibit decreased cofilin-S3 phosphorylation when compared with wild-type levels. Cofilin-S3 phosphorylation functions as a marker of mature dendritic spines, as cofilin inactivation results in F-actin assembly and is associated with the later stages of LTP (Calabrese et al., 2014). In addition, the absence of NLG1 prevented dynamic regulation of cofilin phosphorylation in response to KCl-induced neuronal excitation of brain slices, suggesting that cofilin phosphorylation depends on NLG1 both basally and in an activity-dependent manner. Remarkably, incubation with recombinant NLG1-CTD increased spine-associated cofilin phosphorylation in cultured neurons and rescued cofilin phosphorylation in NLG1 knockout mouse brain slices. Using full-length or truncated NLG1 constructs with a wild-type or mutated PDB sequence, Liu et al. (2016) demonstrated that NLG1-induced cofilin phosphorylation depends on both NLG1 cleavage and an intact PBD sequence within the released CTD. As the NLG1-CTD alone induced spine-associated cofilin phosphorylation, the researchers investigated its impact on actin assembly associated with synapse formation and function. In cultured neurons, recombinant NLG1-CTD increased F-actin levels together with spine and synapse formation. Similarly, intravenous injection of NLG1-CTD increased spine density in the CA1 region of the mouse hippocampus. This increased spine and synapse formation resulted in a corresponding increase in the frequency of excitatory postsynaptic currents, which was inhibited by a peptide that blocked cofilin phosphorylation. Together, these results establish that the NLG1-CTD requires cofilin phosphorylation to strengthen synaptic connections, prompting Liu et al. (2016) to investigate the mechanism underlying NLG1-induced cofilin phosphorylation.SPAR is a known regulator of the actin cytoskeleton that is hypothesized to bind to NLG1 (Craig and Kang, 2007). Using brain lysates and HEK293 cells expressing both NLG1 and SPAR, Liu et al. (2016) demonstrated that SPAR interacts with NLG1-CTD via its PBD domain. In brain slices, KCl-mediated excitation, which induces proteolytic cleavage of endogenous NLG1, increased the association of NLG1 and SPAR, suggesting that the interaction occurs in response to activity-dependent release of an intracellular CTD. To test whether this interaction regulates cofilin phosphorylation, Liu et al. (2016) expressed SPAR in HEK293 cells, where it decreased cofilin-S3 phosphorylation. However, incubation with a recombinant NLG1-CTD containing an intact PBD restored cofilin phosphorylation, demonstrating that this interaction alleviates SPAR-mediated repression of cofilin phosphorylation. In neurons, NLG1-CTD reduced the levels of synaptic SPAR, as assessed by both immunofluorescence and Western blotting of purified synaptosomes. SPAR is known to negatively regulate Rap1 signaling, and Rap1 signaling is important for Rac1 activation and spine morphogenesis (Pak et al., 2001; Maillet et al., 2003). In cultured neurons, a Rap1 inhibitor prevented NLG1-CTD–induced cofilin phosphorylation, whereas treatment with recombinant NLG1-CTD without Rap1 inhibition activated Rac1 signaling, leading to phosphorylation of its downstream targets, LIMK1 and cofilin. The results demonstrate that the CTD of NLG1 binds and displaces SPAR from the spine, alleviating its inhibition on Rap1 signaling. In turn, increased Rap1 signaling promotes Rac1 activation, leading to LIMK-1 and cofilin phosphorylation (Fig. 1). Lastly, these NLG-driven changes in actin assembly were found to simultaneously inhibit long-term depression, an activity-dependent reduction in the efficacy of synapses, and facilitate LTP, as determined by whole-cell patch clamping of brain slices incubated with NLG1-CTD.Open in a separate windowFigure 1.NLG’s CTD strengthens the synapse from within through dynamic actin remodeling. Excitatory activation of NMDA receptors (NMDAR) results in sequential cleavage of NLG1 (Suzuki et al., 2012). Liu et al. (2016) describe how the CTD of NLG1 interacts with SPAR, a negative regulator of Rap GTPase activity. This activity-dependent interaction displaces SPAR and alleviates the local inhibition of Rap activity within the dendritic spine. Rap drives a corresponding increase in Rac activation and phosphorylation of its downstream target, the actin regulator cofilin, thereby increasing F-actin filament assembly within spines. These changes in actin organization ultimately result in increased spine density and promote LTP.This work provides important insights into the mechanism by which NLG1 impacts synapse development and function by highlighting a critical role for SPAR in the regulation of actin assembly mediating synaptic strengthening. Interestingly, the temporal delay between the release of the NLG1-CTD and the subsequent sequestration of SPAR from the PSD could serve to distinguish an early disassembly phase following excitatory stimulation from later LTP consolidation, which is known to rely on both Rac1 activation (Rex et al., 2009) and cofilin phosphorylation (Bosch et al., 2014). Furthermore, it will be of interest to determine whether NLG1’s CTD affects the localization of other proteins known to bind its PBD, such as PSD95 (Irie et al., 1997), and whether these dynamic rearrangements at the postsynaptic scaffold also serve to simultaneously promote actin assembly while alleviating SPAR-mediated negative regulation of actin remodeling. For example, NLG1 has been shown to interact with Kalirin-7 (Owczarek et al., 2015), an activator of Rac1 that binds to PSD95 at the synapse; however, binding to PSD95 reduces Kalirin-7–mediated activation of Rac1 (Penzes et al., 2001). It is therefore attractive to speculate that the activity-dependent release of protein fragments, such as the CTD of NLG1, might alter postsynaptic density interactions that further promote localized Rac1-driven F-actin assembly. Consistent with this hypothesis, adhesion disassembly triggered by the extracellular domain of NLG1’s binding partner (β-neurexin) increases Rac1 activation (Owczarek et al., 2015). Ultimately, more work is necessary to determine how the strengthening effects of the intracellular CTD compete with the destabilizing effects of the extracellular domain (Suzuki et al., 2012). Recent research demonstrates that CAMKII phosphorylates and increases NLG1 surface expression in response to NMDA receptor activation (Bemben et al., 2014). If this phosphorylation event protects NLG1 from cleavage, it could serve to stabilize an adhesive pool of NLG1 while allowing for the release of the CTD from an unprotected population. Alternatively, this phosphorylation event could serve to recruit new NLG1 proteins to the synapse later in the LTP process when adhesions are reestablished. Further research is needed to understand how the adhesive and intracellular signaling capabilities of NLG1 are balanced at discrete stages of synaptic plasticity, and in particular how phosphorylation of NLG1 regulates both its surface expression as well as its cleavage.Consistent with the multiple roles of NLGs in modulating synaptic architecture, it is not surprising that NLG mutations have been implicated in diverse cognitive and neurodevelopmental disorders, such as Alzheimer’s disease and autism (Südhof, 2008; Tristán-Clavijo et al., 2015). In light of this study, it will be interesting to determine how disease-associated NLG mutations contribute to both synaptic adhesion as well as stabilization of the actin cytoskeleton that supports synaptic strengthening. This is particularly important because both Alzheimer’s disease and autism-associated NLG mutant proteins exhibit decreased surface expression (Chubykin et al., 2005; Tristán-Clavijo et al., 2015), although the autism-associated mutant NLG proteins present at the cell surface still promote synapse formation (Chubykin et al., 2005). However, the decreased postsynaptic NLG pool could impair subsequent activity-dependent synaptic strengthening. Likewise, understanding whether binding of the postsynaptic scaffolding protein Shank3 to the CTD of NLG1 (Arons et al., 2012) affects NLG1 cleavage could provide insights into the mechanism by which Shank3 affects activity-dependent synaptic remodeling in autism pathogenesis. The work by Liu et al. (2016), demonstrating that adhesion disassembly coordinates subsequent actin assembly underlying synaptic strengthening, takes an important step toward shedding light on the altered synaptic plasticity underlying both complex neurodevelopmental and neurodegenerative pathologies.     

The Relationship Between Objective Sperm Competition Risk and Men’s Copulatory Interest Is Moderated by Partner’s Time Spent with Other Men

Men who spend a greater proportion of time apart from their female partner since the couple’s last copulation are at greater “objective” sperm competition risk. We propose a novel cue to sperm competition risk: the time she spends with her male friends. Four hundred and twenty men in a committed, heterosexual, sexual relationship completed a questionnaire. The results indicate that men at greater objective sperm competition risk report less time desired until the couple’s next copulation, greater interest in copulating with their partner, and greater anger, frustration, and upset in response to their partner’s sexual rejection, but only among men whose partner spends more time with her male friends. These results remain after controlling statistically for the participant’s age and their partner’s age. We discuss limitations of the current research, and discuss how research in human sperm competition can inform social issues, including men’s partner-directed sexual coercion.     

Travelling with tea: a Tuckerella’s tale

Tuckerella japonica Ehara appears strongly associated with tea (Camellia sinensis (L.) Kuntze, Theaceae) and, due to certain cultural practices in tea production, has in fact become a world traveller, accompanying the greatly coveted tea plant as it spread across the planet. The history of tea production and culture, and its arrival in the USA, provides the backdrop for this traveller’s tale. Tuckerella japonica is morphologically similar to T. flabellifera Miller, described from Tasmania in Australia from Bedfordia salicina (Labill.) D.G. (Asteraceae). These two species have historically been misidentified as each other, creating inaccuracies in the collection records. The implications of this in terms of host plant lists and world distribution are discussed further, along with their morphological separation. The male and immature stages of T. japonica are described for the first time. Tuckerella xinglongensis Lin and Fu, from tea in China, is considered a junior synonym of T. japonica. The loss of the ancestral prostigmatan condition of three nymphal stages during ontogeny is confirmed for males of T. flabellifera, which do not retain a tritonymphal stage.     

Science and Sentiment: Grinnell’s Fact-Based Philosophy of Biodiversity Conservation

At the beginning of the twentieth century, the biologist Joseph Grinnell made a distinction between science and sentiment for producing fact-based generalizations on how to conserve biodiversity. We are inspired by Grinnellian science, which successfully produced a century-long impact on studying and conserving biodiversity that runs orthogonal to some familiar philosophical distinctions such as fact versus value, emotion versus reason and basic versus applied science. According to Grinnell, unlike sentiment-based generalizations, a fact-based generalization traces its diverse commitments and thus becomes tractable for its audience. We argue that foregrounding tractability better explains Grinnell’s practice in the context of his time as well as in the context of current discourse among scientists over the political “biases” of biodiversity research and its problem of “reproducibility.”     

Motor Performance Assessment in Parkinson’s Disease: Association between Objective In-Clinic,Objective In-Home,and Subjective/Semi-Objective Measures

Advances in wearable technology allow for the objective assessment of motor performance in both in-home and in-clinic environments and were used to explore motor impairments in Parkinson’s disease (PD). The aims of this study were to: 1) assess differences between in-clinic and in-home gait speed, and sit-to-stand and stand-to-sit duration in PD patients (in comparison with healthy controls); and 2) determine the objective physical activity measures, including gait, postural balance, instrumented Timed-up-and-go (iTUG), and in-home spontaneous physical activity (SPA), with the highest correlation with subjective/semi-objective measures, including health survey, fall history (fallers vs. non-fallers), fear of falling, pain, Unified Parkinson''s Disease Rating Scale, and PD stage (Hoehn and Yahr). Objective assessments of motor performance were made by measuring physical activities in the same sample of PD patients (n = 15, Age: 71.2±6.3 years) and age-matched healthy controls (n = 35, Age: 71.9±3.8 years). The association between in-clinic and in-home parameters, and between objective parameters and subjective/semi-objective evaluations in the PD group was assessed using linear regression-analysis of variance models and reported as Pearson correlations (R). Both in-home SPA and in-clinic assessments demonstrated strong discriminatory power in detecting impaired motor function in PD. However, mean effect size (0.94±0.37) for in-home measures was smaller compared to in-clinic assessments (1.30±0.34) for parameters that were significantly different between PD and healthy groups. No significant correlation was observed between identical in-clinic and in-home parameters in the PD group (R = 0.10–0.25; p>0.40), while the healthy showed stronger correlation in gait speed, sit-to-stand duration, and stand-to-sit duration (R = 0.36–0.56; p<0.03). This suggests a better correlation between supervised and unsupervised motor function assessments in healthy controls compared to PD group. In the PD group, parameters related to velocity and range-of-motion of lower extremity within gait assessment (R = 0.58–0.84), and turning duration and velocity within iTUG test (R = 0.62–0.77) demonstrated strong correlations with PD stage (p<0.01).     

Property Rights in Fisheries: Iceland’s Experience with ITQs

The fundamental problem of economic inefficiency in fisheries, the so-called common property problem, may be seen to be caused by inadequate or lacking property rights in the underlying natural resources. The introduction of Individual Transferable Quotas (ITQs) into fisheries represents an attempt to correct this failure. ITQs, however, are not property rights in the relevant natural resources, i.e. the fish stocks and their habitat. They are merely harvesting rights and thus far from ideal as property rights. Nevertheless, ITQs have been introduced in numerous fisheries around the world, apparently with generally, even consistently, good economic results. This paper outlines the basic theory of property rights and the strengths and weaknesses of ITQs as property rights in fisheries. The paper goes on to discuss the Icelandic ITQ system and compares its property rights value with that of the New Zealand ITQ system and the Norwegian IQ system. Finally, the paper reviews some measures of the economic outcomes of the ITQ system in Iceland.     

Catecholamine metabolism in children with Asperger’s and Kanner’s syndromes

In a stable state children with Asperger’s and Kanner’s syndromes demonstrate a similar decrease in plasma norepinephrine. In the aggravated state, these changes become more expressed and are characterized by a decrease in plasma tyrosine, norepinephrine, normetanephrine, and by an increase in dopamine and homovanillic acid and a decrease in excretion of norepinephrine and an increase in excretion of homovanillic acid, epinephrine and 3-methoxy-4-hydroxyphenylglycol (MHPG). In the aggravated state children with Kanner’s syndrome were characterized by increased plasma MHPG, decreased excretion of tyrosine and increased expression of normetanephrine. The observed imbalance in dopamine and epinephrine/norepinephrine systems suggests importance of combined analysis of changes in catecholamines and their metabolites as the most informative approach in the study of the effect of autistic disorders.     

When there’s smoke there’s…scleroderma: evidence that patients with scleroderma should stop smoking

There is no treatment for the autoimmune disease scleroderma (systemic sclerosis, SSc), a multisystem disorder characterized by vascular damage and fibrosis. In particular, SSc can severely affect the lung, resulting in pulmonary arterial hypertension and fibrosis. Smoking is well-known to affect pulmonary health, and a recent report (Hudson et al., Arthritis Rheum, in press Oct 8) provides convincing evidence that stopping smoking improves disease outcome in SSc patients. This commentary discusses this recent publication which suggests that physicians should encourage SSc patients to stop smoking immediately.