Is the Genetic Code Optimized for Resource Conservation?

The causes and consequences of the nonrandom structure of the standard genetic code (SGC) have been of long-standing interest. A recent study reported that mutations in present-day protein-coding sequences are less likely to increase proteomic nitrogen and carbon uses under the SGC than under random genetic codes, concluding that the SGC has been selectively optimized for resource conservation. If true, this finding might offer important information on the environment in which the SGC and some of the earliest life forms evolved. However, we here show that the hypothesis of optimization of a genetic code for resource conservation is theoretically untenable. We discover that the aforementioned study estimated the expected mutational effect by inappropriately excluding mutations lowering resource consumptions and including mutations involving stop codons. After remedying these problems, we find no evidence that the SGC is optimized for nitrogen or carbon conservation.     

Is It Worth the Risk? Food Deprivation Effects on Tadpole Anti-Predatory Responses

Predation risk affects foraging behavior and, particularly, the amount of time devoted to the search for food. When exposed to predation risk, food deprived animals should be risk prone and relax behavioral defenses to a wider extent than well fed individuals. To test for this prediction, we used a 2?×?2 factorial design experiment, manipulating both the energetic state (fed vs. fasted) and exposure to an attack-released cue (injured vs. uninjured conspecifics) of common water frog tadpoles (Pelophylax kl. esculentus). Contrary to expectations, food deprivation significantly lowered the activity level of predator-exposed tadpoles. As in this experiment no food resource was added to test containers, energy conserving behavior might have both delayed starvation and lowered the probability of encountering the potential predator. To test for the effect of food availability on behavioral responses, we performed a second experiment, using the same protocol and procedures, except for adding food to all test containers. All tadpoles showed similar levels of activity, while fed tadpoles exposed to alarm cues tended to swim farther from the cage containing the stimulus than in the first experiment. As many anuran larvae can feed on dead conspecifics, prey-borne cues may have been interpreted as the potential presence of both a food source and a predator, fed tadpoles possibly being more confident than fasted tadpoles in their ability to escape predation in case an actual attack occurs.     

Is Scale-Up Worth It? Challenges in Economic Analysis of Diagnostic Tests for Tuberculosis

David Dowdy and colleagues discuss the complexities of costing new TB diagnostic tests, including GeneXpert, and argue that flexible analytic tools are needed for decision-makers to adapt large-sample cost-effectiveness data to local conditions.     

Microtubule Flux: What Is It Good for?

During mitosis in a eukaryotic cell, microtubule subunits continuously move towards spindle poles. A new study has revealed that inhibiting this microtubule flux in mammalian cells has no major effects on chromosome movements; it does, however, increase the probability of erroneous chromosome segregation.     

Is There Enough Science for Conservation Action?

We argue that there is not enough science to appropriately support many of the conservation measures currently being proposed, and hence, we cannot be sure of the objectivity of the conservation actions being implemented. The objectivity claimed to be underlying conservation actions is more assumed than real. We also suggest that the approach to conservation is driven more by moral commitments than by tested concepts, and it is further biased by our anthropocentric evaluation of ecological processes and their outcomes. Conservation science is a young subject, which needs to be nourished while it continues to feed on its roots-ecology and evolutionary biology.     

Sex: Is Giardia Doing It in the Dark?

The protist Giardia has long been considered strictly asexual. Now genes specific for meiotic recombination have been found in the Giardia genome, but their consequences for genetics, epidemiology and evolution remain unknown.     

Genomic Heritability: What Is It?

Whole-genome regression methods are being increasingly used for the analysis and prediction of complex traits and diseases. In human genetics, these methods are commonly used for inferences about genetic parameters, such as the amount of genetic variance among individuals or the proportion of phenotypic variance that can be explained by regression on molecular markers. This is so even though some of the assumptions commonly adopted for data analysis are at odds with important quantitative genetic concepts. In this article we develop theory that leads to a precise definition of parameters arising in high dimensional genomic regressions; we focus on the so-called genomic heritability: the proportion of variance of a trait that can be explained (in the population) by a linear regression on a set of markers. We propose a definition of this parameter that is framed within the classical quantitative genetics theory and show that the genomic heritability and the trait heritability parameters are equal only when all causal variants are typed. Further, we discuss how the genomic variance and genomic heritability, defined as quantitative genetic parameters, relate to parameters of statistical models commonly used for inferences, and indicate potential inferential problems that are assessed further using simulations. When a large proportion of the markers used in the analysis are in LE with QTL the likelihood function can be misspecified. This can induce a sizable finite-sample bias and, possibly, lack of consistency of likelihood (or Bayesian) estimates. This situation can be encountered if the individuals in the sample are distantly related and linkage disequilibrium spans over short regions. This bias does not negate the use of whole-genome regression models as predictive machines; however, our results indicate that caution is needed when using marker-based regressions for inferences about population parameters such as the genomic heritability.     

A Review of Transplantation Practice of the Urologic Organs: Is It Only Achievable for the Kidney?

Transplantation is a viable treatment option for failure of most major organs. Within urology, transplantation of the kidney and ureter are well documented; however, evidence supporting transplantation of other urologic organs is limited. Failure of these organs carries significant morbidity, and transplantation may have a role in management. This article reviews the knowledge, research, and literature surrounding transplantation of each of the urologic organs. Transplantation of the penis, testicle, urethra, vas deferens, and bladder is discussed. Transplantation attempts have been made individually with each of these organs. Penile transplantation has only been performed once in a human. Testicular transplantation research was intertwined with unethical lucrative pursuits. Interest in urethra, bladder, and vas deferens transplantation has decreased as a result of successful surgical reconstructive techniques. Despite years of effort, transplantations of the penis, testicle, urethra, vas deferens, and bladder are not established in current practice. Recent research has shifted toward techniques of reconstruction, tissue engineering, and regenerative medicine.Key words: Urology, Transplantation, Reconstruction, Tissue engineeringOrgan transplantation is still a relatively novel treatment modality; its practice only developed in the latter half of the 20th century, in part due to the advent of immunosuppressive drugs. Key questions driving progress in transplant surgery is how far this science can be pushed, and if any part of the human body can be transplanted.In urology, transplantation of the kidney was previously inconceivable, but is now well established, following the first successful renal transplant performed in 1950. However, there is minimal evidence in the scientific literature of the successful transplantation of other urologic organs.There has, in the past, been great interest in exploring this lesser-known area of urologic transplantation, as the morbidity for patients with failure or damage to urologic organs such as the penis, testicle, or bladder is considerable. There is renewed interest in recent years due to the increased prevalence of devastating injuries to the genitalia caused by improvised explosive devices among soldiers stationed in Afghanistan.¹ There is minimal evidence in the literature addressing how these injuries should be best managed or whether transplantation may have a role in helping such patients.Remarkable progress in transplantation surgery has allowed development of new strategies of treatment for many urologic patients. Greater insight into the practice of transplantation may lead to improved management of other urologic pathologies. We comprehensively reviewed the historical evidence for transplantation of those urologic structures for which the practice is not well established. To our knowledge, no such review exists in the literature.     

Extrapolating Antifungal Animal Data to Humans—Is It Reliable?

This article aimed to review animal models of antifungals and identifies human literature to assess if the extrapolation of results is reliable. Animal studies have helped identify area under the concentration curve to minimum inhibitory concentration ratio targets for new drugs and formulations such as isavuconazole and delayed-release posaconazole that have translated to successful outcomes in humans. Models have also been influential in the identification of possible combination therapies for the treatment of aspergillosis, such as voriconazole and echinocandins. However, challenges are endured with animal models when it comes to replicating the pharmacokinetics of humans which has been exemplified with the newest itraconazole formulation. Additionally, animal models have displayed a survival benefit with the use of iron chelators and amphotericin for mucormycosis which was not demonstrated in humans. Animal models have been a staple in the development and optimization of antifungal agents. They afford the ability to investigate uncommon diseases, such as invasive fungal infections, that would otherwise take years and many resources to complete. Although there are many benefits of animal models, there are also shortcomings. This is why the reliability of extrapolating data from animal models to humans is often scrutinized.     

Worth the ‘EEfRT’? The Effort Expenditure for Rewards Task as an Objective Measure of Motivation and Anhedonia

Background

Of the putative psychopathological endophenotypes in major depressive disorder (MDD), the anhedonic subtype is particularly well supported. Anhedonia is generally assumed to reflect aberrant motivation and reward responsivity. However, research has been limited by a lack of objective measures of reward motivation. We present the Effort-Expenditure for Rewards Task (EEfRT or “effort”), a novel behavioral paradigm as a means of exploring effort-based decision-making in humans. Using the EEfRT, we test the hypothesis that effort-based decision-making is related to trait anhedonia.

Methods/Results

61 undergraduate students participated in the experiment. Subjects completed self-report measures of mood and trait anhedonia, and completed the EEfRT. Across multiple analyses, we found a significant inverse relationship between anhedonia and willingness to expend effort for rewards.

Conclusions

These findings suggest that anhedonia is specifically associated with decreased motivation for rewards, and provide initial validation for the EEfRT as a laboratory-based behavioral measure of reward motivation and effort-based decision-making in humans.     

Why Is the Substomatal Chamber as Large as It Is?

The rate of CO(2) uptake by the mesophyll is examined as a function of the size of the substomatal chamber. Using the techniques of classical electric circuit analysis and a model in which the uptake is linear in the ambient CO(2) concentration, it is shown that the optimal chamber radius is several times larger than is the pore radius. This is somewhat larger than necessary for the reduction of transpirational water loss, and it offers an explanation for the otherwise inexplicably large size of the chamber.     

Tigers of Sundarbans in India: Is the Population a Separate Conservation Unit?

The Sundarbans tiger inhabits a unique mangrove habitat and are morphologically distinct from the recognized tiger subspecies in terms of skull morphometrics and body size. Thus, there is an urgent need to assess their ecological and genetic distinctiveness and determine if Sundarbans tigers should be defined and managed as separate conservation unit. We utilized nine microsatellites and 3 kb from four mitochondrial DNA (mtDNA) genes to estimate genetic variability, population structure, demographic parameters and visualize historic and contemporary connectivity among tiger populations from Sundarbans and mainland India. We also evaluated the traits that determine exchangeability or adaptive differences among tiger populations. Data from both markers suggest that Sundarbans tiger is not a separate tiger subspecies and should be regarded as Bengal tiger (P. t. tigris) subspecies. Maximum likelihood phylogenetic analyses of the mtDNA data revealed reciprocal monophyly. Genetic differentiation was found stronger for mtDNA than nuclear DNA. Microsatellite markers indicated low genetic variation in Sundarbans tigers (He= 0.58) as compared to other mainland populations, such as northern and Peninsular (Hebetween 0.67- 0.70). Molecular data supports migration between mainland and Sundarbans populations until very recent times. We attribute this reduction in gene flow to accelerated fragmentation and habitat alteration in the landscape over the past few centuries. Demographic analyses suggest that Sundarbans tigers have diverged recently from peninsular tiger population within last 2000 years. Sundarbans tigers are the most divergent group of Bengal tigers, and ecologically non-exchangeable with other tiger populations, and thus should be managed as a separate “evolutionarily significant unit” (ESU) following the adaptive evolutionary conservation (AEC) concept.     

Is It Benign or Is It a Pariah? Empirical Evidence for the Impact of the Common Myna (Acridotheres tristis) on Australian Birds

There is widespread concern over the impact of introduced species on biodiversity, but the magnitude of these impacts can be variable. Understanding the impact of an introduced species is essential for effective management. However, empirical evidence of the impact of an introduced species can be difficult to obtain, especially when the impact is through competition. Change in species abundance is often slow and gradual, coinciding with environmental change. As a result, negative impacts on native species through competition are poorly documented. An example of the difficulties associated with obtaining empirical evidence of impact due to competition comes from work on the Common Myna (Acridotheres tristis). The species is listed in the World's top 100 worst invaders, despite a lack of empirical evidence of its negative impacts on native species. We assessed the impact of the Common Myna on native bird abundance, using long-term data both pre and post its invasion. At the outset of our investigation, we postulated that Common Myna establishment would negatively affect the abundance of other cavity-nesting species and bird species that are smaller than it. We found a negative relationship between the establishment of the Common Myna and the long-term abundance of three cavity-nesting species (Sulphur-crested Cockatoo, Crimson Rosella, Laughing Kookaburra) and eight small bird species (Striated Paradoxes, Rufous Whistler, Willie Wagtail, Grey Fantail, Magpie-lark, House Sparrow, Silvereye, Common Blackbird). To the best of our knowledge, this finding has never previously been demonstrated at the population level. We discuss the key elements of our success in finding empirical evidence of a species impact and the implications for prioritisation of introduced species for management. Specifically, prioritization of the Common Myna for management over other species still remains a contentious issue.