Developmental mechanisms of longitudinal stripes in the Japanese four‐lined snake

The developmental mechanisms of color patterns formation and its evolution remain unclear in reptilian sauropsids. We, therefore, studied the pigment cell mechanisms of stripe pattern formation during embryonic development of the snake Elaphe quadrivirgata. We identified 10 post‐ovipositional embryonic developmental stages based on external morphological characteristics. Examination for the temporal changes in differentiation, distribution, and density of pigment cells during embryonic development revealed that melanophores first appeared in myotome and body cavity but not in skin surface at Stage 5. Epidermal melanophores were first recognized at Stage 7, and dermal melanophores and iridophores appeared in Stage 9. Stripe pattern first appeared to establish at Stage 8 as a spatial density gradient of epidermal melanophores between the regions of future dark brown longitudinal stripes and light colored background. Our study, thus, provides a comprehensive pigment‐cell‐based understanding of stripe pattern formation during embryonic development. We briefly discuss the importance of the gene expression studies by considering the biologically relevant theoretical models with standard developmental staging for understanding reptilian color pattern evolution.     

Non‐marine turtle plays important functional roles in Indonesian ecosystems

The Southeast Asian box turtle (Cuora amboinensis) is numerically the most important turtle exported from Indonesia. Listed as Vulnerable by the IUCN, this turtle is heavily harvested and exported for food and traditional medicine in China and for the pet trade primarily in the United States, Europe, and Japan. Despite its significance in global markets, relatively little is known about the species’ ecology or importance to ecosystems. We conducted our research in a national park in Sulawesi, Indonesia, and our objectives were to quantify trophic breadth, capacity for seed dispersal between aquatic and terrestrial ecosystems, and whether ingestion of seeds by C. amboinensis enhances germination. We obtained diet samples from 200 individual turtles and found that the species is omnivorous, exhibiting an ontogenetic shift from more carnivorous to more omnivorous. Both subadults and adults scavenged on other vertebrates. In a seed passage experiment, turtles passed seeds for 2?9 days after ingestion. Radio‐tracked turtles moved, on average, about 35 m per day, indicating that seeds from ingested fruits, given seed passage durations, could be dispersed 70?313 m from the parent tree and potentially between wetland and upland ecosystems. In a seed germination experiment, we found that ingestion of seeds by turtles enhanced germination, as compared with control seeds, for four of six plant species tested. Of these, two are common in the national park, making up a significant proportion of plant biomass in lowland swamp forest and around ephemeral pools in savanna, and are highly valued outside of the park for their lumber for construction of houses, furniture, and boats. Protection of C. amboinensis populations may be important for maintaining trophic linkages that benefit biodiversity, communities, and local economies.     

Cleavage stage porcine embryos may have differing developmental requirements for karyopherins alpha2 and alpha3

Numerous cellular proteins are able to localize to the nucleus due to the fact that they possess a nuclear localization signal (NLS) in their amino acid sequence. Nuclear localization sequences recognized by the importin alpha/beta heterodimer are found in cellular proteins capable of performing many diverse functions, ranging from chromatin remodeling to cell cycle regulation. Evidence has been presented that suggests individual importin alpha homologues are present at varying levels in different adult tissues. Other data have shown that specific subsets of NLSs found in different cellular proteins are recognized by individual importin alpha homologues with varying affinities. This evidence led us to hypothesize that due to the specific cargoes they carry, the mammalian embryo has different developmental requirements for individual importin alpha homologues. The results of the studies presented here indicate that importin alpha/beta-mediated import occurs throughout early cleavage in the porcine embryo, as determined by a reporter protein microinjection assay, and that multiple importin alpha homologues are present throughout early cleavage, as determined by immunocytochemical analysis. An RNA interference approach was used in an attempt to determine the developmental requirements for specific importin alpha homologues during early cleavage in the porcine embryo. Results from this study showed that fertilized porcine embryos injected with double stranded RNA (dsRNA) corresponding to the importin alpha homologue karyopherin alpha3 had significantly fewer nuclei following four days of culture than did embryos injected with dsRNA for another importin alpha homologue, karyopherin alpha2, or two control groups. This is the first report indicating that mammalian embryos may have differential developmental requirements for specific nuclear trafficking pathways.     

Diet‐induced early‐stage atherosclerosis in baboons: Lipoproteins,atherogenesis, and arterial compliance

Background

The purpose of this study was to determine whether dietary manipulation can reliably induce early‐stage atherosclerosis and clinically relevant changes in vascular function in an established, well‐characterized non‐human primate model.

Methods

We fed 112 baboons a high‐cholesterol, high‐fat challenge diet for two years. We assayed circulating biomarkers of cardiovascular disease (CVD) risk, at 0, 7, and 104 weeks into the challenge; assessed arterial compliance noninvasively at 104 weeks; and measured atherosclerotic lesions in three major arteries at necropsy.

Results

We observed evidence of atherosclerosis in all but one baboon fed the two‐year challenge diet. CVD risk biomarkers, the prevalence, size, and complexity of arterial lesions, plus consequent arterial stiffness, were increased in comparison with dietary control animals.

Conclusions

Feeding baboons a high‐cholesterol, high‐fat diet for two years reliably induces atherosclerosis, with risk factor profiles, arterial lesions, and changes in vascular function also seen in humans.     

Characterization of 11 microsatellite marker loci in the Malagasy big‐headed turtle (Erymnochelys madagascariensis)

The Malagasy big‐headed turtle (Erymnochelys madagascariensis) is the only Erymnochelys species living in lakes, rivers and watersheds of western Madagascar. This species is endangered due to over harvesting of natural populations for human consumption. Eleven nuclear microsatellite loci were isolated from a genomic DNA library derived from a free‐ranging Malagasy big‐headed turtle from the Beroboka Classified Forest, Madagascar. Population genetic parameters were estimated on 10 individuals sampled from Ampijoroa and Andranohobaka River, Madagascar, to determine marker utility and as preliminary baseline values to study future populations in these locations.     

Par‐aPKC‐dependent and ‐independent mechanisms cooperatively control cell polarity,Hippo signaling,and cell positioning in 16‐cell stage mouse embryos

In preimplantation mouse embryos, the Hippo signaling pathway plays a central role in regulating the fates of the trophectoderm (TE) and the inner cell mass (ICM). In early blastocysts with more than 32 cells, the Par‐aPKC system controls polarization of the outer cells along the apicobasal axis, and cell polarity suppresses Hippo signaling. Inactivation of Hippo signaling promotes nuclear accumulation of a coactivator protein, Yap, leading to induction of TE‐specific genes. However, whether similar mechanisms operate at earlier stages is not known. Here, we show that slightly different mechanisms operate in 16‐cell stage embryos. Similar to 32‐cell stage embryos, disruption of the Par‐aPKC system activated Hippo signaling and suppressed nuclear Yap and Cdx2 expression in the outer cells. However, unlike 32‐cell stage embryos, 16‐cell stage embryos with a disrupted Par‐aPKC system maintained apical localization of phosphorylated Ezrin/Radixin/Moesin (p‐ERM), and the effects on Yap and Cdx2 were weak. Furthermore, normal 16‐cell stage embryos often contained apolar cells in the outer position. In these cells, the Hippo pathway was strongly activated and Yap was excluded from the nuclei, thus resembling inner cells. Dissociated blastomeres of 8‐cell stage embryos form polar–apolar couplets, which exhibit different levels of nuclear Yap, and the polar cell engulfed the apolar cell. These results suggest that cell polarization at the 16‐cell stage is regulated by both Par‐aPKC‐dependent and ‐independent mechanisms. Asymmetric cell division is involved in cell polarity control, and cell polarity regulates cell positioning and most likely controls Hippo signaling.     

Immunolocalization of beta‐proteins and alpha‐keratin in the epidermis of the soft‐shelled turtle explains the lack of formation of hard corneous material

Immunolocalization of beta‐proteins in the epidermis of the soft‐shelled turtle explains the lack of formation of hard corneous material, Acta Zoologica, Stockholm. The corneous layer of soft‐shelled turtles derives from the accumulation of higher ratio of alpha‐keratins versus beta‐proteins as indicated by gene expression, microscopic, immunocytochemical and Western blotting analysis. Type I and II beta‐proteins of 14–16 kDa, indicated as Tu2 and Tu17, accumulate in the thick and hard corneous layer of the hard‐shelled turtle, but only type II is present in the thinner corneous layer of the soft‐shelled turtle. The presence of proline–proline and proline–cysteine–hinge dipeptides in the beta‐sheet region of all type II beta‐proteins so far isolated from the epidermis of soft‐shelled turtles might impede the formation of beta‐filaments and of the hard corneous material. Western blot analysis suggests that beta‐proteins are low to absent in the corneous layer. The ultrastructural immunolocalization of Tu2 and Tu17 beta‐proteins shows indeed that a diffuse labelling is seen among the numerous alpha‐keratin filaments present in the precorneous and corneous layers of the soft epidermis and that no dense corneous material is formed. Double‐labelling experiments confirm that alpha‐keratin prevails on beta‐proteins. The present observations support the hypothesis that the soft material detected in soft‐shelled turtles derives from the prevalent activation of genes producing type II beta‐proteins and high levels of alpha‐keratins.     

The early‐life environment and individual plasticity in life‐history traits

We tested whether the early‐life environment can influence the extent of individual plasticity in a life‐history trait. We asked: can the early‐life environment explain why, in response to the same adult environmental cue, some individuals invest more than others in current reproduction? Moreover, can it additionally explain why investment in current reproduction trades off against survival in some individuals, but is positively correlated with survival in others? We addressed these questions using the burying beetle, which breeds on small carcasses and sometimes carries phoretic mites. These mites breed alongside the beetle, on the same resource, and are a key component of the beetle's early‐life environment. We exposed female beetles to mites twice during their lives: during their development as larvae and again as adults during their first reproductive event. We measured investment in current reproduction by quantifying average larval mass and recorded the female's life span after breeding to quantify survival. We found no effect of either developing or breeding alongside mites on female reproductive investment, nor on her life span, nor did developing alongside mites influence her size. In post hoc analyses, where we considered the effect of mite number (rather than their mere presence/absence) during the female's adult breeding event, we found that females invested more in current reproduction when exposed to greater mite densities during reproduction, but only if they had been exposed to mites during development as well. Otherwise, they invested less in larvae at greater mite densities. Furthermore, females that had developed with mites exhibited a trade‐off between investment in current reproduction and future survival, whereas these traits were positively correlated in females that had developed without mites. The early‐life environment thus generates individual variation in life‐history plasticity. We discuss whether this is because mites influence the resources available to developing young or serve as important environmental cues.     

Heat shock proteins mediate trade‐offs between early‐life reproduction and late survival in Drosophila melanogaster

Ageing and the resulting increased likelihood mortality are the inescapable fate of organisms because selection pressures on genes that exert their function late in life is weak, promoting the evolution of genes that enhance early‐life reproductive performance at the same time as sacrificing late survival. Heat shock proteins (HSP) are known to buffer various environmental stresses and are also involved in protein homeostasis and longevity. The characteristics of genes for HSPs (hsp) imply that they affect various life‐history traits, which in turn affect longevity; however, little is known about the effects of hsp genes on life‐history traits and their interaction with longevity. In the present study, the effects of hsp genes on multiple fitness traits, such as locomotor activity, total fecundity, early fecundity and survival time, are investigated in Drosophila melanogaster Meigen using RNA interference (RNAi). In egg‐laying females, RNAi knockdown of six hsp genes (hsp22, hsp23, hsp67Ba, hsp67Bb, hsp67Bc and hsp27‐like) does not shorten survival but rather increases it. Knockdown of five of those genes on an individual basis reduces early‐life reproduction, suggesting that several hsp genes mediate the trade‐off between early reproduction and late survival. The data indicate a positive effect of hsp genes on early reproduction and also negative effects on survival time, supporting the antagonistic pleiotropic effects predicted by the optimality theory of ageing.     

Crystal structure of plant light‐harvesting complex shows the active,energy‐transmitting state

Plants dissipate excess excitation energy as heat by non‐photochemical quenching (NPQ). NPQ has been thought to resemble in vitro aggregation quenching of the major antenna complex, light harvesting complex of photosystem II (LHC‐II). Both processes are widely believed to involve a conformational change that creates a quenching centre of two neighbouring pigments within the complex. Using recombinant LHC‐II lacking the pigments implicated in quenching, we show that they have no particular role. Single crystals of LHC‐II emit strong, orientation‐dependent fluorescence with an emission maximum at 680 nm. The average lifetime of the main 680 nm crystal emission at 100 K is 1.31 ns, but only 0.39 ns for LHC‐II aggregates under identical conditions. The strong emission and comparatively long fluorescence lifetimes of single LHC‐II crystals indicate that the complex is unquenched, and that therefore the crystal structure shows the active, energy‐transmitting state of LHC‐II. We conclude that quenching of excitation energy in the light‐harvesting antenna is due to the molecular interaction with external pigments in vitro or other pigment–protein complexes such as PsbS in vivo, and does not require a conformational change within the complex.     

Normal human aging and early‐stage schizophrenia share common molecular profiles

We examined genome‐wide expression datasets from human prefrontal cortex of normal and schizophrenic individuals ranging from 19 to 81 years of age. We found that changes in gene expression that are correlated with aging in normal subjects differ dramatically from those observed with aging in schizophrenic subjects. Only 2.5% of genes were correlated with age in both groups. Surprisingly, we also found a significant overlap (29–34%) between those genes whose expression was correlated with aging in normal subjects and those significantly altered in subjects with early‐stage schizophrenia (within 4 years of diagnosis). This suggests that schizophrenia onset anticipates the normal aging process, and further, that some symptoms of aging, i.e. dementia and psychosis, might be explained by these common molecular profiles.     

RS‐1 enhances CRISPR‐mediated targeted knock‐in in bovine embryos

Targeted knock‐in (KI) can be achieved in embryos by clustered regularly interspaced short palindromic repeats (CRISPR)‐assisted homology directed repair (HDR). However, HDR efficiency is constrained by the competition of nonhomologous end joining. The objective of this study was to explore whether CRISPR‐assisted targeted KI rates can be improved in bovine embryos by exposure to the HDR enhancer RS‐1. In vitro produced zygotes were injected with CRISPR components (300 ng/µl Cas9 messenger RNA and 100 ng/µl single guide RNA against a noncoding region) and a single‐stranded DNA (ssDNA) repair template (100 ng/µl). ssDNA template contained a 6 bp XbaI site insert, allowing targeted KI detection by restriction analysis, flanked by 50 bp homology arms. Following microinjection, zygotes were exposed to 0, 3.75, or 7.5 µM RS‐1 for 24 hr. No differences were noted between groups in terms of development or genome edition rates. However, targeted KI rates were doubled in the group exposed to 7.5 µM RS‐1 compared to the others (52.8% vs. 25% and 23.1%, for 7.5, 0, and 3.75 µM, respectively). In conclusion, transient exposure to 7.5 µM RS‐1 enhances targeted KI rates resulting in approximately half of the embryos containing the intended mutation, hence allowing direct KI generation in embryos.     

Protective role of melatonin in early‐stage and end‐stage liver cirrhosis

The liver is composed of hepatocytes, cholangiocytes, Kupffer cells, sinusoidal endothelial cells, hepatic stellate cells (HSCs) and dendritic cells; all these functional and interstitial cells contribute to the synthesis and secretion functions of liver tissue. However, various hepatotoxic factors including infection, chemicals, high‐fat diet consumption, surgical procedures and genetic mutations, as well as biliary tract diseases such as sclerosing cholangitis and bile duct ligation, ultimately progress into liver cirrhosis after activation of fibrogenesis. Melatonin (MT), a special hormone isolated from the pineal gland, participates in regulating multiple physiological functions including sleep promotion, circadian rhythms and neuroendocrine processes. Current evidence shows that MT protects against liver injury by inhibiting oxidation, inflammation, HSC proliferation and hepatocyte apoptosis, thereby inhibiting the progression of liver cirrhosis. In this review, we summarize the circadian rhythm of liver cirrhosis and its potential mechanisms as well as the therapeutic effects of MT on liver cirrhosis and earlier‐stage liver diseases including liver steatosis, nonalcoholic fatty liver disease and liver fibrosis. Given that MT is an antioxidative and anti‐inflammatory agent that is effective in eliminating liver injury, it is a potential agent with which to reverse liver cirrhosis in its early stage.     

Early‐stage sustainability assessment of biotechnological processes: A case study of citric acid production

Sustainability assessment using a life‐cycle approach is indispensable to contemporary bioprocess development. This assessment is particularly important for early‐stage bioprocess development. As early‐stage investigations of bioprocesses involve the evaluation of their ecological and socioeconomic effects, they can be adjusted more effectively and improved towards sustainability, thereby reducing environmental risk and production costs. Early‐stage sustainability assessment is an important precautionary practice and, despite limited data, a unique opportunity to determine the primary impacts of bioprocess development. To this end, a simple and robust method was applied based on the standardized life‐cycle sustainability assessment methodology and commercially available datasets. In our study, we elaborated on the yeast‐based citric acid production process with Yarrowia lipolytica assessing 11 different substrates in different process modes. The focus of our analysis comprised both cultivation and down‐stream processing. According to our results, the repeated batch raw glycerol based bioprocess alternative showed the best environmental performance. The second‐ and third‐best options were also glycerol‐based. The least sustainable processes were those using molasses, chemically produced ethanol, and soy bean oil. The aggregated results of environmental, economic, and social impacts display waste frying oil as the best‐ranked alternative. The bioprocess with sunflower oil in the batch mode ranked second. The least favorable alternatives were the chemically produced ethanol‐, soy oil‐, refined glycerol‐, and molasses‐based citric acid production processes. The scenario analysis demonstrated that the environmental impact of nutrients and wastewater treatment is negligible, but energy demand of cultivation and down‐stream processing dominated the production process. However, without energy demand the omission of neutralizers almost halves the total impact, and neglecting pasteurization also considerably decreases the environmental impact.     

Test‐compatible confidence intervals for adaptive two‐stage single‐arm designs with binary endpoint

Inference after two‐stage single‐arm designs with binary endpoint is challenging due to the nonunique ordering of the sampling space in multistage designs. We illustrate the problem of specifying test‐compatible confidence intervals for designs with nonconstant second‐stage sample size and present two approaches that guarantee confidence intervals consistent with the test decision. Firstly, we extend the well‐known Clopper–Pearson approach of inverting a family of two‐sided hypothesis tests from the group‐sequential case to designs with fully adaptive sample size. Test compatibility is achieved by using a sample space ordering that is derived from a test‐compatible estimator. The resulting confidence intervals tend to be conservative but assure the nominal coverage probability. In order to assess the possibility of further improving these confidence intervals, we pursue a direct optimization approach minimizing the mean width of the confidence intervals. While the latter approach produces more stable coverage probabilities, it is also slightly anti‐conservative and yields only negligible improvements in mean width. We conclude that the Clopper–Pearson‐type confidence intervals based on a test‐compatible estimator are the best choice if the nominal coverage probability is not to be undershot and compatibility of test decision and confidence interval is to be preserved.