Mitochondrial complex I deficiency leads to the retardation of early embryonic development in Ndufs4 knockout mice
Background The NDUFS4 gene encodes an 18-kD subunit of mitochondria complex I, and mutations in this gene lead to the development of a severe neurodegenerative disease called Leigh syndrome (LS) in humans. To investigate the disease phenotypes and molecular mechanisms of Leigh syndrome, the Ndufs4 knockout (KO) mouse has been widely used as a novel animal model. Because the homozygotes cannot survive beyond child-bearing age, whether Ndufs4 and mitochondrial complex I influence early embryonic development remains unknown. In our study, we attempted to investigate embryonic development in Ndufs4 KO mice, which can be regarded as a Leigh disease model and were created through the CRISPR (clustered regularly interspaced short palindromic repeat) and Cas9 (CRISPR associated)-mediated genome editing system. Methods We first designed a single guide RNA (sgRNA) targeting exon 2 of Ndufs4 to delete the NDUFS4 protein in mouse embryos to mimic Leigh syndrome. Then, we described the phenotypes of our mouse model by forced swimming and the open-field test as well as by assessing other behavioral characteristics. Intracytoplasmic sperm injection (ICSI) was performed to obtain KO embryos to test the influence of NDUFS4 deletion on early embryonic development. Results In this study, we first generated Ndufs4 KO mice with physical and behavioral phenotypes similar to Leigh syndrome using the CRISPR/Cas9 system. The low developmental rate of KO embryos that were derived from knockout gametes indicated that the absence of NDUFS4 impaired the development of preimplantation embryos. Discussion In this paper, we first obtained Ndufs4 KO mice that could mimic Leigh syndrome using the CRISPR/Cas9 system. Then, we identified the role of NDUFS4 in early embryonic development, shedding light on its roles in the respiratory chain and fertility. Our model provides a useful tool with which to investigate the function of Ndufs4. Although the pathological mechanisms of the disease need to be discovered, it helps to understand the pathogenesis of NDUFS4 deficiency in mice and its effects on human diseases.
Wang et al. (2017) Mitochondrial complex I deficiency leads to the retardation of early embryonic development in Ndufs4 knockout mice. PeerJ 5:e3339 https://doi.org/10.7717/peerj.3339
A genome-wide assessment of stages of elevational parapatry in Bornean passerine birds reveals no introgression: implications for processes and patterns of speciation
Topographically complex regions often contain the close juxtaposition of closely related species along elevational gradients. The evolutionary causes of these elevational replacements, and thus the origin and maintenance of a large portion of species diversity along elevational gradients, are usually unclear because ecological differentiation along a gradient or secondary contact following allopatric diversification can produce the same pattern. We used reduced representation genomic sequencing to assess genetic relationships and gene flow between three parapatric pairs of closely related songbird taxa (Arachnothera spiderhunters, Chloropsis leafbirds, and Enicurus forktails) along an elevational gradient in Borneo. Each taxon pair presents a different elevational range distribution across the island, yet results were uniform: little or no gene flow was detected in any pairwise comparisons. These results are congruent with an allopatric “species-pump” model for generation of species diversity and elevational parapatry of congeners on Borneo, rather than in situ generation of species by “ecological speciation” along an elevational gradient.
Moyle et al. (2017) A genome-wide assessment of stages of elevational parapatry in Bornean passerine birds reveals no introgression: implications for processes and patterns of speciation. PeerJ 5:e3335 https://doi.org/10.7717/peerj.3335
Ranking of critical species to preserve the functionality of mutualistic networks using the k-core decomposition
Background Network analysis has become a relevant approach to analyze cascading species extinctions resulting from perturbations on mutualistic interactions as a result of environmental change. In this context, it is essential to be able to point out key species, whose stability would prevent cascading extinctions, and the consequent loss of ecosystem function. In this study, we aim to explain how the k-core decomposition sheds light on the understanding the robustness of bipartite mutualistic networks. Methods We defined three k-magnitudes based on the k-core decomposition: k-radius, k-degree, and k-risk. The first one, k-radius, quantifies the distance from a node to the innermost shell of the partner guild, while k-degree provides a measure of centrality in the k-shell based decomposition. k-risk is a way to measure the vulnerability of a network to the loss of a particular species. Using these magnitudes we analyzed 89 mutualistic networks involving plant pollinators or seed dispersers. Two static extinction procedures were implemented in which k-degree and k-risk were compared against other commonly used ranking indexes, as for example MusRank, explained in detail in Material and Methods. Results When extinctions take place in both guilds, k-risk is the best ranking index if the goal is to identify the key species to preserve the giant component. When species are removed only in the primary class and cascading extinctions are measured in the secondary class, the most effective ranking index to identify the key species to preserve the giant component is k-degree. However, MusRank index was more effective when the goal is to identify the key species to preserve the greatest species richness in the second class. Discussion The k-core decomposition offers a new topological view of the structure of mutualistic networks. The new k-radius, k-degree and k-risk magnitudes take advantage of its properties and provide new insight into the structure of mutualistic networks. The k-risk and k-degree ranking indexes are especially effective approaches to identify key species to preserve when conservation practitioners focus on the preservation of ecosystem functionality over species richness.
García-Algarra et al. (2017) Ranking of critical species to preserve the functionality of mutualistic networks using the k-core decomposition. PeerJ 5:e3321 https://doi.org/10.7717/peerj.3321
Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata
We investigated intra- and inter-colony sequence variation in a population of the dominant Hawaiian coral Montipora capitata by analyzing marker gene and genomic data. Ribosomal ITS1 regions showed evidence of a reticulate history among the colonies, suggesting incomplete rDNA repeat homogenization. Analysis of the mitochondrial genome identified a major (M. capitata) and a minor (M. flabellata) haplotype in single polyp-derived sperm bundle DNA with some colonies containing 2–3 different mtDNA haplotypes. In contrast, Pax-C and newly identified single-copy nuclear genes showed either no sequence differences or minor variations in SNP frequencies segregating among the colonies. Our data suggest past mitochondrial introgression in M. capitata, whereas nuclear single-copy loci show limited variation, highlighting the divergent evolutionary histories of these coral DNA markers.
Putnam et al. (2017) Divergent evolutionary histories of DNA markers in a Hawaiian population of the coral Montipora capitata. PeerJ 5:e3319 https://doi.org/10.7717/peerj.3319
Transcriptome analyses provide insights into the difference of alkaloids biosynthesis in the Chinese goldthread (Coptis chinensis Franch.) from different biotopes
Coptis chinensis Franch., the Chinese goldthread (‘Weilian’ in Chinese), one of the most important medicinal plants from the family Ranunculaceae, and its rhizome has been widely used in Traditional Chinese Medicine for centuries. Here, we analyzed the chemical components and the transcriptome of the Chinese goldthread from three biotopes, including Zhenping, Zunyi and Shizhu. We built comprehensive, high-quality de novo transcriptome assemblies of the Chinese goldthread from short-read RNA-Sequencing data, obtaining 155,710 transcripts and 56,071 unigenes. More than 98.39% and 95.97% of core eukaryotic genes were found in the transcripts and unigenes respectively, indicating that this unigene set capture the majority of the coding genes. A total of 520,462, 493,718, and 507,247 heterozygous SNPs were identified in the three accessions from Zhenping, Zunyi, and Shizhu respectively, indicating high polymorphism in coding regions of the Chinese goldthread (∼1%). Chemical analyses of the rhizome identified six major components, including berberine, palmatine, coptisine, epiberberine, columbamine, and jatrorrhizine. Berberine has the highest concentrations, followed by coptisine, palmatine, and epiberberine sequentially for all the three accessions. The drug quality of the accession from Shizhu may be the highest among these accessions. Differential analyses of the transcriptome identified four pivotal candidate enzymes, including aspartate aminotransferaseprotein, polyphenol oxidase, primary-amine oxidase, and tyrosine decarboxylase, were significantly differentially expressed and may be responsible for the difference of alkaloids contents in the accessions from different biotopes.
Chen et al. (2017) Transcriptome analyses provide insights into the difference of alkaloids biosynthesis in the Chinese goldthread (Coptis chinensis Franch.) from different biotopes. PeerJ 5:e3303 https://doi.org/10.7717/peerj.3303
Body composition estimation from selected slices: equations computed from a new semi-automatic thresholding method developed on whole-body CT scans
Background Estimating volumes and masses of total body components is important for the study and treatment monitoring of nutrition and nutrition-related disorders, cancer, joint replacement, energy-expenditure and exercise physiology. While several equations have been offered for estimating total body components from MRI slices, no reliable and tested method exists for CT scans. For the first time, body composition data was derived from 41 high-resolution whole-body CT scans. From these data, we defined equations for estimating volumes and masses of total body AT and LT from corresponding tissue areas measured in selected CT scan slices. Methods We present a new semi-automatic approach to defining the density cutoff between adipose tissue (AT) and lean tissue (LT) in such material. An intra-class correlation coefficient (ICC) was used to validate the method. The equations for estimating the whole-body composition volume and mass from areas measured in selected slices were modeled with ordinary least squares (OLS) linear regressions and support vector machine regression (SVMR). Results and Discussion The best predictive equation for total body AT volume was based on the AT area of a single slice located between the 4th and 5th lumbar vertebrae (L4-L5) and produced lower prediction errors (|PE| = 1.86 liters, %PE = 8.77) than previous equations also based on CT scans. The LT area of the mid-thigh provided the lowest prediction errors (|PE| = 2.52 liters, %PE = 7.08) for estimating whole-body LT volume. We also present equations to predict total body AT and LT masses from a slice located at L4-L5 that resulted in reduced error compared with the previously published equations based on CT scans. The multislice SVMR predictor gave the theoretical upper limit for prediction precision of volumes and cross-validated the results.
Lacoste Jeanson et al. (2017) Body composition estimation from selected slices: equations computed from a new semi-automatic thresholding method developed on whole-body CT scans. PeerJ 5:e3302 https://doi.org/10.7717/peerj.3302
Toxicity, repellency and flushing out in Triatoma infestans (Hemiptera: Reduviidae) exposed to the repellents DEET and IR3535
DEET and IR3535 are insect repellents present worldwide in commercial products; their efficacy has been mainly evaluated in mosquitoes. This study compares the toxicological effects and the behavioral responses induced by both repellents on the blood-sucking bug Triatoma infestans Klug (Hemiptera: Reduviidae), one of the main vectors of Chagas disease. When applied topically, the Median Lethal Dose (72 h) for DEET was 220.8 µg/insect. Using IR3535, topical application of 500 µg/insect killed no nymphs. The minimum concentration that produced repellency was the same for both compounds: 1,15 µg/cm2. The effect of a mixture DEET:IR3535 1:1 was similar to that of their pure components. Flushing out was assessed in a chamber with a shelter containing groups of ten nymphs. The repellents were aerosolized on the shelter and the number of insects leaving it was recorded for 60 min. During that time, 0.006 g/m3 of the positive control tetramethrin flushed out 76.7% of the nymphs, while 1.76 g/m3 of DEET or IR3535 flushed out 30 and 0%, respectively. The concentrations required for both compounds to produce toxicity or flushing out are too high to have any practical applications. However, they showed a promising repellency. Additional research should be done to evaluate their possible use for personal protection against T. infestans bites.
Reynoso et al. (2017) Toxicity, repellency and flushing out in Triatoma infestans (Hemiptera: Reduviidae) exposed to the repellents DEET and IR3535. PeerJ 5:e3292 https://doi.org/10.7717/peerj.3292
Face recognition is similarly affected by viewpoint in school-aged children and adults
There is an ongoing debate on the question when face processing abilities mature. One aspect that has been part of this debate is the ability to recognize faces in and across different viewpoints. Here, we tested 128 participants consisting of school-age children (ages, 5–10 years) and adults (ages, 19–37 years) in two experiments to investigate the effects of different viewpoints (including front, three-quarter, profile view) on face recognition during development. Furthermore, we compared recognition performance for faces to that of another object category (cars). In the first experiment (n = 88) we tested if the pattern of performance for faces presented in different viewpoints is similar in school-aged children and adults. Participants completed a two-alternative-forced-choice (2AFC) memory task comprising images of both faces and cars in front, three-quarter and profile view, which were presented in the same viewpoint during learning and testing. In the second experiment (n = 40) we tested if face recognition is similarly affected by viewpoint changes in children and adults. In this experiment the 2AFC memory task included a change of viewpoint between learning and testing. While in both experiments we found higher recognition performance for faces with increasing age, the overall pattern of both viewpoint and viewpoint-change-effects and also the difference between view-change- and no-change-conditions was similar across age groups. In contrast to faces, no viewpoint effects were observed in cars (experiment 1), viewpoint change effects, however, were similar for cars and faces (experiment 2). In sum, our results suggest early maturity of the ability to recognize faces in and across different viewpoints.
Nordt et al. (2017) Face recognition is similarly affected by viewpoint in school-aged children and adults. PeerJ 5:e3253 https://doi.org/10.7717/peerj.3253
Lygistorrhinidae (Diptera: Bibionomorpha: Sciaroidea) in early Eocene Cambay amber
One new genus and three new species of Lygistorrhinidae in early Eocene Cambay amber from India are described, which significantly increases our knowledge about this group in the Eocene. Lygistorrhina indica n. sp. is the oldest fossil known from this extant genus. Indorrhina sahnii n. gen. et sp. shows morphological similarities to each of the two extant genera Lygistorrhina and Asiorrhina. Palaeognoriste orientale is the third species known from a group that has only been recorded from Eocene Baltic amber before. The latter finding reveals faunal links between Cambay amber and the probably slightly younger Baltic amber, adding further evidence that faunal exchange between Europe/Asia and India took place before the formation of Cambay amber.
Stebner et al. (2017) Lygistorrhinidae (Diptera: Bibionomorpha: Sciaroidea) in early Eocene Cambay amber. PeerJ 5:e3313 https://doi.org/10.7717/peerj.3313
Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities
Sequencing environmental DNA (eDNA) is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes. A variety of pre-treatment techniques for screening eDNA and eRNA derived operational taxonomic units (OTUs) have been employed prior to statistical analyses, including removing singleton taxa (i.e., OTUs found only once) and discarding those not present in both eDNA and eRNA datasets. In this study, we used bacterial (16S ribosomal RNA gene) and eukaryotic (18S ribosomal RNA gene) eDNA- and eRNA-derived data from benthic communities collected at increasing distances along a transect from an oil production platform (Taranaki, New Zealand). Macro-infauna (visual classification of benthic invertebrates) and physico-chemical data were analyzed in parallel. We tested the effect of removing singleton taxa, and removing taxa not present in the eDNA and eRNA libraries from the same environmental sample (trimmed by shared OTUs), by comparing the impact of the oil production platform on alpha- and beta-diversity of the eDNA/eRNA-based biological assemblages, and by correlating these to the morphologically identified macro-faunal communities and the physico-chemical data. When trimmed by singletons, presence/absence information from eRNA data represented the best proxy to detect changes on species diversity for both bacteria and eukaryotes. However, assessment of quantitative beta-diversity from read abundance information of bacteria eRNA did not, contrary to eDNA, reveal any impact from the oil production activity. Overall, the data appeared more robust when trimmed by shared OTUs, showing a greater effect of the platform on alpha- and beta-diversity. Trimming by shared OTUs likely removes taxa derived from legacy DNA and technical artefacts introduced through reverse transcriptase, polymerase-chain-reaction and sequencing. Findings from our scoping study suggest that metabarcoding-based biomonitoring surveys should, if funds, time and expertise allow, be assessed using both eDNA and eRNA products.
Laroche et al. (2017) Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities. PeerJ 5:e3347 https://doi.org/10.7717/peerj.3347