Detecting telomere elongation in longitudinal datasets: analysis of a proposal by Simons, Stulp and Nakagawa
Telomere shortening has emerged as an important biomarker of aging. Longitudinal studies consistently find that, although telomere length shortens over time on average, there is a subset of individuals for whom telomere length is observed to increase. This apparent lengthening could either be a genuine biological phenomenon, or simply due to measurement and sampling error. Simons, Stulp & Nakagawa (2014) recently proposed a statistical test for detecting when the amount of apparent lengthening in a dataset exceeds that which should be expected due to error, and thus indicating that genuine elongation may be operative in some individuals. However, the test is based on a restrictive assumption, namely that each individual’s true rate of telomere change is constant over time. It is not currently known whether this assumption is true. Here we show, using simulated datasets, that with perfect measurement and large sample size, the test has high power to detect true lengthening as long as the true rate of change is either constant, or moderately stable, over time. If the true rate of change varies randomly from year to year, the test systematically returns type-II errors (false negatives; that is, failures to detect lengthening even when a substantial fraction of the population truly lengthens each year). We also consider the impact of measurement error. Using estimates of the magnitude of annual attrition and of measurement error derived from the human telomere literature, we show that power of the test is likely to be low in several empirically-realistic scenarios, even in large samples. Thus, whilst a significant result of the proposed test is likely to indicate that true lengthening is present in a data set, type-II errors are a likely outcome, either if measurement error is substantial, and/or the true rate of telomere change varies substantially over time within individuals.
Nettle et al. (2017) Detecting telomere elongation in longitudinal datasets: analysis of a proposal by Simons, Stulp and Nakagawa. PeerJ 5:e3265 https://doi.org/10.7717/peerj.3265
First report of bats (Mammalia: Chiroptera) from the Gray Fossil Site (late Miocene or early Pliocene), Tennessee, USA
Thousands of vertebrate fossils have been recovered from the Gray Fossil Site, Tennessee, dating to the Miocene-Pliocene boundary. Among these are but eight specimens of bats representing two different taxa referable to the family Vespertilionidae. Comparison of the fossils with Neogene and Quaternary bats reveals that seven of the eight specimens pertain to a species of Eptesicus that cannot be distinguished from recent North American Eptesicus fuscus. The remaining specimen, a horizontal ramus with m3, is from a smaller vespertilionid bat that cannot confidently be assigned to a genus. Although many vespertilionid genera can be excluded through comparisons, and many extinct named taxa cannot be compared due to nonequivalence of preserved skeletal elements, the second taxon shows morphological similarities to small-bodied taxa with three lower premolar alveoli, three distinct m3 talonid cusps, and m3 postcristid showing the myotodont condition. It resembles especially Nycticeius humeralis and small species of Eptesicus. Eptesicus cf. E. fuscus potentially inhabited eastern North America continuously since the late Hemphillian land mammal age, when other evidence from the Gray Fossil Site indicates the presence in the southern Appalachian Mountains of a warm, subtropical, oak-hickory-conifer forest having autochthonous North American as well as allochthonous biogeographical ties to eastern Asia and tropical-subtropical Middle America.
Czaplewski (2017) First report of bats (Mammalia: Chiroptera) from the Gray Fossil Site (late Miocene or early Pliocene), Tennessee, USA. PeerJ 5:e3263 https://doi.org/10.7717/peerj.3263
Evolution of developmental sequences in lepidosaurs
Background Lepidosaurs, a group including rhynchocephalians and squamates, are one of the major clades of extant vertebrates. Although there has been extensive phylogenetic work on this clade, its interrelationships are a matter of debate. Morphological and molecular data suggest very different relationships within squamates. Despite this, relatively few studies have assessed the utility of other types of data for inferring squamate phylogeny. Methods We used developmental sequences of 20 events in 29 species of lepidosaurs. These sequences were analysed using event-pairing and continuous analysis. They were transformed into cladistic characters and analysed in TNT. Ancestral state reconstructions were performed on two main phylogenetic hypotheses of squamates (morphological and molecular). Results Cladistic analyses conducted using characters generated by these methods do not resemble any previously published phylogeny. Ancestral state reconstructions are equally consistent with both morphological and molecular hypotheses of squamate phylogeny. Only several inferred heterochronic events are common to all methods and phylogenies. Discussion Results of the cladistic analyses, and the fact that reconstructions of heterochronic events show more similarities between certain methods rather than phylogenetic hypotheses, suggest that phylogenetic signal is at best weak in the studied developmental events. Possibly the developmental sequences analysed here evolve too quickly to recover deep divergences within Squamata.
Skawiński et al. (2017) Evolution of developmental sequences in lepidosaurs. PeerJ 5:e3262 https://doi.org/10.7717/peerj.3262
Prediction of post-translational modification sites using multiple kernel support vector machine
Protein post-translational modification (PTM) is an important mechanism that is involved in the regulation of protein function. Considering the high-cost and labor-intensive of experimental identification, many computational prediction methods are currently available for the prediction of PTM sites by using protein local sequence information in the context of conserved motif. Here we proposed a novel computational method by using the combination of multiple kernel support vector machines (SVM) for predicting PTM sites including phosphorylation, O-linked glycosylation, acetylation, sulfation and nitration. To largely make use of local sequence information and site-modification relationships, we developed a local sequence kernel and Gaussian interaction profile kernel, respectively. Multiple kernels were further combined to train SVM for efficiently leveraging kernel information to boost predictive performance. We compared the proposed method with existing PTM prediction methods. The experimental results revealed that the proposed method performed comparable or better performance than the existing prediction methods, suggesting the feasibility of the developed kernels and the usefulness of the proposed method in PTM sites prediction.
Wang et al. (2017) Prediction of post-translational modification sites using multiple kernel support vector machine. PeerJ 5:e3261 https://doi.org/10.7717/peerj.3261
A Profile Hidden Markov Model to investigate the distribution and frequency of LanB-encoding lantibiotic modification genes in the human oral and gut microbiome
Background The human microbiota plays a key role in health and disease, and bacteriocins, which are small, bacterially produced, antimicrobial peptides, are likely to have an important function in the stability and dynamics of this community. Here we examined the density and distribution of the subclass I lantibiotic modification protein, LanB, in human oral and stool microbiome datasets using a specially constructed profile Hidden Markov Model (HMM). Methods The model was validated by correctly identifying known lanB genes in the genomes of known bacteriocin producers more effectively than other methods, while being sensitive enough to differentiate between different subclasses of lantibiotic modification proteins. This approach was compared with two existing methods to screen both genomic and metagenomic datasets obtained from the Human Microbiome Project (HMP). Results Of the methods evaluated, the new profile HMM identified the greatest number of putative LanB proteins in the stool and oral metagenome data while BlastP identified the fewest. In addition, the model identified more LanB proteins than a pre-existing Pfam lanthionine dehydratase model. Searching the gastrointestinal tract subset of the HMP reference genome database with the new HMM identified seven putative subclass I lantibiotic producers, including two members of the Coprobacillus genus. Conclusions These findings establish custom profile HMMs as a potentially powerful tool in the search for novel bioactive producers with the power to benefit human health, and reinforce the repertoire of apparent bacteriocin-encoding gene clusters that may have been overlooked by culture-dependent mining efforts to date.
Walsh et al. (2017) A Profile Hidden Markov Model to investigate the distribution and frequency of LanB-encoding lantibiotic modification genes in the human oral and gut microbiome. PeerJ 5:e3254 https://doi.org/10.7717/peerj.3254
Octahedral ruthenium (II) polypyridyl complexes as antimicrobial agents against mycobacterium
Tuberculosis is one of the world’s deadliest infectious disease with 1.5 millions deaths annually. It is imperative to discover novel compounds with potent activity against M. tuberculosis. In this study, susceptibilities of M. smegmatis to the octahedral ruthenium(II) polypyridyl complexes, 1 {[(bpy)3Ru] (PF6)2 (bpy = 2,2′-bipyridine)}, 2 {[(phen)2Ru(dppz)](PF6)2 (phen = 1,10-phenanthroline, dppz = dipyridophenazine)} and 3 {[(phen)3Ru](PF6)2} were measured by broth microdilution and reported as the MIC values. Toxicities of complex 3 to LO2 and hepG2 cell lines were also measured. Complex 2 inhibited the growth of M. smegmatis with MIC value of 2 µg/mL, while complex 3 was bactericidal with MIC value of 26 µg/mL. Furthermore, the bactericidal activity of complex 3 was dependent on reactive oxygen species production. Complex 3 showed no cytotoxicity against LO2 and hepG2 cell lines at concentration as high as 64 µg/mL, paving the way for further optimization and development as a novel antibacterial agent for the treatment of M. tuberculosis infection.
Liao et al. (2017) Octahedral ruthenium (II) polypyridyl complexes as antimicrobial agents against mycobacterium. PeerJ 5:e3252 https://doi.org/10.7717/peerj.3252
Pitfalls associated with evaluating enzymatic quorum quenching activity: the case of MomL and its effect on Pseudomonas aeruginosa and Acinetobacter baumannii biofilms
Background The enzymatic degradation of quorums sensing (QS) molecules (called quorum quenching, QQ) has been considered as a promising anti-virulence therapy to treat biofilm-related infections and combat antibiotic resistance. The recently-discovered QQ enzyme MomL has been reported to efficiently degrade different N-acyl homoserine lactones (AHLs) of various Gram-negative pathogens. Here we investigated the effect of MomL on biofilms formed by two important nosocomial pathogens, Pseudomonas aeruginosa and Acinetobacter baumannii. Methods MomL was expressed in E.coli BL21 and purified. The activity of MomL on AHLs with hydroxyl substituent was tested. Biofilms of P. aeruginosa PAO1 and Acinetobacter strains were formed in 96-well microtiter plates. Biofilm formation was evaluated by crystal violet staining, plating and fluorescence microscopy. The effect of MomL on biofilm susceptibility to antibiotics was also tested. We further evaluated MomL in dual-species biofilms formed by P. aeruginosa and A. baumannii, and in biofilms formed in a wound model. The effect of MomL on virulence of A. baumannii was also tested in the Caenorhabditis elegans model. Results MomL reduced biofilm formation and increased biofilm susceptibility to different antibiotics in biofilms of P. aeruginosa PAO1 and A. baumannii LMG 10531 formed in microtiter plates in vitro. However, no significant differences were detected in the dual-species biofilm and in wound model biofilms. In addition, MomL did not affect virulence of A. baumannii in the C. elegans model. Finally, the effect of MomL on biofilm of Acinetobacter strains seems to be strain-dependent. Discussion Our results indicate that although MomL showed a promising anti-biofilm effect against P. aeruginosa and A. baumanii biofilms formed in microtiter plates, the effect on biofilm formation under conditions more likely to mimic the real-life situation was much less pronounced or even absent. Our data indicate that in order to obtain a better picture of potential applicability of QQ enzymes for the treatment of biofilm-related infections, more elaborate model systems need to be used.
Zhang et al. (2017) Pitfalls associated with evaluating enzymatic quorum quenching activity: the case of MomL and its effect on Pseudomonas aeruginosa and Acinetobacter baumannii biofilms. PeerJ 5:e3251 https://doi.org/10.7717/peerj.3251
The genetics of venom ontogeny in the eastern diamondback rattlesnake (Crotalus adamanteus)
The same selective forces that give rise to rapid inter- and intraspecific divergence in snake venoms can also favor differences in venoms across life-history stages. Ontogenetic changes in venom composition are well known and widespread in snakes but have not been investigated to the level of unambiguously identifying the specific loci involved. The eastern diamondback rattlesnake was previously shown to undergo an ontogenetic shift in venom composition at sexual maturity, and this shift accounted for more venom variation than geography. To characterize the genetics underlying the ontogenetic venom compositional change in C. adamanteus, we sequenced adult/juvenile pairs of venom-gland transcriptomes from five populations previously shown to have different adult venom compositions. We identified a total of 59 putative toxin transcripts for C. adamanteus, and 12 of these were involved in the ontogenetic change. Three toxins were downregulated, and nine were upregulated in adults relative to juveniles. Adults and juveniles expressed similar total levels of snake-venom metalloproteinases but differed substantially in their featured paralogs, and adults expressed higher levels of Bradykinin-potentiating and C-type natriuretic peptides, nerve growth factor, and specific paralogs of phospholipases A2 and snake venom serine proteinases. Juvenile venom was more toxic to mice, indicating that the expression differences resulted in a phenotypically, and therefore potentially ecologically, significant difference in venom function. We also showed that adult and juvenile venom-gland transcriptomes for a species with known ontogenetic venom variation were equally effective at individually providing a full characterization of the venom genes of a species but that any particular individual was likely to lack several toxins in their transcriptome. A full characterization of a species’ venom-gene complement therefore requires sequencing more than one individual, although the ages of the individuals are unimportant.
Rokyta et al. (2017) The genetics of venom ontogeny in the eastern diamondback rattlesnake (Crotalus adamanteus). PeerJ 5:e3249 https://doi.org/10.7717/peerj.3249
Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge
Background Zostera marina (also known as eelgrass) is a foundation species in coastal and marine ecosystems worldwide and is a model for studies of seagrasses (a paraphyletic group in the order Alismatales) that include all the known fully submerged marine angiosperms. In recent years, there has been a growing appreciation of the potential importance of the microbial communities (i.e., microbiomes) associated with various plant species. Here we report a study of variation in Z. marina microbiomes from a field site in Bodega Bay, CA. Methods We characterized and then compared the microbial communities of root, leaf and sediment samples (using 16S ribosomal RNA gene PCR and sequencing) and associated environmental parameters from the inside, edge and outside of a single subtidal Z. marina patch. Multiple comparative approaches were used to examine associations between microbiome features (e.g., diversity, taxonomic composition) and environmental parameters and to compare sample types and sites. Results Microbial communities differed significantly between sample types (root, leaf and sediment) and in sediments from different sites (inside, edge, outside). Carbon:Nitrogen ratio and eelgrass density were both significantly correlated to sediment community composition. Enrichment of certain taxonomic groups in each sample type was detected and analyzed in regard to possible functional implications (especially regarding sulfur metabolism). Discussion Our results are mostly consistent with prior work on seagrass associated microbiomes with a few differences and additional findings. From a functional point of view, the most significant finding is that many of the taxa that differ significantly between sample types and sites are closely related to ones commonly associated with various aspects of sulfur and nitrogen metabolism. Though not a traditional model organism, we believe that Z. marina can become a model for studies of marine plant-microbiome interactions.
Ettinger et al. (2017) Microbial communities in sediment from Zostera marina patches, but not the Z. marina leaf or root microbiomes, vary in relation to distance from patch edge. PeerJ 5:e3246 https://doi.org/10.7717/peerj.3246
On the entry of an emerging arbovirus into host cells: Mayaro virus takes the highway to the cytoplasm through fusion with early endosomes and caveolae-derived vesicles
Mayaro virus (MAYV) is an emergent sylvatic alphavirus in South America, related to sporadic outbreaks of a chikungunya-like human febrile illness accompanied by severe arthralgia. Despite its high potential for urban emergence, MAYV is still an obscure virus with scarce information about its infection cycle, including the corresponding early events. Even for prototypical alphaviruses, the cell entry mechanism still has some rough edges to trim: although clathrin-mediated endocytosis is quoted as the putative route, alternative paths as distinct as direct virus genome injection through the cell plasma membrane seems to be possible. Our aim was to clarify crucial details on the entry route exploited by MAYV to gain access into the host cell. Tracking the virus since its first contact with the surface of Vero cells by fluorescence microscopy, we show that its entry occurs by a fast endocytic process and relies on fusion with acidic endosomal compartments. Moreover, blocking clathrin-mediated endocytosis or depleting cholesterol from the cell membrane leads to a strong inhibition of viral infection, as assessed by plaque assays. Following this clue, we found that early endosomes and caveolae-derived vesicles are both implicated as target membranes for MAYV fusion. Our findings unravel the very first events that culminate in a productive infection by MAYV and shed light on potential targets for a rational antiviral therapy, besides providing a better comprehension of the entry routes exploited by alphaviruses to get into the cell.
Carvalho et al. (2017) On the entry of an emerging arbovirus into host cells: Mayaro virus takes the highway to the cytoplasm through fusion with early endosomes and caveolae-derived vesicles. PeerJ 5:e3245 https://doi.org/10.7717/peerj.3245