The key role of microtubules in hypoxia preconditioning-induced nuclear translocation of HIF-1α in rat cardiomyocytes
Background Hypoxia-inducible factor (HIF)-1 is involved in the regulation of hypoxic preconditioning in cardiomyocytes. Under hypoxic conditions, HIF-1α accumulates and is translocated to the nucleus, where it forms an active complex with HIF-1β and activates transcription of approximately 60 kinds of hypoxia-adaptive genes. Microtubules are hollow tubular structures in the cell that maintain cellular morphology and that transport substances. This study attempted to clarify the role of microtubule structure in the endonuclear aggregation of HIF-1α following hypoxic preconditioning of cardiomyocytes. Methods Primary rat cardiomyocytes were isolated and cultured. The cardiomyocyte culture system was used to establish a hypoxia model and a hypoxic preconditioning model. Interventions were performed on primary cardiomyocytes using a microtubule-depolymerizing agent and different concentrations of a microtubule stabilizer. The microtubule structure and the degree of HIF-1α nuclear aggregation were observed by confocal laser scanning microscopy. The expression of HIF-1α in the cytoplasm and nucleus was detected using Western blotting. Cardiomyocyte energy content, reflected by adenosine triphosphate/adenosine diphosphate (ATP/ADP), and key glycolytic enzymes were monitored by colorimetry and high-performance liquid chromatography (HPLC). Reactive oxygen species (ROS) production was also used to comprehensively assess whether microtubule stabilization can enhance the myocardial protective effect of hypoxic preconditioning. Results During prolonged hypoxia, it was found that the destruction of the microtubule network structure of cardiomyocytes was gradually aggravated. After this preconditioning, an abundance of HIF-1α was clustered in the nucleus. When the microtubules were depolymerized and hypoxia pretreatment was performed, HIF-1α clustering occurred around the nucleus, and HIF-1α nuclear expression was low. The levels of key glycolytic enzymes were significantly higher in the microtubule stabilizer group than in the hypoxia group. Additionally, the levels of lactate dehydrogenase and ROS were significantly lower in the microtubule stabilizer group than in the hypoxia group. Conclusion The microtubules of cardiomyocytes may be involved in the process of HIF-1α endonuclear aggregation, helping to enhance the anti-hypoxic ability of cardiomyocytes.
Guo et al. (2017) The key role of microtubules in hypoxia preconditioning-induced nuclear translocation of HIF-1α in rat cardiomyocytes. PeerJ 5:e3662 https://doi.org/10.7717/peerj.3662
Genome-wide identification of CBL family and expression analysis of CBLs in response to potassium deficiency in cotton
Calcineurin B-like (CBL) proteins, as calcium sensors, play pivotal roles in plant responses to diverse abiotic stresses and in growth and development through interaction with CBL-interacting protein kinases (CIPKs). However, knowledge about functions and evolution of CBLs in Gossypium plants is scarce. Here, we conducted a genome-wide survey and identified 13, 13 and 22 CBL genes in the progenitor diploid Gossypium arboreum and Gossypium raimondii, and the cultivated allotetraploid Gossypium hirsutum, respectively. Analysis of physical properties, chromosomal locations, conserved domains and phylogeny indicated rather conserved nature of CBLs among the three Gossypium species. Moreover, these CBLs have closer genetic evolutionary relationship with the CBLs from cocoa than with those from other plants. Most CBL genes underwent evolution under purifying selection in the three Gossypium plants. Additionally, nearly all G. hirsutum CBL (GhCBL) genes were expressed in the root, stem, leaf, flower and fiber. Many GhCBLs were preferentially expressed in the flower while several GhCBLs were mainly expressed in roots. Expression patterns of GhCBL genes in response to potassium deficiency were also studied. The expression of most GhCBLs were moderately induced in roots after treatments with low-potassium stress. Yeast two-hybrid experiments indicated that GhCBL1-2, GhCBL1-3, GhCBL4-4, GhCBL8, GhCBL9 and GhCBL10-3 interacted with GhCIPK23, respectively. Our results provided a comprehensive view of the CBLs and valuable information for researchers to further investigate the roles and functional mechanisms of the CBLs in Gossypium.
Lu et al. (2017) Genome-wide identification of CBL family and expression analysis of CBLs in response to potassium deficiency in cotton. PeerJ 5:e3653 https://doi.org/10.7717/peerj.3653
Freeze-thaw decellularization of the trabecular meshwork in an ex vivo eye perfusion model
Objective The trabecular meshwork (TM) is the primary substrate of outflow resistance in glaucomatous eyes. Repopulating diseased TM with fresh, functional TM cells might be a viable therapeutic approach. Decellularized TM scaffolds have previously been produced by ablating cells with suicide gene therapy or saponin, which risks incomplete cell removal or dissolution of the extracellular matrix, respectively. We hypothesized that improved trabecular meshwork cell ablation would result from freeze-thaw cycles compared to chemical treatment. Materials and Methods We obtained 24 porcine eyes from a local abattoir, dissected and mounted them in an anterior segment perfusion within two hours of sacrifice. Intraocular pressure (IOP) was recorded continuously by a pressure transducer system. After 72 h of IOP stabilization, eight eyes were assigned to freeze-thaw (F) ablation (−80 °C × 2), to 0.02% saponin (S) treatment, or the control group (C), respectively. The TM was transduced with an eGFP expressing feline immunodeficiency viral (FIV) vector and tracked via fluorescent microscopy to confirm ablation. Following treatment, the eyes were perfused with standard tissue culture media for 180 h. TM histology was assessed by hematoxylin and eosin staining. TM viability was evaluated by a calcein AM/propidium iodide (PI) assay. The TM extracellular matrix was stained with Picro Sirius Red. We measured IOP and modeled it with a linear mixed effects model using a B-spline function of time with five degrees of freedom. Results F and S experienced a similar IOP reduction of 30% from baseline (P = 0.64). IOP reduction of about 30% occurred in F within 24 h and in S within 48 h. Live visualization of eGFP demonstrated that F conferred a complete ablation of all TM cells and only a partial ablation in S. Histological analysis and Picro Sirius staining confirmed that no TM cells survived in F while the extracellular matrix remained. The viability assay showed very low PI and no calcein staining in F in contrast to many PI-labeled, dead TM cells and calcein-labeled viable TM cells in S. Conclusion We developed a rapid TM ablation method that uses cyclic freezing that is free of biological or chemical agents and able to produce a decellularized TM scaffold with preserved TM extracellular matrix in an organotypic perfusion culture.
Dang et al. (2017) Freeze-thaw decellularization of the trabecular meshwork in an ex vivo eye perfusion model. PeerJ 5:e3629 https://doi.org/10.7717/peerj.3629
Microbial communities in the reef water at Kham Island, lower Gulf of Thailand
Coral reefs are among the most biodiverse habitats on Earth, but knowledge of their associated marinemicrobiome remains limited. To increase the understanding of the coral reef ecosystem in the lower Gulf of Thailand, this study utilized 16S and 18S rRNA gene-based pyrosequencing to identify the prokaryotic and eukaryotic microbiota present in the reef water at Kham Island, Trat province, Thailand (N6.97 E100.86). The obtained result was then compared with the published microbiota from different coral reef water and marine sites. The coral reefs at Kham Island are of the fringe type. The reefs remain preserved and abundant. The community similarity indices (i.e., Lennon similarity index, Yue & Clayton similarity index) indicated that the prokaryotic composition of Kham was closely related to that of Kra, another fringing reef site in the lower Gulf of Thailand, followed by coral reef water microbiota at GS048b (Cooks Bay, Fr. Polynesia), Palmyra (Northern Line Islands, United States) and GS108b (Coccos Keeling, Australia), respectively. Additionally, the microbial eukaryotic populations at Kham was analyzed and compared with the available database at Kra. Both eukaryotic microbiota, in summer and winter seasons, were correlated. An abundance of Dinophysis acuminata was noted in the summer season, in accordance with its reported cause of diarrhoeatic shellfish outbreak in the summer season elsewhere. The slightly lower biodiversity in Kham than at Kra might reflect the partly habitat difference due to coastal anthropogenic activities and minor water circulation, as Kham locates close to the mainland and is surrounded by islands (e.g., Chang and Kut islands). The global marine microbiota comparison suggested relatively similar microbial structures among coral sites irrespective of geographical location, supporting the importance of coral-associated marine microbiomes, and Spearman’s correlation analysis between community membership and factors of shore distance and seawater temperature indicated potential correlation of these factors (p-values < 0.05) with Kham, Kra, and some other coral and coastal sites. Together, this study provided the second marine microbial database for the coral reef of the lower Gulf of Thailand, and a comparison of the coral-associated marine microbial diversity among global ocean sites.
Somboonna et al. (2017) Microbial communities in the reef water at Kham Island, lower Gulf of Thailand. PeerJ 5:e3625 https://doi.org/10.7717/peerj.3625
Characterisation of microsatellite and SNP markers from Miseq and genotyping-by-sequencing data among parapatric Urophora cardui (Tephritidae) populations
Phylogeographic analyses of the gall fly Urophora cardui have in earlier studies based on allozymes and mtDNA identified small-scale, parapatrically diverged populations within an expanding Western Palearctic population. However, the low polymorphism of these markers prohibited an accurate delimitation of the evolutionary origin of the parapatric divergence. Urophora cardui from the Western Palearctic have been introduced into Canada as biological control agents of the host plant Cirsium arvense. Here, we characterise 12 microsatellite loci with hexa-, penta- and tetra-nucleotide repeat motifs and report a genotyping-by-sequencing SNP protocol. We test the markers for genetic variation among three parapatric U. cardui populations. Microsatellite variability (N = 59 individuals) was high: expected heterozygosity/locus/population (0.60–0.90), allele number/locus/population (5–21). One locus was alternatively sex-linked in males or females. Cross-species amplification in the sister species U. stylata was successful or partially successful for seven loci. For genotyping-by-sequencing (N = 18 individuals), different DNA extraction methods did not affect data quality. Depending on sequence sorting criteria, 1,177–2,347 unlinked SNPs and 1,750–4,469 parsimony informative sites were found in 3,514–5,767 loci recovered after paralog filtering. Both marker systems quantified the same population partitions with high probabilities. Many and highly differentiated loci in both marker systems indicate genome-wide diversification and genetically distinct populations.
Johannesen et al. (2017) Characterisation of microsatellite and SNP markers from Miseq and genotyping-by-sequencing data among parapatric Urophora cardui (Tephritidae) populations. PeerJ 5:e3582 https://doi.org/10.7717/peerj.3582
Extensive analysis of native and non-native Centaurea solstitialis L. populations across the world shows no traces of polyploidization
Centaurea solstitialis L. (yellow starthistle, Asteraceae) is a Eurasian native plant introduced as an exotic into North and South America, and Australia, where it is regarded as a noxious invasive. Changes in ploidy level have been found to be responsible for numerous plant biological invasions, as they are involved in trait shifts critical to invasive success, like increased growth rate and biomass, longer life-span, or polycarpy. C. solstitialis had been reported to be diploid (2n = 2x = 16 chromosomes), however, actual data are scarce and sometimes contradictory. We determined for the first time the absolute nuclear DNA content by flow cytometry and estimated ploidy level in 52 natural populations of C. solstitialis across its native and non-native ranges, around the world. All the C. solstitialis populations screened were found to be homogeneously diploid (average 2C value of 1.72 pg, SD = ±0.06 pg), with no significant variation in DNA content between invasive and non-invasive genotypes. We did not find any meaningful difference among the extensive number of native and non-native C. solstitialis populations sampled around the globe, indicating that the species invasive success is not due to changes in genome size or ploidy level.
Irimia et al. (2017) Extensive analysis of native and non-native Centaurea solstitialis L. populations across the world shows no traces of polyploidization. PeerJ 5:e3531 https://doi.org/10.7717/peerj.3531
Extinction models vary in the information they require, the simplest considering the rate of certain sightings only. More complicated methods include uncertain sightings and allow for variation in the reliability of uncertain sightings. Generally extinction models require expert opinion, either as a prior belief that a species is extinct, or to establish the quality of a sighting record, or both. Is this subjectivity necessary? We present two models to explore whether the individual quality of sightings, judged by experts, is strongly informative of the probability of extinction: the ‘quality breakpoint method’ and the ‘quality as variance method’. For the first method we use the Barbary lion as an exemplar. For the second method we use the Barbary lion, Alaotra grebe, Jamaican petrel and Pohnpei starling as exemplars. The ‘quality breakpoint method’ uses certain and uncertain sighting records, and the quality of uncertain records, to establish whether a change point in the rate of sightings can be established using a simultaneous Bayesian optimisation with a non-informative prior. For the Barbary lion, there is a change in subjective quality of sightings around 1930. Unexpectedly sighting quality increases after this date. This suggests that including quality scores from experts can lead to irregular effects and may not offer reliable results. As an alternative, we use quality as a measure of variance around the sightings, not a change in quality. This leads to predictions with larger standard deviations, however the results remain consistent across any prior belief of extinction. Nonetheless, replacing actual quality scores with random quality scores showed little difference, inferring that the quality scores from experts are superfluous. Therefore, we deem the expensive process of obtaining pooled expert estimates as unnecessary, and even when used we recommend that sighting data should have minimal input from experts in terms of assessing the sighting quality at a fine scale. Rather, sightings should be classed as certain or uncertain, using a framework that is as independent of human bias as possible.
Lee et al. (2017) Are extinction opinions extinct?. PeerJ 5:e3663 https://doi.org/10.7717/peerj.3663
Quid est Clea helena? Evidence for a previously unrecognized radiation of assassin snails (Gastropoda: Buccinoidea: Nassariidae)
The genus Clea from SE Asia is from one of only two unrelated families among the megadiverse predatory marine Neogastropoda to have successfully conquered continental waters. While little is known about their anatomy, life history and ecology, interest has grown exponentially in recent years owing to their increasing popularity as aquarium pets. However, the systematic affinities of the genus and the validity of the included species have not been robustly explored. Differences in shell, operculum and radula characters support separation of Clea as presently defined into two distinct genera: Clea, for the type species Clea nigricans and its allies, and Anentome for Clea helena and allies. A five-gene mitochondrial (COI, 16S, 12S) and nuclear (H3, 28S) gene dataset confirms the placement of Anentome as a somewhat isolated offshoot of the family Nassariidae and sister to the estuarine Nassodonta. Anatomical data corroborate this grouping and, in conjunction with their phylogenetic placement, support their recognition as a new subfamily, the Anentominae. The assassin snail Anentome helena, a popular import through the aquarium trade so named for their voracious appetite for other snails, is found to comprise a complex of at least four species. None of these likely represents true Anentome helena described from Java, including a specimen purchased through the aquarium trade under this name in the US and one that was recently found introduced in Singapore, both of which were supported as conspecific with a species from Thailand. The introduction of Anentome “helena” through the aquarium trade constitutes a significant threat to native aquatic snail faunas which are often already highly imperiled. Comprehensive systematic revision of this previously unrecognized species complex is urgently needed to facilitate communication and manage this emerging threat.
Strong et al. (2017) Quid est Clea helena? Evidence for a previously unrecognized radiation of assassin snails (Gastropoda: Buccinoidea: Nassariidae). PeerJ 5:e3638 https://doi.org/10.7717/peerj.3638
Atrial fibrillation and psychological factors: a systematic review
Background Psychological factors have been suggested to have an influence in Atrial Fibrillation (AF) onset, progression, severity and outcomes, but their role is unclear and mainly focused on anxiety and depression. Methods A systematic electronic search had been conducted to identify studies exploring different psychological factors in AF. The search retrieved 832 articles that were reviewed according to inclusion criteria: observational study with a control/comparison group; use of standardized and validated instruments for psychological assessment. Results were summarized qualitatively and quantitatively by effect size measure (Cohen’s d and its 95% confidence interval). Cochrane Collaboration guidelines and the PRISMA Statement were adopted. Results Eight studies were included in the systematic review. Depression was the most studied construct/ but only one study showed a clear link with AF. The remaining studies showed small and non-significant (95% CI [−0.25–1.00]) differences between AF and controls, no differences in frequency of depression history (95% CI [−0.14–0.22]) or in case frequency (95% CI [−0.50–0.04]). Miscellaneous results were found as far as anxiety: AF patients showed higher levels when compared to healthy subjects (95% CI [2.05–2.95]), but findings were inconsistent when compared to other heart diseases. Considering personality and life-events preceding AF, we respectively found a large (95% CI [1.87–2.49]) and a moderate to large effect (95% CI [0.48–0.98]). Discussion The small number of studies does not allow to draw clear-cut conclusions on the involvement of psychological factors in AF. Promising lines of research are related to personality and adverse life-events, and to the increase of longitudinal design studies. Some methodological problems could be overcome by including clinical psychologists in the implementation of research protocols.
Galli et al. (2017) Atrial fibrillation and psychological factors: a systematic review. PeerJ 5:e3537 https://doi.org/10.7717/peerj.3537
Ecological interactions and the Netflix problem
Species interactions are a key component of ecosystems but we generally have an incomplete picture of who-eats-who in a given community. Different techniques have been devised to predict species interactions using theoretical models or abundances. Here, we explore the K nearest neighbour approach, with a special emphasis on recommendation, along with a supervised machine learning technique. Recommenders are algorithms developed for companies like Netflix to predict whether a customer will like a product given the preferences of similar customers. These machine learning techniques are well-suited to study binary ecological interactions since they focus on positive-only data. By removing a prey from a predator, we find that recommenders can guess the missing prey around 50% of the times on the first try, with up to 881 possibilities. Traits do not improve significantly the results for the K nearest neighbour, although a simple test with a supervised learning approach (random forests) show we can predict interactions with high accuracy using only three traits per species. This result shows that binary interactions can be predicted without regard to the ecological community given only three variables: body mass and two variables for the species’ phylogeny. These techniques are complementary, as recommenders can predict interactions in the absence of traits, using only information about other species’ interactions, while supervised learning algorithms such as random forests base their predictions on traits only but do not exploit other species’ interactions. Further work should focus on developing custom similarity measures specialized for ecology to improve the KNN algorithms and using richer data to capture indirect relationships between species.
Desjardins-Proulx et al. (2017) Ecological interactions and the Netflix problem. PeerJ 5:e3644 https://doi.org/10.7717/peerj.3644