Feeding response of the tropical copepod Acartia erythraea to short-term thermal stress: more animal-derived food was consumed
The objective of this study was to explore the feeding response of tropical copepods to short-term thermal shock and provide insight into the potential impact of coastal power plants on the trophic dynamics of tropical coastal ecosystems. Feeding experiments were conducted at three different temperatures (29 °C, 33 °C, and 35 °C) using the copepod Acartia erythraea, collected from Sanya Bay, China. The grazing rate of A. erythraea decreased dramatically in the high temperature treatment. Analysis of 18S rDNA clone libraries revealed that the diet of copepods from different treatments was mainly comprised of diatoms, metazoans, and protozoans; A. erythraea exhibited an obvious feeding preference shift with temperature, with a change from a diatom-dominated diet at 29 °C to a metazoan-dominated diet at 35 °C, and the omnivory index shifted from 0.1 to 2.84 correspondingly. Furthermore, A. erythraea showed a positive feeding response to plant food (i.e., phytoplankton and land plants) in the control treatment (29 °C), but a positive response to animal prey (i.e., metazoans and protozoans) at temperatures exceeding 33 °C, as evaluated by the Ivlev’s selectivity index. Our results suggest that copepods could regulate their food intake by considering their energy demands when exposed to short-term thermal stress, which might influence the pathway of materials moving up the trophic system. However, further studies are required to elucidate the effects of elevated temperature on feeding of different organisms in order to predict the influence of thermal pollution on the food web of tropical coastal ecosystems.
Environmental Contamination and Remediation
Hu et al. (2018) Feeding response of the tropical copepod Acartia erythraea to short-term thermal stress: more animal-derived food was consumed. PeerJ 6:e6129 https://doi.org/10.7717/peerj.6129
Transposons and pathogenicity in Xanthomonas: acquisition of murein lytic transglycosylases by TnXax1 enhances Xanthomonas citri subsp. citri 306 virulence and fitness
Xanthomonas citri subsp. citri 306 (XccA) is the causal agent of type A citrus canker (CC), one of the most significant citriculture diseases. Murein lytic transglycosylases (LT), potentially involved in XccA pathogenicity, are enzymes responsible for peptidoglycan structure assembly, remodeling and degradation. They directly impact cell wall expansion during bacterial growth, septum division allowing cell separation, cell wall remodeling allowing flagellar assembly, bacterial conjugation, muropeptide recycling, and secretion system assembly, in particular the Type 3 Secretion System involved in bacterial virulence, which play a fundamental role in XccA pathogenicity. Information about the XccA LT arsenal is patchy: little is known about family diversity, their exact role or their connection to virulence in this bacterium. Among the LTs with possible involvement in virulence, two paralogue open reading frames (ORFs) (one on the chromosome and one in plasmid pXAC64) are passenger genes of the Tn3 family transposon TnXax1, known to play a significant role in the evolution and emergence of pathogenicity in Xanthomonadales and to carry a variety of virulence determinants. This study addresses LT diversity in the XccA genome and examines the role of plasmid and chromosomal TnXax1 LT passenger genes using site-directed deletion mutagenesis and functional characterization. We identified 13 XccA LTs: 12 belong to families 1A, 1B, 1C, 1D (two copies), 1F, 1G, 3A, 3B (two copies), 5A, 6A and one which is non-categorized. The non-categorized LT is exclusive to the Xanthomonas genus and related to the 3B family but contains an additional domain linked to carbohydrate metabolism. The categorized LTs are probably involved in cell wall remodeling to allow insertion of type 3, 4 and 6 secretion systems, flagellum assembly, division and recycling of cell wall and degradation and control of peptidoglycan production. The TnXax1 passenger LT genes (3B family) are not essential to XccA or for CC development but are implicated in peptidoglycan metabolism, directly impacting bacterial fitness and CC symptom enhancement in susceptible hosts (e.g., Citrus sinensis). This underlines the role of TnXax1 as a virulence and pathogenicity-propagating agent in XccA and suggests that LT acquisition by horizontal gene transfer mediated by TnXax1 may improve bacterial fitness, conferring adaptive advantages to the plant-pathogen interaction process.
Oliveira et al. (2018) Transposons and pathogenicity in Xanthomonas: acquisition of murein lytic transglycosylases by TnXax1 enhances Xanthomonas citri subsp. citri 306 virulence and fitness. PeerJ 6:e6111 https://doi.org/10.7717/peerj.6111
First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes
There is a gradual shift from representing a species’ genome by a single reference genome sequence to a pan-genome representation. Pan-genomes are the abstract representations of the genomes of all the strains that are present in the population or species. In this study, we employed a pan-genomic approach to analyze the intraspecific mitochondrial genome diversity of Fusarium graminearum. We present an improved reference mitochondrial genome for F. graminearum with an intron-exon annotation that was verified using RNA-seq data. Each of the 24 studied isolates had a distinct mitochondrial sequence. Length variation in the F. graminearum mitogenome was found to be largely due to variation of intron regions (99.98%). The “intronless” mitogenome length was found to be quite stable and could be informative when comparing species. The coding regions showed high conservation, while the variability of intergenic regions was highest. However, the most important variable parts are the intron regions, because they contain approximately half of the variable sites, make up more than half of the mitogenome, and show presence/absence variation. Furthermore, our analyses show that the mitogenome of F. graminearum is recombining, as was previously shown in F. oxysporum, indicating that mitogenome recombination is a common phenomenon in Fusarium. The majority of mitochondrial introns in F. graminearum belongs to group I introns, which are associated with homing endonuclease genes (HEGs). Mitochondrial introns containing HE genes may spread within populations through homing, where the endonuclease recognizes and cleaves the recognition site in the target gene. After cleavage of the “host” gene, it is replaced by the gene copy containing the intron with HEG. We propose to use introns unique to a population for tracking the spread of the given population, because introns can spread through vertical inheritance, recombination as well as via horizontal transfer. We demonstrate how pooled sequencing of strains can be used for mining mitogenome data. The usage of pooled sequencing offers a scalable solution for population analysis and for species level comparisons studies. This study may serve as a basis for future mitochondrial genome variability studies and representations.
Brankovics et al. (2018) First steps towards mitochondrial pan-genomics: detailed analysis of Fusarium graminearum mitogenomes. PeerJ 6:e5963 https://doi.org/10.7717/peerj.5963
Iberian pig adaptation to acorn consumption: II. Net portal appearance of amino acids
In Iberian pig outdoor production, pigs are fed equilibrated diets until the final fattening period when grazing pigs consume mainly acorns from oak trees. Acorns are rich in energy but poor in crude protein where lysine is the first limiting amino acid (AA). Net portal appearance (NPA) is very useful to ascertain AA available for liver and peripheral tissues. The aim of this study was to determine NPA of AA in Iberian gilts fed with acorns and to ascertain if there was an effect of acorn feeding over time. Two sampling periods were carried out (after one day and after one week of acorn feeding) with six gilts (34 kg average BW) set up with three catheters: in carotid artery and portal vein for blood sampling, and ileal vein for a marker infusion to measure portal plasma flow (PPF). Pigs were fed at 2.5 × ME for maintenance a standard diet in two meals, at 09:00 (0.25) and 15:00 h (the remaining 0.75). The day previous to first sampling, pig diet was replaced by 2.4 kg of acorn. A serial blood collection was done at −5 min, 0.5, 1, 1.5, 2, 2.5, 3, 3.5, 4, 5 and 6 h after feeding 0.25 of total daily acorn ration. Following identical protocol, one week later the second sampling was done. NPA of sum of essential AA (EAA) was poor. Although increased NPA of histidine (P < 0.001), leucine, phenylalanine and valine (0.05 < P < 0.08) was found after one week of acorn consumption, the sum of EAA did not change. Furthermore, fractional absorption (NPA/AA intake) of EAA, non-essential AA (NEAA) and total AA was 97, 44 and 49% lower, respectively, at the beginning of eating acorn than a week later. Supplementation, with some of the EAA and NEAA to Iberian pigs during the grazing period would be beneficial to overcome the increased portal-drained viscera (PDV) utilization of AA observed in the present study.
Lachica et al. (2018) Iberian pig adaptation to acorn consumption: II. Net portal appearance of amino acids. PeerJ 6:e6137 https://doi.org/10.7717/peerj.6137
ScanFold: an approach for genome-wide discovery of local RNA structural elements—applications to Zika virus and HIV
In addition to encoding RNA primary structures, genomes also encode RNA secondary and tertiary structures that play roles in gene regulation and, in the case of RNA viruses, genome replication. Methods for the identification of functional RNA structures in genomes typically rely on scanning analysis windows, where multiple partially-overlapping windows are used to predict RNA structures and folding metrics to deduce regions likely to form functional structure. Separate structural models are produced for each window, where the step size can greatly affect the returned model. This makes deducing unique local structures challenging, as the same nucleotides in each window can be alternatively base paired. We are presenting here a new approach where all base pairs from analysis windows are considered and weighted by favorable folding. This results in unique base pairing throughout the genome and the generation of local regions/structures that can be ranked by their propensity to form unusually thermodynamically stable folds. We applied this approach to the Zika virus (ZIKV) and HIV-1 genomes. ZIKV is linked to a variety of neurological ailments including microcephaly and Guillain–Barré syndrome and its (+)-sense RNA genome encodes two, previously described, functionally essential structured RNA regions. HIV, the cause of AIDS, contains multiple functional RNA motifs in its genome, which have been extensively studied. Our approach is able to successfully identify and model the structures of known functional motifs in both viruses, while also finding additional regions likely to form functional structures. All data have been archived at the RNAStructuromeDB (www.structurome.bb.iastate.edu), a repository of RNA folding data for humans and their pathogens.
Andrews et al. (2018) ScanFold: an approach for genome-wide discovery of local RNA structural elements—applications to Zika virus and HIV. PeerJ 6:e6136 https://doi.org/10.7717/peerj.6136
Effects of ultraviolet radiation on metabolic rate and fitness of Aedes albopictus and Culex pipiens mosquitoes
Natural and anthropogenic changes (e.g., land use change, pollution) will alter many environmental factors in the coming years, including the amount of solar radiation reaching the earth’s surface. Alterations in solar radiation exposure is likely to impact the ecologies of many living organisms, including invertebrates that inhabit aquatic habitats. In this study, we assessed the effect of UV-B radiation on the metabolic rates and fitness (survival, development time, body size) of Aedes albopictus and Culex pipiens mosquitoes and the activity of their microbial food resources in experimental aquatic microcosms. We exposed single-species cohorts of newly hatched Ae. albopictus and Cx. pipiens larvae and a control treatment with no larvae to three UV-B conditions that mimicked those in full-sun and shade in the field and to a control condition with no UV-B radiation. Our results indicated that UV-B radiation affected the metabolic rates of both Ae. albopictus and Cx. pipiens larvae, with significantly higher rates found in full-sun compared to shade and no-UV conditions, 8 and 15 days after exposure began. Ae. albopictus and Cx. pipiens survival was also affected by UV-B radiation condition, with significantly lower survival in full-sun compared to shade and no UV-B conditions. Microbial metabolic rates were consistently significantly lower in full-sun compared to shade and no-UV conditions, especially at 8 days of exposure. These results show that UV-B radiation at levels found in open spaces showed strong and important impacts on the metabolic rates and survival of Ae. albopictus and Cx. pipiens larvae. Decreased survival of Ae. albopictus and Cx. pipiens with higher UV-B radiation levels may be caused by both direct exposure to radiation as well as the indirect effects of reduced microbial food, resulting in greater metabolic demands and stress. Negative impacts of UV-B radiation on the survival of Ae. albopictus and Cx. pipiens are likely to have important implications for the distribution and abundance of these mosquitoes, and the transmission of pathogens that these two broadly distributed mosquitoes vector.
Villena et al. (2018) Effects of ultraviolet radiation on metabolic rate and fitness of Aedes albopictus and Culex pipiens mosquitoes. PeerJ 6:e6133 https://doi.org/10.7717/peerj.6133
Local persistence of Mann’s soft-haired mouse Abrothrix manni (Rodentia, Sigmodontinae) during Quaternary glaciations in southern Chile
Quaternary climatic oscillations have impacted Patagonian sigmodontine fauna, leaving traceable genetic footprints. In southern Chile, changes in the landscape included transitions to different vegetation formations as well as the extension of ice sheets. In this study, we focus on the Valdivian forest endemic and recently described sigmodontine species Abrothrix manni. We aim to assess the genetic structure of this species, testing for the existence of intraspecific lineages, and inferring the recent demographic history of the species. Analyses were based on the first 801 bp of the mitochondrial gene Cytocrhome-b from 49 individuals of A. manni collected at 10 localities that covers most part of its geographic distribution. Genealogical analyses recovered two main intraspecific lineages that are geographically segregated and present an intermediate site of secondary contact. Historical demography shows signal of recent population decrease. Based on these results, we proposed that current genetic diversity of A. manni differentiated in at least two distinct refugial areas in southern Chile. This scenario, in addition to be unique among those uncovered for the so far studied Valdivian forest rodents, is noteworthy because of the reduced geographic scale inhabited by the species.
Valdez et al. (2018) Local persistence of Mann’s soft-haired mouse Abrothrix manni (Rodentia, Sigmodontinae) during Quaternary glaciations in southern Chile. PeerJ 6:e6130 https://doi.org/10.7717/peerj.6130
Elevated CD3low double negative T lymphocyte is associated with pneumonia and its severity in pediatric patients
Background Previous studies have shown that the adaptive immunity function of T cells in disease states correlates with CD3 surface expression closely. During routine assessment of TBNK subsets in peripheral blood of pediatric patients by flow cytometry, we noticed that variable expression levels of CD3 on CD3+CD4−CD8− double-negative T (DNT) lymphocytes in different patients. The objective of this study was to assess the relationship of CD3 expression levels on DNT cells with disease severity. Methods In this prospective study, we investigated the frequencies of circulating CD4−CD8− DNT cell subsets with CD3low or CD3high phenotype by flow cytometry in 76 pediatric patients with pneumonia, 55 patients with severe pneumonia (SP), and 29 healthy controls (Con). Results The numbers of circulating DNT cells were similar in all groups; however, the frequency of CD3low DNT cell subsets was significantly increased in patients with pneumonia (p < 0.001) and SP (p < 0.001). The elevated CD3low DNT cell frequency showed a positive correlation with the clinical severity of pneumonia. On sub-group analysis, the frequency of CD3low DNT cells was only elevated in children with pneumonia aged <5 years, while no association was observed with the causative pathogen of pneumonia. Conclusions These findings suggest that CD3 expression levels on DNT cell subsets of peripheral lymphocytes may be a valuable biomarker for evaluation of immune response in pediatric infectious disease. CD3low DNT cells were elevated in children with pneumonia aged <5 years, which indicates that it may be an important research target in pediatric infectious diseases.
Wang et al. (2018) Elevated CD3low double negative T lymphocyte is associated with pneumonia and its severity in pediatric patients. PeerJ 6:e6114 https://doi.org/10.7717/peerj.6114
Morphological characterization and staging of bumble bee pupae
Bumble bees (Hymenoptera: Apidae, Bombus) are important pollinators and models for studying mechanisms underlying developmental plasticity, such as factors influencing size, immunity, and social behaviors. Research on such processes, as well as expanding use of gene-manipulation and gene expression technologies, requires a detailed understanding of how these bees develop. Developmental research often uses time-staging of pupae, however dramatic size differences in these bees can generate variation in developmental timing. To study developmental mechanisms in bumble bees, appropriate staging of developing bees using morphology is necessary. In this study, we describe morphological changes across development in several bumble bee species and use this to establish morphology-based staging criteria, establishing 20 distinct illustrated stages. These criteria, defined largely by eye and cuticle pigmentation patterns, are generalizable across members of the subgenus Pyrobombus, and can be used as a framework for study of other bumble bee subgenera. We examine the effects of temperature, caste, size, and species on pupal development, revealing that pupal duration shifts with each of these factors, confirming the importance of staging pupae based on morphology rather than age and the need for standardizing sampling.
Tian et al. (2018) Morphological characterization and staging of bumble bee pupae. PeerJ 6:e6089 https://doi.org/10.7717/peerj.6089
Nanocontainer designed from an infectious hypodermal and hematopoietic necrosis virus (IHHNV) has excellent physical stability and ability to deliver shrimp tissues
Background A virus-like particle (VLP) is an excellent tool for a compound delivery system due to its simple composition, symmetrical structure and self-assembly. Its surface modification both chemically and genetically is established, leading to the target-specific delivery and improved encapsulation efficiency. However, its physical stabilities against many harsh conditions that guarantee long term storage and oral administration have been much less studied. Methods IHHNV-VLPs were reconstructed from recombinant IHHNV capsid protein in E. coli. Their physical properties against three strong physical conditions including long term storage (0–30 days) in 4 °C, physical stabilities against broad ranged pH (4–9) and against three types of digestive enzymes were tested. Disassembly and reassembly of VLPs for encapsidating an enhanced green fluorescent protein tagged plasmid DNA (EGFP-VLPs) were controlled by the use of reducing agent (DTT) and calcium specific chelating agent (EGTA). Lastly, delivering ability of EGFP-VLPs was performed in vivo by intramuscular injection and traced the expression of GFP in the shrimp tissues 24 hr post-injection. Results Upon its purification, IHHNV-VLPs were able to be kept at 4 °C up to 30 days with only slight degradation. They were very stable in basic condition (pH 8–9) and to a lesser extent in acidic condition (pH 4–6) while they could stand digestions of trypsin and chymotrypsin better than pepsin. As similar with many other non-enveloped viruses, the assembly of IHHNV-VLPs was dependent on both disulfide bridging and calcium ions which allowed us to control disassembly and reassembly of these VLPs to pack EGFP plasmid DNA. IHHNV-VLPs could deliver EGFP plasmids into shrimp muscles and gills as evident by RT-PCR and confocal microscopy demonstrating the expression of GFP in the targeted tissues. Discussion There are extensive data in which capsid proteins of the non-enveloped viruses in the form of VLPs are constructed and used as nano-containers for therapeutic compound delivery. However, the bottleneck of its application as an excellent delivery container for oral administration would rely solely on physical stability and interacting ability of VLPs to the host cells. These properties are retained for IHHNV-VLPs reported herein. Thus, IHHNV-VLPs would stand as a good applicable nanocontainer to carry therapeutic agents towards the targeting tissues against ionic and digestive conditions via oral administration in aquaculture field.
Kiatmetha et al. (2018) Nanocontainer designed from an infectious hypodermal and hematopoietic necrosis virus (IHHNV) has excellent physical stability and ability to deliver shrimp tissues. PeerJ 6:e6079 https://doi.org/10.7717/peerj.6079