A morphological and molecular study of Hydrodynastes gigas (Serpentes, Dipsadidae), a widespread species from South America
Background Studies with integrative approaches (based on different lines of evidence) are fundamental for understanding the diversity of organisms. Different data sources can improve the understanding of the taxonomy and evolution of snakes. We used this integrative approach to verify the taxonomic status of Hydrodynastes gigas (Duméril, Bibron & Duméril, 1854), given its wide distribution throughout South America, including the validity of the recently described Hydrodynastes melanogigas Franco, Fernandes & Bentim, 2007. Methods We performed a phylogenetic analysis of Bayesian Inference with mtDNA 16S and Cytb, and nuDNA Cmos and NT3 concatenated (1,902 bp). In addition, we performed traditional morphometric analyses, meristic, hemipenis morphology and coloration pattern of H. gigas and H. melanogigas. Results According to molecular and morphological characters, H. gigas is widely distributed throughout South America. We found no evidence to support that H. gigas and H. melanogigas species are distinct lineages, therefore, H. melanogigas is a junior synonym of H. gigas. Thus, the melanic pattern of H. melanogigas is the result of a polymorphism of H. gigas. Melanic populations of H. gigas can be found in the Tocantins-Araguaia basin.
Carvalho et al. (2020) A morphological and molecular study of Hydrodynastes gigas (Serpentes, Dipsadidae), a widespread species from South America. PeerJ 8:e10073 https://doi.org/10.7717/peerj.10073
Remote sensing inversion and spatial variation of land surface temperature over mining areas of Jixi, Heilongjiang, China
Background Jixi is a typical mining city in China that has undergone dramatic changes in its land-use pattern of mining areas over the development of its coal resources. The impacts of coal mining activities have greatly affected the regional land surface temperature and ecological system. Methods The Landsat 8 Operational Land Imager (OLI) data from 2015 and 2019 were used from the Jiguan, Didao, and Chengzihe District of Jixi in Heilongjiang, China as the study area. The calculations to determine the land-use classification, vegetation coverage, and land surface temperature (LST) were performed using ArcGIS10.5 and ENVI 5.3 software packages. A correlation analysis revealed the impact of land-use type, vegetation coverage, and coal mining activities on LSTs. Results The results show significant spatial differentiation in the LSTs of Jixi City. The LSTs for various land-use types were ranked from high to low as follows: mining land > construction land > grassland > cultivated land > forest land > water area. The LST was lower in areas with high vegetation coverage than in other areas. For every 0.1 increase in vegetation coverage, the LST is expected to drop by approximately 0.75 °C. An analysis of mining land patches indicates that the patch area of mining lands has a significant positive correlation with both the average and maximum patch temperatures. The average patch temperature shows a logarithmic increase with the growth of the patch area, and within 200,000 m2, the average patch temperature increases significantly. The maximum patch temperature shows a linear increase with the patch area growth, and for every 100,000 m2 increase in the patch area of mining lands, the maximum patch temperature increases by approximately 0.81 °C. The higher the average patch temperature of mining land, the higher the temperature in its buffer zone, and the greater its influence scope. This study provides a useful reference for exploring the warming effects caused by coal mining activities and the definition of its influence scope.
Environmental Contamination and Remediation
Spatial and Geographic Information Science
Cao et al. (2020) Remote sensing inversion and spatial variation of land surface temperature over mining areas of Jixi, Heilongjiang, China. PeerJ 8:e10257 https://doi.org/10.7717/peerj.10257
Pro-inflammatory response ensured by LPS and Pam3CSK4 in RAW 264.7 cells did not improve a fungistatic effect on Cryptococcus gattii infection
Background The macrophage lineage is characterized by plasticity due to the acquisition of distinct functional phenotypes, and two major subsets are evaluated; classical M1 activation (strong microbicidal activity) and alternative M2 activation (immunoregulatory functions). The M1 subset expresses inducible nitric oxide synthase (iNOS), which is a primary marker to identify these cells, whereas M2 macrophages are characterized by expression of Arginase-1, found in inflammatory zone 1 (Fizz1), chitinase-like molecule (Ym-1), and CD206. The micro-environmental stimuli and signals in tissues are critical in the macrophage polarization. Toll-like receptors (TLR) ligands, such as lipopolysaccharide (LPS), palmitoyl-3-cysteine-serine-lysine-4 (Pam3CSK4), and ArtinM (mannose-binding lectin) are inductors of M1 subset. The impact of TLR2 and TLR4 signals to fight against Cryptococcus gattii infection is unknown, which is a fungal pathogen that preferentially infects the lung of immunocompetent individuals. The macrophages initiate an immune response to combat the C. gattii, then we evaluated in RAW 264.7 cell the effect of TLR2 and TLR4 agonists on the macrophage polarization dynamic and the impact on the growth of C. gattii. Methods and Results We demonstrated that P3C4, LPS, and ArtinM induced an increase in the levels of iNOS transcripts in RAW 264.7 cells, whereas the relative expression of arginase-1, Ym-1, and Fizz1 was significantly increased in the presence of IL-4 alone. The effects of TLR2 and TLR4 agonists on repolarization from the M2 to M1 subset was evaluated, and the first stimulus was composed of IL-4 and, after 24 h of incubation, the cells were submitted to a second stimulus of P3C4, LPS, ArtinM, or Medium. These TLR agonists induced the production of TNF-α in polarized RAW 264.7 cells to the M2 subset, moreover the measurement of M1/M2 markers using qRT-PCR demonstrated that a second stimulus with LPS for 24 h induced a significant augmentation of levels of iNOS mRNA. This impact of TLR2 and TLR4 agonists in the activation of the RAW 264.7 macrophage was assayed in the presence of C. gattii, the macrophages stimulated with TLR2 and TLR4 agonists for 24 h and co-cultured with C. gattii, as a second stimulus, reached high levels of TNF-α even after incubation with different concentrations of C. gattii. The activation of RAW 264.7 cells induced by TLR2 and TLR4 agonists favored the phagocytosis of C. gattii and inhibited the growth of yeast in the early period of infection. However, RAW 264.7 cells incubated with C. gattii in the presence of TLR2 and TLR4 agonists did not result a significant difference in the colony forming unit (CFU) assay in the early period of C. gattii infection, compared to negative control. Conclusion Polarized RAW 264.7 cells to the M1 subset with TLR2 and TLR4 agonists did not inhibit the growth of C. gattii, whereas robust immunity was identified that could dysregulate host tolerance to this pathogen.
de Campos et al. (2020) Pro-inflammatory response ensured by LPS and Pam3CSK4 in RAW 264.7 cells did not improve a fungistatic effect on Cryptococcus gattii infection. PeerJ 8:e10295 https://doi.org/10.7717/peerj.10295
Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect
Gymnosperms such as ginkgo, conifers, cycads, and gnetophytes are vital components of land ecosystems, and they have significant economic and ecologic value, as well as important roles as forest vegetation. In this study, we investigated the structural variation and evolution of chloroplast transfer RNAs (tRNAs) in gymnosperms. Chloroplasts are important organelles in photosynthetic plants. tRNAs are key participants in translation where they act as adapter molecules between the information level of nucleic acids and functional level of proteins. The basic structures of gymnosperm chloroplast tRNAs were found to have family-specific conserved sequences. The tRNAΨ -loop was observed to contain a conforming sequence, i.e., U-U-C-N-A-N2. In gymnosperms, tRNAIle was found to encode a “CAU” anticodon, which is usually encoded by tRNAMet. Phylogenetic analysis suggested that plastid tRNAs have a common polyphyletic evolutionary pattern, i.e., rooted in abundant common ancestors. Analyses of duplication and loss events in chloroplast tRNAs showed that gymnosperm tRNAs have experienced little more gene loss than gene duplication. Transition and transversion analysis showed that the tRNAs are iso-acceptor specific and they have experienced unequal evolutionary rates. These results provide new insights into the structural variation and evolution of gymnosperm chloroplast tRNAs, which may improve our comprehensive understanding of the biological characteristics of the tRNA family.
Zhang et al. (2020) Evolutionary analysis of chloroplast tRNA of Gymnosperm revealed the novel structural variation and evolutionary aspect. PeerJ 8:e10312 https://doi.org/10.7717/peerj.10312
Three new deep-sea species of Thyasiridae (Mollusca: Bivalvia) from the abyssal plain of the northwestern Pacific Ocean and hadal depths of the Kuril-Kamchatka Trench
The Thyasiridae is the most species-rich family of bivalves in the abyssal and hadal zones of the northwestern Pacific Ocean. In recent years, with at least 14 thyasirid species found in that region at depths exceeding 3,000 m. Some of them are the numerically dominant species in bottom communities. However, all members in that family have not yet been identified to the species level. Based on the material collected from 1953 to 2016 by five deep-sea expeditions, three new species of Thyasiridae (Mollusca: Bivalvia) are described from the abyssal and hadal zones of the northwestern Pacific. “Axinulus” roseus sp. nov. was found in the Kuril-Kamchatka Trench at 9,000–9,583 m depth. This species has a large rhomboidal shell with strong commarginal sculpture, a well defined, long and deep lunule and escutcheon without an auricle, a ctenidium consisting of a single demibranch, extensively lobed lateral pouches, and a large prodissoconch with specific sculpture. It is one of the dominant species in terms of abundance in macrobenthic communities in the deepest basin of the Kuril-Kamchatka Trench with a population density of up to 396 ind. m−2. The species has a shell length of up to 9.0 mm and it is the largest thyasirid with a single demibranch. “Axinulus” oliveri sp. nov. was found in a vast region of the northwestern Pacific on the abyssal plain adjacent to the Kuril-Kamchatka Trench, on the abyssal slope of the Kuril Islands, and in the Kuril-Kamchatka Trench at 4,648–6,168 m depth. This species is characterized by its ovate-rhomboidal shell, a well defined, deep and long escutcheon with a distinct auricle, a ctenidium with a single demibranch, and extensively lobed lateral pouches. It is widespread in the northwestern Pacific and forms populations with a density of up to 36 ind. m−2. Scanning electron microscopic observation of the gills of “A.” roseus sp. nov. and “A.” oliveri sp. nov. revealed that these species are not chemosymbiotic. “Axinulus” roseus sp. nov. and “A.” oliveri sp. nov. are provisionally assigned to the genus Axinulus, because they differ from the type species of the genus in a number of morphological and anatomical features. Parathyasira fragilis sp. nov. was found on the abyssal plain adjacent to the Kuril-Kamchatka Trench at 5,249–5,399 m depth. This species is distinguished by its very thin, fragile, dorsoventrally elongated, rhomboidal shell with very long anterodorsal margin and a long, wide, flat lunule. The taxonomic position of the new species is discussed.
Kamenev (2020) Three new deep-sea species of Thyasiridae (Mollusca: Bivalvia) from the abyssal plain of the northwestern Pacific Ocean and hadal depths of the Kuril-Kamchatka Trench. PeerJ 8:e10405 https://doi.org/10.7717/peerj.10405
Partial revision of the neustonic genus Scapholeberis Schoedler, 1858 (Crustacea: Cladocera): decoding of the barcoding results
Water fleas (Crustacea: Cladocera) are among the most intensively studied freshwater invertebrates. However, ecologically important daphniids that live on the surface layer (neuston) remain taxonomically confused. Here we attempt to reconcile genetic and morphological information for the neustonic genus Scapholeberis Schoedler, 1858 (Cladocera: Daphniidae) and present the first revision of the Scapholeberis kingii species group. We analyzed new and existing mitochondrial DNA sequences (сytochrome C oxidase subunit I gene region) together with morphology for all but one of the known species of the neustonic daphniids. Morphological comparisons of available populations, belonging to the Scapholeberis kingii species group from several Australian, Asian and African localities, revealed, that they are almost identical according to parthenogenetic females. However, Australian populations can be reliably distinguished from Asian ones based on the morphology of gamogenetic females. Mitochondrial DNA data analyses revealed divergent lineages (>17% for the DNA barcoding COI region) for the three different species (Australia, Asia and Africa). Based on this set of data, we redescribed S. kingii Sars, 1888 from Australia, its terra typica, and described a new species, S. smirnovi sp.nov. from the Russian Far East, Korea and Japan. The status of populations from Ethiopia and the Republic of South Africa remained unclear, because in the African material and the putative type material, we found only parthenogenetic females. Our results provide an integrative revision of the S. kingii species group and improve the taxonomic scaffold used for barcoding and genomics for the remaining species groups in the daphniid genus Scapholeberis.
Garibian et al. (2020) Partial revision of the neustonic genus Scapholeberis Schoedler, 1858 (Crustacea: Cladocera): decoding of the barcoding results. PeerJ 8:e10410 https://doi.org/10.7717/peerj.10410
Antibacterial activity of human defensins against Staphylococcus aureus and Escherichia coli
Background The global problem of antibiotic resistance requires the search for and development of new methods of treatment. One of the promising strategies is the use of low doses of antimicrobial peptides, in particular, human defensins HNP-1, hBD-1, and hBD-3, in combination with antibacterial drugs already used in clinical practice. This approach may be used to increase the effectiveness of conventional antibiotics. However, this requires thorough study of the effectiveness of defensins in combination with antibiotics against a large number of bacterial strains with known phenotypes of antibiotic resistance. The aim of this work was to study the antibacterial effect of HNP-1, hBD-1 and hBD-3 in combination with rifampicin or amikacin against clinical isolates of Staphylococcus aureus (n = 27) and Escherichia coli (n = 24) collected from hospitalized patients. Methods The standard checkerboard assay was used to determine minimum inhibitory concentrations (MICs) of antimicrobials. The combined microbicidal effects of two substances (defensin + conventional antibiotic) were assessed by the fractional inhibitory concentration index (FICI). Results The highest anti-staphylococcal activity (including methicillin-resistant strains) among defensins was demonstrated by hBD-3 that had MIC of 1 (0.5–4) mg/L (hereinafter, MIC values are presented as median and interquartile range). The MIC of HNP-1 against S. aureus was 4 (2–8) mg/L; the MIC of hBD-1 was 8 (4–8) mg/L. Against E. coli, the most effective was also found to be hBD-3 that had MIC of 4 (4–8) mg/L; the MIC of HNP-1 was 12 (4–32) mg/L. The combinations of HNP-1 + rifampicin and hBD-3 + rifampicin demonstrated synergistic effects against S. aureus. Against E. coli, combinations of HNP-1 + amikacin and hBD-3 + amikacin also showed synergy of action.
Bolatchiev (2020) Antibacterial activity of human defensins against Staphylococcus aureus and Escherichia coli. PeerJ 8:e10455 https://doi.org/10.7717/peerj.10455
miR-224, miR-147b and miR-31 associated with lymph node metastasis and prognosis for lung adenocarcinoma by regulating PRPF4B, WDR82 or NR3C2
Background The present study is to screen lymph node metastasis-related microRNAs (miRNAs) in lung adenocarcinoma (LUAD) and uncover their underlying mechanisms. Methods The miRNA microarray dataset was collected from the Gene Expression Omnibus database under accession number GSE64859. The differentially expressed miRNAs (DEMs) were identified using a t-test. Target genes of DEMs were predicted through the miRWalk2.0 database. The function of these target genes was annotated with the clusterProfiler and the Database for Annotation, Visualization and Integrated Discovery (DAVID) tools. Protein-protein interaction network was established using the STRING database to extract hub target genes. The expressions and associations with survival and lymph node metastasis of miRNAs and target genes were validated by analysis of The Cancer Genome Atlas (TCGA) dataset. Results Eight DEMs were identified between lymph node metastasis and non-metastasis samples of GSE64859 dataset. miRNA-target gene pairs were predicted between six DEMs and 251 target genes (i.e. hsa-miR-224-PRPF4B, hsa-miR-147b-WDR82 and hsa-miR-31-NR3C2). The clusterProfiler analysis showed WDR82 was involved in the mRNA surveillance pathway, while the GO enrichment analysis using the DAVID database indicated PRPF4B participated in the protein phosphorylation and NR3C2 was related with the transcription, DNA-templated. WDR82 and PRPF4B may be hub genes because they could interact with others. Two DEMs (miR-31-5p and miR-31-3p) and 45 target genes (including PRPF4B and NR3C2) were significantly associated with overall survival. The expressions of miR-224 and miR-147b were validated to be upregulated, while WDR82, PRPF4B and NR3C2 were downregulated in lymph node metastasis samples of TCGA datasets compared with non-metastasis samples. Also, there were significantly negative expression correlations between miR-147b and WDR82, between miR-224 and PRPF4B, as well as between miR-31 and NR3C2 in LUAD samples. Conclusions The present study identified several crucial miRNA-mRNA interaction pairs, which may provide novel explanations for the lymph node metastasis and poor prognosis for LUAD patients.
Wang et al. (2020) miR-224, miR-147b and miR-31 associated with lymph node metastasis and prognosis for lung adenocarcinoma by regulating PRPF4B, WDR82 or NR3C2. PeerJ 8:e9704 https://doi.org/10.7717/peerj.9704
The Italian record of the Cretaceous shark, Ptychodus latissimus Agassiz, 1835 (Chondrichthyes; Elasmobranchii)
Associated and isolated teeth of the extinct elasmobranch Ptychodus latissimus Agassiz, 1835 from the Upper Cretaceous Scaglia Rossa pelagic limestone of northern Italy are described and discussed here in detail for the first time. The dentition of this widely distributed species consists of low-crowned molariform teeth that exhibit marked and strong occlusal ornamentations suitable for crushing hard-shelled prey. The associated tooth sets and isolated teeth analyzed here are heterogeneous in size and crown outline, but unambiguously belong to a single species. Re-examination of this Italian material consisting of ca. 30 specimens mostly coming from historical collections allows for a rigorous assessment of the intraspecific variability of P. latissimus, including the identification of three different tooth “morphotypes” based on their positions within the jaws. The relatively flat crowns and occlusal sharp and thick ridges indicate a high adaptation for crushing hard-shelled prey in P. latissimus indicating that the durophagous adaptations of this species were certainly more pronounced than in all other species of Ptychodus. We hypothesize that P. latissimus was a third-level predator occupying habitats with abundant thick-shelled prey, such as inoceramid bivalves and ammonites.
Amadori et al. (2020) The Italian record of the Cretaceous shark, Ptychodus latissimus Agassiz, 1835 (Chondrichthyes; Elasmobranchii). PeerJ 8:e10167 https://doi.org/10.7717/peerj.10167
Hissing of geese: caller identity encoded in a non-vocal acoustic signal
Non-vocal, or unvoiced, signals surprisingly have received very little attention until recently especially when compared to other acoustic signals. Some sounds made by terrestrial vertebrates are produced not only by the larynx but also by the syrinx. Furthermore, some birds are known to produce several types of non-syrinx sounds. Besides mechanical sounds produced by feathers, bills and/or wings, sounds can be also produced by constriction, anywhere along the pathway from the lungs to the lips or nostrils (in mammals), or to the bill (in birds), resulting in turbulent, aerodynamic sounds. These noises often emulate whispering, snorting or hissing. Even though hissing sounds have been studied in mammals and reptiles, only a few studies have analyzed hissing sounds in birds. Presently, only the hissing of small, nesting passerines as a defense against their respective predators have been studied. We studied hissing in domestic goose. This bird represents a ground nesting non-passerine bird which frequently produces hissing out of the nest in comparison to passerines producing hissing during nesting in holes e.g., parids. Compared to vocally produced alarm calls, almost nothing is known about how non-vocal hissing sounds potentially encode information about a caller’s identity. Therefore, we aimed to test whether non-vocal air expirations can encode an individual’s identity similar to those sounds generated by the syrinx or the larynx. We analyzed 217 hissing sounds from 22 individual geese. We calculated the Potential for Individual Coding (PIC) comparing the coefficient of variation both within and among individuals. In addition, we conducted a series of 15 a stepwise discriminant function analysis (DFA) models. All 16 acoustic variables showed a higher coefficient of variation among individuals. Twelve DFA models revealed 51.2–54.4% classification result (cross-validated output) and all 15 models showed 60.8–68.2% classification output based on conventional DFA in comparison to a 4.5% success rate when classification by chance. This indicates the stability of the DFA results even when using different combinations of variables. Our findings showed that an individual’s identity could be encoded with respect to the energy distribution at the beginning of a signal and the lowest frequencies. Body weight did not influence an individual’s sound expression. Recognition of hissing mates in dangerous situations could increase the probability of their surviving via a more efficient anti-predator response.
Policht et al. (2020) Hissing of geese: caller identity encoded in a non-vocal acoustic signal. PeerJ 8:e10197 https://doi.org/10.7717/peerj.10197