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1
Authors: Thanh Dat Ta, Nomar Espinosa Waminal, Thi Hong Nguyen, Remnyl Joyce Pellerin, Hyun Hee Kim
Published: Mar 2021
Authors: Thanh Dat Ta, Nomar Espinosa Waminal, Thi Hong Nguyen, Remnyl Joyce Pellerin, Hyun Hee Kim
Published: Mar 2021
Abstract Background DNA tandem repeats (TRs) are often abundant and occupy discrete regions in eukaryotic genomes. These TRs often cause or generate chromosomal rearrangements, which, in turn, drive chromosome evolution and speciation. Tracing the chromosomal distribution of TRs could therefore provide insights into the chromosome dynamics and speciation among closely related taxa. The basic chromosome number in the genus Senna is 2 n  = 28, but dysploid species like Senna tora have also been observed. Objective To understand the dynamics of these TRs and their impact on S. tora dysploidization. Methods We performed a comparative fluorescence in situ hybridization (FISH) analysis among nine closely related Senna species and compared the chromosomal distribution of these repeats from a cytotaxonomic perspective by using the ITS1-5.8S-ITS2 sequence to infer phylogenetic relationships. Results Of the nine S. tora TRs, two did not show any FISH signal whereas seven TRs showed similar and contrasting patterns to other Senna species. StoTR01_86, which was localized in the pericentromeric regions in all S. tora , but not at the nucleolar organizer region (NOR) site, was colocalized at the NOR site in all species except in S. siamea . StoTR02_7_tel was mostly localized at chromosome termini, but some species had an interstitial telomeric repeat in a few chromosomes. StoTR05_180 was distributed in the subtelomeric region in most species and was highly amplified in the pericentromeric region in some species. StoTR06_159 was either absent or colocalized in the NOR site in some species, and StoIGS_463, which was localized at the NOR site in S. tora , was either absent or localized at the subtelomeric or pericentromeric regions in other species. Conclusions These data suggest that TRs play important roles in S. tora dysploidy and suggest the involvement of 45S rDNA intergenic spacers in “carrying” repeats during genome reshuffling.
2
Authors: Yuichi Iwasaki, Kiyan Sorgog
Published: Mar 2021
Authors: Yuichi Iwasaki, Kiyan Sorgog
Published: Mar 2021
Estimation of species sensitivity distributions (SSDs) is a crucial approach to predicting ecological risks and water quality benchmarks, but the amount of data required to implement this approach is a serious constraint on the application of SSDs to chemicals for which there are few or no toxicity data. The development of statistical models to directly estimate the mean and standard deviation (SD) of the logarithms of log-normally distributed SSDs has recently been proposed to overcome this problem. To predict these two parameters, we developed multiple linear regression models that included, in addition to readily obtainable descriptors, the mean and SD of the logarithms of the concentrations that are acutely toxic to one algal, one crustacean, and one fish species, as predictors. We hypothesized that use of the three species’ mean and SD would improve the accuracy of the predicted means and SDs of the logarithms of the SSDs. We derived SSDs for 60 chemicals based on quality-assured acute toxicity data. Forty-five of the chemicals were used for model fitting, and 15 for external validation. Our results supported previous findings that models developed on the basis of only descriptors such as log K OW had limited ability to predict the mean and SD of SSD (e.g., r 2 = 0.62 and 0.49, respectively). Inclusion of the three species’ mean and SD, in addition to the descriptors, in the models markedly improved the predictions of the means and SDs of SSDs (e.g., r 2 = 0.96 and 0.75, respectively). We conclude that use of the three species’ mean and SD is promising for more accurately estimating an SSD and thus the hazardous concentration for 5% of species in cases where limited ecotoxicity data are available.
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2
Authors: Attila Ősi, János Magyar, Károly Rosta, Matthew Vickaryous
Published: Mar 2021
Authors: Attila Ősi, János Magyar, Károly Rosta, Matthew Vickaryous
Published: Mar 2021
Bony cranial ornamentation is developed by many groups of vertebrates, including ankylosaur dinosaurs. To date, the morphology and ontogenetic origin of ankylosaurian cranial ornamentation has primarily focused on a limited number of species from only one of the two major lineages, Ankylosauridae. For members of the sister group Nodosauridae, less is known. Here, we provide new details of the cranial anatomy of the nodosaurid Hungarosaurus from the Santonian of Europe. Based on a number of previously described and newly identified fragmentary skulls and skull elements, we recognize three different size classes of Hungarosaurus . We interpret these size classes as representing different stages of ontogeny. Cranial ornamentation is already well-developed in the earliest ontogenetic stage represented herein, suggesting that the presence of outgrowths may have played a role in intra- and interspecific recognition. We find no evidence that cranial ornamentation in Hungarosaurus involves the contribution of coossified osteoderms. Instead, available evidence indicates that cranial ornamentation forms as a result of the elaboration of individual elements. Although individual differences and sexual dimorphism cannot be excluded, the observed variation in Hungarosaurus cranial ornamentation appears to be associated with ontogeny.
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2
Authors: Enrique J. Gomez, Jose A. Delgado, Juan M. Gonzalez
Published: Mar 2021
Authors: Enrique J. Gomez, Jose A. Delgado, Juan M. Gonzalez
Published: Mar 2021
Soils are highly heterogeneous and support highly diverse microbial communities. Microbial extracellular enzymes breakdown complex polymers into small assimilable molecules representing the limiting step of soil organic matter mineralization. This process occurs on to soil particles although currently it is typically estimated in laboratory aqueous solutions. Herein, estimates of microbial extracellular enzyme activity were obtained over a broad range of temperatures and water availabilities frequently observed at soil upper layers. A Pseudomonas strain presented optimum extracellular enzyme activities at high water activity whereas a desiccation resistant bacterium ( Deinococcus ) and a soil thermophilic isolate ( Parageobacillus ) showed optimum extracellular enzyme activity under dried (i.e., water activities ranging 0.5–0.8) rather that wet conditions. Different unamended soils presented a distinctive response of extracellular enzyme activity as a function of temperature and water availability. This study presents a procedure to obtain realistic estimates of microbial extracellular enzyme activity under natural soil conditions of extreme water availability and temperature. Improving estimates of microbial extracellular enzyme activity contribute to better understand the role of microorganisms in soils.
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Authors: Sonali Garg, Robin Suyesh, Sandeep Das, Mark A. Bee, S. D. Biju
Published: Mar 2021
Authors: Sonali Garg, Robin Suyesh, Sandeep Das, Mark A. Bee, S. D. Biju
Published: Mar 2021
The genus Raorchestes is a large radiation of Old World tree frogs for which the Western Ghats in Peninsular India is the major center for origin and diversification. Extensive studies on this group during the past two decades have resolved long-standing taxonomic confusions and uncovered several new species, resulting in a four-fold increase in the number of known Raorchestes frogs from this region. Our ongoing research has revealed another five new species in the genus, formally described as Raorchestes drutaahu sp. nov., Raorchestes kakkayamensis sp. nov., Raorchestes keirasabinae sp. nov., Raorchestes sanjappai sp. nov., and Raorchestes vellikkannan sp. nov., all from the State of Kerala in southern Western Ghats. Based on new collections, we also provide insights on the taxonomic identity of three previously known taxa. Furthermore, since attempts for an up-to-date comprehensive study of this taxonomically challenging genus using multiple integrative taxonomic approaches have been lacking, here we review the systematic affinities of all known Raorchestes species and define 16 species groups based on evidence from multi-gene (2,327 bp) phylogenetic analyses, several morphological characters (including eye colouration and pattern), and acoustic parameters (temporal and spectral properties, as well as calling height). The results of our study present novel insights to facilitate a better working taxonomy for this rather speciose and morphologically conserved radiation of shrub frogs. This will further enable proper field identification, provide momentum for multi-disciplinary studies, as well as assist conservation of one of the most colourful and acoustically diverse frog groups of the Western Ghats biodiversity hotspot.
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1
Authors: Taku, Ongeziwe, et al
Published: Mar 2021
Authors: Taku, Ongeziwe, et al
Published: Mar 2021
Background South African women of reproductive age have a high burden of sexually transmitted infections (STIs), including human papillomavirus (HPV) infection. However, there is limited information on the prevalence of sexually transmitted pathogens in women from rural Eastern Cape Province, South Africa. The study aims at determining the prevalence of sexually transmitted pathogens and co-infection with high-risk (HR) HPV among women from rural Eastern Cape Province, South Africa. Methods A total of 205 cervical specimens were collected from women aged ≥ 30 years from a rural community-based clinic. The samples were tested for a panel of pathogenic STIs [ Chlamydia trachomatis (serovars A-K & L1-L3), Haemophilus ducreyi , Herpes Simplex Virus (Types 1 & 2), Neisseria gonorrhoeae , Treponema pallidum , Trichomonas vaginalis ( TV ), and pathobionts [ Mycoplasma genitalium (MG), Mycoplasma hominis ( MH ) and Ureaplasma spp. ( UP )] using a multiplex PCR STD direct flow chip assay through a manual Hybrispot platform (Master Diagnostica, Granada, Spain). HR-HPV detection was performed by Hybrid Capture-2 assay. Results High-risk HPV prevalence was 32.2% (66/205) and HIV-1 prevalence was 38.5% (79/205). The overall prevalence of six pathogenic STIs was 22.9% (47/205), with TV having the highest prevalence (15.6%; 32/205). UP (70.2%, 144/205) and MH (36.6%, 75/205) were the most frequently detected pathobionts. Co-infection with ≥ 2 pathogens pathobionts was observed among 52.7% (108/205) participants. Of the six pathogenic STIs, three participants had more than one STI (1.46%) with the presence of MH and UP . HSV-2 (OR: 4.17, CI [1.184–14.690]) and HIV infection (OR: 2.11, CI [1.145–3.873]) were independent STIs associated with HR-HPV infection. Conclusions The high prevalence of pathogenic STIs underscores the need to improve syndromic management policy by implementing effective strategies of prevention, screening tests, and management. HSV-2 and HIV positive remain strongly associated with HR-HPV infection.
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Authors: Abubakar Shettima, Intan H. Ishak, Syahirah Hanisah Abdul Rais, Hadura Abu Hasan, Nurulhasanah Othman
Published: Mar 2021
Authors: Abubakar Shettima, Intan H. Ishak, Syahirah Hanisah Abdul Rais, Hadura Abu Hasan, Nurulhasanah Othman
Published: Mar 2021
Background Proteomic analyses have broadened the horizons of vector control measures by identifying proteins associated with different biological and physiological processes and give further insight into the mosquitoes’ biology, mechanism of insecticide resistance and pathogens-mosquitoes interaction. Female Ae. aegypti ingests human blood to acquire the requisite nutrients to make eggs. During blood ingestion, female mosquitoes transmit different pathogens. Therefore, this study aimed to determine the best protein extraction method for mass spectrometry analysis which will allow a better proteome profiling for female mosquitoes. Methods In this present study, two protein extractions methods were performed to analyze female Ae. aegyti proteome, via TCA acetone precipitation extraction method and a commercial protein extraction reagent CytoBuster TM . Then, protein identification was performed by LC-ESI-MS/MS and followed by functional protein annotation analysis. Results The CytoBuster TM reagent gave the highest protein yield with a mean of 475.90 µg compared to TCA acetone precipitation extraction showed 283.15 µg mean of protein. LC-ESI-MS/MS identified 1,290 and 890 proteins from the CytoBuster TM reagent and TCA acetone precipitation, respectively. When comparing the protein class categories in both methods, there were three additional categories for proteins identified using CytoBuster TM reagent. The proteins were related to scaffold/adaptor protein (PC00226), protein binding activity modulator (PC00095) and intercellular signal molecule (PC00207). In conclusion, the CytoBuster TM protein extraction reagent showed a better performance for the extraction of proteins in term of the protein yield, proteome coverage and extraction speed.
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Authors: Añazco, Diego, et al
Published: Mar 2021
Authors: Añazco, Diego, et al
Published: Mar 2021
Background Preprints are preliminary reports that have not been peer-reviewed. In December 2019, a novel coronavirus appeared in China, and since then, scientific production, including preprints, has drastically increased. In this study, we intend to evaluate how often preprints about COVID-19 were published in scholarly journals and cited. Methods We searched the iSearch COVID-19 portfolio to identify all preprints related to COVID-19 posted on bioRxiv, medRxiv, and Research Square from January 1, 2020, to May 31, 2020. We used a custom-designed program to obtain metadata using the Crossref public API. After that, we determined the publication rate and made comparisons based on citation counts using non-parametric methods. Also, we compared the publication rate, citation counts, and time interval from posting on a preprint server to publication in a scholarly journal among the three different preprint servers. Results Our sample included 5,061 preprints, out of which 288 were published in scholarly journals and 4,773 remained unpublished (publication rate of 5.7%). We found that articles published in scholarly journals had a significantly higher total citation count than unpublished preprints within our sample ( p < 0.001), and that preprints that were eventually published had a higher citation count as preprints when compared to unpublished preprints ( p < 0.001). As well, we found that published preprints had a significantly higher citation count after publication in a scholarly journal compared to as a preprint ( p < 0.001). Our results also show that medRxiv had the highest publication rate, while bioRxiv had the highest citation count and shortest time interval from posting on a preprint server to publication in a scholarly journal. Conclusions We found a remarkably low publication rate for preprints within our sample, despite accelerated time to publication by multiple scholarly journals. These findings could be partially attributed to the unprecedented surge in scientific production observed during the COVID-19 pandemic, which might saturate reviewing and editing processes in scholarly journals. However, our findings show that preprints had a significantly lower scientific impact, which might suggest that some preprints have lower quality and will not be able to endure peer-reviewing processes to be published in a peer-reviewed journal.
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Authors: Tong, Xinxin, et al
Published: Mar 2021
Authors: Tong, Xinxin, et al
Published: Mar 2021
In this study, using an isobaric tags for relative and absolute quantitation (iTRAQ ) approach coupled with LC-MS / MS and bioinformatics, the proteomes were analyzed for the crucial three stages covering the fruiting body development of Ophiocordyceps sinensis , including sclerotium (ST), primordium (PR) and mature fruiting body (MF), with a focus on fruiting body development-related proteins and the potential mechanisms of the development. A total of 1,875 proteins were identified. Principal Component Analysis (PCA) demonstrated that the protein patterns between PR and MF were more similar than ST. Differentially accumulated proteins (DAPs) analysis showed that there were 510, 173 and 514 DAPs in the comparisons of ST vs. PR, PR vs. MF and ST vs. MF, respectively. A total of 62 shared DAPs were identified and primarily enriched in proteins related to ‘carbon transport and mechanism’, ‘the response to oxidative stress’, ‘antioxidative activity’ and ‘translation’. KEGG and GO databases showed that the DAPs were enriched in terms of ‘primary metabolisms (amino acid/fatty acid/energy metabolism)’, ‘the response to oxidative stress’ and ‘peroxidase’. Furthermore, 34 DAPs involved in reactive oxygen species (ROS) metabolism were identified and clustered across the three stages using hierarchical clustering implemented in hCluster R package . It was suggested that their roles and the underlying mechanisms may be stage-specific. ROS may play a role in fungal pathogenicity in ST, the fruit-body initiation in PR, sexual reproduction and highland adaptation in MF. Crucial ROS-related proteins were identified, such as superoxide dismutase (SOD, T5A6F1), Nor-1 (T5AFX3), electron transport protein (T5AHD1), histidine phosphotransferase (HPt, T5A9Z5) and Glutathione peroxidase (T5A9V1). Besides, the accumulation of ROS at the three stages were assayed using 2,7-dichlorofuorescin diacetate (DCFH-DA) stanning. A much stronger ROS accumulation was detected at the stage MF, compared to the stages of PR and ST. Sections of ST and fruit-body part of MF were stained by DCFH-DA and observed under the fluorescencemicroscope, showing ROS was distributed within the conidiospore and ascus. Besides, SOD activity increased across the three stages, while CAT activity has a strong increasement in MF compared to the stages of ST and PR. It was suggested that ROS may act in gradient-dependent manner to regulate the fruiting body development. The coding region sequences of six DAPs were analyzed at mRNA level by quantitative real-time PCR (qRT-PCR). The results support the result of DAPs analysis and the proteome sequencing data. Our findings offer the perspective of proteome to understand the biology of fruiting body development and highland adaptation in O. sinensis , which would inform the big industry of this valuable fungus.
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