Clostridium manihotivorum sp. nov., a novel mesophilic anaerobic bacterium that produces cassava pulp-degrading enzymes
Background Cassava pulp is a promising starch-based biomasses, which consists of residual starch granules entrapped in plant cell wall containing non-starch polysaccharides, cellulose and hemicellulose. Strain CT4T, a novel mesophilic anaerobic bacterium isolated from soil collected from a cassava pulp landfill, has a strong ability to degrade polysaccharides in cassava pulp. This study explored a rarely described species within the genus Clostridium that possessed a group of cassava pulp-degrading enzymes. Methods A novel mesophilic anaerobic bacterium, the strain CT4T, was identified based on phylogenetic, genomic, phenotypic and chemotaxonomic analysis. The complete genome of the strain CT4T was obtained following whole-genome sequencing, assembly and annotation using both Illumina and Oxford Nanopore Technology (ONT) platforms. Results Analysis based on the 16S rRNA gene sequence indicated that strain CT4T is a species of genus Clostridium. Analysis of the whole-genome average amino acid identity (AAI) of strain CT4T and the other 665 closely related species of the genus Clostridium revealed a separated strain CT4T from the others. The results revealed that the genome consisted of a 6.3 Mb circular chromosome with 5,664 protein-coding sequences. Genome analysis result of strain CT4T revealed that it contained a set of genes encoding amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. A comparative genomic analysis of strain CT4T with closely related species with available genomic information, C. amylolyticum SW408T, showed that strain CT4T contained more genes encoding cassava pulp-degrading enzymes, which comprised a complex mixture of amylolytic-, hemicellulolytic-, cellulolytic- and pectinolytic enzymes. This work presents the potential for saccharification of strain CT4T in the utilization of cassava pulp. Based on phylogenetic, genomic, phenotypic and chemotaxonomic data, we propose a novel species for which the name Clostridium manihotivorum sp. nov. is suggested, with the type strain CT4T (= TBRC 11758T = NBRC 114534T).
Cheawchanlertfa et al. (2020) Clostridium manihotivorum sp. nov., a novel mesophilic anaerobic bacterium that produces cassava pulp-degrading enzymes. PeerJ 8:e10343 https://doi.org/10.7717/peerj.10343
Effects of microhabitat on rodent-mediated seed removal of endangered Kmeria septentrionalis in the karst habitat
Seed removal behaviors of rodents are largely influenced by microhabitat. Although the karst ecosystem is composed of a broad variety of microhabitats, we have no information on how they affect such behaviors. We investigated rodents’ seed removal behaviors in four karst microhabitats (stone cavern, stone groove, stone surface, and soil surface) using three types of Kmeria septentrionalis seeds: fresh, black (intact seeds with black aril that dehydrates and darkens), and exposed (clean seeds without the aril). We show that Rattus norvegicus, Leopoldamys edwardsi and Rattus flavipectus were the predominant seed predators. Even though all seed types experienced a high removal rate in all four microhabitats, but rodents preferentially removed seeds from the three stone microhabitats (stone caves: 69.71 ± 2.74%; stone surface: 60.53 ± 2.90%; stone groove: 56.94 ± 2.91%) compared to the soil surface (53.90 ± 2.92%). Seeds that had been altered by being exposed to the environment were more attractive to rodents than fresh seeds (76.25 ± 2.20% versus 36.18 ± 2.29%). The seed removal behavior of rodents was significantly affected by the microhabitat and seed type. Finally, seeds that had fallen on the soil surface microhabitat incurred a lower predation risk than seeds fallen on other microhabitats, which increased their probability to germinate. Our results indicate that the lower predation rate of seeds from the endangered K. septentrionalis dropped on the soil surface increases trees’ likelihood of survival.
Wang et al. (2020) Effects of microhabitat on rodent-mediated seed removal of endangered Kmeria septentrionalis in the karst habitat. PeerJ 8:e10378 https://doi.org/10.7717/peerj.10378
Temporal expression profiles of lncRNA and mRNA in human embryonic stem cell-derived motor neurons during differentiation
Background Human embryonic stem cells (hESC) have been an invaluable research tool to study motor neuron development and disorders. However, transcriptional regulation of multiple temporal stages from ESCs to spinal motor neurons (MNs) has not yet been fully elucidated. Thus, the goals of this study were to profile the time-course expression patterns of lncRNAs during MN differentiation of ESCs and to clarify the potential mechanisms of the lncRNAs that are related to MN differentiation. Methods We utilized our previous protocol which can harvest motor neuron in more than 90% purity from hESCs. Then, differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs) during MN differentiation were identified through RNA sequencing. Bioinformatic analyses were performed to assess potential biological functions of genes. We also performed qRT-PCR to validate the DElncRNAs and DEmRNAs. Results A total of 441 lncRNAs and 1,068 mRNAs at day 6, 443 and 1,175 at day 12, and 338 lncRNAs and 68 mRNAs at day 18 were differentially expressed compared with day 0. Bioinformatic analyses identified that several key regulatory genes including POU5F1, TDGF1, SOX17, LEFTY2 and ZSCAN10, which involved in the regulation of embryonic development. We also predicted 283 target genes of DElncRNAs, in which 6 mRNAs were differentially expressed. Significant fold changes in lncRNAs (NCAM1-AS) and mRNAs (HOXA3) were confirmed by qRT-PCR. Then, through predicted overlapped miRNA verification, we constructed a lncRNA NCAM1-AS-miRNA-HOXA3 network.
Sun et al. (2020) Temporal expression profiles of lncRNA and mRNA in human embryonic stem cell-derived motor neurons during differentiation. PeerJ 8:e10075 https://doi.org/10.7717/peerj.10075
Regional infectious risk prediction of COVID-19 based on geo-spatial data
After the first confirmed case of the novel coronavirus disease (COVID-19) was found, it is of considerable significance to divide the risk levels of various provinces or provincial municipalities in Mainland China and predict the spatial distribution characteristics of infectious diseases. In this paper, we predict the epidemic risk of each province based on geographical proximity information, spatial inverse distance information, economic distance and Baidu migration index. A simulation study revealed that the information based on geographical economy matrix and migration index could well predict the spatial spread of the epidemic. The results reveal that the accuracy rate of the prediction is over 87.10% with a rank difference of 3.1. The results based on prior information will guide government agencies and medical and health institutions to implement responses to major public health emergencies when facing the epidemic situation.
Cheng et al. (2020) Regional infectious risk prediction of COVID-19 based on geo-spatial data. PeerJ 8:e10139 https://doi.org/10.7717/peerj.10139
Identification of L-asparaginases from Streptomyces strains with competitive activity and immunogenic profiles: a bioinformatic approach
The enzyme L-asparaginase from Escherichia coli is a therapeutic enzyme that has been a cornerstone in the clinical treatment of acute lymphoblastic leukemia for the last decades. However, treatment effectiveness is limited by the highly immunogenic nature of the protein and its cross-reactivity towards L-glutamine. In this work, a bioinformatic approach was used to identify, select and computationally characterize L-asparaginases from Streptomyces through sequence-based screening analyses, immunoinformatics, homology modeling, and molecular docking studies. Based on its predicted low immunogenicity and excellent enzymatic activity, we selected a previously uncharacterized L-asparaginase from Streptomyces scabrisporus. Furthermore, two putative asparaginase binding sites were identified and a 3D model is proposed. These promising features allow us to propose L-asparaginase from S. scabrisporus as an alternative for the treatment of acute lymphocytic leukemia.
González-Torres et al. (2020) Identification of L-asparaginases from Streptomyces strains with competitive activity and immunogenic profiles: a bioinformatic approach. PeerJ 8:e10276 https://doi.org/10.7717/peerj.10276
The optimal platelet concentration in platelet-rich plasma for proliferation of human cells in vitro—diversity, biases, and possible basic experimental principles for further research in the field: A review
Background In the last decades, several in vitro studies have tested the effect of plate-rich plasma (PRP) on the proliferation of human cells in search of a wizard for the use of PRP in a clinical setting. However, the literature displays striking differences regarding this question despite the relatively similar experimental design. The aim of this review is twofold: describe and explain this diversity and suggest basic principles for further in vitro studies in the field. The optimal platelet concentration in vivo will also be discussed. Methods A search in mainly EMBASE and PubMed was performed to identify in vitro studies that investigate the effect of different PRP concentrations on human cell proliferation. The assessment of bias was based on the principles of “Good Cell Culture Practice” and adapted. Results In total, 965 in vitro studies were detected. After the initial screening, 31 studies remained for full-text screening. A total of 16 studies met the criteria of final inclusion and appeared relatively sound. In general, the studies state consistently that PRP stimulates the proliferation of the human cell. Two main types of experimental techniques were detected: 1. The Fixed PRP Concentration Group using a fixed PRP concentration throughout the experiment, which leads to a substantial decrease in nutrition available at higher concentrations. 2. The Fixed PRP Volume Group using a fixed PRP-to-media ratio (Vol/Vol) throughout the experiment. A general tendency was observed in both groups: when the PRP to media ratio increased (Vol/Vol), the proliferation rate decreased. Further, The Low Leukocyte group observed a substantial higher optimal PRP concentration than The High leukocyte group. No prominent tendencies was seen regarding anticoagulants, activation methods, and blood donor (age or sex). Discussion Two major biases regarding optimal proliferation in vitro is pointed out: 1. Too high PRP volume. It is speculated that the techniques used by some studies led to an adverse growth condition and even cell starvation at higher concentrations. 2. High leukocyte levels. Reduced proliferation rate due to proinflammatory substances released during degranulation of leukocytes. Conclusions The two main biases may explain the bell-shaped effect of PRP and the detrimental effects at higher platelet concentrations observed in several studies. These biases may also explain the low optimal PRP concentration observed in some studies. Even if one universal optimal PRP concentration does not exist, the review indicates that PRP concentrations in the upper parts of the scale is optimal or at least beneficial. Finally, following basic experimental principles are suggested. 1: The PRP/media ratio (Vol/Vol) should be kept as constant. 2: The PRP/media ratio should provide a sufficient nutrition supply, that is, PRP ≤ 10% (Vol/Vol). 3: The cell density per well (cells/mL) should be defined. 4: Leukocyte level should be kept low, preferable depleted (< 0.1 PLT/µL).
Straum (2020) The optimal platelet concentration in platelet-rich plasma for proliferation of human cells in vitro—diversity, biases, and possible basic experimental principles for further research in the field: A review. PeerJ 8:e10303 https://doi.org/10.7717/peerj.10303
Cytokine RT-qPCR and ddPCR for immunological investigations of the endangered Australian sea lion (Neophoca cinerea) and other mammals
Measurement of cytokine gene expression by reverse transcription quantitative polymerase chain reaction (RT-qPCR) is used widely to assess the immune system of animals and to identify biomarkers of disease, but its application is limited in wildlife species due to a lack of species-specific reagents. The free-ranging endangered Australian sea lion (Neophoca cinerea) experiences significant clinical disease and high pup mortality due to intestinal hookworm infection. Developing immunological tools specific to the species will aid in the assessment of drivers of disease and its impact in population demographics. This study describes the development and validation of cross-reactive RT-qPCR assays to measure five important cytokines involved in innate and Th1/Th2 responses (IL-6, TNFα, IFNγ, IL-4 and IL-10) in unstimulated blood samples from a range of different mammalian species including the Australian sea lion. All RT-qPCR assays efficiencies ranged between 87% (Ovis aries TNFα) and 111% (Bos taurus IL-10) and had strong linearity (R2). IL-4 and IFNγ gene expression for N. cinerea fell below the dynamic range (and therefore quantifiable limits) of RT-qPCR assays but were able to be quantified using the novel droplet digital PCR (ddPCR). This study delivers new immunological tools for eco-immunologists studying cytokine gene expression in wildlife species and is to our knowledge, the first cytokine ddPCR approach to be reported in a pinniped species.
Meza Cerda et al. (2020) Cytokine RT-qPCR and ddPCR for immunological investigations of the endangered Australian sea lion (Neophoca cinerea) and other mammals. PeerJ 8:e10306 https://doi.org/10.7717/peerj.10306
Combined application of biochar and nitrogen fertilizer improves rice yield, microbial activity and N-metabolism in a pot experiment
The excessive use of synthetic nitrogen (N) fertilizers in rice (Oryza sativa L.) has resulted in high N loss, soil degradation, and environmental pollution in a changing climate. Soil biochar amendment is proposed as a climate change mitigation tool that supports carbon sequestration and reduces N losses and greenhouse gas (GHG) emissions from the soil. The current study evaluated the impact of four different rates of biochar (B) (C/B0-0 t ha−1, B1-20 t ha−1, B2-40 t ha−1, and B3-60 t ha−1) and two N levels (N1; low (270 kg N ha−1) and N2; high (360 kg N ha−1)), on rice (cultivar Zhenguiai) grown in pots. Significant increases in the average soil microbial biomass N (SMBN) (88%) and carbon (87%) were recorded at the highest rate of 60-ton ha−1B and 360 kg N ha−1 compared to the control (N1C) during both seasons (S1 and S2). The photochemical efficiency (Fv/Fm), quantum yield of the photosystem (PS) II (ΦPS II), electron transport rate (ETR), and photochemical quenching (qP) were enhanced at low rates of biochar applications (20 to 40 t B ha−1) for high and low N rates across the seasons. Nitrate reductase (NR), glutamine synthetase (GS), and glutamine 2-oxoglutarate aminotransferase (GOGAT) activity were, on average, 39%, 55%, and 63% higher in the N1B3, N2B2, and N2B3 treatments, respectively than the N1C. The grain quality was higher in the N1B3 treatment than the N1C, i.e., the protein content (PC), amylose content (AC), percent brown rice (BRP), and percent milled rice (MRP) were, on average, 16%, 28%, 4.6%, and 5% higher, respectively in both seasons. The results of this study indicated that biochar addition to the soil in combination with N fertilizers increased the dry matter (DM) content, N uptake, and grain yield of rice by 24%, 27%, and 64%, respectively, compared to the N1C.
Ali et al. (2020) Combined application of biochar and nitrogen fertilizer improves rice yield, microbial activity and N-metabolism in a pot experiment. PeerJ 8:e10311 https://doi.org/10.7717/peerj.10311
Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform
Marine organisms are important to global food security as they are the largest source of animal proteins feeding mankind. Genomics-assisted aquaculture can increase yield while preserving the environment to ensure sufficient and sustainable production for global food security. However, only few high-quality genome sequences of marine organisms, especially shellfish, are available to the public partly because of the difficulty in the sequence assembly due to the complex nature of their genomes. A key step for a successful genome sequencing is the preparation of high-quality high molecular weight (HMW) genomic DNA. This study evaluated the effectiveness of five DNA extraction protocols (CTAB, Genomic-tip, Mollusc DNA, TIANamp Marine Animals DNA, and Sbeadex livestock kits) in obtaining shrimp HMW DNA for a long-read sequencing platform. DNA samples were assessed for quality and quantity using a Qubit fluorometer, NanoDrop spectrophotometer and pulsed-field gel electrophoresis. Among the five extraction methods examined without further optimization, the Genomic-tip kit yielded genomic DNA with the highest quality. However, further modifications of these established protocols might yield even better DNA quality and quantity. To further investigate whether the obtained genomic DNA could be used in a long-read sequencing application, DNA samples from the top three extraction methods (CTAB method, Genomic-tip and Mollusc DNA kits) were used for Pacific Biosciences (PacBio) library construction and sequencing. Genomic DNA obtained from Genomic-tip and Mollusc DNA kits allowed successful library construction, while the DNA obtained from the CTAB method did not. Genomic DNA isolated using the Genomic-tip kit yielded a higher number of long reads (N50 of 14.57 Kb) than those obtained from Mollusc DNA kits (N50 of 9.74 Kb). Thus, this study identified an effective extraction method for high-quality HMW genomic DNA of shrimp that can be applied to other marine organisms for a long-read sequencing platform.
Angthong et al. (2020) Optimization of high molecular weight DNA extraction methods in shrimp for a long-read sequencing platform. PeerJ 8:e10340 https://doi.org/10.7717/peerj.10340
Identification of the important environmental factors influencing natural vegetation succession following cropland abandonment on the Loess Plateau, China
Identification of typical vegetation succession types and their important influencing factors is an important prerequisite to implement differential vegetation and soil management after land abandonment on the Loess Plateau, China. However, there is no reported study specifically on the identification of vegetation types and their important factors as well as the thresholds of the important factors for classification of the vegetation types, based on the medium- to long-term succession of natural vegetation after cropland abandonment. We collected vegetation and soil data on the natural vegetation with the longest 60-year-old forest communities that developed after cropland abandonment and analyzed the data using two-way indicator species analysis, detrended correspondence analysis, direct canonical correspondence analysis and classification tree model. The vegetation communities were classified into five distinct vegetation types, including Artemisia scoparia, Lespedeza davurica and Stipa bungeana, Artemisia giraldii pamp, Sophora viciifolia, Quercus liaotungensis and Biota orientalis. The years after cropland abandonment and soil C/N were further identified as important factors determining the types of vegetation. Likewise, it was observed that most of the investigated soil nutrient variables and soil texture-related variables improved with the vegetation succession while soil water in the surface layers showed a decreasing trend. These findings may provide an ecological basis for site-specific management of vegetation types after cropland abandonment in the medium-long term on the Loess Plateau. Our results encourage further exploration of vegetation succession and their important factors based on longer periods of vegetation succession after cropland abandonment under more soil and climatic conditions on the mountainous areas as the Loess Plateau.
Zhang et al. (2020) Identification of the important environmental factors influencing natural vegetation succession following cropland abandonment on the Loess Plateau, China. PeerJ 8:e10349 https://doi.org/10.7717/peerj.10349