Eur J Pharmacol. 2021 Mar 19:174057. doi: 10.1016/j.ejphar.2021.174057. Online ahead of print.

ABSTRACT

Immunotoxins are protein-based drugs consist of a target-specific binding domain and a cytotoxic domain to eliminate target cells. Such compounds are potentially therapeutic to combat diseases such as cancer. Generally, the B-subunit of Shiga toxin (STXB) receptor, globotriaosylceramide (Gb3), is expressed in high amounts on a number of human tumors cancer cells. In this study, we evaluated a new antitumor candidate called DT389-STXB chimeric protein, which genetically fused the DT to B-subunit of Shiga-like toxin (STXB). First a chimeric protein, encoding DT389-STXB was synthesized. The optimized chimeric protein expressed in E.coli BL21 (DE3) and confirmed by anti-His western blot analysis. T47D, SKBR3, 4T1 and MCF7 cell lines were treated separately with purified DT389-STXB recombinant protein and functional activity of DT389-STXB was analyzed by the cell enzyme-linked immunosorbentassay (ELISA), MTT, ICC, western blot and apoptosis tests. The results indicated that the recombinant DT389-STXB fusion protein with a molecular weight of 53 kDa was successfully expressed in E.coli BL21 (DE3) and the anti-His western-blot was used to confirm the presence of the protein. The DT389-STXB fusion protein attached to T47D, SKBR3 and 4T1 cell lines with the proper affinity and induced dose-dependent cytotoxicity against GB3-expressing cancer cells in vitro. Our results showed that DT389-STXB fusion protein may be a promising candidate for antitumor therapy agent against breast cancer; however, further studies are required to explore its efficacy in vivo for therapeutic applications.

PMID:33753109 | DOI:10.1016/j.ejphar.2021.174057

Mol Genet Metab. 2021 Mar 11:S1096-7192(21)00062-7. doi: 10.1016/j.ymgme.2021.03.005. Online ahead of print.

ABSTRACT

Leigh syndrome is a severe mitochondrial neurodegenerative disease with no effective treatment. In the Ndufs4-/- mouse model of Leigh syndrome, continuously breathing 11% O2 (hypoxia) prevents neurodegeneration and leads to a dramatic extension (~5-fold) in lifespan. We investigated the effect of hypoxia on the brain metabolism of Ndufs4-/- mice by studying blood gas tensions and metabolite levels in simultaneously sampled arterial and cerebral internal jugular venous (IJV) blood. Relatively healthy Ndufs4-/- and wildtype (WT) mice breathing air until postnatal age ~38 d were compared to Ndufs4-/- and WT mice breathing air until ~38 days old followed by 4-weeks of breathing 11% O2. Compared to WT control mice, Ndufs4-/- mice breathing air have reduced brain O2 consumption as evidenced by an elevated partial pressure of O2 in IJV blood (PijvO2) despite a normal PO2 in arterial blood, and higher lactate/pyruvate (L/P) ratios in IJV plasma revealed by metabolic profiling. In Ndufs4-/- mice, hypoxia treatment normalized the cerebral venous PijvO2 and L/P ratios, and decreased levels of nicotinate in IJV plasma. Brain concentrations of nicotinamide adenine dinucleotide (NAD+) were lower in Ndufs4-/- mice breathing air than in WT mice, but preserved at WT levels with hypoxia treatment. Although mild hypoxia (17% O2) has been shown to be an ineffective therapy for Ndufs4-/- mice, we find that when combined with nicotinic acid supplementation it provides a modest improvement in neurodegeneration and lifespan. Therapies targeting both brain hyperoxia and NAD+ deficiency may hold promise for treating Leigh syndrome.

PMID:33752971 | DOI:10.1016/j.ymgme.2021.03.005

BMC Bioinformatics. 2021 Mar 22;22(1):143. doi: 10.1186/s12859-021-04062-2.

ABSTRACT

BACKGROUND: Recently, many computational methods have been proposed to predict cancer genes. One typical kind of method is to find the differentially expressed genes between tumour and normal samples. However, there are also some genes, for example, 'dark' genes, that play important roles at the network level but are difficult to find by traditional differential gene expression analysis. In addition, network controllability methods, such as the minimum feedback vertex set (MFVS) method, have been used frequently in cancer gene prediction. However, the weights of vertices (or genes) are ignored in the traditional MFVS methods, leading to difficulty in finding the optimal solution because of the existence of many possible MFVSs.

RESULTS: Here, we introduce a novel method, called weighted MFVS (WMFVS), which integrates the gene differential expression value with MFVS to select the maximum-weighted MFVS from all possible MFVSs in a protein interaction network. Our experimental results show that WMFVS achieves better performance than using traditional bio-data or network-data analyses alone.

CONCLUSION: This method balances the advantage of differential gene expression analyses and network analyses, improves the low accuracy of differential gene expression analyses and decreases the instability of pure network analyses. Furthermore, WMFVS can be easily applied to various kinds of networks, providing a useful framework for data analysis and prediction.

PMID:33752597 | DOI:10.1186/s12859-021-04062-2

MAbs. 2021 Jan-Dec;13(1):1902034. doi: 10.1080/19420862.2021.1902034.

ABSTRACT

Dual targeting of surface receptors with bispecific antibodies is attracting increasing interest in cancer therapy. Here, we present a novel bivalent and bispecific antagonistic molecule (Dab-Fc) targeting human epidermal growth factors 2 and 3 (HER2 and HER3) derived from the Db-Ig platform, which was developed for the generation of multivalent and multispecific antibody molecules. Dab-Fc comprises the variable domains of the anti-HER2 antibody trastuzumab and the anti-HER3 antibody 3-43 assembled into a diabody-like structure stabilized by CH1 and CL domains and further fused to a human γ1 Fc region. The resulting Dab-Fc 2 × 3 molecule retained unhindered binding to both antigens and was able to bind both antigens sequentially. In cellular experiments, the Dab-Fc 2 × 3 molecule strongly bound to different tumor cell lines expressing HER2 and HER3 and was efficiently internalized. This was associated with potent inhibition of the proliferation and migration of these tumor cell lines. Furthermore, IgG-like pharmacokinetics and anti-tumoral activity were demonstrated in a xenograft tumor model of the gastric cancer cell-line NCI-N87. These results illustrate the suitability of our versatile Db-Ig platform technology for the generation of bivalent bispecific molecules, which has been successfully used here for the dual targeting of HER2 and HER3.

PMID:33752566 | DOI:10.1080/19420862.2021.1902034

Water Res. 2021 Mar 7;196:117014. doi: 10.1016/j.watres.2021.117014. Online ahead of print.

ABSTRACT

Freshwater lakes are threatened by harmful cyanobacterial blooms, whose basic unit is Cyanobacterial Aggregate (CA). CA-attached bacteria play a significant role through different blooming stages with substantial variation of their taxonomic structure. However, little is known about their functional variations and functional links with cyanobacteria due to the lack of reference genomes. In this longitudinal study, we collected 16 CA samples from Lake Taihu, one of China's largest freshwater lakes, from April 2015 to February 2016, and sequenced their V4 region of 16S rRNA genes, full metagenomes (MG), and metatranscriptomes (MT). The analysis of these data revealed the dynamics of microbial taxonomic and functional structure in CAs, influenced by both external environmental factors and internal metabolism. 55 OTUs, 456 genes, and 37 transcripts showed significantly differential abundance across the early, middle, and late blooming stages (ANOVA test, P < 0.05). Total nitrogen and total phosphorus were proved to be the most important environmental drivers of microbial taxonomic and functional variations in CAs (Mantel's r > 0.25, P < 0.05). We constructed 161 high-quality metagenome-assembled genomes (MAGs), out of which 22 were cyanobacterial strains with diverse energy pathways, transporters and prokaryotic defense systems. Based on these MAGs, we constructed a cyanobacteria-bacteria co-nitrogen-pathway and a cyanobacteria-bacteria co-phosphorus-pathway, by which we demonstrated how nitrogen and phosphorus influence the dynamics of the microbial structure to a certain extent by affecting these co-pathways. Overall, these results characterized the taxonomic, functional, and transcriptional variations of microbes in CAs through different blooming stages. Genome assembly and metabolic analysis of cyanobacteria and their attached bacteria suggested that the material exchange and signal transduction do, indeed, exist among them. Our understanding of the underlying molecular pathways for cyanobacterial blooms could lead to the control of blooms by interventional strategies to disrupt critical microbes' expression.

PMID:33751971 | DOI:10.1016/j.watres.2021.117014

EMBO Mol Med. 2021 Mar 10:e13162. doi: 10.15252/emmm.202013162. Online ahead of print.

ABSTRACT

Metastasis is the main cause of deaths related to solid cancers. Active transcriptional programmes are known to regulate the metastatic cascade but the molecular determinants of metastatic colonization remain elusive. Using an inducible piggyBac (PB) transposon mutagenesis screen, we have shown that overexpression of the transcription factor nuclear factor IB (NFIB) alone is sufficient to enhance primary mammary tumour growth and lung metastatic colonization. Mechanistically and functionally, NFIB directly increases expression of the oxidoreductase ERO1A, which enhances HIF1α-VEGFA-mediated angiogenesis and colonization, the last and fatal step of the metastatic cascade. NFIB is thus clinically relevant: it is preferentially expressed in the poor-prognostic group of basal-like breast cancers, and high expression of the NFIB/ERO1A/VEGFA pathway correlates with reduced breast cancer patient survival.

PMID:33751828 | DOI:10.15252/emmm.202013162

J Phycol. 2021 Mar 9. doi: 10.1111/jpy.13163. Online ahead of print.

ABSTRACT

The biological communities of mountain lakes are suspected to be highly sensitive to global warming and associated catchment changes. To identify the parameters determining algal community responses, subfossil pigments from 21 different mountain lakes in the Bavarian-Tyrolean Limestone Alps were investigated. Sediment cores were radio-isotopically dated, and their pigment preservation evaluated. General additive models (GAM) of pigment compositions were calculated with temperature as the explanatory variable and generalised linear models with several lake parameters explaining log-transformed GAM p-values. Lake depth and trophic state were identified as major control variables of the algal community and productivity changes. Shifts in a deep oligotrophic alpine lake (lg(p) = -1.04) were half as strong as in a shallow mesotrophic alpine lake (lg(p) = -1.86) with faster warming and higher productivity forcing the development of biomass. Phytoplankton and macrophyte pigments increased clearly with warming, at lower altitudes, and decreased at the treeline, so that periphytic pigments dominated alpine sediments. This pattern is probably the result of interactions of UV radiation and allochthonous inputs of DOM. Our findings suggest that (sub)alpine shallow lakes with higher nutrient levels are most vulnerable to climate change-driven changes whereas deep, nutrient-poor lakes appear more resilient.

PMID:33751611 | DOI:10.1111/jpy.13163

Antonie Van Leeuwenhoek. 2021 Mar 9. doi: 10.1007/s10482-021-01551-5. Online ahead of print.

ABSTRACT

The marine phycosphere harbors unique cross-kingdom associations with ecological relevance. During investigating the diversity of phycosphere microbiota of marine harmful algal blooms dinoflagellates, a faint yellow-pigmented bacterium, designated as strain LZ-8, was isolated from paralytic shellfish poisoning toxin-producing dinoflagellate Alexandrium catenella LZT09. The new isolate appeared to have growth-promoting potential toward its algal host. Molecular analysis using 16S rRNA gene, housekeeping rpoD gene and whole-genome sequence comparison indicated that strain LZ-8T was a novel gammaproteobacterium of the family Alteromonadaceae. The major fatty acids of strain LZ-8T were C16:0, C18:1 ω9c, C12:0 3-OH, summed feature 3, C16:1 ω9c, C12:0 and summed feature 9. The major isoprenoid quinone was Q-9. Polar lipids were diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, unidentified phospholipid, two unidentified aminolipids and six unidentified polar lipids. The genomic DNA G+C content was 57.36 mol%. Based on genome sequencing, several biosynthetic gene clusters responsible for bacterial biosynthesis of carotenoids and siderophores that may involve in algae-bacterial interactions were identified in the genome of strain LZ-8T. The polyphasic characterization indicated that strain LZ-8T represents a novel Marinobacter species. The name Marinobacter alexandrii sp. nov., type strain LZ-8T (= CCTCC AB 2018386T = KCTC 72198T) is proposed.

PMID:33751267 | DOI:10.1007/s10482-021-01551-5

Plant Cell. 2021 Mar 5:koab076. doi: 10.1093/plcell/koab076. Online ahead of print.

ABSTRACT

Angiosperms have evolved the phloem for the long-distance transport of metabolites. The complex process of phloem development involves genes that only occur in vascular plant lineages. For example, in Arabidopsis thaliana, the BREVIS RADIX (BRX) gene is required for continuous root protophloem differentiation, together with PROTEIN KINASE ASSOCIATED WITH BRX (PAX). BRX and its BRX-LIKE (BRXL) homologs are composed of four highly conserved domains including the signature tandem BRX domains that are separated by variable spacers. Nevertheless, BRX family proteins have functionally diverged. For instance, BRXL2 can only partially replace BRX in the root protophloem. This divergence is reflected in physiologically relevant differences in protein behavior, such as auxin-induced plasma membrane dissociation of BRX, which is not observed for BRXL2. Here we dissected the differential functions of BRX family proteins using a set of amino acid substitutions and domain swaps. Our data suggest that the plasma membrane-associated tandem BRX domains are both necessary and sufficient to convey the biological outputs of BRX function and therefore constitute an important regulatory entity. Moreover, PAX target phosphosites in the linker between the two BRX domains mediate the auxin-induced plasma membrane dissociation. Engineering these sites into BRXL2 renders this modified protein auxin-responsive and thereby increases its biological activity in the root protophloem context.

PMID:33751121 | DOI:10.1093/plcell/koab076

Plant Cell. 2021 Mar 22;33(1):11-26. doi: 10.1093/plcell/koaa015.

ABSTRACT

Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom long-term establishment of genome duplications suggests a link with environmental conditions. Whole-genome duplications seem to correlate with periods of extinction or global change, while polyploids often thrive in harsh or disturbed environments. Evidence is also accumulating that biotic interactions, for instance, with pathogens or mutualists, affect polyploids differently than nonpolyploids. Here, we review recent findings and insights on the effect of both abiotic and biotic stress on polyploids versus nonpolyploids and propose that stress response in general is an important and even determining factor in the establishment and success of polyploidy.

PMID:33751096 | DOI:10.1093/plcell/koaa015

PLoS Biol. 2021 Mar 22;19(3):e3001128. doi: 10.1371/journal.pbio.3001128. eCollection 2021 Mar.

ABSTRACT

The scientific community is focused on developing antiviral therapies to mitigate the impacts of the ongoing novel coronavirus disease 2019 (COVID-19) outbreak. This will be facilitated by improved understanding of viral dynamics within infected hosts. Here, using a mathematical model in combination with published viral load data, we compare within-host viral dynamics of SARS-CoV-2 with analogous dynamics of MERS-CoV and SARS-CoV. Our quantitative analyses using a mathematical model revealed that the within-host reproduction number at symptom onset of SARS-CoV-2 was statistically significantly larger than that of MERS-CoV and similar to that of SARS-CoV. In addition, the time from symptom onset to the viral load peak for SARS-CoV-2 infection was shorter than those of MERS-CoV and SARS-CoV. These findings suggest the difficulty of controlling SARS-CoV-2 infection by antivirals. We further used the viral dynamics model to predict the efficacy of potential antiviral drugs that have different modes of action. The efficacy was measured by the reduction in the viral load area under the curve (AUC). Our results indicate that therapies that block de novo infection or virus production are likely to be effective if and only if initiated before the viral load peak (which appears 2-3 days after symptom onset), but therapies that promote cytotoxicity of infected cells are likely to have effects with less sensitivity to the timing of treatment initiation. Furthermore, combining a therapy that promotes cytotoxicity and one that blocks de novo infection or virus production synergistically reduces the AUC with early treatment. Our unique modeling approach provides insights into the pathogenesis of SARS-CoV-2 and may be useful for development of antiviral therapies.

PMID:33750978 | DOI:10.1371/journal.pbio.3001128

Commun Biol. 2021 Mar 9;4(1):316. doi: 10.1038/s42003-021-01841-8.

ABSTRACT

Broad spectrum antibiotics cause both transient and lasting damage to the ecology of the gut microbiome. Antibiotic-induced loss of gut bacterial diversity has been linked to susceptibility to enteric infections. Prior work on subtherapeutic antibiotic treatment in humans and non-human animals has suggested that entire gut communities may exhibit tolerance phenotypes. In this study, we validate the existence of these community tolerance phenotypes in the murine gut and explore how antibiotic treatment duration or a diet enriched in antimicrobial phytochemicals might influence the frequency of this phenotype. Almost a third of mice exhibited whole-community tolerance to a high dose of the β-lactam antibiotic cefoperazone, independent of antibiotic treatment duration or dietary phytochemical amendment. We observed few compositional differences between non-responder microbiota during antibiotic treatment and the untreated control microbiota. However, gene expression was vastly different between non-responder microbiota and controls during treatment, with non-responder communities showing an upregulation of antimicrobial tolerance genes, like efflux transporters, and a down-regulation of central metabolism. Future work should focus on what specific host- or microbiome-associated factors are responsible for tipping communities between responder and non-responder phenotypes so that we might learn to harness this phenomenon to protect our microbiota from routine antibiotic treatment.

PMID:33750910 | DOI:10.1038/s42003-021-01841-8

Br J Cancer. 2021 Mar 10. doi: 10.1038/s41416-020-01253-1. Online ahead of print.

ABSTRACT

BACKGROUND: Oral and gut microbiomes have emerged as potential biomarkers in cancer. We characterised the oral and gut microbiomes in a prospective observational cohort of HPV+ oropharyngeal squamous cell carcinoma (OPSCC) patients and evaluated the impact of chemoradiotherapy (CRT).

METHODS: Saliva, oropharyngeal swabs over the tumour site and stool were collected at baseline and post-CRT. 16S RNA and shotgun metagenomic sequencing were used to generate taxonomic profiles, including relative abundance (RA), bacterial density, α-diversity and β-diversity.

RESULTS: A total of 132 samples from 22 patients were analysed. Baseline saliva and swabs had similar taxonomic composition (R2 = 0.006; p = 0.827). Oropharyngeal swabs and stool taxonomic composition varied significantly by stage, with increased oral RA of Fusobacterium nucleatum observed in stage III disease (p < 0.05). CRT significantly reduced the species richness and increased the RA of gut-associated taxa in oropharyngeal swabs (p < 0.05), while it had no effect in stool samples. These findings remained significant when adjusted by stage, smoking status and antibiotic use.

CONCLUSIONS: Baseline oral and gut microbiomes differ by stage in this HPV+ cohort. CRT caused a shift towards a gut-like microbiome composition in oropharyngeal swabs. Stage-specific features and the transitions in oral microbiome might have prognostic and therapeutic implications.

PMID:33750907 | DOI:10.1038/s41416-020-01253-1

Hortic Res. 2021 Mar 10;8(1):62. doi: 10.1038/s41438-021-00494-2.

ABSTRACT

The nonrandom three-dimensional organization of chromatin plays an important role in the regulation of gene expression. However, it remains unclear whether this organization is conserved and whether it is involved in regulating gene expression during speciation after whole-genome duplication (WGD) in plants. In this study, high-resolution interaction maps were generated using high-throughput chromatin conformation capture (Hi-C) techniques for two poplar species, Populus euphratica and Populus alba var. pyramidalis, which diverged ~14 Mya after a common WGD. We examined the similarities and differences in the hierarchical chromatin organization between the two species, including A/B compartment regions and topologically associating domains (TADs), as well as in their DNA methylation and gene expression patterns. We found that chromatin status was strongly associated with epigenetic modifications and gene transcriptional activity, yet the conservation of hierarchical chromatin organization across the two species was low. The divergence of gene expression between WGD-derived paralogs was associated with the strength of chromatin interactions, and colocalized paralogs exhibited strong similarities in epigenetic modifications and expression levels. Thus, the spatial localization of duplicated genes is highly correlated with biased expression during the diploidization process. This study provides new insights into the evolution of chromatin organization and transcriptional regulation during the speciation process of poplars after WGD.

PMID:33750794 | DOI:10.1038/s41438-021-00494-2

Nat Commun. 2021 Mar 9;12(1):1546. doi: 10.1038/s41467-021-21143-1.

ABSTRACT

Many bacterial pathogens rely on virulent type III secretion systems (T3SSs) or injectisomes to translocate effector proteins in order to establish infection. The central component of the injectisome is the needle complex which assembles a continuous conduit crossing the bacterial envelope and the host cell membrane to mediate effector protein translocation. However, the molecular principles underlying type III secretion remain elusive. Here, we report a structure of an active Salmonella enterica serovar Typhimurium needle complex engaged with the effector protein SptP in two functional states, revealing the complete 800Å-long secretion conduit and unraveling the critical role of the export apparatus (EA) subcomplex in type III secretion. Unfolded substrates enter the EA through a hydrophilic constriction formed by SpaQ proteins, which enables side chain-independent substrate transport. Above, a methionine gasket formed by SpaP proteins functions as a gate that dilates to accommodate substrates while preventing leaky pore formation. Following gate penetration, a moveable SpaR loop first folds up to then support substrate transport. Together, these findings establish the molecular basis for substrate translocation through T3SSs and improve our understanding of bacterial pathogenicity and motility.

PMID:33750771 | DOI:10.1038/s41467-021-21143-1

J Genet Genomics. 2020 Nov 7:S1673-8527(20)30168-5. doi: 10.1016/j.jgg.2020.04.008. Online ahead of print.

ABSTRACT

There is an increasing interest in understanding how three-dimensional (3D) organization of the genome is regulated. Different strategies have been employed to identify genome-wide chromatin interactions. However, due to current limitations in resolving genomic contacts, visualization and validation of these genomic loci with sub-kilobase resolution remain unsolved to date. Here, we describe Tn5 transposase-based Fluorescence in situ hybridization (Tn5-FISH), a PCR-based, cost-effective imaging method, which can co-localize the genomic loci with sub-kilobase resolution, dissect genome architecture, and verify chromatin interactions detected by chromatin configuration capture (3C)-derived methods. To validate this method, short-range interactions in keratin-encoding gene (KRT) locus in topologically associated domain (TAD) were imaged by triple-color Tn5-FISH, indicating that Tn5-FISH is very useful to verify short-range chromatin interactions inside the contact domain and TAD. Therefore, Tn5-FISH can be a powerful molecular tool for the clinical detection of cytogenetic changes in numerous genetic diseases such as cancers.

PMID:33750643 | DOI:10.1016/j.jgg.2020.04.008

BMC Genomics. 2021 Mar 9;22(1):167. doi: 10.1186/s12864-021-07490-9.

ABSTRACT

BACKGROUND: Suaeda glauca (S. glauca) is a halophyte widely distributed in saline and sandy beaches, with strong saline-alkali tolerance. It is also admired as a landscape plant with high development prospects and scientific research value. The S. glauca chloroplast (cp) genome has recently been reported; however, the mitochondria (mt) genome is still unexplored.

RESULTS: The mt genome of S. glauca were assembled based on the reads from Pacbio and Illumina sequencing platforms. The circular mt genome of S. glauca has a length of 474,330 bp. The base composition of the S. glauca mt genome showed A (28.00%), T (27.93%), C (21.62%), and G (22.45%). S. glauca mt genome contains 61 genes, including 27 protein-coding genes, 29 tRNA genes, and 5 rRNA genes. The sequence repeats, RNA editing, and gene migration from cp to mt were observed in S. glauca mt genome. Phylogenetic analysis based on the mt genomes of S. glauca and other 28 taxa reflects an exact evolutionary and taxonomic status of S. glauca. Furthermore, the investigation on mt genome characteristics, including genome size, GC contents, genome organization, and gene repeats of S. gulaca genome, was investigated compared to other land plants, indicating the variation of the mt genome in plants. However, the subsequently Ka/Ks analysis revealed that most of the protein-coding genes in mt genome had undergone negative selections, reflecting the importance of those genes in the mt genomes.

CONCLUSIONS: In this study, we reported the mt genome assembly and annotation of a halophytic model plant S. glauca. The subsequent analysis provided us a comprehensive understanding of the S. glauca mt genome, which might facilitate the research on the salt-tolerant plant species.

PMID:33750312 | DOI:10.1186/s12864-021-07490-9

BMC Genomics. 2021 Mar 9;22(1):168. doi: 10.1186/s12864-021-07491-8.

ABSTRACT

BACKGROUND: Colourless microalgae of the Prototheca genus are the only known plants that have consistently been implicated in a range of clinically relevant opportunistic infections in both animals and humans. The Prototheca algae are emerging pathogens, whose incidence has increased importantly over the past two decades. Prototheca wickerhamii is a major human pathogen, responsible for at least 115 cases worldwide. Although the algae are receiving more attention nowadays, there is still a substantial knowledge gap regarding their biology, and pathogenicity in particular. Here we report, for the first time, the complete nuclear genome, organelle genomes, and transcriptome of the P. wickerhamii type strain ATCC 16529.

RESULTS: The assembled genome size was of 16.7 Mbp, making it the smallest and most compact genome sequenced so far among the protothecans. Key features of the genome included a high overall GC content (64.5%), a high number (6081) and proportion (45.9%) of protein-coding genes, and a low repetitive sequence content (2.2%). The vast majority (90.6%) of the predicted genes were confirmed with the corresponding transcripts upon RNA-sequencing analysis. Most (93.2%) of the genes had their putative function assigned when searched against the InterProScan database. A fourth (23.3%) of the genes were annotated with an enzymatic activity possibly associated with the adaptation to the human host environment. The P. wickerhamii genome encoded a wide array of possible virulence factors, including those already identified in two model opportunistic fungal pathogens, i.e. Candida albicans and Trichophyton rubrum, and thought to be involved in invasion of the host or elicitation of the adaptive stress response. Approximately 6% of the P. wickerhamii genes matched a Pathogen-Host Interaction Database entry and had a previously experimentally proven role in the disease development. Furthermore, genes coding for proteins (e.g. ATPase, malate dehydrogenase) hitherto considered as potential virulence factors of Prototheca spp. were demonstrated in the P. wickerhamii genome.

CONCLUSIONS: Overall, this study is the first to describe the genetic make-up of P. wickerhamii and discovers proteins possibly involved in the development of protothecosis.

PMID:33750287 | DOI:10.1186/s12864-021-07491-8

Plant Biotechnol J. 2021 Mar 22. doi: 10.1111/pbi.13583. Online ahead of print.

ABSTRACT

The generation of new ideas and scientific hypotheses is often the result of extensive literature and database searches, but, with the growing wealth of public and private knowledge, the process of searching diverse and interconnected data to generate new insights into genes, gene networks, traits and diseases is becoming both more complex and more time-consuming. To guide this technically challenging data integration task and to make gene discovery and hypotheses generation easier for researchers, we have developed a comprehensive software package called KnetMiner which is open-source and containerised for easy use. KnetMiner is an integrated, intelligent, interactive gene and gene network discovery platform that supports scientists discover and understand the biological stories of complex traits and diseases across species. It features fast algorithms for generating rich interactive gene networks and prioritizing candidate genes based on knowledge mining approaches. KnetMiner is used in many plant science institutions and has been adopted by several plant breeding organisations to accelerate gene discovery. The software is generic and customizable and can therefore be readily applied to new species and data types, for example it has been applied to pest insects and fungal pathogens; and most recently repurposed to support COVID-19 research. Here we give an overview of the main approaches to using KnetMiner and we report plant-centric case studies for identifying genes, gene networks and trait relationships in Triticum aestivum (bread wheat), as well as, an evidence-based approach to rank candidate genes under a large Arabidopsis thaliana QTL. KnetMiner is available at: https://knetminer.org.

PMID:33750020 | DOI:10.1111/pbi.13583

Indoor Air. 2021 Mar 22. doi: 10.1111/ina.12821. Online ahead of print.

ABSTRACT

Screening the volatiles isolated from a standard polypropylene material consisting of a polypropylene homopolymer, the filler talcum, and a mixture of antioxidants, for odor-active compounds by application of an aroma extract dilution analysis revealed 30 odorants with flavor dilution factors ranging from 1 to 64. Eighteen odor-active compounds were subsequently quantitated by gas chromatography-mass spectrometry using stable isotopically substituted odorants as internal standards, and their odor activity values (OAVs) were calculated as ratios of the concentrations to the odor threshold values. Five odorants showed OAVs ≥1, among which were hex-1-en-3-one (OAV 12), butanoic acid (OAV 3), as well as 4-methylphenol, butan-1-ol, and 2-tert-butylphenol (all OAV 1). A comparative analysis of polypropylene materials with different additives suggested plastic-like, pungent smelling hex-1-en-3-one as an ubiquitous key odorant. Odor-active amounts of alkylphenols, in particular plastic-like, phenolic smelling 2-tert-butylphenol, were additionally formed in the presence of talcum and phenolic antioxidants. Whereas the precursors of the phenols were thus obvious, the origin of hex-1-en-3-one was unknown. Injection molding showed only little influence on odorant concentrations.

PMID:33749958 | DOI:10.1111/ina.12821