Microbiome Research and Multi-Omics Integration for Personalized Medicine in Asthma

Asthma is a multifactorial inflammatory disorder of the respiratory system characterized by high diversity in clinical manifestations, underlying pathological mechanisms and response to treatment. It is generally established that human microbiota plays an essential role in shaping a healthy immune response, while its perturbation can cause chronic inflammation related to a wide range of diseases, including asthma. Systems biology approaches encompassing microbiome analysis can offer valuable platforms towards a global understanding of asthma complexity and improving patients’ classification, status monitoring and therapeutic choices. In the present review, we summarize recent studies exploring the contribution of microbiota dysbiosis to asthma pathogenesis and heterogeneity in the context of asthma phenotypes–endotypes and administered medication. We subsequently focus on emerging efforts to gain deeper insights into microbiota–host interactions driving asthma complexity by integrating microbiome and host multi-omics data. One of the most prominent achievements of these research efforts is the association of refractory neutrophilic asthma with certain microbial signatures, including predominant pathogenic bacterial taxa (such as Proteobacteria phyla, Gammaproteobacteria class, especially species from Haemophilus and Moraxella genera). Overall, despite existing challenges, large-scale multi-omics endeavors may provide promising biomarkers and therapeutic targets for future development of novel microbe-based personalized strategies for diagnosis, prevention and/or treatment of uncontrollable asthma.

The functional evolution of termite gut microbiota

SUMMARYTermites primarily feed on lignocellulose or soil in association with specific gut microbes. The functioning of the termite gut microbiota is partly understood in a handful of wood-feeding pest species, but remains largely unknown in other taxa. We intend to feel this gap and provide a global understanding of the functional evolution of termite gut microbiota. We sequenced the gut metagenomes of 145 samples representative of the termite diversity. We show that the prokaryotic fraction of the gut microbiota of all termites possesses similar genes for carbohydrate and nitrogen metabolisms, in proportions varying with termite phylogenetic position and diet. The presence of a conserved set of gut prokaryotic genes implies that key nutritional functions were present in the ancestor of modern termites. Furthermore, the abundance of these genes largely correlated with the host phylogeny. Finally, we found that the adaptation to a diet of soil by some termite lineages was accompanied by a change in the stoichiometry of genes involved in important nutritional functions rather than by the acquisition of new genes and pathways. Our results reveal that the composition and function of termite gut prokaryotic communities have been remarkably conserved since termites first appeared ∼150 million years ago. Therefore, the “world smallest bioreactor” has been operating as a multipartite symbiosis composed of termites, archaea, bacteria, and cellulolytic flagellates since its inception.

Latvian Students’ Understanding of Global Problems and Readiness to Get Involved in Solving Them in OECD PISA 2018 Comparison

Students’ life in the modern globalized world gives them many new possibilities and at the same time also creates new serious challenges putting forward also new requirements. Students’ understanding of the global problems (climate changes and global warming, global health (including pandemics), migration, international conflicts, famine or insufficient food, the causes of poverty, etc.) become more and more important. The aim of the study is to analyze the results of Latvia’s fifteen years old students in the OECD PISA 2018 in the aspect of the global competence paying a more detailed attention to the students’ understanding of the global problems and their readiness to take action for collective well-being. The research questions are follows: 1) What is Latvian students’ global competence in the international comparison and what is its relation to the characteristics of students, their families and school; 2) What is Latvian students’ understanding of the global problems and readiness to get involved in their solution? The descriptive statistical analysis employs the data from surveys/questionnaires (66 countries) and tests (27 countries) included in PISA 2018 international data basis. Latvian students’ performance in the cognitive test of the global competence is considerably higher than the average of the participating countries, and as regards the OECD countries we are on the average level. In Latvia, students of capital Riga schools have the highest level of global understanding, it is lower in other cities and even lower in rural schools. Latvian students have a slightly lower readiness to get involved in solving the global phenomena and participation in concrete activities than the average in OECD countries.

Transcriptome Analysis Reveals the Senescence Process Controlling the Flower Opening and Closure Rhythm in the Waterlilies (Nymphaea L.)

Most waterlily flowers open at dawn and close after noon usually for three to four days, and thereafter wilt. The short lifespan of flowers restricts the development of the flower postharvest industry. The termination of flower movements is a key event during flower aging process. However, it is still unclear when the senescence process initiates and how it terminates the movement rhythm. In this study, we observed that the opening diameter of flowers was the smallest on the fourth (last) flowering day. Subsequent transcriptome profiles generated from petals at different flowering stages showed that the multiple signaling pathways were activated at the last closure stage (Time 3, T3) of the flowers, including Ca2+, reactive oxygen species and far red light signaling pathways, as well as auxin, ethylene and jasmonic acid signaling pathways. Moreover, In terms of cell metabolism regulation, the genes related to hydrolase (protease, phospholipase, nuclease) were upregulated at T3 stage, indicating that petals entered the senescence stage at that time; and the genes related to water transport and cell wall modification were also differentially regulated at T3 stage, which would affect the ability of cell expand and contract, and eventually lead to petal not open after the fourth day. Collectively, our data provided a new insight into the termination of flower opening in the waterlilies, and a global understanding of the senescence process of those opening-closure rhythm flowers.

Heterologous Complementation of SPO11-1 and -2 Depends on the Splicing Pattern

In the past, major findings in meiosis have been achieved, but questions towards the global understanding of meiosis remain concealed. In plants, one of these questions covers the need for two diverse meiotic active SPO11 proteins. In Arabidopsis and other plants, both meiotic SPO11 are indispensable in a functional form for double strand break induction during meiotic prophase I. This stands in contrast to mammals and fungi, where a single SPO11 is present and sufficient. We aimed to investigate the specific function and evolution of both meiotic SPO11 paralogs in land plants. By performing immunostaining of both SPO11-1 and -2, an investigation of the spatiotemporal localization of each SPO11 during meiosis was achieved. We further exchanged SPO11-1 and -2 in Arabidopsis and could show a species-specific function of the respective SPO11. By additional changes of regions between SPO11-1 and -2, a sequence-specific function for both the SPO11 proteins was revealed. Furthermore, the previous findings about the aberrant splicing of each SPO11 were refined by narrowing them down to a specific developmental phase. These findings let us suggest that the function of both SPO11 paralogs is highly sequence specific and that the orthologs are species specific.

BOTANICAL MYTHS: FAKE NEWS OF THE CONTEMPORARY WORLD

The myths take many forms depending on the cultures in which we find them; however, their function is always to explain natural phenomena that occur in their surroundings. As observed throughout human history, it is an inherent condition for the human species to believe in the metaphysical and to use their individual and introspective thinking as a way to achieve their dreams and goals, something that works as a responsible 'driving force' in many cases, for governing and inspiring the human individual. Additionally, populations or part of communities that obtain their livelihood and/or subsistence directly from agricultural activity spontaneously express a greater willingness to believe in the 'infallible' agroforestry myths, which explain the possible botanical phenomena. In light of this, our present study lists the main physiological bases refuting different botanical myths based on evidence proven in original articles. Furthermore, our phenomenological approach was carried out in an eclectic way in the field of botany and is not linked to any specific authority or philosophical school. Finally, we explore and integrate different, mutually compatible approaches to provide the reader with a global understanding of the 'infallibility' of botanical myths.

Japanese Bronze Bells in Switzerland

Western museums hold numerous Japanese objects, typically gathered by collectors during travels in Japan and then donated to local institutions. This simple scenario is by no means always the case, as can be seen with the numerous Japanese bronze bells in Swiss museum collections. The story of how the bells changed from holding significant functions within Japanese monastic and secular communities to being sold for their materiality and sheer weight as they travel across the globe tells a complex story of how objects change in meaning as they travel. As the bells were eventually relegated to museum archives, their stories help to shed light on global transfers, interculturality, and cultural misunderstandings, as they narrowly escape destruction. Their stories show the futility of claiming global understanding of art when, despite globalization, we are in the end products of our own localized traditions and understandings.

Comparative transcriptome analysis reveals regulatory network and regulators associated with proanthocyanidin accumulation in persimmon

Background Proanthocyanidins (PAs) are important plant secondary metabolites that confer flavor, nutritional value, and resistance to pathogens. Persimmon is one of the PA richest crops. Mature fruits can be inedible because of the astringency caused by high PA levels and need to go through a de-astringency treatment before consumption. The molecular basis for PA accumulation is poorly known, particularly transcriptional regulators. We characterised three genotypes (‘Luotiantianshi’ (LT), ‘Mopanshi’ (MP), and ‘Youhou’ (YH)) with different PA accumulation patterns using an approach that combined PacBio full-length sequencing and Illumina-based RNA sequencing to build high-quality full-length transcriptomes. Additionally, we analysed transcriptome dynamics of the three genotypes (LT, MP, and YH) at four key fruit developmental stages. Results A total of 96,463 transcripts were obtained. We identified 80,075 protein-coding sequences (CDSs), 71,137 simple sequence repeats (SSRs), and 27,845 long noncoding RNAs (lncRNAs). Pearson correlation coefficient (PCC), principal component analysis (PCA), and differentially expressed transcripts (DETs) analyses indicated that the four different developmental stages within a genotype exhibited similar transcriptome activities. A total of 2,164 transcripts specific to each fruit developmental stage were detected. The transcripts specific to early stages were attributed to phenylpropanoid and flavonoid biosynthesis. Co-expression network analyses revealed MEbrown and MEblue modules were strongly associated to PA accumulation. From these two modules, 20 hub TFs are potential regulators for PA accumulation. Among them, Cluster_78388 (SBP protein), Cluster_63454 (bZIP protein), and Cluster_66595 (MYB protein) appear to involve in the PA biosynthesis in Chinese genotypes. Conclusions This is the first high-quality reference transcriptome for commercial persimmon. Our work provides insights into the molecular pathways underlying PA accumulation and enhances our global understanding of transcriptome dynamics throughout fruit development.