Systematics Research Articles

Identification of Target PTEN-Based miR-425 and miR-576 as Potential Diagnostic and Immunotherapeutic Biomarkers of Colorectal Cancer With Liver Metastasis.

A major complication of colorectal cancer (CRC), one of the most common and fatal types of cancers, is secondary liver metastasis. For patients with this fate, there are very few biomarkers available in clinical application, and the disease remains incurable. Recently, increasing studies demonstrated that tumorigenesis and development are closely related to immune escape, indicating that the roles of immune-related indicators might have been neglected in the past in colorectal cancer liver metastases (CRLM). Here, we unveil that elevated miR-425 and miR-576 promote CRLM through inhibiting PTEN-mediated cellular immune function. Specifically, miR-425 and miR-576 were identified for their significant upregulation in CRLM compared with the primary CRC tissues based on GSE81581 (n = 8) and GSE44121 (n = 18) datasets. Besides, we determined that the two microRNAs (miRNAs) coparticipated in restraining P53 and transforming growth factor beta (TGF-β) signaling pathways associated with tumor metastasis, and both shortened the overall survival of the patients with metastatic susceptibility. Notably, in situ hybridization on relatively large samples of paired CRC tissues (n = 157) not only substantiated that the expression of miR-425 and miR-576 was dramatically upregulated in CRLM but also revealed that they were closely related to tumor deterioration, especially liver metastases. Moreover, we further confirmed that the combination of miR-425 and miR-576 was an effective predictive model for liver metastases and poor clinical outcomes. Mechanically, downregulated PTEN (GSE81558, n = 6) was verified to be a shared target of miR-425 and miR-576 acting as metastasis-related oncogenes, on account of the presence of binding sites (+2928–+2934 and +4371–+4378, respectively) and the collaborative suppression of P53/TGF-β signaling in CRLM, which was further confirmed in CRC cells (HCT116 and SW480) based on systematic molecular biology experiments. Importantly, the target PTEN was strongly associated with microsatellite instability, tumor microenvironment, and immune cell infiltration. Thus, we speculate that miR-425 and miR-576 are novel biomarkers for CRLM prevention and immunotherapy and upstream inhibitors of the PTEN-P53/TGF-β function axis.

Using weighted gene co-expression network analysis (WGCNA) to identify the hub genes related to hypoxic adaptation in yak (Bos grunniens).

As a mammal living at the highest altitude in the world, the yak has strong adaptability to the harsh natural environment (such as low temperature, scarce food, especially low oxygen) of Qinghai-Tibet Plateau (QTP) after a long process of natural selection. Here, we used Weighted Correlation Network Analysis (WGCNA), a systematic biology method, to identify hypoxic adaptation-related modules and hub genes. The research of the adaptability of yak against hypoxia is of great significance to identify the genetic characteristics and yak breeding. Based on the transcriptome sequencing data (PRJNA362606), the R package DESeq2 and WGCNA were conducted to analyze differentially expressed genes (DEGs) and construct the gene co-expression network. The module hub genes were identified and characterized by the correlation of gene and trait, module membership (kME). In addition, GO and KEGG enrichment analyses were used to explore the functions of hub genes. Our results revealed that 1098, 1429, and 1645 DEGs were identified in muscle, spleen, and lung, respectively. Besides, a total of 13 gene co-expression modules were detected, of which two hypoxic adaptation-related modules (saddlebrown and turquoise) were found. We identified 39 and 150 hub genes in these two modules. Functional enrichment analyses showed that 12 GO terms and 18 KEGG pathways were enriched in the saddlebrown module while 85 GO terms and 22 KEGG pathways were enriched in the turquoise module. The significant pathways related to hypoxia adaptation include FoxO signaling pathway, Thermogenesis pathway, and Retrograde endocannabinoid signaling pathway, etc. CONCLUSIONS: In this study, we obtained two hypoxia-related specific modules and identified hub genes based on the connectivity by constructing a weighted gene co-expression network. Function enrichment analysis of two modules revealed mitochondrion is the most important organelle for hypoxia adaptation. Moreover, the insulin-related pathways and thermogenic-related pathways played a major role. The results of this study provide theoretical guidance for further understanding the molecular mechanism of yak adaptation to hypoxia.

Engineering Escherichia coli for production of geraniol by systematic synthetic biology approaches and laboratory-evolved fusion tags

Geraniol is a valuable monoterpene extensively used in the fragrance, food, and cosmetic industries. Increasing environmental concerns and supply gaps have motivated efforts to advance the microbial production of geraniol from renewable feedstocks. In this study, we first constructed a platform geraniol Escherichia coli strain by bioprospecting the key enzymes geranyl diphosphate synthase (GPPS) and geraniol synthase (GES) and selection of a host cell background. This strategy led to a 46.4-fold increase in geraniol titer to 964.3 mg/L. We propose that the expression level of eukaryotic GES can be further optimized through fusion tag evolution engineering. To this end, we manipulated GES to maximize flux towards the targeted product geraniol from precursor geranyl diphosphate (GPP) via the utilization of fusion tags. Additionally, we developed a high-throughput screening system to monitor fusion tag variants. This common plug-and-play toolbox proved to be a robust approach for systematic modulation of protein expression and can be used to tune biosynthetic metabolic pathways. Finally, by combining a modified E1* fusion tag, we achieved 2124.1 mg/L of geraniol in shake flask cultures, which reached 27.2% of the maximum theoretical yield and was the highest titer ever reported. We propose that this strategy has set a good reference for enhancing a broader range of terpenoid production in microbial cell factories, which might open new possibilities for the bio-production of other valuable chemicals.

Risk Compounds, Preclinical Toxicity Evaluation, and Potential Mechanisms of Chinese Materia Medica-Induced Cardiotoxicity.

Chinese materia medica (CMM) has been applied for the prevention and treatment of diseases for thousands of years. However, arrhythmia, myocardial ischemia, heart failure, and other cardiac adverse reactions during CMM application were gradually reported. CMM-induced cardiotoxicity has aroused widespread attention. Our review aimed to summarize the risk compounds, preclinical toxicity evaluation, and potential mechanisms of CMM-induced cardiotoxicity. All relevant articles published on the PubMed, Embase, and China National Knowledge Infrastructure (CNKI) databases for the latest twenty years were searched and manually extracted. The risk substances of CMM-induced cardiotoxicity are relatively complex. A single CMM usually contains various risk compounds, and the same risk substance may exist in various CMM. The active and risk substances in CMM may be transformed into each other under different conditions, such as drug dosage, medication methods, and body status. Generally, the risk compounds of CMM-induced cardiotoxicity can be classified into alkaloids, terpenoids, steroids, heavy metals, organic acids, toxic proteins, and peptides. Traditional evaluation methods of chemical drug-induced cardiotoxicity primarily include cardiac function monitoring, endomyocardial biopsy, myocardial zymogram, and biomarker determination. In the preclinical stage, CMM-induced cardiotoxicity should be systematically evaluated at the overall, tissue, cellular, and molecular levels, including cardiac function, histopathology, cytology, myocardial zymogram, and biomarkers. Thanks to the development of systematic biology, the higher specificity and sensitivity of biomarkers, such as genes, proteins, and metabolic small molecules, are gradually applied for evaluating CMM-induced cardiotoxicity. Previous studies on the mechanisms of CMM-induced cardiotoxicity focused on a single drug, monomer or components of CMM. The interaction among ion homeostasis (sodium, potassium, and calcium ions), oxidative damage, mitochondrial injury, apoptosis and autophagy, and metabolic disturbance is involved in CMM-induced cardiotoxicity. Clarification on the risk compounds, preclinical toxicity evaluation, and potential mechanisms of CMM-induced cardiotoxicity must be beneficial to guide new CMM development and post-marketed CMM reevaluation.

The Health Status of Rohingya Refugees, a Systematics Review

The Health Status of Rohingya Refugees, a Systematics Review

Mumetopia interfeles sp. nov., a new species of Anthomyzidae (Diptera) occurring en masse in an urban grassy habitat in Chile: its taxonomy, phylogeny and biology

A new species of Anthomyzidae (Diptera), viz., Mumetopia interfeles Roháček sp. nov. (both sexes), is described from Chile, based on a large series collected from a small grassy area (consisting of a non-native species, Hordeum murinum L.) among houses in the city of Valparaíso. Its systematic affiliation, phylogenetic relationships, and biology are discussed. Cases of mass occurrence of adult Anthomyzidae, particularly those in anthropogenic habitats, are reviewed and general features of them discussed. A phylogenetic hypothesis is proposed for the relationships of the new species and the Chamaebosca group of genera within Anthomyzidae (64 species in dataset), based on Bayesian inference and maximum likelihood analyses of seven DNA markers (12S, 16S, 28S, COI, COII, CytB, ITS2). Taxonomic limits of the genus Mumetopia Melander, 1913 are discussed. Based on a new molecular hypothesis and a previous cladistic analysis of morphological data (Roháček & Barber 2009), a broadened, better-supported concept of Mumetopia (s. str.) is proposed to include M. interfeles sp. nov. (and its unnamed relatives) and externally aberrant, undescribed species endemic to the Juan Fernández Islands. Apart from Anthomyzidae (M. interfeles sp. nov. only), the community of Diptera associated with H. murinum was dominated by phytophagous Chloropidae: Ceratobarys sacculicornis (Enderlein, 1911) occurred in extremely high numbers similar to those of M. interfeles sp. nov., while the less abundant Opetiophora sp. represents the first record of the genus from South America.

Who are we now? A demographic assessment of three evolution societies.

Scientific societies have the potential to catalyze support for communities that have been historically excluded from science. Many of these societies have formed committees to propose and administer initiatives to promote the career and well-being of their members, with a special emphasis on racial and ethnic minorities. Yet, these societies are rarely armed with data to inform their proposals. Three of the evolution societies (American Society of Naturalists, "ASN"; Society of Systematic Biologists, "SSB"; Society for the Study of Evolution, "SSE") have also formed Diversity, Equity, and Inclusion committees in the last few years. As a first step in determining the needs of the societies, these committees collected data on the demographic characteristics of the societies' constituents by surveying the attendants of the Evolution 2019 meeting. Here, we report the proportions for different demographic groups in attendance at the meeting and compare these proportions to the demographics of recipients of Ph.D. degrees either in evolutionary biology or in the broader life sciences, as well as population demographics of the USA. Our results indicate that historically excluded groups are still underrepresented across US-based evolutionary biology professional societies. We explore whether demographic composition differs at different professional stages and find that representation for women and LGBTQ+ members decreases as the career stage progresses. We also find some evidence for heterogeneity across societies in terms of racial composition. Finally, we discuss the caveats and limitations of our procedures. Our results will serve to inform future efforts to collect demographic data at the society levels, which should in turn be used to design and implement evidence-based initiatives for inclusion and equity. This report should be a starting point for systematic efforts to characterize the ever-changing representation in evolutionary biology and to work toward the inclusion of all groups.

Secretary's Report, 2020 : American Society of Naturalists.

Secretary's Report, 2020 : American Society of Naturalists.

Body size data collected non-invasively from drone images indicate a morphologically distinct Chilean blue whale (Balaenoptera musculus) taxon

The blue whaleBalaenoptera musculus(Linnaeus, 1758) was the target of intense commercial whaling in the 20thcentury, and current populations remain drastically below pre-whaling abundances. Reducing uncertainty in subspecific taxonomy would enable targeted conservation strategies for the recovery of unique intraspecific diversity. Currently, there are 2 named blue whale subspecies in the temperate to polar Southern Hemisphere: the Antarctic blue whaleB. m. intermediaand the pygmy blue whaleB. m. brevicauda. These subspecies have distinct morphologies, genetics, and acoustics. In 2019, the Society for Marine Mammalogy’s Committee on Taxonomy agreed that evidence supports a third (and presently unnamed) subspecies of Southern Hemisphere blue whale subspecies, the Chilean blue whale. Whaling data indicate that the Chilean blue whale is intermediate in body length between pygmy and Antarctic blue whales. We collected body size data from blue whales in the Gulfo Corcovado, Chile, during the austral summers of 2015 and 2017 using aerial photogrammetry from a remotely controlled drone to test the hypothesis that the Chilean blue whale is morphologically distinct from other Southern Hemisphere blue whale subspecies. We found the Chilean whale to be morphologically intermediate in both overall body length and relative tail length, thereby joining other diverse data in supporting the Chilean blue whale as a unique subspecific taxon. Additional photogrammetry studies of Antarctic, pygmy, and Chilean blue whales will help examine unique morphological variation within this species of conservation concern. To our knowledge, this is the first non-invasive small drone study to test a hypothesis for systematic biology.

Collections‐based systematics and biogeography in the 21st century: A tribute to Dr. Vicki Funk

Collections‐based systematics and biogeography in the 21st century: A tribute to Dr. Vicki Funk

Synthetic Biology Driven Biosynthesis of Unnatural Tropolone Sesquiterpenoids.

Tropolone sesquiterpenoids (TS) are an intriguing family of biologically active fungal meroterpenoids that arise through a unique intermolecular hetero Diels–Alder (hDA) reaction between humulene and tropolones. Here, we report on the combinatorial biosynthesis of a series of unprecedented analogs of the TS pycnidione 1 and xenovulene A 2. In a systematic synthetic biology driven approach, we recombined genes from three TS biosynthetic gene clusters (pycnidione 1, xenovulene A 2 and eupenifeldin 3) in the fungal host Aspergillus oryzae NSAR1. Rational design of the reconstituted pathways granted control over the number of hDA reactions taking place, the chemical nature of the fused polyketide moiety (tropolono‐ vs. monobenzo‐pyranyl) and the degree of hydroxylation. Formation of unexpected monobenzopyranyl sesquiterpenoids was investigated using isotope‐feeding studies to reveal a new and highly unusual oxidative ring contraction rearrangement.

The Sensing Liver: Localization and Ligands for Hepatic Murine Olfactory and Taste Receptors.

Sensory receptors, including olfactory receptors (ORs), taste receptors (TRs), and opsins (Opns) have recently been found in a variety of non-sensory tissues where they have distinct physiological functions. As G protein-coupled receptors (GPCRs), these proteins can serve as important chemosensors by sensing and interpreting chemical cues in the environment. We reasoned that the liver, the largest metabolic organ in the body, is primed to take advantage of some of these sensory receptors in order to sense and regulate blood content and metabolism. In this study, we report the expression of novel hepatic sensory receptors – including 7 ORs, 6 bitter TRs, and 1 Opn – identified through a systematic molecular biology screening approach. We further determined that several of these receptors are expressed within hepatocytes, the parenchymal cells of the liver. Finally, we uncovered several agonists of the previously orphaned hepatic ORs. These compounds fall under two classes: methylpyrazines and monoterpenes. In particular, the latter chemicals are plant and fungal-derived compounds with known hepatic protective effects. Collectively, this study sheds light on the chemosensory functions of the liver and unveils potentially important regulators of hepatic homeostasis.

Quantifying shortfalls in the knowledge on Neotropical Auchenipteridae fishes

AbstractThe Neotropics harbour the greatest diversity of freshwater fish on Earth. Despite recent advances in characterizing the fish fauna, the total number of species, distributional range, evolution and ecological traits remain uncertain. Thus, we quantify shortfalls in the knowledge of taxonomy (Linnean shortfall), geographic distribution (Wallacean shortfall), evolutionary relationships (Darwinian shortfall) and feeding habits (Raunkiæran shortfall) of Auchenipteridae driftwood catfishes, one of the most representative groups of the Siluriformes family in the Neotropics. We find a steep increase in the historical accumulation of valid species over time, suggesting that 45% of the total number predicted remains to be described. Auchenipterids also remain under‐collected; only 45% of the ecoregions and less than 3% of the one‐degree grid cells covering the Neotropics are reasonably sampled. The topologies of recent phylogenies are more similar to each other than former ones, showing a tendency towards a robust phylogenetic hypothesis for this family. Current knowledge on feeding habits is biased towards a few genera and species and is still expanding with every new published study. Our study highlights specific knowledge gaps that need to be addressed: a considerable number of Auchenipteridae species remain to be described; and most of valid species lack reliable information on their geographic distribution and feeding habitat. It implies that research on fish systematic biology needs to advance and it will require a concerted effort of taxonomists, ecologists and biogeographers to reduce these gaps.

A disciplina de Libras nos cursos de Letras do Instituto Federal de Educação, Ciência e Tecnologia do Ceará: uma análise comparativa de ementas

Este trabalho tem como objetivo analisar as ementas das disciplinas de Libras e Introdução ao Estudo de Libras dos cursos de Licenciatura em Letras do Instituto Federal de Educação, Ciência e Tecnologia do Ceará (IFCE), que funcionam nos câmpus Baturité, Camocim, Crateús, Tauá, Tianguá e Umirim. Trata-se de um estudo documental exploratório de abordagem qualitativa. A coleta de dados se deu no site oficial da instituição, onde estão disponibilizados os Projetos Pedagógicos de Curso (PPC). Adotou-se a análise comparativa em núcleos temáticos de acordo com Bonitatibus (1989) e Minayo et. al. (2015). Observou-se nas ementas a presença majoritária dos Fundamentos Linguísticos e Comunicação em Libras em detrimento dos Fundamentos da Educação de Surdos e da Educação de Surdos na Perspectiva Inclusiva. O estudo sugere novas pesquisas sistemáticas que analisem as ementas das disciplinas em questão nas mais diversas Licenciaturas da instituição, para confirmar ou refutar as hipóteses aqui levantadas e compreender o currículo do IFCE em sua totalidade.

Review of the Neotropical Peiratine genus Thymbreus Stål (Hemiptera: Reduviidae)

Summary The peiratine genus Thymbreus Stål, 1859 is reviewed and a revised diagnosis is given. Three species are recognized, redescribed and illustrated. A key is provided to help separate species of Thymbreus. The publication dates of Thymbreus and its type species, Thymbreus pyrrhopterus Stål, 1859, Opinus pyrrhopterus Stål, 1860 as well as T. ocellatus (Signoret, 1862) are clarified. Lectotypes of T. crocinopterus Stål, 1862, Pirates semirufus Walker, 1873, T. pyrrhopterus Stål, 1859 and O. pyrrhopterus Stål, 1860 are designated. Systematic position, distribution, and biology of this genus are briefly discussed.

In memory of Professor Tang Yan‐Cheng: New perspectives in systematic and evolutionary biology

In memory of Professor Tang Yan‐Cheng: New perspectives in systematic and evolutionary biology

A conjoint analysis of epilepsy and migraine through network-and-pathway-based method.

Epilepsy and migraine are both considered as paroxysmal neurologic disorders. Previous studies have reported some cases with comorbidity of these two diseases. As the underlying molecular mechanism remains unclear, we performed a network-and-pathway-based method with candidate gene sets of epilepsy and migraine to explore it. : Comparing the candidate genes between epilepsy and migraine, we identified 21 common genes. Functional enrichment analysis indicated that epilepsy and migraine are dysfunctional in the similar biological processes, such as glutamatergic transmissions, channel activities, and transporter activities. We also explored many shared pathways between these two diseases such as neuroactive ligand-receptor interaction. By combining systematical analysis and previous studies review, we finally identified six essential genes associated with the comorbidity of epilepsy and migraine. This is the first time to address the common ground of epilepsy and migraine by a systematic biology method. The present study provides a novel way to explain the potential mechanisms of these two diseases and a new set of therapeutic targets.

Shining a light on species delimitation in the tree genus Engelhardia Leschenault ex Blume (Juglandaceae)

Enhanced efficacy in species delimitation is critically important in biology given the pending biodiversity crisis under global warming and anthropogenic activity. In particular, delineation of traditional classifications in view of the complexity of species requires an integrative approach to effectively define species boundaries, and this is a major focus of systematic biology. Here, we explored species delimitation of Engelhardia in tropical and subtropical Asia. In total, 716 individuals in 71 populations were genotyped using five chloroplast regions, one nuclear DNA region (nrITS), and 11 nuclear simple sequence repeats (nSSR). Phylogenetic trees were constructed and relationships among species were assessed. Molecular analyses were then combined with 14 morphological characteristics of 720 specimens to further explore the species boundaries of Engelhardia. Integrating phylogenetic and morphological clusters provided well-resolved relationships to delineate seven species. The results suggested that: first, that E. fenzelii, E. roxburghiana, E. hainanensis, E. apoensis, and E. serrata are distinct species; second, E. spicata var. spicata, E. spicata var. aceriflora, E. spicata var. colebrookeana, and E. rigida should be combined under E. spicata and treated as a species complex; third, E. serrata var. cambodica should be raised to species level and named E. villosa. We illuminated that bias thresholds determining the cluster number for delimiting species boundaries were substantially reduced when morphological data were incorporated. Our results urge caution when using the concepts of subspecies and varieties in order to prevent confusion, particularly with respect to species delimitation for tropical and subtropical species. In some cases, re-ranking or combining subspecies and/or varieties may enable more accurate species delimitation.

Advances on systems metabolic engineering of Bacillus subtilis as a chassis cell

The Gram-positive model bacterium Bacillus subtilis, has been broadly applied in various fields because of its low pathogenicity and strong protein secretion ability, as well as its well-developed fermentation technology. B. subtilis is considered as an attractive host in the field of metabolic engineering, in particular for protein expression and secretion, so it has been well studied and applied in genetic engineering. In this review, we discussed why B. subtilis is a good chassis cell for metabolic engineering. We also summarized the latest research progress in systematic biology, synthetic biology and evolution-based engineering of B. subtilis, and showed systemic metabolic engineering expedite the harnessing B. subtilis for bioproduction.

Challenges facing systematic biology

AbstractSystematic biology is fundamental for providing organized information about the living world. It clarifies what organisms share our planet, and it also reveals the basic short‐term and long‐term processes that have given rise to this diversity. Human society is rapidly modernizing, largely through increased digital communications tied closely to satellite innovations. Communication is now global and instantaneous, allied with an awareness of place made possible by global positioning technology. Despite many positive recent developments, numerous tensions remain that threaten a tranquil world order and negatively impact biodiversity, such as between developed and developing countries, democratic and authoritarian governments, and among religious groups. The increasing human population is also bringing pressures to bear on global biodiversity through activities that result in air and water pollution, topsoil erosion, deforestation, ozone depletion, global warming, and taxic loss. The systematic biology community has been unable to respond effectively to these many new challenges due to fragmentation and lack of cohesion. Systematists have tended to focus more on issues relevant to their own taxonomic groups (e.g., bacteria, ferns, fungi, reptiles, mammals, etc.) and much less on global concerns. Systematists must become better organized to allow the global priority of inventorying the planet to be achieved as soon as practicable. A global organization, an International Federation for Systematic Biology, should be formed to serve as a coordinator to help articulate five‐year and longer plans. Large‐scale funding (billions of dollars) must be sought to allow implementation of shared goals. Projects must be created that more obviously connect in some fashion to major societal problems such as poverty, water resources, food production, and human health. The astronomy and nuclear physics communities provide models of successful planning and implementation, the former on understanding the extreme distant reality of our existence, and the latter on the extremely small atomic dimensions. Systematic biology focuses largely on understanding the middle range of reality that we can see and more easily directly experience. Making the case for understanding at this level should, in principle, be the easiest of all. Fundamental is that projects be simple in concept, visionary in perspective, and offering economic stimulus for participants (i.e., the creation of new jobs).