Exosomes: the key of sophisticated cell–cell communication and targeted metastasis in pancreatic cancer

Pancreatic cancer is one of the most common malignancies. Unfortunately, the lack of effective methods of treatment and diagnosis has led to poor prognosis coupled with a very high mortality rate. So far, the pathogenesis and progression mechanisms of pancreatic cancer have been poorly characterized. Exosomes are small vesicles secreted by most cells, contain lipids, proteins, and nucleic acids, and are involved in diverse functions such as intercellular communications, biological processes, and cell signaling. In pancreatic cancer, exosomes are enriched with multiple signaling molecules that mediate intercellular communication with control of immune suppression, mutual promotion between pancreas stellate cells and pancreatic cancer cells, and reprogramming of normal cells. In addition, exosomes can regulate the pancreatic cancer microenvironment and promote the growth and survival of pancreatic cancer. Exosomes can also build pre-metastatic micro-ecological niches and facilitate the targeting of pancreatic cancer. The ability of exosomes to load cargo and target allows them to be of great clinical value as a biomarker mediator for targeted drugs in pancreatic cancer.

Review: Insects—A Source of Safe and Sustainable Food?— “Jein” (Yes and No)

For almost a decade, edible insects have become promoted on a wider basis as one way to combat world hunger and malnourishment, although attempts to do so have a longer history. Contemporary researchers and consumers, particularly those without an entomophagous background, have been rising safety and sustainability concerns. The present contribution seeks a substantiated answer to the question posed above. The possible answer consists of different factors that have been taken into consideration. First, the species and its life cycle. It is mandatory to realize that what is labeled as “edible insects” stands for more than 2,140 animal species, not counting other edible, non-crustacean arthropods. Their life cycles are as diverse as the ecological niches these animals can fill and last between some days to several years and many of them may—or may not—be reproduced in the different farming systems. Second, the level of knowledge concerning the food use of a given species is important, be it traditional, newly created by research, or a combination of both. Third, the existence of a traditional method of making the use of the insect safe and sustainable, ideally from both the traditional and the modern points of view. Fourth, the degree of effectiveness of these measures despite globalization changes in the food-supplying network. Fifth, farming conditions, particularly housing, feeding (type, composition, and contaminants), animal health and animal welfare. Sixth, processing, transport, and storage conditions of both traditional and novel insect-based foodstuffs, and seventh, consumer awareness and acceptance of these products. These main variables create a complex web of possibilities, just as with other foodstuffs that are either harvested from the wild or farmed. In this way, food safety may be reached when proper hygiene protocols are observed (which usually include heating steps) and the animals do not contain chemical residues or environment contaminants. A varying degree of sustainability can be achieved if the aforementioned variables are heeded. Hence, the question if insects can be safe and sustainable can be answered with “jein,” a German portmanteau word joining “yes” (“ja”) and “no” (“nein”).

Targeted Genome Mining Reveals the Psychrophilic Clostridium estertheticum Complex as a Potential Source for Novel Bacteriocins, Including Cesin A and Estercticin A

Antimicrobial resistance in pathogenic bacteria is considered a major public health issue necessitating the discovery of alternative antimicrobial compounds. In this regard, targeted genome mining in bacteria occupying under-explored ecological niches has the potential to reveal such compounds, including bacteriocins. In this study, we determined the bacteriocin biosynthetic potential of the psychrophilic Clostridium estertheticum complex (CEC) through a combination of genome mining and phenotypic screening assays. The genome mining was performed in 40 CEC genomes using antiSMASH. The production of bacteriocin-like compounds was phenotypically validated through agar well (primary screening) and disk diffusion (secondary screening) assays using cell free supernatants (CFS) and partially purified extracts, respectively. Stability of four selected CFS against proteolytic enzymes, temperature and pH was determined while one CFS was analyzed by HRMS and MS/MS to identify potential bacteriocins. Twenty novel bacteriocin biosynthetic gene clusters (BBGC), which were classified into eight (six lantibiotics and two sactipeptides) distinct groups, were discovered in 18 genomes belonging to C. estertheticum (n = 12), C. tagluense (n = 3) and genomospecies2 (n = 3). Primary screening linked six BBGC with narrow antimicrobial activity against closely related clostridia species. All four preselected CFS retained activity after exposure to different proteolytic, temperature and pH conditions. Secondary screening linked BBGC1 and BBGC7 encoding a lantibiotic and sactipeptide, respectively, with activity against Bacillus cereus while lantibiotic-encoding BBGC2 and BBGC3 were linked with activity against B. cereus, Staphylococcus aureus (methicillin-resistant), Escherichia coli and Pseudomonas aeruginosa. MS/MS analysis revealed that C. estertheticum CF004 produces cesin A, a short natural variant of nisin, and HRMS indicated the production of a novel sactipeptide named estercticin A. Therefore, we have shown the CEC, in particular C. estertheticum, is a source of novel and stable bacteriocins that have activities against clinically relevant pathogens.

Competing for space of aphids

Diversity of ecological niches among aphid entomocenosis increased, most likely, in the process of evolution, due to unsuitability for one or two species selection in the direction of direct competition compared with the advantage of selection in the direction of differentiation niches, reliable provision of resources of different types in terms of maintaining of both species and the relative independence from the competition with other species for resources of host plants....

Late Pleistocene-dated divergence between South Hemisphere populations of the non-conventional yeast L. cidri.

Most organisms belonging to the Saccharomycotina subphylum have high genetic diversity and a vast repertoire of metabolisms and lifestyles, which explains its ecological versatility. The yeast Lachancea cidri is an ideal model for exploring the interplay between genetics, ecological function and evolution. L. cidri is a species that diverged from the Saccharomyces lineage before the whole-genome duplication and exhibits a broad distribution across the South Hemisphere, thus displaying an important ecological success. Here, we applied phylogenomics to investigate the adaptive genetic variation of L. cidri isolates obtained from natural environments in Australia and South America. Our approach revealed the presence of two main lineages according to their geographic distribution (Aus and SoAm). Estimation of the divergence time suggest that South American and Australian lineages diverged near the last glacial maximum event during the Pleistocene (64-8 KYA), consistent with the presence of multiple glacial refugia. Interestingly, we found that the French reference strain belongs to the Australian lineage, with a recent divergence (405-51 YA), likely associated to human movements. Additionally, species delimitation analysis identified different evolutionary units within the South American lineage and, together with parameters like Pi (π) and FST, revealed that Patagonia contains most of the genetic diversity of this species. These results agree with phenotypic characterizations, demonstrating a greater phenotypic diversity in the South American lineage. These findings support the idea of a Pleistocene-dated divergence between South Hemisphere lineages, where the Nothofagus and Araucaria ecological niches likely favored the extensive distribution of L. cidri in Patagonia.

Diversity of cave Phlebotomines (Diptera: Psychodidae) from a Colombian cave

Sandflies are vector species of Leishmania, among many other pathogens, with a global distribution and a variety of ecological niches. Previous samplings have found that karstic formations (i.e., caves and folds formed by the erosion of limestone) serve as a natural habitat to sandfly species. The majority of samplings of cave sandfly diversity have occurred in Brazil and to date none have studied the species composition in a cave in the Northern Andes. We collected sandflies in the Cave-Los Guacharos-, in the state of Antioquia, Colombia. The sampling was carried out during two consecutive nights in September 2019. CDC-type light traps were installed inside the cavern and in other surrounding karst systems (caves and folds). In total, we identified 18 species of sandfly from the cave and surrounding karst systems, including three new records for Colombia (Bichromomyia olmeca nociva, Brumptomyia brumpti, and Warileya leponti), and provide the first karstic reports for four other species (Lutzomyia gomezi, Lutzomyia hartmanni, Pintomyia ovallesi, and Psychodopygus panamensis). We then used the results of our survey and published literature to test two hypotheses. First, that sandfly diversity in Neotropical caves is richest nearer to the equator and second that there is a phylogenetic signal of karstic habitat use in sandflies. Counter to our predictions, we found no evidence that diversity follows a latitudinal gradient. Further, we find no evidence of a phylogenetic signal of karstic habitat use, instead finding that the use of caves likely evolved multiple times across several genera. Our results highlight the importance of a wide sampling to understand the natural habitat of sandflies and other disease vectors.

Form, Function, Agency: Sources of Natural Purpose in Animal Evolution

The origination and evolution of multicellular form and function is generally thought to be based on gene-based variation, with natural selection changing the populational composition in the respective variants over time. The criterion for evolutionary success is differential fitness, the relative capacity to leave progeny in the next generation. Theoretical considerations show that this model implies that phenotypic evolution will generally be gradual, based on variations of small effect. But the fossil record of early phylogenesis, notably for the metazoans, or animals, does not support the gradualist scenario. Moreover, discordances of phenotype and genotype in extant species, along with the existence of a pan-metazoan developmental genetic toolkit, does not support the gene-variation-based evolutionary mechanism, at least at the level of phyla. Most importantly, all life-forms, including the cells that constitute animal embryos, exhibit agency, and associations of cells (even constructed ones with no history of natural selection) exhibit novel kinds of agency. This strongly suggests that new multicellular forms can invent new ways of life (e.g., ecological niches) and can persist without supplanting their populational cohorts. This chapter describes how anatomical (e.g., segments, appendages) and functional (e.g., muscle, nerve) phenotypes can emerge without cycles of gradual selection from inherent properties of metazoan cells and their aggregates. While such phenotypic “add-ons” could provide enablements for exploration of new niches, it is implausible that they arose as adaptations to external challenges. Reproductive fitness, which is essential for understanding biogeography and ecology, is unlikely to have played a role in phylum-level evolution.

Whole-Genome Sequencing and Annotation of the Yeast Clavispora santaluciae Reveals Important Insights about Its Adaptation to the Vineyard Environment

Clavispora santaluciae was recently described as a novel non-Saccharomyces yeast species, isolated from grapes of Azores vineyards, a Portuguese archipelago with particular environmental conditions, and from Italian grapes infected with Drosophila suzukii. In the present work, the genome of five Clavispora santaluciae strains was sequenced, assembled, and annotated for the first time, using robust pipelines, and a combination of both long- and short-read sequencing platforms. Genome comparisons revealed specific differences between strains of Clavispora santaluciae reflecting their isolation in two separate ecological niches—Azorean and Italian vineyards—as well as mechanisms of adaptation to the intricate and arduous environmental features of the geographical location from which they were isolated. In particular, relevant differences were detected in the number of coding genes (shared and unique) and transposable elements, the amount and diversity of non-coding RNAs, and the enzymatic potential of each strain through the analysis of their CAZyome. A comparative study was also conducted between the Clavispora santaluciae genome and those of the remaining species of the Metschnikowiaceae family. Our phylogenetic and genomic analysis, comprising 126 yeast strains (alignment of 2362 common proteins) allowed the establishment of a robust phylogram of Metschnikowiaceae and detailed incongruencies to be clarified in the future.

Insights Into Comparative Analyses and Phylogenomic Implications of Acer (Sapindaceae) Inferred From Complete Chloroplast Genomes

Acer L. (Sapindaceae) is one of the most diverse and widespread plant genera in the Northern Hemisphere. It comprises 124–156 recognized species, with approximately half being native to Asia. Owing to its numerous morphological features and hybridization, this genus is taxonomically and phylogenetically ranked as one of the most challenging plant taxa. Here, we report the complete chloroplast genome sequences of five Acer species and compare them with those of 43 published Acer species. The chloroplast genomes were 149,103–158,458 bp in length. We conducted a sliding window analysis to find three relatively highly variable regions (psbN-rps14, rpl32-trnL, and ycf1) with a high potential for developing practical genetic markers. A total of 76–103 SSR loci were identified in 48 Acer species. The positive selection analysis of Acer species chloroplast genes showed that two genes (psaI and psbK) were positively selected, implying that light level is a selection pressure for Acer species. Using Bayes empirical Bayes methods, we also identified that 20 cp gene sites have undergone positive selection, which might result from adaptation to specific ecological niches. In phylogenetic analysis, we have reconfirmed that Acer pictum subsp. mono and A. truncatum as sister species. Our results strongly support the sister relationships between sections Platanoidea and Macrantha and between sections Trifoliata and Pentaphylla. Moreover, series Glabra and Arguta are proposed to promote to the section level. The chloroplast genomic resources provided in this study assist taxonomic and phylogenomic resolution within Acer and the Sapindaceae family.

Ecomorphic Structure Transformation of Soil Macrofauna Amid Recreational Impact

The level of reacreation load on the components of urban green areas is increasing, so identifying the effective management tools in these ecosystems is becoming crucial for ensuring the maintenance of soil biota habitats. The purpose of this study is to reveal a pattern of structuring community of soil macrofauna under a recreational impact based on an ecomorphic approach. The article assesses the level of recreational transformation of the soil macrofauna of public green spaces in the city of Melitopol on the territory of Novooleksandrivskyi Park. For research purposes, a testing site was allocated in an area with a high level of recreational load, with samples taken within this site. To collect soil macrofauna and assess soil properties at each point of the testing site, soil and zoological tests were carried out and the following soil indicators were measured: temperature, electrical conductivity, humidity and soil penetration resistance, litter depth and grass stand height. The community ordination was performed using two approaches: OMI and RLQ analysis. The study found that the ecological niches of soil macrofauna in recreational conditions are spatially structured. The main factors for structuring the ecological niche of soil macrofauna within the study area are soil penetration resistance in the range of the entire measured layer, soil moisture, and distance to trees. As for the number of species, the basis of the coenomorphic structure of soil macrofauna are silvants (45.5%) and pratants (24.2%). As for the species abundance, the basis of the coenomorphic structure of macrofauna comprises pratants (64.5%), slightly less stepants (19.1%) and silvants (16.1%), and sporadic occurrence of paludants (0.2%). Such coenomorphic structure can be considered as ecologically labile. Zoophages, hemiaerophobes, and megatrophs are tolerant to a high level of recreational load. The area corresponding to the highest level of recreational load is vacant. This indicates factual absence of soil macrofauna species that could exist amid intense recreational exposure