Subcohort Research Articles

Taxonomical composition and functional analysis of biofilms sampled from a nuclear storage pool.

Sampling small amounts of biofilm from harsh environments such as the biofilm present on the walls of a radioactive material storage pool offers few analytical options if taxonomic characterization and estimation of the different biomass contributions are the objectives. Although 16S/18S rRNA amplification on extracted DNA and sequencing is the most widely applied method, its reliability in terms of quantitation has been questioned as yields can be species-dependent. Here, we propose a tandem-mass spectrometry proteotyping approach consisting of acquiring peptide data and interpreting then against a generalist database without any a priori. The peptide sequence information is transformed into useful taxonomical information that allows to obtain the different biomass contributions at different taxonomical ranks. This new methodology is applied for the first time to analyze the composition of biofilms from minute quantities of material collected from a pool used to store radioactive sources in a nuclear facility. For these biofilms, we report the identification of three genera, namely Sphingomonas, Caulobacter, and Acidovorax, and their functional characterization by metaproteomics which shows that these organisms are metabolic active. Differential expression of Gene Ontology GOslim terms between the two main microorganisms highlights their metabolic specialization.

Revision of the Barremian fern Coniopteris laciniata from Las Hoyas and El Montsec (Spain): Highlighting its importance in the evolution of vegetation during the Early Cretaceous

AbstractThe species Coniopteris laciniata and Sphenopteris wonnacottii are heterophyllous ferns recovered from two Spanish Barremian localities, Las Hoyas and El Montsec respectively. The similarities between these species, observed in a study of a total of 66 hand specimens from both localities, indicate that they are conspecific. Following the rule of priority in botanical nomenclature, and because there are doubts about the assignment of this species to a higher taxonomic rank, the name Coniopteris is maintained. Characters of this fern and additional characters of other species of Coniopteris would support a diversification of polypod ferns during the Early Cretaceous. Metric architecture analyses suggest that the heterophylly of the plant was probably caused by the submersion of the apical part of fronds in water during their development, which would be consistent with the taphonomy of the remains in both localities.

Mammals of Yakutia: Changes in the understanding of the composition of the mammal fauna over the past 50 years and an Annotated List. Part 2. Carnivorous, Cetaceans, and Artiodactyls

This study presents data on the mammal fauna including Carnivora (5 families, 12 genera, and 17 species), Cetacea (2 families, 3 genera, and 3 species), and Artiodactyla (3 families, 8 genera, and 3 species). A total number of 28 species demonstarted an increase in the richness of these taxa over the past 50 years due to the introduction of one carnivorous species and two ungulate species. Among the latter, only the introduction of musk ox can be considered successful. In addition, sporadic occurrences of four species that were not part of the original fauna in Yakutia have been registered. The northern sea lion and bowhead whale can colonize marine regions of Yakutia, whereas the Asian badger can colonize its terrestrial regions if the current climate trend stays unchanged. The tiger is unlikely to survive the Yakutian conditions, due to both low temperatures and low density of the ungulates, which constitute the major part of its food supply. At present, the complete list of species that inhabit the terrestrial and marine areas of Yakutia includes 70 representatives of the Mammalia class. The major part of the mammalian fauna of the region consists of indigenous species, whereas the share of non-native species was only approximately 10%. The changes in the composition of the mammalian fauna over the last 50 years are connected with a better current knowledge of the regional fauna, introduction, and changes in the taxonomic rank of species and subspecies. Moreover, four new species were identified: Chiroptera (2), Insectivora (1), and Rodentia (1). Some clarifications have been made to the taxonomic rank of species and subspecies belonging to the genera Ochotona, Urocitellus, and Alexandromys (Microtus). The use of genetic approach can clarify the taxonomic rank of a number of species. More complete and precise data on the composition of the faunistic list, geographic ranges of these species can be obtained by covering the territorial gaps in the previous studies and additional research on understudied taxa, in particular chiropterans and marine mammals.

Abstract 3156: Meta-analysis of lung cancer single-cell RNA data reveals novel gene modules associated with lineage, stage, and genetic alterations

Abstract Objective: Combinations of somatic alterations, epigenetic changes, and interactions with cells in the tumor microenvironment can induce gene expression changes in cancer cells. Single-cell RNA-seq can provide valuable insights into the heterogeneity of cancer cells within and across tumor samples. We performed a meta-analysis of single-cell RNA-seq (scRNA-seq) datasets containing primary tumor samples from patients with non-small-cell-lung cancer (NSCLC) to characterize modules of co-expressed genes and determine associations with histological, genetic, and immune features. Methods: scRNA-seq data of 116,260 cells from 127 NSCLC samples including lung adenocarcinomas (LUADs) and lung squamous cell carcinomas (LUSCs) were collected and merged from 12 datasets. Cancer cells were identified by inferring copy number variations (CNVs). Celda was used to identify 163 gene co-expression modules across cancer cells. MAST was used to assess association of each module with histology, stage, and study. CaDrA was used to identify combinations of genomic features associated with gene modules projected into TCGA bulk RNA-seq. Result: Broad biological category of modules included those related to lineage, cell cycle and proliferation, extracellular matrix production (ECM), epithelial-to-mesenchymal transition (EMT), antigen presentation, xenobiotic metabolism, stress response, chemokine signaling, interferon signaling, housekeeping, and other general cellular processes. The modules most strongly associated with study-specific effects were enriched in housekeeping and ribosomal genes. Several ECM and cell-cycling modules were induced in advanced LUADs while MHC class II modules were reduced in late stage disease. Several modules containing different surfactant proteins or secretoglobins were identified and displayed heterogeneity within and across early-stage LUADs. Three modules in LUSCs were enriched for detoxification enzymes and associated with somatic mutations in different members of the Nrf2 pathway. A module of genes involved in keratinization displayed intra- and inter-tumoral heterogeneity across LUSCs and was associated with neutrophil infiltration scores in samples from TCGA. Conclusion: We employed a novel meta-analysis approach to study gene co-expression patterns that are active in lung cancer cells profiled with single-cell RNA-seq. Characterization of these modules revealed the biological processes and cancer hallmarks active within and across lung tumors. Citation Format: Rui Hong, Sarah Mazzilli, Stefano Monti, Avrum Spira, Joshua D. Campbell. Meta-analysis of lung cancer single-cell RNA data reveals novel gene modules associated with lineage, stage, and genetic alterations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3156.

Study of the diets of two coexisting species – invasive Chinese sleeper (Perccottus glenii Dybowski, 1877) and native European perch (Perca fluviatilis Linnaeus, 1758)

In Poland, the Chinese sleeper Perccottus glenii is one of the alien fish species which, by effectively competing with native species, may contribute to the weakening of their population and a reduction of the biodiversity. The aim of this paper is to study the diets of two coexisting species: the native European perch Perca fluviatilis and the invasive Chinese sleeper. The fish were collected from a watercourse used for draining water from a fishing farm, located in the Nida River water system (Poland), using the electrofishing method. The captured fish were killed, preserved in a 4% formaldehyde solution and the stomachs of the fish were dissected. Then, based on the materials collected from these stomachs, the abundance and taxonomic rankings of the individual diet components (quantity of individuals in the individual taxa) were determined. The overlap of the P. fluviatilis and P. glenii feeding spectra was studied using a principal component analysis (PCA). The analysis of the data collected demonstrated that the diets of these two species overlaps considerably. At the same time, the analysis of the major diet components showed that the niche used by P. fluviatilis is broader than that used by P. glenii. It seems that, due to its high level of plasticity, P. fluviatilis is able to withstand the pressures of P. glenii and is also able to limit its abundance. Both species frequently choose fish as their prey, including juvenile common carp Cyprinus carpio Linnaeus, 1758, which indicates that together with native predators, P. glenii may pose a considerable threat to farmed juvenile Cyprinidae.

A taxonomic treatment of the violets (Violaceae) of the northeastern United States and adjacent Canada 1

A taxonomic treatment is presented for the violets (Violaceae) confirmed in the range described in the second edition of Gleason and Cronquist's Manual of Vascular Plants of Northeastern United States and Adjacent Canada, in advance of the new treatment of this manual that is in preparation. Recent field, herbarium, and laboratory investigations of eastern North America's violet flora by the author and students have reexamined eastern North American violet taxa and utilized multiple sources of evidence filtered through modern species concepts to delimit taxa and assign appropriate taxonomic rank. Results have led to the recognition of 58 native and eight introduced species, one subspecies, one variety and one form, 10 informal variants, and 113 wild hybrids in our region, representing the genera Cubelium, Pombalia, and Viola. In Viola, two new species are described and three new combinations are made (one to species rank, one to subspecies, and one to forma), and eight names are typified. Viola taxa are distributed across five sections and nine subsections and are representative of most of the infrageneric taxonomic diversity in North America overall. Anomalous variants in Viola emarginata, Viola palmata, Viola septentrionalis, and Viola sororia currently lack sufficient information for taxonomic decisions but are presented to encourage study, collection, and documentation. Six potential taxa occur adjacent to or very near our region and may eventually be discovered in our area; they are included in the keys and briefly described with figures. The treatment includes introductory text, dichotomous keys, synonymy with some type information, detailed descriptions, and other information, as well as color figures of habit and plant structures and US county-level geographic distribution maps for nearly all included taxa.

DL-TODA: A Deep Learning Tool for Omics Data Analysis.

Metagenomics is a technique for genome-wide profiling of microbiomes; this technique generates billions of DNA sequences called reads. Given the multiplication of metagenomic projects, computational tools are necessary to enable the efficient and accurate classification of metagenomic reads without needing to construct a reference database. The program DL-TODA presented here aims to classify metagenomic reads using a deep learning model trained on over 3000 bacterial species. A convolutional neural network architecture originally designed for computer vision was applied for the modeling of species-specific features. Using synthetic testing data simulated with 2454 genomes from 639 species, DL-TODA was shown to classify nearly 75% of the reads with high confidence. The classification accuracy of DL-TODA was over 0.98 at taxonomic ranks above the genus level, making it comparable with Kraken2 and Centrifuge, two state-of-the-art taxonomic classification tools. DL-TODA also achieved an accuracy of 0.97 at the species level, which is higher than 0.93 by Kraken2 and 0.85 by Centrifuge on the same test set. Application of DL-TODA to the human oral and cropland soil metagenomes further demonstrated its use in analyzing microbiomes from diverse environments. Compared to Centrifuge and Kraken2, DL-TODA predicted distinct relative abundance rankings and is less biased toward a single taxon.

Draft Genome Sequences of Algoriphagus sp. Strain PAP.12 and Roseivirga sp. Strain PAP.19, Isolated from Marine Samples from Papua, Indonesia.

Algoriphagus sp. strain PAP.12 (EXT111900) and Roseivirga sp. strain PAP.19 (EXT111901) were isolated from marine samples. Here, we report their draft genome sequences, 5.032 Mbp and 4.583 Mbp in size, respectively, and rate their specialized metabolite production capacity. Taxonomic ranks established by genome-based analysis indicate that Algoriphagus sp. strain PAP.12 represents a candidate new species.

Temporal dynamics of geothermal microbial communities in Aotearoa-New Zealand.

Microbial biogeography studies, in particular for geothermal-associated habitats, have focused on spatial patterns and/or individual sites, which have limited ability to describe the dynamics of ecosystem behaviour. Here, we report the first comprehensive temporal study of bacterial and archaeal communities from an extensive range of geothermal features in Aotearoa-New Zealand. One hundred and fifteen water column samples from 31 geothermal ecosystems were taken over a 34-month period to ascertain microbial community stability (control sites), community response to both natural and anthropogenic disturbances in the local environment (disturbed sites) and temporal variation in spring diversity across different pH values (pH 3, 5, 7, 9) all at a similar temperature of 60-70°C (pH sites). Identical methodologies were employed to measure microbial diversity via 16S rRNA gene amplicon sequencing, along with 44 physicochemical parameters from each feature, to ensure confidence in comparing samples across timeframes. Our results indicated temperature and associated groundwater physicochemistry were the most likely parameters to vary stochastically in these geothermal features, with community abundances rather than composition more readily affected by a changing environment. However, variation in pH (pH ±1) had a more significant effect on community structure than temperature (±20°C), with alpha diversity failing to adequately measure temporal microbial disparity in geothermal features outside of circumneutral conditions. While a substantial physicochemical disturbance was required to shift community structures at the phylum level, geothermal ecosystems were resilient at this broad taxonomic rank and returned to a pre-disturbed state if environmental conditions re-established. These findings highlight the diverse controls between different microbial communities within the same habitat-type, expanding our understanding of temporal dynamics in extreme ecosystems.

Assessment of fungal spores and spore-like diversity in environmental samples by targeted lysis

At particular stages during their life cycles, fungi use multiple strategies to form specialized structures to survive unfavorable environmental conditions. These strategies encompass sporulation, as well as cell-wall melanization, multicellular tissue formation or even dimorphism. The resulting structures are not only used to disperse to other environments, but also to survive long periods of time awaiting favorable growth conditions. As a result, these specialized fungal structures are part of the microbial seed bank, which is known to influence the microbial community composition and contribute to the maintenance of diversity. Despite the importance of the microbial seed bank in the environment, methods to study the diversity of fungal structures with improved resistance only target spores dispersing in the air, omitting the high diversity of these structures in terms of morphology and environmental distribution. In this study, we applied a separation method based on cell lysis to enrich lysis-resistant fungal structures (for instance, spores, sclerotia, melanized yeast) to obtain a proxy of the composition of the fungal seed bank. This approach was first evaluated in-vitro in selected species. The results obtained showed that DNA from fungal spores and from yeast was only obtained after the application of the enrichment method, while mycelium was always lysed. After validation, we compared the diversity of the total and lysis-resistant fractions in the polyextreme environment of the Salar de Huasco, a high-altitude athalassohaline wetland in the Chilean Altiplano. Environmental samples were collected from the salt flat and from microbial mats in small surrounding ponds. Both the lake sediments and microbial mats were dominated by Ascomycota and Basidiomycota, however, the diversity and composition of each environment differed at lower taxonomic ranks. Members of the phylum Chytridiomycota were enriched in the lysis-resistant fraction, while members of the phylum Rozellomycota were never detected in this fraction. Moreover, we show that the community composition of the lysis-resistant fraction reflects the diversity of life cycles and survival strategies developed by fungi in the environment. To the best of our knowledge this is the first time that the fungal diversity is explored in the Salar de Huasco. In addition, the method presented here provides a simple and culture independent approach to assess the diversity of fungal lysis-resistant cells in the environment.

Upregulated Genes in Contact Co-culture of Osteoblasts and Sympathetic Neuronal Cells

Many works have been done on the interaction between neurons and osteoblasts. However, the cells used in our previous study were derived from mouse and rat, and it is impossible to exclude the possibility of cross-reactivity of the mouse and rat probes Osteoblasts cell line labeled with red fluorescent protein and sympathetic neuronal cell line labeled with green fluorescent protein were generated. A DNA microarray analysis was conducted by using these cell line in co-culture system. It was filtered for genes with a ratio more than 2.0-fold in the biological process category by the search term “axon” and cellular component by the search term “membrane”. Eight genes, i.e., neuropilin 1, growth associated protein 43, dopamine receptor D2, plexin A2, disabled 1, ephrin receptor A7, ephrin B2, and fibronectin leucine rich transmembrane protein 3 were found. The molecules expressed on the plasma membrane of osteoblasts were upregulated in contact co-culture with sympathetic neuronal cells. It was filtered for genes with a ratio more than 2.0-fold in the biological process category by the search term “osteoblast” and cellular component by the search term “membrane”. Four genes, i.e., gap junction protein, alpha 1, collagen, type VI, alpha 1 and bone morphogenetic protein 4 were found. The molecules expressed on the plasma membrane of neurons were upregulated in co-culture with osteoblasts. These molecules may be candidates for factors that promote osteoblast differentiation and neural differentiation.

A Taxonomic Hierarchy of Blockchain Consensus Algorithms: An Evolutionary Phylogeny Approach

Countless endeavors have been undertaken to address the Byzantine Generals Problem, a generalization of the Two Generals Problem. The emergence of proof of work (PoW) for Bitcoin has led to various consensus algorithms diverging, and comparable existing consensus algorithms are being gradually utilized interchangeably, or only developed for each specific application domain. Our approach employs an evolutionary phylogeny method to classify blockchain consensus algorithms based on their historical development and current usage. To demonstrate the relatedness and lineage of distinct algorithms, as well as to support the recapitulation theory, which posits that the evolutionary history of its mainnets is mirrored in the development of an individual consensus algorithm, we present a taxonomy. We have created a comprehensive classification of past and present consensus algorithms that serves to organize this swift consensus algorithm evolution period. By recognizing similarities, we have compiled a list of different verified consensus algorithms and performed clustering on over 38 of these. Our new taxonomic tree presents five taxonomic ranks, including the evolutionary process and decision-making method, as a technique for analyzing correlation. Through the examination of the evolution and utilization of these algorithms, we have developed a systematic and hierarchical taxonomy that enables the grouping of consensus algorithms into distinct categories. The proposed method classifies various consensus algorithms according to taxonomic ranks and aims to reveal the direction of research on the application of blockchain consensus algorithms for each domain.

A generic AI pipeline for identifying known species and discovering new species

To counterattack the current biodiversity crisis, we need innovative tools and technologies that can greatly improve species identification and discovery at scale. Here, we describe a data analysis pipeline to automatically identify biological sound categories in soundscape data and accelerate the discovery of new species. The pipeline consists of two components: (1) Unsupervised audio event detection and clustering that enables automatic detection and categorization of biological sounds in large audio datasets and (2) supervised deep learning-based signal detection that enables automated cluster labeling and detection of known sound categories in new audio. We evaluated the results of our unsupervised analysis tools applied to a labeled dataset of ∼18 h of recordings from Panama. Experts assigned a label to each sound event with a max frequency of 6 kHz. Our results show that clusters generally had high homogeneity and completeness and indicate that our cluster analysis tool can successfully detect and group like-sounds together, improving data processing and species identification. In addition, we were able to implement these analytical tools in a user-friendly data analysis platform that will provide scientists, wildlife managers, conservationists, and public and private environmental organizations with the information they need to make informed conservation and management decisions.

Gut Microbiota Composition in the First and Third Trimester of Pregnancy among Malay Women is Associated with Body Mass Index: A Pilot Study.

This study has analysed the pattern of gut microbiota during the first and third trimesters among pregnant Malay women. This was a pilot prospective observational study involving 12 pregnant Malay women without any endocrine disorders and on neither antibiotics nor probiotics. Demographic details and anthropometric measurements were obtained, and the faecal 16S ribosomal ribonucleic acid (rRNA) metagenome microbiota of the first and third trimesters (T1 and T3) were analysed. Univariate and multivariate statistics, partial least squares discriminant analysis (PLSDA) and Kendall rank correlation testing were used to identify key genera and associations with pregnancy trimester and body mass index (BMI). The most abundant phyla were Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria, with significant differences in composition at the genus level demonstrated between T1 and T3. Sequencing showed a statistically significant difference in beta diversity between normal and abnormal BMI at all taxonomic ranks (R 2 = 0.60; Q 2 = 0.23) and genus levels (R 2 = 0.57; Q 2 = 0.37). The relative abundances of Akkermansia (P < 0.05; false discovery rate [FDR] < 0.05), Olsenella (P < 0.05; FDR < 0.05) and Oscillospira (P < 0.05; FDR < 0.05) were found to be significantly higher in normal BMI cases by 2.4, 3.4 and 3.1 times, respectively. Three genera (Akkermansia, Olsenella and Oscillospira) were correlated with normal BMI during pregnancy. All three could be promising biotherapeutic targets in body weight regulation during pregnancy, subsequently reducing complications associated with higher BMI.

An extreme environment drives local adaptation ofGenista tinctoria(Fabaceae) from the Mefite (Ansanto Valley, southern Italy)

AbstractThe Mefite in the Ansanto Valley is one of the largest and oldest cold natural carbon dioxide springs (CNCDS) known in the world. This site is characterized by toxic concentrations of CO2 and other harmful gases, and few plant species can survive in this environment. Among these plants, there is an aberrant Genista tinctoria population previously described as G. anxantica. This study aims to advance understanding of evolution over small geographical scales in an extreme environment using G. tinctoria populations from low and high CO2 environments. To investigate differentiation of the Mefite population, we analysed plastid sequences and microsatellite data for populations in the surrounding area. Considering the genetic results, it is evident that the population of the Mefite has an exclusive genetic pattern from both plastid and nuclear points of view with the presence of significant genetic barriers for both genomes analysed, which would point to the isolation of this population from neighbouring G. tinctoria populations. The population of G. tinctoria from the Mefite shows evidence of genetic differentiation from the nearby populations and the genetic indices show discrete variation. Recruitment was confirmed in the Mefite population, an indication that fitness is maintained despite the extreme local conditions. Our results indicate that the potent selection pressure imposed by the Mefite atmosphere has driven genetic differentiation of the local population from nearby G. tinctoria populations. A correct taxonomic rank evaluation and some conservation remarks are also proposed. Our study demonstrates that CO2 concentrations can influence population differentiation and adaptation in plants in a similar way to atmospheric sulphur, herbicides or edaphic conditions.

Body plan of Dickinsonia, the oldest mobile animals

ABSTRACTMaterials collected on the territory of the southeastern White Sea area, including diversely preserved body imprints, combined body-trace fossils, specimens with signs of intravital damage and regeneration, and extended ontogenetic series, make it possible to significantly widen the data on the body plan and biology of Dickinsonia, the oldest known mobile animal, included in the Late Precambrian taxon of high rank, Proarticulata. A number of reconstructed anatomical features were added to the obvious directly observed features of Dickinsonia, such as a consistent body shape lacking lateral appendages and temporary outgrowths, transverse differentiation, and anterior–posterior polarity. These reconstructed features include dorsoventral polarity, ciliated mucus-secreting epithelium underlain by a basal lamina, two rows of blind food-gathering pockets, absence of a through-gut, nervous system of diffusive type, axial support band and muscle fibres. Such a set of features indicates the affinity of Dickinsonia and Proarticulata as a whole (the only known Ediacaran Metazoa) to Urbilateria, a hypothetical ancestor of bilaterally symmetrical animals.

Identification of the regulatory network and potential markers for type 2 diabetes mellitus related to internal exposure to metals in Chinese adults.

People intake metals from their environment. This study investigated type 2 diabetes mellitus (T2DM) related to internal exposure to metals and attempted to identify possible biomarkers. A total of 734 Chinese adults were enrolled, and urinary levels of ten metals were measured. Multinomial logistic regression model was used to assess the association between metals and impaired fasting glucose (IFG) and T2DM. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein-protein interaction were used to explore the pathogenesis of T2DM related to metals. After adjustment, lead (Pb) was positively associated with IFG (odds ratio [OR] 1.31, 95% confidence interval [CI] 1.06-1.61) and T2DM (OR 1.41, 95% CI 1.01-1.98), but cobalt was negatively associated with IFG (OR 0.57, 95% CI 0.34-0.95). Transcriptome analysis showed 69 target genes involved in the Pb-target network of T2DM. GO enrichment indicated that the target genes are enriched mainly in the biological process category. KEGG enrichment indicated that Pb exposure leads to non-alcoholic fatty liver disease, lipid and atherosclerosis, and insulin resistance. Moreover, there is alteration of four key pathways, and six algorithms were used to identify 12 possible genes in T2DM related to Pb. SOD2 and ICAM1 show strong similarity in expression, suggesting a functional correlation between these key genes. This study reveals that SOD2 and ICAM1 may be potential targets of Pb exposure-induced T2DM and provides novel insight into the biological effects and underlying mechanism of T2DM related to internal exposure to metals in the Chinese population.

Comparison of genomic and transcriptional microbiome analysis in gastric cancer patients and healthy individuals.

Helicobacter pylori and the stomach microbiome play a crucial role in gastric carcinogenesis, and detailed characterization of the microbiome is necessary for a better understanding of the pathophysiology of the disease. There are two common modalities for microbiome analysis: DNA (16S rRNA gene) and RNA (16S rRNA transcript) sequencing. The implications from the use of one or another sequencing approach on the characterization and comparability of the mucosal microbiome in gastric cancer (GC) are poorly studied. To characterize the microbiota of GC using 16S rRNA gene and its transcript and determine difference in the bacterial composition. In this study, 316 DNA and RNA samples extracted from 105 individual stomach biopsies were included. The study cohort consisted of 29 healthy control individuals and 76 patients with GC. Gastric tissue biopsy samples were collected from damaged mucosa and healthy mucosa at least 5 cm from the tumor tissue. From the controls, healthy stomach mucosa biopsies were collected. From all biopsies RNA and DNA were extracted. RNA was reverse transcribed into cDNA. V1-V2 region of bacterial 16S rRNA gene from all samples were amplified and sequenced on an Illumina MiSeq platform. Bray-Curtis algorithm was used to construct sample-similarity matrices abundances of taxonomic ranks in each sample type. For significant differences between groups permutational multivariate analysis of variance and Mann-Whitney test followed by false-discovery rate test were used. Microbial analysis revealed that only a portion of phylotypes (18%-30%) overlapped between microbial profiles obtained from DNA and RNA samples. Detailed analysis revealed differences between GC and controls depending on the chosen modality, identifying 17 genera at the DNA level and 27 genera at the RNA level. Ten of those bacteria were found to be different from the control group at both levels. The key taxa showed congruent results in various tests used; however, differences in 7 bacteria taxa were found uniquely only at the DNA level, and 17 uniquely only at the RNA level. Furthermore, RNA sequencing was more sensitive for detecting differences in bacterial richness, as well as differences in the relative abundance of Reyranella and Sediminibacterium according to the type of GC. In each study group (control, tumor, and tumor adjacent) were found differences between DNA and RNA bacterial profiles. Comprehensive microbial study provides evidence for the effect of choice of sequencing modality on the microbiota profile, as well as on the identified differences between case and control.

Sex Determination and the Human Person

Abstract: For many species that reproduce sexually, how sex is expressed at different points across lifespan is highly contingent and dependent on various environmental factors. For example, in many species of fish, environmental cues can trigger a natural process of sex transition where a female transitions to male. For many species of turtle, incubation temperature influences the likelihood that turtle eggs will hatch males or females. What is the case for Homo sapiens? Is human sex expression influenced by contingent environmental factors like we see in fish and turtles, with whom we share common ancestry and DNA? Our paper explores the current biological science of sex determination and how it applies to philosophical and theological accounts of the human person. We argue that while human sex determination is not susceptible to environmental cues to the same degree we see in other species, there is sufficient variability among the pathways of human sex development to complicate simplistic biological categories of male and female.

Molecular and ionomic responses of Solanum lycopersicum L. (cv. Micro-Tom) plants treated with a novel calcium-based plant biostimulant

In this study, we investigated the leaf treatment effects of a novel trace elements calcium-based fluid mixture with a supposed biostimulant action on Solanum lycopersicum L. cv. Micro-Tom. Seedlings were grown on standard peat substrate and treated with two different products: a calcium-based fluid mixture and a common calcium fertilizer, CaCl2. Both treatments were compared to an untreated control. We first investigated the effects of treatments on fruit yield and dry matter production in greenhouse-grown tomato. These effects were then assessed in leaves by gene expression profiling of 60 genes involved in different biological pathways and functional categories, and by ionomic analysis. Leaf treatment on tomato with the calcium-based fluid mixture allowed the highest fruit yield per plant (6.17 fruits plant−1) and above-ground dry matter (13.99 g plant−1) to be obtained. Also, 4 genes related to the nutrient transporter category, NCX, NRAMP3, SI BOR2, and CHLM, were upregulated in plants treated with the novel product. CRK, a gene related to the calcium-dependent protein kinases (CDPK), was upregulated in plants treated with the novel product whereas SODCC.1, a gene related to the superoxide dismutase family, was downregulated in the same plants. A substantial reduction of elemental contents was observed for CaCl2-treated plants, while the novel Ca-based mixture increased the leaf mineral content of Zn (+61%) and Mn (+65%). These results highlighted the biostimulant activity of the novel product resulting in changes in fruit yield and dry matter production, gene expression, and ionome profiles of tomato leaves.