Early Settlement Research Articles

Segmented filamentous bacteria-based treatment to elicit protection against Enterobacteriaceae in Layer chickens.

Gut microbes like segmented filamentous bacteria (SFB) play a key role in gut maturation during early life, as demonstrated in humans and mice. Our previous study demonstrated oral inoculation of ileum-spores containing SFB to chickens after hatch increases early SFB gut colonization, which increases immune maturation and resistance to bacteria, like Salmonella, as tested in vitro; however, more studies are needed for treatment optimization and in vivo testing. The objectives of this study were to (1) test a treatment that includes both spores and filamentous SFB, (2) validate antimicrobial ability of the treatment in layer hens in vivo, and (3) elucidate its molecular mechanism. One-day-old specific pathogen-free layers (n = 12 per group) were orally treated with either PBS (CON) or SFB-based treatment (SFB). At 4 days post-inoculation (DPI), both CON and SFB groups were orally challenged with Salmonella Typhimurium. Total Enterobacteriaceae and Salmonella were examined by plating and enumeration in feces at 7,10 and 14 dpi; and in the ileum, cecum, and spleen at 16 dpi in euthanized birds. The presence and levels of SFB were determined from ilea scrapings via microscopy and qPCR, respectively. Relative gene expression of host-derived antimicrobial peptides and cytokines in the distal ileum was determined by RT-qPCR. At 10 and 14 dpi, a significant decrease in total Enterobacteriaceae was observed in the feces of the SFB group. At necropsy, the level of SFB was significantly higher in the SFB group than in the CON group, while a significant decrease in total Enterobacteriaceae and Salmonella was observed in the ceca of the SFB group. RT-qPCR revealed increased expression of β-defensin 14, and cytokines IL-10 and IFNγ. The introduction of SFB at hatch as a prophylactic treatment may benefit commercial partners as well as consumers by reducing the incidence of Enterobacteriaceae in food animals. Reduction of these bacteria in animals would, in turn, increase animal health, productivity, and safety for consumers. Studies to optimize the treatment for poultry industry applications are ongoing in our lab.

Early colonization of sessile megabenthos on electrolytic carbonated structures (Alicante's harbor, Western Mediterranean)

Biofouling of different artificial substrates was studied to determine the differences in biofouling assemblages among different substrates. However, studies on biofouling on natural substrates like electrolytic carbonated ones are lacking. These substrates have a great potential for coral reef restoration in tropical areas and for biofilter construction. Thus, this study was developed to examine the colonization of sessile macrofouling in the port of Alicante (SE Spain, Western Mediterranean) on two types of substrates: electrolytic carbonated and bare steel (as control) over three months of immersion (October 2019–January 2020). The community diversity was studied through different biotic parameters and abundance of assemblages, and preference of organisms according to their status and functional group (active filter feeders). Univariate and multivariate analyses (PERMANOVA and SIMPER) were also applied to examine the differences between carbonate and control substrates. The carbonated substrate had a more structured community and higher abundance, recruitment, and diversity indexes than the bare steel. Moreover, filter feeders (Porifera, Bivalvia, and Ascidiacea) were more abundant, and most of them only appeared in the carbonated substrate. These results show the potential of carbonated structures as biofilters.

Microbiome convergence and deterministic community assembly along successional biocrust gradients on potash salt heaps.

Potash mining, typically performed for agricultural fertilizer production, can create piles of residual salt waste that are ecologically detrimental and difficult to revegetate. Biological soil crusts (biocrusts) have been found growing on and around these heaps, suggesting resilience to the hypersaline environment. We set out to understand the community dynamics of biocrust formation by examining two succesionary salinity gradients at historical mining sites using a high throughput amplicon sequencing. Bare heaps were distinct, with little overlap between sites, and were characterized by high salinity, low nutrient availability, and specialized, low diversity microbial communities, dominated by Halobacteria, Chloroflexia, and Deinococci. 'Initial' stages of biocrust development were dominated by site-specific Cyanobacteria, with significant overlap between sites. Established biocrusts were the most diverse, with large proportions of Alphaproteobacteria, Anaerolineae, and Planctomycetacia. Along the salinity gradient at both sites, salinity decreased, pH decreased, and nutrients and Chlorophyll a increased. Microbiomes between sites converged during succession and community assembly process analysis revealed biocrusts at both sites were dominated by deterministic, niche-based processes; indicating a high degree of phylogenetic turnover. We posit early cyanobacterial colonization is essential for biocrust initiation, and facilitates later establishment of plant and other higher-level biota.

Integrated multi-omic analyses provide insight into colon adenoma susceptibility modulation by the gut microbiota.

Colon cancer onset is strongly associated with the differences in microbial taxa in the gastrointestinal tract. Although recent studies highlight the role of individual taxa, the effect of a complex gut microbiome (GM) on the metabolome and host transcriptome is still unknown. We used a multi-omics approach to determine how differences in the GM affect the susceptibility to adenoma development in a rat model of human colon cancer. Ultra-high performance liquid chromatography mass spectrometry of feces collected prior to observable disease onset identified putative metabolite profiles that likely predict future disease severity. Transcriptome analyses performed after disease onset from normal colonic epithelium and tumor tissues show a correlation between GM and host gene expression. Integrated pathway analyses of the metabolome and transcriptome based on putatively identified metabolic features indicate that bile acid biosynthesis is enriched in rats with high tumors along with increased fatty acid metabolism and mucin biosynthesis. Targeted pyrosequencing of the Pirc allele indicates that the GM alters the mechanism of adenoma development and may drive an epigenetic pathway of tumor suppressor silencing. This study reveals how untargeted metabolomics identifies signatures of susceptibility and integrated analyses uncover pathways of differential mechanisms of loss of tumor suppressor gene function and for potential prevention and therapeutic intervention. IMPORTANCE The association between the gut microbiome and colon cancer is significant but difficult to test in model systems. This study highlights the association of differences in the pathogen-free gut microbiome to changes in the host transcriptome and metabolome that correlate with colon adenoma initiation and development in a rat genetic model of early colon cancer. The utilization of a multi-omics approach integrating metabolomics and transcriptomics reveals differences in pathways including bile acid biosynthesis and fatty acid metabolism. The study also shows that differences in gut microbiomes significantly alter the mechanism of adenoma formation, shifting from genetic changes to epigenetic changes that initiate the early loss of tumor suppressor function. These findings enhance our understanding of the gut microbiome's role in colon cancer susceptibility, offer insights into potential biomarkers and therapeutic targets, and may pave the way for future prevention and intervention strategies.

Biofilm-induced effect on the buoyancy of plastic debris: An experimental study

Plastic floating on the ocean surface represents about 1 % of all plastic in the ocean, despite the buoyancy of most plastics. Biofouling can help to sink debris, which could explain this discrepancy. A set of laboratory experiments was conducted to investigate biofilm-induced effects on the buoyancy of different plastic debris. Ten materials of different densities (buoyant/non-buoyant), sizes (micro/meso/macro), and shapes (irregular/spherical/cylindrical/flat), including facemasks and cotton swabs, were evaluated. Biofilm was incubated in these materials from a few weeks to three months to investigate the effect of different growth levels on their buoyancy. Biofilm levels and rising/settling velocities were measured and compared at seven time-points. The results show a hindered buoyancy for solid materials, while hollow and open materials showed the opposite trend in early biofilm colonization stages. A relationship was established between biofilm-growth and equivalent sphere diameter that can be used to improve predictive modeling of plastic-debris transport.

Longitudinal anellome dynamics inthe upper respiratory tract ofchildren with acute respiratory tract infections.

Anelloviruses (AVs) are ubiquitous in humans and are the most abundant components of the commensal virome. Previous studies on the diversity, transmission, and persistence of AVs mainly focused on the blood or transplanted tissues from adults; however, the profile of the anellome in the respiratory tract in children are barely known. We investigated the anellome profile and their dynamics in the upper respiratory tract from a cohort of children with acute respiratory tract infections (ARTIs). Different to that in adult, betatorquevirus is the most abundant genus, followed by alphatorquevirus. We found that the relative abundance of betatorquevirus was higher in earlier time points, and in contrast, the abundance of alphatorquevirus was higher in later time points; these results might suggest that betatorquevirus decreased with age and alphatorquevirus increased with age in childhood. No difference regarding the diversity and abundance of anellome was found between single and multiple ARTIs, consistent with the idea that AV is not associated with certain disease. Most AVs are transient, and a small proportion (8 per cent) of them were found to be possibly persistent, with persistence time ranging from 1 month to as long as 56 months. Furthermore, the individual respiratory anellome appeared to be unique and dynamic, and the replacement of existing AVs with new ones are common over different time points. These findings demonstrate that betatorquevirus may be the early colonizer in children, and the individual respiratory anellome is unique, which are featured by both chronic infections and AV community replacement.

Direct interaction of small non-coding RNAs CjNC140 and CjNC110 optimizes expression of key pathogenic phenotypes of Campylobacter jejuni.

Small non-coding RNAs (sRNAs) are important players in modulating gene expression in bacterial pathogens, but their functions are largely undetermined in Campylobacter jejuni, an important cause of foodborne gastroenteritis in humans. In this study, we elucidated the functions of sRNA CjNC140 and its interaction with CjNC110, a previously characterized sRNA involved in the regulation of several virulence phenotypes of C. jejuni. Inactivation of CjNC140 increased motility, autoagglutination, L-methionine concentration, autoinducer-2 production, hydrogen peroxide resistance, and early chicken colonization, indicating a primarily inhibitory role of CjNC140 for these phenotypes. Apart from motility, all these effects directly contrasted the previously demonstrated positive regulation by CjNC110, suggesting that CjNC110 and CjNC140 operate in an opposite manner to modulate physiologic processes in C. jejuni. RNAseq and northern blotting further demonstrated that expression of CjNC140 increased in the absence of CjNC110, while expression of CjNC110 decreased in the absence of CjNC140, suggesting a possibility of their direct interaction. Indeed, electrophoretic mobility shift assay demonstrated a direct binding between the two sRNAs via GA- (CjNC110) and CU- (CjNC140) rich stem-loops. Additionally, RNAseq and follow-up experiments identified that CjNC140 positively regulates p19, which encodes a key iron uptake transporter in Campylobacter. Furthermore, computational analysis revealed both CjNC140 and CjNC110 are highly conserved in C. jejuni, and the predicted secondary structures support CjNC140 as a functional homolog of the iron regulatory sRNA, RyhB. These findings establish CjNC140 and CjNC110 as a key checks-and- balances mechanism in maintaining homeostasis of gene expression and optimizing phenotypes critical for C. jejuni pathobiology. IMPORTANCE Gene regulation is critical to all aspects of pathogenesis of bacterial disease, and small non-coding RNAs (sRNAs) represent a new frontier in gene regulation of bacteria. In Campylobacter jejuni, the role of sRNAs remains largely unexplored. Here, we investigate the role of two highly conserved sRNAs, CjNC110 and CjNC140, and demonstrate that CjNC140 displays a primarily inhibitory role in contrast to a primarily activating role for CjNC110 for several key virulence-associated phenotypes. Our results also revealed that the sRNA regulatory pathway is intertwined with the iron uptake system, another virulence mechanism critical for in vivo colonization. These findings open a new direction for understanding C. jejuni pathobiology and identify potential targets for intervention for this major foodborne pathogen.

Chemical and elementary characterization of Spongiophyton nanum: Understanding the phylogeny, paleoenvironment, and fossilization processes of an enigmatic flora

The record of thalloid macrofossils in the North-Northwest region of the Paraná Basin is less studied compared to that of invertebrate paleofauna in the same area. Consequently, the lack of important information regarding the niches occupied by thalloid embryophytes during early land colonization in this coastal paleoenvironment is evident. This study presents the first chemical and elemental data on Spongiophyton for this region of the basin, offering insights into its paleoenvironment and fossilization processes and providing considerations about the phylogeny of this enigmatic assemblage Spongiophyton nanum Kräusel emend. Chaloner et al. (1974) collected fragments from an outcropping rock in Jaciara, Mato Grosso, Brazil, and studied them using scanning electron microscope/energy X-ray dispersive spectrometer (EDS) and Fourier transform infrared (FTIR) spectroscopy techniques. The EDS analysis showed the highest elemental concentration of carbon, oxygen, and calcium as the main elements of the cuticle composition. Silicon and aluminum were better represented inside the pores than in other areas of the cuticle. The high carbon concentration in the cuticle suggested an anoxic condition prevalent during the deposition of the fine-grained sediments, which prevented its oxidation before and during diagenesis. The carbon present in the EDS spectra was restricted to the cuticle area, and the FTIR spectra indicated the presence of some functional groups, both related to the original organic matter, possibly cutin. Based on elemental characterization, the fossilization of S. nanum may involve more than one process, such as carbonification and mineralization, and S. nanum has more affinities with lichen groups.

DLGNet: A dual-branch lesion-aware network with the supervised Gaussian Mixture model for colon lesions classification in colonoscopy images.

Colorectal cancer is one of the malignant tumors with the highest mortality due to the lack of obvious early symptoms. It is usually in the advanced stage when it is discovered. Thus the automatic and accurate classification of early colon lesions is of great significance for clinically estimating the status of colon lesions and formulating appropriate diagnostic programs. However, it is challenging to classify full-stage colon lesions due to the large inter-class similarities and intra-class differences of the images. In this work, we propose a novel dual-branch lesion-aware neural network (DLGNet) to classify intestinal lesions by exploring the intrinsic relationship between diseases, composed of four modules: lesion location module, dual-branch classification module, attention guidance module, and inter-class Gaussian loss function. Specifically, the elaborate dual-branch module integrates the original image and the lesion patch obtained by the lesion localization module to explore and interact with lesion-specific features from a global and local perspective. Also, the feature-guided module guides the model to pay attention to the disease-specific features by learning remote dependencies through spatial and channel attention after network feature learning. Finally, the inter-class Gaussian loss function is proposed, which assumes that each feature extracted by the network is an independent Gaussian distribution, and the inter-class clustering is more compact, thereby improving the discriminative ability of the network. The extensive experiments on the collected 2568 colonoscopy images have an average accuracy of 91.50%, and the proposed method surpasses the state-of-the-art methods. This study is the first time that colon lesions are classified at each stage and achieves promising colon disease classification performance. To motivate the community, we have made our code publicly available via https://github.com/soleilssss/DLGNet.

Role of Candida species in the occurrence of dental caries in Thi Qar Governorate

Dental caries is a multifactorial disease associated with many factors such as cariogenic microorganisms. Candida is known to be associated with early colonization of cariogenic leading to dental caries. The current study aims to isolation and diagnosis Candida species from caries lesions and the surrounding dental plaque in relation to dental caries. This study was conducted during July 2021–December 2022 in Thi-Qar governorate. Samples were collected from 100 patients using sterile procedures for ages from 4 to 65 years for both genders for various factors such as daily intake of sweets, daily brushing of teeth and smoking. Eighty three Candida isolates of six species were isolated, C. albicans was 44, C. glabrata 11, C. dubliniensis 14, C. tropicalis 10, C. krusei 3 and C. utilis 1, in all age groups and for both genders. The current study proved the existence and role of different species of Candida in causing caries disease, not just C. albicans.

Whole-body microbiota of newborn calves and their response to prenatal vitamin and mineral supplementation.

Early life microbial colonization and factors affecting colonization patterns are gaining interest due to recent developments suggesting that early life microbiome may play a role in Developmental Origins of Health and Disease. In cattle, limited information exists on the early microbial colonization of anatomical sites involved in bovine health beyond the gastrointestinal tract. Here, we investigated 1) the initial microbial colonization of seven different anatomical locations in newborn calves and 2) whether these early life microbial communities and 3) serum cytokine profiles are influenced by prenatal vitamin and mineral (VTM) supplementation. Samples were collected from the hoof, liver, lung, nasal cavity, eye, rumen (tissue and fluid), and vagina of beef calves that were born from dams that either received or did not receive VTM supplementation throughout gestation (n = 7/group). Calves were separated from dams immediately after birth and fed commercial colostrum and milk replacer until euthanasia at 30 h post-initial colostrum feeding. The microbiota of all samples was assessed using 16S rRNA gene sequencing and qPCR. Calf serum was subjected to multiplex quantification of 15 bovine cytokines and chemokines. Our results indicated that the hoof, eye, liver, lung, nasal cavity, and vagina of newborn calves were colonized by site-specific microbiota, whose community structure differed from the ruminal-associated communities (0.64 ≥ R2 ≥ 0.12, p ≤ 0.003). The ruminal fluid microbial community was the only one that differed by treatment (p < 0.01). However, differences (p < 0.05) by treatment were detected in microbial richness (vagina); diversity (ruminal tissue, fluid, and eye); composition at the phylum and genus level (ruminal tissue, fluid, and vagina); and in total bacterial abundance (eye and vagina). From serum cytokines evaluated, concentration of chemokine IP-10 was greater (p = 0.02) in VTM calves compared to control calves. Overall, our results suggest that upon birth, the whole-body of newborn calves are colonized by relatively rich, diverse, and site-specific bacterial communities. Noticeable differences were observed in ruminal, vaginal, and ocular microbiota of newborn calves in response to prenatal VTM supplementation. These findings can derive future hypotheses regarding the initial microbial colonization of different body sites, and on maternal micronutrient consumption as a factor that may influence early life microbial colonization.

Genomic and Functional Characterization of Longitudinal Pseudomonas aeruginosa Isolates from Young Patients with Cystic Fibrosis.

Individuals with cystic fibrosis (CF) suffer from frequent and recurring microbial airway infections. The Gram-negative bacterium Pseudomonas aeruginosa is one of the most common organisms isolated from CF patient airways. P. aeruginosa establishes chronic infections that persist throughout a patient's lifetime and is a major cause of morbidity and mortality. Throughout the course of infection, P. aeruginosa must evolve and adapt from an initial state of early, transient colonization to chronic colonization of the airways. Here, we examined isolates of P. aeruginosa from children under the age of 3 years old with CF to determine genetic adaptations the bacterium undergoes during this early stage of colonization and infection. These isolates were collected when early aggressive antimicrobial therapy was not the standard of care and therefore highlight strain evolution under limited antibiotic pressure. Examination of specific phenotypic adaptations, such as lipid A palmitoylation, antibiotic resistance, and loss of quorum sensing, did not reveal a clear genetic basis for such changes. Additionally, we demonstrate that the geography of patient origin, within the United States or among other countries, does not appear to significantly influence genetic adaptation. In summary, our results support the long-standing model that patients acquire individual isolates of P. aeruginosa that subsequently become hyperadapted to the patient-specific airway environment. This study provides a multipatient genomic analysis of isolates from young CF patients in the United States and contributes data regarding early colonization and adaptation to the growing body of research about P. aeruginosa evolution in the context of CF airway disease. IMPORTANCE Chronic lung infection with Pseudomonas aeruginosa is of major concern for patients with cystic fibrosis (CF). During infection, P. aeruginosa undergoes genomic and functional adaptation to the hyperinflammatory CF airway, resulting in worsening lung function and pulmonary decline. All studies that describe these adaptations use P. aeruginosa obtained from older children or adults during late chronic lung infection; however, children with CF can be infected with P. aeruginosa as early as 3 months of age. Therefore, it is unclear when these genomic and functional adaptations occur over the course of CF lung infection, as access to P. aeruginosa isolates in children during early infection is limited. Here, we present a unique cohort of CF patients who were identified as being infected with P. aeruginosa at an early age prior to aggressive antibiotic therapy. Furthermore, we performed genomic and functional characterization of these isolates to address whether chronic CF P. aeruginosa phenotypes are present during early infection.

Emotional connection and ease of learning the Spanish language among young adult Chavacano speakers

Chavacano was the product of early Spanish colonization. It was able to adapt to the dynamic of the Philippine culture for centuries. Then, it later became a separate language spoken mostly in Cavite and Zamboanga Peninsula. This study was exploratory research that contextualize the ease of learning Spanish language based on linguistic, cultural, and emotional domains. Eight students who are native Chavacano speakers in Zamboanga City were interviewed for the study. The findings indicated that the close resemblance of lexical and phonological components of Chavacano to Spanish influenced the learning of the native speakers. Cognates played an essential role in cognition and interpreting basic words from Spanish to simpler ideas in Chavacano. Cognition guessing was determined to be a major contributor to language learning for orthographies. For native Chavacano speakers, cognition guessing was a mechanism for language learning in Spanish where learners happened to deduce the meaning of a word by comparing it to a language they know. Additionally, social-cultural relatedness between Chavacano and Spanish mediated the learning in certain manner. Learners were able to emotionally relate themselves to the culture of their target language which in turn influenced language transfer. Such mechanism was firstly observed in learning the second language but later also applied in bilingualism and foreign languages. This study established theoretical connection of ease of learning the Spanish language through phonology, lexical similarities, and its sociocultural resemblance to Chavacano.

A Globally Distributed Bacteroides caccae Strain Is the Most Prevalent Mother-Child Shared Bacteroidaceae Strain in a Large Scandinavian Cohort.

Bacteroides and Phocaeicola, members of the family Bacteroidaceae, are among the first microbes to colonize the human infant gut. While it is known that these microbes can be transmitted from mother to child, our understanding of the specific strains that are shared and potentially transmitted is limited. In this study, we aimed to investigate the shared strains of Bacteroides and Phocaeicola in mothers and their infants. We analyzed fecal samples from pregnant woman recruited at 18 weeks of gestation from the PreventADALL study, as well as offspring samples from early infancy, including skin swab samples taken within 10 min after birth, the first available fecal sample (meconium), and fecal samples at 3 months of age. We screened 464 meconium samples for Bacteroidaceae, with subsequent selection of 144 mother-child pairs for longitudinal analysis, based on the presence of Bacteroidaceae, longitudinal sample availability, and delivery mode. Our results showed that Bacteroidaceae members were mainly detected in samples from vaginally delivered infants. We identified high prevalences of Phocaeicola vulgatus, Phocaeicola dorei, Bacteroides caccae, and Bacteroides thetaiotaomicron in mothers and vaginally born infants. However, at the strain level, we observed high prevalences of only two strains: a B. caccae strain and a P. vulgatus strain. Notably, the B. caccae strain was identified as a novel component of mother-child shared strains, and its high prevalence was also observed in publicly available metagenomes worldwide. Our findings suggest that mode of delivery may play a role in shaping the early colonization of the infant gut microbiota, in particular the colonization of Bacteroidaceae members. IMPORTANCE Our study provides evidence that Bacteroidaceae strains present on infants' skin within 10 min after birth, in meconium samples, and in fecal samples at 3 months of age in vaginally delivered infants are shared with their mothers. Using strain resolution analyses, we identified two strains, belonging to Bacteroides caccae and Phocaeicola vulgatus, as shared between mothers and their infants. Interestingly, the B. caccae strain showed a high prevalence worldwide, while the P. vulgatus strain was less common. Our findings also showed that vaginal delivery was associated with early colonization of Bacteroidaceae members, whereas cesarean section delivery was associated with delayed colonization. Given the potential for these microbes to influence the colonic environment, our results suggest that understanding the bacterial-host relationship at the strain level may have implications for infant health and development later in life.

Succession of Fungal Community during Outdoor Deterioration of Round Bamboo

Bamboo’s mechanical and aesthetic properties are significantly influenced by fungi. However, few studies have been conducted to investigate the structure and dynamics of fungal communities in bamboo during its natural deterioration. In this study, fungal community succession and characteristic variations of round bamboo in roofed and unroofed environments over a period of 13 weeks of deterioration were deciphered using high-throughput sequencing and multiple characterization methods. A total of 459 fungal Operational Taxonomic Units (OTUs) from eight phyla were identified. The fungal community’s richness of roofed bamboo samples showed an increasing trend, whereas that of unroofed bamboo samples presented a declining trend during deterioration. Ascomycota and Basidiomycota were the dominant phyla throughout the deterioration process in two different environments: Basidiomycota was found to be an early colonizer of unroofed bamboo samples. Principal Coordinates Analysis (PCoA) analysis suggested that the deterioration time had a greater impact on fungal community variation compared to the exposure conditions. Redundancy analysis (RDA) further revealed that temperature was a major environmental factor that contributed to the variation in fungal communities. Additionally, the bamboo epidermis presented a descending total amount of cell wall components in both roofed and unroofed conditions. The correlation analysis between the fungal community and relative abundance of three major cell wall components elucidated that Cladosporium was negatively correlated with hemicellulose in roofed samples, whereas they presented a positive correlation with hemicellulose and a negative correlation with lignin in unroofed samples. Furthermore, the contact angle decreased during the deterioration process in the roofed as well as unroofed samples, which could arise from the degradation of lignin. Our findings provide novel insights into the fungal community succession on round bamboo during its natural deterioration and give useful information for round bamboo protection.

Evolutionary and ecologic controls on benthos distribution from an upper Cambrian incised estuarine valley: Implications for the early colonization of marginal-marine settings

Estuarine deposits of the Furongian Pico de Halcón Member of Argentina contain trace and body fossils that allow assessing the role of evolutionary and environmental factors on early colonization of marginal-marine environments. The outer region of the estuary was characterized by a subtidal sandbody flanked by tidal flats. Vertical burrows of suspension feeders and probably passive predators are abundant in the high-energy areas of the outer estuary. Horizontal trilobite and vermiform trace fossils record the activities of mobile deposit, detritus, and suspension feeders in more protected settings. Arthropod trackways, vertical burrows, and horizontal vermiform burrows have been recorded in middle estuarine deposits. The occurrence of trackways attests the ability of some late Cambrian marine arthropods to periodically migrate inland following tidal channels or via salt-water wedges. No trace and body fossils have been found in inner valley areas. Outer and middle estuarine deposits contain the trilobite Neoparabolina frequens argentina. Its record in brackish-water settings is envisaged as a result of its generalist nature and ability (physiologic or behavioral) to cope with a wide array of conditions, flexible resource requirements, and successful spreading.Although trace-fossil distribution along the salinity gradient reflects the basics of the “brackish-water model”, the remarkably low ichnodiversity in the middle estuary and the lack of trace fossils in the inner estuary are interpreted as reflecting evolutionary controls. Teichichnus assemblages, forming monospecific occurrences or with Planolites, in fine-grained, heterolithic facies seem to be remarkably persistent through geologic time. The studied trace fossils yield insights on attempts of some clades to expand into stressful brackish-water settings early in their evolutionary histories. In addition, comparison of the environmental tolerance of the Furongian benthos with other occurrences in younger early Paleozoic estuarine settings allows to track early steps of the colonization of brackish-water environments as it developed during the Ordovician Radiation.

Nutrient availability and acid erosion determine the early colonization of limestone by lithobiontic microorganisms.

Microorganisms, including the pioneer microorganisms that play a role in the early colonization of rock, are extremely important biological factors in rock deterioration. The interaction of microorganisms with limestone leads to biodeterioration, accelerates soil formation, and plays an important role in the restoration of degraded ecosystems that cannot be ignored. However, the process of microbial colonization of sterile limestone in the early stages of ecological succession is unclear, as are the factors that affect the colonization. Acid erosion (both organic and inorganic), nutrient availability, and water availability are thought to be key factors affecting the colonization of lithobiontic microorganisms. In this study, organic acid (Oa), inorganic acid (Ia), inorganic acid + nutrient solution (Ia + Nut), nutrient solution (Nut), and rain shade (RS) treatments were applied to sterilized limestone, and the interaction between microorganisms and limestone was investigated using high-throughput sequencing techniques to assess the microorganisms on the limestone after 60 days of natural placement. The results were as follows: (1) The abundance of fungi was higher than that of bacteria in the early colonization of limestone, and the dominant bacterial phyla were Proteobacteria, Bacteroidota, and Actinobacteriota, while the dominant fungal phyla were Ascomycota, Basidiomycota, and Chytridiomycota. (2) Acid erosion and nutrient availability shaped different microbial communities in different ways, with bacteria being more sensitive to the environmental stresses than fungi, and the higher the acidity (Ia and Oa)/nutrient concentration, the greater the differences in microbial communities compared to the control (based on principal coordinate analysis). (3) Fungal communities were highly resistant to environmental stress and competitive, while bacterial communities were highly resilient to environmental stress and stable. In conclusion, our results indicate that limestone exhibits high bioreceptivity and can be rapidly colonized by microorganisms within 60 days in its natural environment, and both nutrient availability and acid erosion of limestone are important determinants of early microbial colonization.

Settlement of the Tropical Box Mussel, Septifer bilocularis: Effects of Site, Position, and Substratum

The box tropical mussel Septifer bilocularis lives attached to a hard substratum, forming a dense aggregation or patch. The aggregation occurs at the time of larvae settlement in response to different cues. Larvae may have a positive response whereas larvae may settle and attach to the substratum, while in a negative response, postpone settling occurs. Byssus threads are produced and attached to the substratum, and for some reason, they are affected by many variables. We studied whether the attachment was affected by sites, position in the patch, and substratum. Large and small patches of mussel beds were selected arbitrarily, each in 3 replicates. Substrata of palm, coconut, polypropylene fibres, and mussel shells with byssus threads, each in 4 replicates, were distributed randomly into a PVC plate with 16 holes. The PVC plates with experimental substrata were placed along the edge and in the middle of large and small patches. A three-factorial ANOVA was then performed on samples of sites, position in patches, and substratum as main effects. A significant effect of sites, position within patches, and substratum as well were found. A significantly high number of new settlers in small patches than in other positions within patches occurred. The larger number of new settlers was found on coconut, palm, and polypropylene fibres, while low numbers on the mussel shells with byssus threads were found. The new settlers of S. bilocularis (&lt;1 mm) with transparent shells were observed attached to coconut, palm, and polypropylene fibres. In contrast, the new settlers ranged from &gt;1 mm to 3 mm with dark green shells attached to mussel shells with byssus threads. This study suggests that early settlement occurs when mussels’ larvae first settle and attach to coconut, palm, and polypropylene fibres before reattaching to adult shells with byssus threads.

Preliminary study of microRNA expression profiling in non-metastatic colorectal cancer.

e15528 Background: MicroRNAs (miRNAs) are non-coding single-stranded RNAs (18–25 nucleotides in length) that regulate gene expression at the posttranscriptional level by promoting the degradation of mRNAs or by blocking mRNA translation. However, the clinical significance in colon cancer is not yet determined. This study aims to identify differentially expressed miRNAs in colorectal cancer by comparing colon cancerous tissues with normal tissues, exploring the potential roles. Methods: The miRNA expression microarray was employed on tumors from patients diagnosed with adenocarcinoma of the colon. The pilot study included samples from 6 patients (3 women and 3 men), aged 55 to 72 years (mean 62.5±8.4 years). The tumour was located in the rectum, TNM status was as follows: cT (all patients at stage T3), cN (3 patients – N1, 3 patients – Nx), cM (all patients at stage M0). Average tumor size 4.6±2.5 cm. Normal colon tissue was used as a control. The studies were performed with the consent of the patient and according to the protocol accepted by the Bioethics Committee at the Medical University of Lublin No. KE-0254/12/2018. The material was collected during tumor removal surgery, then transported and stored in RNAlater. In the next step, microRNAs were isolated using the RNeasy Micro Kit (Qiagen). The quality and quantity of isolated RNA was assessed with NanoDrop 2000c followed by Bioanalyzer 2100 (Agilent), for the next step samples with RIN above 7. The microRNA expression profile was then evaluated using the GeneChip™ miRNA 4.0 Array (Applied Biosystems). Results: On the basis of a pilot microarray study, the profile of differentially expressed miRNAs was successfully screened. 1.39% of 36 222 tested genes showed a significant at least twofold increase in expression, while 1.75% showed a significant at least twofold decrease in expression. Three novel, not yet described in literature, miRNAs i.e. miR-3154 (p-value 0.015), miR-3921 (p-value 0.036), and miR-5006 (p-value 0.007) appeared to be involved in colorectal carcinogenesis. Conclusions: The present study suggests that mentioned miRNAs after confirmation on a greater group of patients may be used as diagnostic markers for the detection of early stage colon cancer in the general population. This paper was created as part of the project “The Best of the Best! 4. 0.” implemented under the Operational Programme: Knowledge Education Development 2014-2020 and co-financed by the European Social Fund.

Electronic frailty index predicts 30-day mortality from chemotherapy in breast, colorectal and lung cancer.

12009 Background: Older and frail patients with cancer (Ca) often receive less aggressive treatment and as a result have worse survival. Current methods of assessing fitness (performance status) for intensive treatment such as chemotherapy are inadequate. The complexity of geriatric assessments, lack of training and time pressures in busy clinics, mean that better solutions are needed. A UK initiative - the electronic frailty index (eFI) - is derived from a cumulative deficit frailty model and provides a measure of frailty alongside pre-existing conditions such as issues with mobility, fractures, falls, memory, sight, hearing , anaemia, tremor, diabetes, heart, thyroid, skin, respiratory, cerebrovascular, circulation, social vulnerability, and polypharmacy (36 fields) (Clegg et al). Patients are classified into the following groups: no frailty, mild, moderate or severe frailty. We used the same methodology to investigate whether eFI predicts adverse outcomes of chemotherapy in frail patients with Ca. Methods: The study conducted retrospective data analysis of Ca patients treated with chemotherapy from Public Health England (PHE) Systemic Chemotherapy Dataset (SACT) years 2015-2018. Eligible patients had stage II - III breast Ca, stage III colon Ca or stage IIIB–IV non-small-cell lung Ca (NSCLC). The data from SACT was linked with hospital episodes' statistics (obtained from NHS-Digital) to calculate 30-day SACT mortality, overall survival and hospital admissions. EFI was calculated from the above 35 fields; polypharmacy was not available from NHS-Digital data. Results: The eFI was calculated for 78799 patients: colorectal 17951, lung 22052, and breast 38796. 20388 patients were ≥ 70y. o. and 58411 were &lt; 70y.o. Most patients were fit with an eFI score of 0-69% (54563), 19% (15,295) had mild frailty, 7.7% (6104)- moderate, and 3.6% (2837) had severe frailty. 4.2% (3356) of patients died within 30 days of SACT. For colorectal Ca patients the risk of dying within 30 days of SACT in patients ≥70y.o was twice that of the &lt; 70y.o (OR 2.04 -CI 1.58 - 2.64); patients with mild eFI did not differ- OR: 1.07 (CI 0.78-1.45), moderate frailty: 1.6 (CI 1.1-2.33) and severe frailty: 2.13 (CI 1.34-3.39). In breast Ca patients, 30-day mortality for ≥70y.o. was 6.38 times higher than for &lt; 70y.o (95% CI 4.29-9.49); eFI for mild frailty- OR of 1.45 (95% CI 0.78-2.71), moderate frailty-OR of 3.5 (95%CI 1.82-6.75) and severe frailty 5.73 (95% CI 2.66-12.3). The 30-day mortality in lung cancer in ≥70y.o and &lt; 70y.o did not differ with OR 0.95 (95% CI 0.88-1.03) for ≥70y.o. Patients with mild frailty had OR for 30-day mortality of 1.17 (95% CI 1.07-1.28), moderate frailty-OR of 1.28 (95%CI 1.15-1.44) and severe frailty 1.48 (95% CI 1.28-1.77). Conclusions: The eFI closely predicts poor outcomes from SACT, particularly in early breast and colon cancer, and requires further evaluation in a prospective study.