Biology subjects

Silamikelis, I.

Publications and source records attributed to Silamikelis, I..

6 recordsLinked to original sources

bioRxiv2025

Colorectal adenoma presence is associated with decreased menaquinone pathway functions in the gut microbiome of patients undergoing routine colonoscopy

BackgroundColorectal cancer (CRC) is among the most common malignancies worldwide, with colorectal adenomas recognized as well-established precursors to CRC. Changes in gut microbiota appear to be linked to CRC by promoting chronic inflammation, immune dysfunction, and metabolic issues that drive tumor growth and progression. ObjectivesTo explore the relationship between gut microbiome composition and the presence of colorectal adenomas in patients undergoing routine colonoscopy. Materials and methodsPatients were selected from those receiving standard colonoscopy based on strict inclusion and exclusion criteria, to minimize potential confounding factors such as previous colorectal surgeries, inflammatory bowel diseases, and the use of antibiotics or probiotics. Fecal samples were collected before bowel preparation for the colonoscopy procedure, and metagenomic shotgun sequencing was used to analyze the composition and functions of the gut microbiome. ResultsOverall, 136 participants were recruited, and 56 of them had colorectal adenomas. Although no distinction was observed in alpha diversity, beta diversity analysis indicated significant differences between the adenoma-positive and adenoma-negative groups. Signs of dysbiosis were found in patients with adenomas: increased abundance of the genera Bacteroides and Prevotella and decreased abundance of Faecalibacterium and Anaerostipes species. Beta diversity analysis showed statistically significant differences in the structure of the microbiota. Significant differences in the relative abundance of UBA7597 sp003448195 were observed between groups. Functionally, decreased vitamin K2, SCFA (propionate) synthesis, along with lower Stickland fermentation activity was observed, indicating altered microbial metabolism. These changes may compromise epithelial barrier support, anti-inflammatory signaling, and energy metabolism in the colon. ConclusionsThe discovery of microbial taxa and functional pathways associated with the presence of adenomas underscores the potential of microbiota-based biomarkers and therapeutic strategies in the prevention and management of colorectal cancer.

bioinformatics↗

bioRxiv2024

Common mycelial network mediated inter-plant signals modulate plant biotic stress responses and defence against foliar pathogens

Arbuscular mycorrhizal fungi (AMF) are ubiquitous root symbionts that form common mycelial networks (CMN), linking multiple plants underground. CMN are hypothesized to play a role for information exchange between plants for neighbour-primed defences. However, the key transcriptomic and metabolome responses in receiver plant associated with inter-plant CMN connections remain yet to be elucidated. Additionally, the confounding effects of hyphal damage from CMN disconnection have not been clearly resolved. To uncover the contribution of CMN integrity to neighbour-primed plant defences, we used model AMF Rhizophagus irregularis to inter-connect two Medicago truncatula plants and explored the effect of sender wounding and flg22 elicitation on receiver plants leaf responses and pathogen tolerance. For the first time, we demonstrate that changes in receivers biotic stress and defence signalling pathways rely on CMN-mediated inter-plant signals, not on mycelial network damage. This response was associated with distinct leaf isoprenoid production, including volatile monoterpenes and triterpene saponins. Furthermore, CMN-mediated signals from stressed senders enhanced receiver resistance to Fusarium sporotrichoides whilst simultaneously increasing susceptibility to Botrytis cinerea. Our findings highlight the critical role of CMN in inter-plant signalling for pathogen-specific susceptibility and resistance which can be a key for understanding plant community-level defence in nature and agroecosystems.

plant biology↗

bioRxiv2024

Investigation of plant virus-like particle formation in bacterial and yeast expression systems

Virus-like particles (VLPs) have garnered significant attention due to their potential applications in various fields, particularly in biomedicine, where they are used for drug delivery, vaccine development, and as diagnostic tools. Plant virus-derived VLPs have been especially successful, leading to a surge in research aimed at developing new VLPs. Despite this growing interest, not all attempts at VLP formation are successful. Understanding the factors that contribute to successful VLP assembly is crucial for advancing this field. In this study, we focus on the coat proteins (CPs) of three plant viruses belonging to the Sobemovirus genus as a model to investigate the process of VLP formation. Our findings demonstrated that the strong binding of CPs to ssDNA can be a major reason for unsuccessful VLP production. This issue can potentially be overcome by transitioning from an episomal to a chromosome-integrated expression system. By doing so, we aim to elucidate the mechanisms that facilitate successful VLP assembly. Our findings provide valuable insights into the properties of sobemovirus CPs and highlight their potential for encapsulating foreign nucleic acids, thereby providing additional applications as nanocontainers or vaccine platforms with interior modification capabilities for enhanced immune response. Moreover, our RNA-Seq data indicates that sobemovirus-derived VLPs predominantly package their CP mRNA, irrespective of the expression system used. This characteristic can be utilized for the functional encapsulation of nucleic acids, enhancing the versatility and utility of these VLPs in various biotechnological applications.

molecular biology↗

bioRxiv2023

Ryegrass mottle virus complete genome determination and development of infectious cDNA by combining two methods - 3' RACE and 5' RACE-seq

Sobemovirus ryegrass mottle virus (RGMoV) is a single-stranded positive virus with a 30 nm viral particle size. It exhibits T=3 symmetry, with 180 coat protein (CP) subunits forming the virus structure. The RGMoV genome comprises five open reading frames, encoding P1, Px, a membrane-anchored 3C-like serine protease, a virus genome-linked protein, P16, an RNA-dependent RNA polymerase, and a coat protein. The RGMoV genome size varies, ranging from 4175 nt (MW411579.1) to 4253 nt (MW411579.1) in deposited sequences. An earlier deposited RGMoV complete genome sequence of 4212 nt length (EF091714.1) was utilized to develop an infectious complementary DNA (icDNA) construct for in vitro gRNA transcription from the T7 promoter. However, when the transcribed gRNA was introduced to oat plants, it failed to induce viral infection. This indicated the potential absence of certain sequences in either the 5 or 3 untranslated regions (UTR) or both. To resolve this, the complete sequence of the 3 UTR was determined through 3 end RACE, while the 5 UTR was identified using high-throughput sequencing (HTS) - 5 RACE-seq. Only the icDNA vector containing both newly identified UTR sequences proved infectious, resulting in classical viral infection symptoms and subsequent propagation of progeny viruses, exhibiting the ability to cause repeated infection in oat plants after at least one passage. The successful generation of the icDNA highlights the synergistic potential of utilizing both methods when one approach alone fails. Furthermore, this study demonstrates the reliability of HTS as a method for determining the complete genome sequence of viral genomes.

molecular biology↗

bioRxiv2022

OverFlap PCR - a reliable approach for generation of plasmid DNA libraries containing random sequences without template bias.

Over the decades the improvement of naturally occurring proteins and creation of novel ones has been the primary goal for many practical biotechnology researchers and it is widely recognized that randomization of protein sequences coupled to various effect screening methodologies is one of the most powerful techniques for fast, efficient and purposeful approach for acquisition of desired improvements. Over the years considerable advancements have been made in this field, however development of PCR based or template guided methodologies has been hampered by the resulting template sequence bias. In this article we present novel whole plasmid amplification based approach, which we named OverFlap PCR, for randomization of virtually any region of the plasmid DNA, without introduction of mentioned bias.

molecular biology↗

bioRxiv2020

Metformin strongly affects gut microbiome composition in high-fat diet-induced type 2 diabetes mouse model of both sexes

Effects of metformin, the first-line drug for type 2 diabetes therapy, on gut microbiome composition in type 2 diabetes have been described in various studies both in human subjects and animals. However, the details of the molecular mechanisms of metformin action have not been fully understood. Moreover, there is a significant lack of information on how metformin affects gut microbiome composition in female mice models, as most of the existing studies have focused on males only. Our study aimed to examine metformin-induced alterations in gut microbiome diversity and composition of high-fat diet-induced type 2 diabetes mouse model, employing a randomized block, factorial study design, and including 24 experimental units allocated to 8 treatment groups. We performed shotgun metagenomic sequencing using DNA obtained from fecal samples representing gut microbiome before and after ten weeks-long metformin treatment. We identified 100 metformin-related differentially abundant species in high-fat diet-fed mice before and after the treatment, with most of the species abundances increased. In contrast, no significant changes were observed in control diet-fed mice.We also observed sex-specific differences in response to metformin treatment. Males experienced more pronounced changes in metabolic markers, while, in females, the extent of changes in gut microbiome representatives was more marked, indicated by 53 differentially abundant species with more remarkable Log fold changes compared to the combined-sex analysis. Our results suggest that both sexes of animals should be included in future studies focusing on metformin effects on the gut microbiome.

microbiology↗