Biology subjects

Geiger, A.

Publications and source records attributed to Geiger, A..

5 recordsLinked to original sources

bioRxiv2026

Silvicultural practices and interannual variation shape ectomycorrhizal fungal diversity and community composition in an oak-hornbeam forest in northern Hungary

Ectomycorrhizal (ECM) fungi are well-known for their crucial roles in forest health and productivity, yet their responses to various forest management practices are understudied, particularly in oak-dominated forests. The purpose of this study was to better understand the effects of silvicultural treatments on the diversity and community composition of ECM fungi in an oak-hornbeam forest in northern Hungary. We analyzed ITS2 rDNA metabarcoding data of soil-borne fungi to compare richness and community composition of ECM fungi among forest treatment types (clear-cutting, gap-cutting, preparation-cutting, tree retention in clear-cut areas, and control) and between sampling years (2020 and 2021). We found 268 ECM fungal genotypes, with the most diverse phylogenetic clades being /russula-lactarius (52), /tomentella-thelephora (47), /inocybe (40), /sebacina (27), and /cortinarius (20). We found significant compositional difference of ECM fungi among silvicultural treatments in both years, with some variations in richness. There were also small, but still significant compositional differences between the two years. Treatment effect was partly explained by altered environmental variables, such as relative humidity and soil temperature. These results highlight the importance of forest structure and the abiotic environment in driving community dynamics of plant-symbiotic fungi, with potential implications for forest health and productivity.

ecology↗

bioRxiv2024

Enhancing gRNA Transcript levels by Reducing the Scaffold Poly-T Tract for Optimal SpCas9- and SaCas9-mediated Gene Editing

Ensuring sufficient gRNA transcript levels is critical for obtaining optimal CRISPR-Cas9 gene editing efficiency. The standard gRNA scaffold contains a sequence of four thymine nucleotides (4T), which is known to inhibit transcription from Pol III promoters such as the U6 promoter. Our study showed that using standard plasmid transfection protocols, the presence of these 4Ts did not significantly affect editing efficiency, as most of the gRNAs tested (55 gRNAs) achieved near-perfect editing outcomes. We observed that gRNAs with lower activity were T-rich and had reduced gRNA transcript levels. However, this issue can be effectively resolved by increasing transcript levels, which can be readily achieved by shortening the 4T sequences. In this study, we demonstrated this by modifying the sequences to 3TC. Although the 3TC scaffold modification did not improve editing efficiency for already efficient gRNAs when high vector quantities were available, it proved highly beneficial under conditions of limited vector availability, where the 3TC scaffold yielded higher editing efficiency. Additionally, we demonstrated that the 3TC scaffold is compatible with SpCas9 high-fidelity variants and ABEmax base editing, enhancing their editing efficiency. Another commonly used natural Cas9 variant, SaCas9, also benefited from the 3TC scaffold sequence modification, which increased gRNA transcription and subsequently improved editing activity. This modification was applied to the EDIT-101 therapeutic strategy, where it demonstrated marked improvements in performance. This study highlights the importance of shortening the 4T sequences in the gRNA scaffold to optimize gRNA transcript expression for enhanced CRISPR-Cas9 gene editing efficiency. This optimization is particularly important for therapeutic applications, where the quantity of vector is often limited, ensuring more effective and optimal outcomes.

molecular biology↗

bioRxiv2024

Test Retest Reliability of Meta Analytic Networks During Naturalistic Viewing

Functional connectivity analyses have given considerable insights into human brain function and organization. As research moves towards clinical application, test-retest reliability has become a main focus of the field. So far, the majority of studies have relied on resting-state paradigms to examine brain connectivity, based on its low demand and ease of implementation. However, the reliability of resting-state measures is mostly moderate, potentially due to its unconstrained nature. Recently, naturalistic viewing paradigms have gained popularity because they probe the human brain under more ecologically valid conditions, thereby possibly increasing reliability. Therefore, we here compared the reliability of graph metrics extracted from resting-state and naturalistic viewing in functional networks, across two sessions. We show that naturalistic viewing can increase reliability over resting-state, but that its effect varies between stimuli and networks. Furthermore, we demonstrate that the effect of naturalistic viewing differs between two cohorts with Asian and European cultural backgrounds. Taken together, our study encourages the use of naturalistic viewing to increase reliability, but emphasizes the need to carefully select the appropriate stimulus and network for the respective research question.

neuroscience↗

bioRxiv2020

Bacteriome diversity of blackflies gut and association with Onchocerca volvulus, the causative agent of onchocerciasis in Mbam valley (Center Region, Cameroon)

BackgroundVector control using larvicides is the main alternative strategy to address limits of preventive chemotherapy using ivermectin to fight onchocerciasis. However, it remains substantially limited by implementation difficulties, ecological concerns and resistance of vector populations. Therefore, efficient and environmentally safe alternative control strategies are still needed. This study explores the role of blackfly bacterial communities both on vector competence and refractoriness to O. volvulus infection in order to determine their potential as a novel vector control-based approach to fight onchocerciasis. Principal findingsA total of 1,270 blackflies were dissected and the infection rate was 10.1%, indicative of ongoing transmission of onchocerciasis in the surveyed communities. Sequencing process revealed 19 phyla and 210 genera, highlighting the diversity of gut blackflies bacterial communities. Wolbachia was the predominant genus with 70% of relative abundance of blackflies gut bacterial communities. Serratia sp and Acidomonas genera were significantly abundant among infected blackflies (p=0.043 and p=0.027, respectively), whereas other genera as Brevibacterium were associated with the absence of infection (p=0.008). Conclusion/SignificanceThis study revealed that blackfly native bacteria are potentially involved in infection by O. volvulus, either by facilitating or preventing the parasite infestation of the vector. These bacteria represent an interesting potential as a biological target for a novel approach of vector control to fight onchocerciasis. Author summaryStudies of arthropods involved in vector-borne diseases (tsetse flies, mosquitoes, and drosophila) demonstrated the importance of their native bacteria either to ease infection and transmission of human pathogenic microorganisms including parasites or on the contrary to induce host protective effects against these parasites. Indeed, some native bacteria of arthropod vectors are now recognized to be associated either with the resistance of their hosts to parasitic infections, or the reduction of their hosts viability in case of the parasite infestation, thus highlighting the potential of such bacteria to be used as biological tool for vector control strategies. However, such bacteria have never been described on blackfly, an arthropod transmitting Onchocerca volvulus, which is the parasite responsible of onchocerciasis commonly known as river blindness. This study aimed to fill this gap by investigating the bacterial diversity of blackfly bacteriome and describing the possible role of bacteria communities in susceptibility/resistance features of the blackflies to O. volvulus infection, and therefore their potential as biological targets or tool for vector control. The screening of these blackflies native bacteria during this study, highlighted some bacteria genera of interest with significant association either with the absence of O. volvulus in blackfly or with vector infection.

molecular biology↗

bioRxiv2020

Confronting the COVID-19 Pandemic with Systems Biology

Using a Systems Biology approach, we integrated genomic, transcriptomic, proteomic, and molecular structure information to provide a holistic understanding of the COVID-19 pandemic. The expression data analysis of the Renin Angiotensin System indicates mild nasal, oral or throat infections are likely and that the gastrointestinal tissues are a common primary target of SARS-CoV-2. Extreme symptoms in the lower respiratory system likely result from a secondary-infection possibly by a comorbidity-driven upregulation of ACE2 in the lung. The remarkable differences in expression of other RAS elements, the elimination of macrophages and the activation of cytokines in COVID-19 bronchoalveolar samples suggest that a functional immune deficiency is a critical outcome of COVID-19. We posit that using a non-respiratory system as a major pathway of infection is likely determining the unprecedented global spread of this coronavirus. One Sentence SummaryA Systems Approach Indicates Non-respiratory Pathways of Infection as Key for the COVID-19 Pandemic

systems biology↗