Biology subjects

Nikolic, D.

Publications and source records attributed to Nikolic, D..

6 recordsLinked to original sources

bioRxiv2025

Outer Membrane Vesicles (OMVs) Produced by Plant Beneficial Rhizospheric Bacteria Enter Root Epidermal Cells

Extracellular vesicles (EVs) are shown to play an important role in the interaction between bacteria and human cells, as well as between fungi and plants; however, much less is known about their role in plant-bacteria relations. Outer membrane vesicles (OMVs), EVs produced by Gram-negative bacteria, were shown to have both immuno-activating and immuno-suppressive effects on plants, and a direct interaction of OMVs with plant cell membranes was shown for one phytopathogenic bacterial strain. Data on OMVs participation in the symbiotic relationship between plant-beneficial bacteria and plants are even more limited, and are mainly related to the rhizobia-legume interaction. To investigate the interaction of OMVs of non-rhizobial phytobeneficial bacteria with plant cells, we isolated and characterized OMVs produced by Paraburkholderia phytofirmans PsJN, a strain well known for its growth-promoting and stress-protective effects in a wide range of plant species. Using OMVs labelled with fluorescent lipid-binding dye VybrantTM DiD and confocal laser scanning microscopy, we showed that PsJN-OMVs interact directly with the root hairs and epidermal cells of Arabidopsis thaliana and tomato. Moreover, by employing octadecyl-rhodamine B chloride (R18), we demonstrated that PsJN-OMVs can fuse with plant cell membranes. The findings presented in our study are an important step in elucidating the potential role of OMVs in the early stages of root colonization and the establishment of symbiotic relationships. Increasing our understanding in this area could pave the way for the use of these nano-vehicles to develop eco-friendly solutions for overcoming environmental challenges and supporting sustainable agriculture.

plant biology↗

bioRxiv2024

Enable, Empower, Succeed: Harnessing Open Science for Antimicrobial Resistance Containment

Antimicrobial resistance (AMR) poses a significant threat to global health, particularly in Western sub-Saharan Africa where 27.3 deaths per 100,000 lives are affected, and surveillance and control measures are often limited. Genomics research plays a crucial role in understanding the emergence, spread and containment measures of AMR. However, its implementation in such settings is particularly challenging due to limited human capacity. This manuscript outlines a three-day bioinformatics workshop in Cameroon, highlighting efforts to build human capacity for genomics research to support AMR surveillance using readily accessible and user-friendly web-based tools. The workshop introduced participants to basic next-generation sequencing concepts, data file formats used in bacterial genomics, data sharing procedures and considerations, as well as the use of web-based bioinformatics software to analyse genomic data, including in silico prediction of AMR, phylogenetics analyses, and a quick introduction to Linux(C) command line. We provide a detailed description of the relevant training approaches used, including workshop structure, the selection and planning, and utilization of freely available web-based tools, and the evaluation methods employed. Our approach aimed to overcome limitations such as inadequate infrastructure, limited access to computational resources, and scarcity of expertise. By leveraging the power of freely available web-based tools, we demonstrated how participants can acquire fundamental bioinformatics skills, enhance their understanding of biological data analysis, and contribute to the field, even in an underprivileged environment. Our findings highlight the effectiveness of this training approach in empowering local researchers and bridging the bioinformatics gap in genomics surveillance of AMR in resource-constrained settings. Building human capacity for genomics research globally, and especially in resource-constrained settings, is imperative for ensuring global health and sustainable containment of AMR. Data summaryThe authors confirm that all supporting data, code and protocols have been provided within the article or through supplementary data files. Impact StatementAntimicrobial resistance (AMR) is a major global health threat, especially in Western sub-Saharan Africa, where 27.3 deaths per 100,000 lives occur. Genomics research play an instrumental role for understanding AMRs emergence, spread, and containment measures. However, its implementation in these settings is challenging due to limited human capacity. A three-day bioinformatics workshop in Cameroon aimed to build human capacity for genomics research using web-based tools. Participants were introduced to next-generation sequencing concepts, data file formats, data sharing procedures, and web-based bioinformatics software for analysing genomic data. The workshop aimed to overcome limitations like inadequate infrastructure, computational resources, and expertise scarcity. The findings show the effectiveness of this training approach in empowering local researchers and bridging the bioinformatics gap in genomics surveillance of AMR in resource-constrained settings.

scientific communication and education↗

bioRxiv2021

Train-the-Trainer as an Effective Approach to Building Global Networks of Experts in Genomic Surveillance of AMR

Advanced genomics and sequencing technologies are increasingly becoming critical for global health applications such as pathogen and antimicrobial resistance (AMR) surveillance. Limited resources challenge capacity development in low- and middle-income countries (LMICs), with few countries having genomics facilities and adequately trained staff. Training research and public health experts who are directly involved in the establishment of such facilities offers an effective, but limited, solution to a growing need. Instead, training them to impart their knowledge and skills to others provides a sustainable model for scaling up the much needed capacity and capability for genomic sequencing and analysis locally with global impact. We designed and developed a Train-the-Trainer course integrating pedagogical aspects with genomic and bioinformatics activities. The course was delivered to 18 participants from 12 countries in Africa, Asia, and Latin America. A combination of teaching strategies culminating in a group project created a foundation for continued development at home institutions. Upon follow-up after 6 months, at least 40% of trainees had initiated training programs and collaborations to build capacity at local, national, and regional level. This work provides a framework for implementing a training and capacity building program for the application of genomics tools and resources in AMR surveillance. 40-word summaryThis work provides a framework for implementing a training and capacity building program for the application of genomics tools and resources in AMR surveillance. We outline a Train-the-Trainer course integrating pedagogical aspects with genomic and bioinformatics activities.

scientific communication and education↗

bioRxiv2019

Quickly fading afterimages: hierarchical adaptations in human perception

Afterimages result from a prolonged exposure to still visual stimuli. They are best detectable when viewed against uniform backgrounds and can persist for multiple seconds. Consequently, the dynamics of afterimages appears to be slow by their very nature. To the contrary, we report here that about 50% of an afterimage intensity can be erased rapidly--within less than a second. The prerequisite is that subjects view a rich visual content to erase the afterimage; fast erasure of afterimages does not occur if subjects view a blank screen. Moreover, we find evidence that fast removal of afterimages is a skill learned with practice as our subjects were always more effective in cleaning up afterimages in later parts of the experiment. These results can be explained by a tri-level hierarchy of adaptive mechanisms, as has been proposed by the theory of practopoiesis.

neuroscience↗

bioRxiv2018

Visual exposure optimizes stimulus encoding in primary visual cortex

The brain adapts to the sensory environment. For example, simple sensory exposure can modify the response properties of early sensory neurons. How these changes affect the overall encoding and maintenance of stimulus information across neuronal populations remains unclear. We perform parallel recordings in the primary visual cortex of anesthetized cats and find that brief, repetitive exposure to structured visual stimuli enhances stimulus encoding by decreasing the selectivity and increasing the range of the neuronal responses that persist after stimulus presentation. Low-dimensional projection methods and simple classifiers demonstrate that visual exposure increases the segregation of persistent neuronal population responses into stimulus-specific clusters. These observed refinements preserve the representational details required for stimulus reconstruction and are detectable in post-exposure spontaneous activity. Assuming response facilitation and recurrent network interactions as the core mechanisms underlying stimulus persistence, we show that the exposure-driven segregation of stimulus responses can arise through strictly local plasticity mechanisms, also in the absence of firing rate changes. Our findings provide evidence for the existence of an automatic, unguided optimization process that enhances the encoding power of neuronal populations in early visual cortex, thus potentially benefiting simple readouts at higher stages of visual processing.

neuroscience↗

bioRxiv2017

Dynamics of pollen tube growth and embryo sac development in Pozna Plava plum cultivar related to fruit set

A newly released, late ripening plum cultivar Pozna Plava sets fruit poorly, although it produces high quality fruit. This study aimed to evaluate which factors in the reproductive process could be related to the lack of fruit set. In two consecutive years, establishment of a suitable polleniser and the stage of ovule development at anthesis as well as initial and final fruit set have been studied. In addition to this, the impact made by temperature fluctuations on the interaction between male gametophytes and female sporophytes was also analysed. Growth of the pollen tubes in the style and penetration into the nucellus as well as fruit set were more effective in cross-pollination than in open and self-pollination. A relative delay in ovule development was observed, and most ovules had an embryo sac with eight nuclei. Considering the results of the quantitiative parameter study of pollen tube growth in the ovary as well as the results of the stage of ovule development, a conclusion can be made that this cultivar is characterised by an extremely short effective period of pollination.

plant biology↗