ABSTRACTS 1) How to prepare samples for electron microscope without killing yourself[LŠ1] The process of sample preparation for electron microscopes requires many steps including possibl[INS: e :INS] [DEL: y :DEL] [DEL: frightening and :DEL] dangerous [LŠ2] procedures. In this presentation, two sample preparation processes will be briefly introduced with a special focus on potentially dangerous steps[INS: , :INS] [DEL: . :DEL] [INS: n :INS] [DEL: N :DEL] amely, the preparation of plant chromosomes for [INS: electron microscope :INS] scanning [DEL: electron microscope :DEL] [DEL: will be presented followed by :DEL] [INS: and :INS] [DEL: :DEL] protein sample preparation for transmission cryoelectron tomography. The difference between scanning and transmission electron microscope requirements will [DEL: also :DEL] be [DEL: mentioned :DEL] [INS: addressed :INS] . 2) Piece by piece: Creating the[LŠ3] picture of organism response to metal nanoparticles with different methods Lead and cadmium are environmental pollutants causing harmful effects in multiple organ systems. [DEL: However :DEL] [INS: Although :INS] [DEL: , :DEL] the toxic effects of their nanoforms are not yet fully known[INS: , :INS] [DEL: and :DEL] [INS: :INS] it has been determined that they have a unique inflammatory blueprint. In this presentation, the design of [DEL: the :DEL] inhalation experiments using whole-body inhalation chambers with female mice will be introduced, together with the wide spectrum of different methods used for investigating organism response to metal nanoparticles exposure. Various methods for the proper[LŠ4] evaluation of samples include: biochemical analyses, immunohistochemistry and immunofluorescence, Western blot, qPCR, RNA Scope, transmission electron microscopy, atomic absorption spectrometry, LA-ICP-MS and lipid LC-MS. [INS: A c :INS] [DEL: C :DEL] ombination [LŠ5] of these advanced methodological approaches will expand knowledge about pathological changes in the organs. 3) [INS: A n :INS] [DEL: N :DEL] ew insight into molecular functions of AGR2 in colorectal cancer In recent years, the role of Anterior gradient protein AGR2 in tumour development and progression has be[INS: en :INS] [DEL: come :DEL] [INS: studied :INS] more intensively[DEL: studied :DEL] . The contribution of AGR2 to malignant transformation, drug resistance and the development of metastases ha[INS: s :INS] [INS: [LŠ6] :INS] [DEL: ve :DEL] already been reported by others as well as our group. However, the mechanism of [INS: the/its :INS] action[INS: s :INS] [LŠ7] and the scope of AGR2 functions remain largely unclear especially in colorectal cancer (CRC) where the role of AGR2 has been minimally studied. This project aims to i) elucidate the molecular reprogramming of AGR2 expression during metastasis, ii) clarify the molecular pathways associated with AGR2 in cell adhesion and iii) describe the role of AGR2 in regulating gene expression at the post-transcriptional level through RNA-protein interactions. Together th[INS: ese :INS] [DEL: is :DEL] could bring new findings contributing to the understanding of these complex mechanisms and may help in future research or even diagnosis and treatment of colorectal cancer on which this project is focused 4) Know your enemy: Bringing the infection cycle of human enteroviruses to light Echovirus 18 (E18) is a common cause of encephalitis and meningitis. However, the structure and life cycle of E18 and many other viruses from Enterovirus genera are still unknown.[LŠ8] The in vitro approach of virus purification lacks information [DEL: on :DEL] [INS: about/regarding :INS] the replication cycle of the virus in natural conditions. In this project, the focused-ion beam milling (FIBM) is used to create lamellas within the infected cells and image them using cryogenic electron tomography (cryo-ET). [INS: A :INS] 3D reconstruction of cell sections identifies the structure of the replicating viruses and their intermediate states and addresses the morphological changes of the infected cells in situ. Data [DEL: of :DEL] [INS: regarding :INS] human echovirus 18 might serve as a reference for further experiments on other enterovirus species. Th[INS: is :INS] [DEL: e :DEL] research [DEL: might :DEL] [INS: may :INS] [INS: [LŠ9] :INS] [INS: :INS] lead to a better understanding of virus biology and enabling the development of antiviral treatment 5) Exploring cell wall proteins in plants The cell wall is an important structure for plants as it determines [DEL: a :DEL] [INS: the :INS] shape of cells, enables a connection of cells, [INS: and :INS] provides a basic mechanical strength. The cell wall consists of biopolymers such as cellulose, pectins and lignin. Cellulose and lignin are the most abundant polymers on Earth and their modifications have an application in a wide range of industries such as food, paper, textiles [DEL: or :DEL] [INS: and :INS] [INS: [LŠ10] :INS] [INS: :INS] pharmaceutical industries. In the cell wall, many proteins can be found including expansins. Expansins are cell wall-loosening proteins activated during cell wall acidification, first described in cucumber seedlings. Expansins are known to disrupt bonds in the cell wall structure. To investigate the cell wall biomechanical properties of plants, Gateway cloning strategy was used, as well as, [INS: a :INS] chemically inducible activation system which was devised to regulate transgene expression in plants. [INS: In addition to :INS] [DEL: Apart from :DEL] these methods, confocal laser scanning microscopy and GUS staining were applied and will be included in this presentation. Initial results show the expression pattern of expansin 1 in different tissue layer of plants. 6) Can we do science without animal testing? Research involving laboratory animals is [INS: considered :INS] necessary to ensure human and animal health and to protect the environment. In the absence of human data, it is the most reliable methodology [DEL: to :DEL] [INS: when :INS] detect[INS: ing :INS] important toxic properties of chemicals and [DEL: to :DEL] estimat[INS: ing :INS] [DEL: e :DEL] risks to human and environmental health. Animal research can be debated on many grounds: ethical reasons, utility, reliability, price. These points are crucial to deciding whether animal testing should be conducted, but it does not stop the fact that it is currently happening. In 2014, approximately 7 million animals were used in research and teaching in Australia. In the U.S, approximately 1 million animals were used. However, this value [DEL: is :DEL] exclud[INS: es :INS] [DEL: i :DEL] [DEL: ng :DEL] mice, birds, and rats- these other excluded animals could account for up to 90% of the actual testing done. Computer modeling is a promising field. Modeling can be used to do disease and treatment in silico tests and interpret data from human clinical trials. Bioinformatics is also a growing field using similar technologies. In vitro technologies like organs-on-chips aim to mimic the functions and microstructure of human’s living organs. There are several new technologies being used and the question still remains: can we do science without animal testing? 7) Exons in, introns out: The importance of correct splicing Splicing is one of the post-transcriptional modifications that transform[INS: s :INS] the precursor mRNA to mature mRNA that can be translated into [DEL: the :DEL] functional protein. During splicing, introns (non-coding regions) are removed and exons (coding regions)[INS: :INS] are joined together [DEL: thanks :DEL] [INS: due :INS] [INS: [LŠ11] :INS] [INS: :INS] to the splicing machinery known as spliceosome. The correct recognition of exons is driven by many factors, especially by splice sites quality, exon length, secondary mRNA structure, or presence of splicing regulatory elements. Even a single point mutation can influence the spliceosomal function. In this presentation, the basic conditions of the splicing process will be introduced with a more detailed focus on pseudoexons –activation events, methodology, and effects of pseudoexon inclusion on human genetic disorders. Deeper insight into the splicing process and pseudoexon recognition may bring valuable information, [INS: which :INS] [DEL: that :DEL] c[INS: ould :INS] [INS: [LŠ12] :INS] [DEL: an :DEL] be used [DEL: even :DEL] [DEL: [LŠ13] :DEL] [DEL: :DEL] in clinical practice. 8) Gap Junction Intercellular Communication : A Biomarker of Testicular Toxicity Effects of the individual chemical responses are well reported in the literature; [DEL: thereby :DEL] [INS: yet :INS] , overlooking the consequences of mixture exposure. There is worldwide decline in [DEL: the :DEL] male fertility and exposure to organochlorines and their mixture pose a risk to the male reproductive health. [INS: The m :INS] [DEL: M :DEL] ale reproductive system is an understudied system and previously conducted studies have shown the interreference[LŠ14] of the organochlorine cocktail with reproductive health. Testicular GJIC plays a vital role in spermatogenesis and steroidogenesis; however, they are often overlooked due to the lack of HCS ([INS: H :INS] [DEL: h :DEL] igh [INS: C :INS] [DEL: c :DEL] ontent [INS: S :INS] [DEL: s :DEL] creening) method. In this study, we assessed the effects of organochlorine cocktails on gap junction intercellular communication (GJIC) in murine male prepubertal testicular (Leydig Tm3 and Sertoli Tm4) cells using the multiparametric scrape load dye transfer (SLDT) assay. The organochlorine mixture inhibited testicular GJIC at the non-cytotoxic concentrations in both Leydig (Tm3) and Sertoli cells (Tm4), respectively. In conclusion, GJIC is an important marker of the testicular toxicity as the inhibition in GJIC could lead to the cancer formation in further stages. 9) Antimicrobial peptides: A solution to bacterial antibiotic resistance? [INS: The d :INS] [DEL: D :DEL] iscovery of antibiotics [INS: has :INS] enabled the development of our society as we know today. Previously deathly diseases [INS: have :INS] bec[INS: o :INS] [DEL: a :DEL] me a mere discomfort.[LŠ15] However, in the 21st century, we may experience the end of this antibiotic era due to the rapid emergence of antibiotic-resistant bacterial strains. According to the WHO, resistant bacteria might cause more than 10 million deaths a year worldwide by 2050. To prevent such a scenario from happening, new types of antibiotics are desperately[LŠ16] needed. Antimicrobial peptides constitute a class of potential novel therapeutics. Despite being highly active against various pathogens, their clinical use is often prevented [DEL: due to :DEL] [INS: for :INS] multiple reasons, cytotoxicity being one of them. The presented project aims to reveal amino acid patterns responsible for the peptide selectivity towards bacterial cells, exploiting the differences in cellular membrane lipid composition. Such knowledge will enable modifications of existing antimicrobial peptides to enhance their selectivity as well as the design of novel antimicrobial peptides with low cytotoxicity. Such an improvement of the peptides would increase their chances of progressing into the clinical trials. 10) Telomeres in plants and humans – not so similar, not so different Although the principles of telomere biology are conserved [LŠ17] and point to common evolutionary roots of eukaryotes, their implications for cell and organism survival, senescence, and aging are not shared among kingdoms[LŠ18] . In particular, plants show specific features of their growth and development. The requirement to finish the incomplete replication of chromosome ends is common for all organisms with linear chromosomes. In eukaryotes, this requirement is commonly solved by a specific nucleoprotein enzyme complex called telomerase. It consists of two major subunits in most of the organisms: telomerase RNA (TR) and telomerase reverse transcriptase (TERT). However, [INS: the :INS] holoenzyme of functional telomerase is composed of many other proteins that can regulate telomerase biogenesis or its access to the telomeres. We recently demonstrated that some protein homologues participate in TERT biogenesis also in plants. Since the genuine plant RNA subunit of telomerase has been identified only recently, it has yet to be found out if the assembly of the telomerase holoenzyme into catalytically active complex is aided by snoRNA proteins, as it is in mammals. In this presentation, [INS: the :INS] differences between human and plant telomere biology will be shown, with [INS: an :INS] emphasis on the comparison of telomere associated proteins acting in humans and in A. thaliana model plant[LŠ19] . The knowledge of plant telomere biology could help us to understand how efficient are plant molecular systems in ensuring maintenance of genome stability. 11) Structural insight into [DEL: the :DEL] lectins: finding a new substitution for antibiotics Lectins are ubiquitous proteins and glycoproteins with the ability to specifically, non-covalently and reversibly bind to [DEL: the :DEL] mono-, oligo- and polysaccharides. These sugar-binding proteins play [INS: an :INS] important role in many processes occurring in nature such as cell-cell interaction or recognition of the host by the pathogen. Since lectins are involved in the host-pathogen interaction, we can use our results and knowledge for drug development in a so-called [LŠ20] antiadhesive therapy to overcome th[INS: is :INS] [DEL: e :DEL] antibiotic resistance related issue. To understand [INS: the :INS] lectin[DEL: s :DEL] function and mechanism of action[LŠ21] , we need to obtain the high-resolution structure of the studied protein. Structural data describes key residues involved in interaction and allows us to find substances for antiadhesive therapy. 12) Making Good's Buffers Good for Freezing: [INS: T :INS] [DEL: t :DEL] he Acidity Changes and their Elimination via Mixing with Sodium Phosphate Three Good's buffers (HEPES, MOPS, and MES), both pure and mixed with sodium phosphate buffers (Na-P), are investigated in terms of the freezing-induced acidity changes in their operational pH ranges. The Good's buffers have the tendency to basify upon freezing and, more intensively, at lower pHs. The acidity [INS: levels :INS] var[INS: y :INS] [DEL: ies :DEL] most prominently in MES, where the change may reach the value of two. [DEL: Importantly :DEL] [INS: It is significant that :INS] [DEL: , :DEL] the Good's buffers are shown to mitigate the strong acidification in the Na-P buffer. Diverse concentrations of the Good's buffers are added to cancel out the strong, freezing-induced drop in 50mM Na-P that markedly contributes to the solution's acidity; These buffer blends are[INS: , :INS] therefore[INS: , :INS] proposed to be applied in maintaining approximately the acidity of solutions even after the freezing process and, as such, should limit the stresses for frozen chemicals and biochemicals. 13) Characterization of CA IX enzyme structural and interaction implications for targeting tumors and metastases – [INS: Killing t :INS] [DEL: T :DEL] wo birds with one stone[LŠ22] Human carbonic anhydrases (CAs) are a family of zinc metalloenzymes that play an essential role in the acid-base balance. Up t[INS: ill now :INS] [DEL: o date :DEL] , 15 human isoforms of CA have been identified, some of them are involved in cancer growth. Unfortunately, CAs share high sequence homology in enzymatic active sites, where most inhibitors are designed. This homology causes inhibitor binding to off-target isoforms present in healthy tissue. Unlike other human carbonic anhydrases, the carbonic anhydrase IX (CAIX) has a unique intrinsically disordered part (IDP) that participates in catalytic activity. The cancer cells upregulate CAIX to preserve physiological conditions inside the cancer cells while maintaining extracellular acidic pH. CAIX expression is essential to cancer cell growth, metastasis, and contributes to increased resistance to conventional radiation therapy and chemotherapy. While the catalytic domain of CAIX has been successfully crystallized, attempts to obtain crystal structure of extracellular CAIX [INS: have :INS] ended in failure and [INS: the :INS] structure of the IDP region CAIX remains unresolved despite rising evidence of its biological relevance. Nuclear magnetic resonance (NMR) will be employed to characterize the structure of IDP region of CAIX and its interaction with isoform-specific inhibitors. 14) Molecular Dynamics (MD) Simulation on DNA 4-way Junction, Reliable or Not? Molecular Dynamics (MD) simulation is a widely used technique analyzing the physical movement of molecules at the atomistic level. In nucleic acids studies[INS: . :INS] [DEL: , :DEL] MD simulation promotes our[LŠ23] understanding [DEL: on :DEL] [INS: in :INS] the key interactions stabilizing standard-form DNA/RNA, the structural mechanism of conformation transitions, the interactions between nucleic acids and proteins, etc.[LŠ24] However, compared with other molecules like proteins, this modelling technique is not mature[DEL: d :DEL] enough to return fully reliable results of nucleic acids simulations. The abundant nucleic acids structures contribute to the major difficulties of MD simulation on nucleic acids. From our simulation research on DNA 4-way junction, a special DNA structure appear[INS: s :INS] in gene recombination and DNA reparation, we [INS: have :INS] notice[INS: d :INS] [INS: /noticed :INS] [LŠ25] incorrect descriptions of MD simulation on the junction dynamics. In order to reproduce the practical junction behaviour, several strategies that bias the simulation balance can be applied. Nevertheless, even if th[INS: e :INS] [DEL: o :DEL] se strategies correct the junction simulation, they are still limited to the scenario of DNA 4-way junction application. The simulation of DNA 4-way junction works as an example to show the obstacle of acquiring a general MD simulation parameter set or protocol to have a satisfying[LŠ26] performance on nucleic acids MD simulation. ________________________________ [LŠ1]Your title is entertaining and great for a presentation, but would be a little informal, for academic texts. [LŠ2]No need to use the word “frightening” as the idea the procedures are dangerous has already been presented. [LŠ3]I would change ‘the to ‘a’ as there may well be more than one definitive picture. [LŠ4]The word ’proper’ may seem to be quite subjective, unless you have a definition in your field. Perhaps, an adjective like ’robust’ could be used. [LŠ5]Perhaps, the beginning might be modified a little by saying something like ‘it is hoped/expected that…..’ [LŠ6]The contribution seems to be the subject. [LŠ7]Not sure here, whether one particular action or more actions are presented. [LŠ8]It might be more effective to join your first two sentences together. [LŠ9]Might is a little bit too weak for a final sentence. [LŠ10]It is a list. [LŠ11]‘Thanks to’ is correct but slightly informal. [LŠ12]I’m not sure why you have used the word ‘even’? Is it very unusual to use things like this in clinical practice? It may be better to remove ‘ even’ and change the word ’can’ to ‘could’ to suggest possibility. [LŠ13]I’m not sure why you have used the word ‘even’? Is it very unusual to use things like this in clinical practice? It may be better to remove ‘ even’ and change the word ’can’ to ‘could’ to suggest possibility. [LŠ14]Inter-reference or interference? [LŠ15]This claim might need some example. [LŠ16]I would avoid using extreme language like ‘desperately’, your reader or audience may think your research is biased. [LŠ17]I am not sure what is meant. [LŠ18]Which kingdoms? [LŠ19]Is there only one? ? If more, this would need to be pluralised. [LŠ20]‘so called’ is a correct phrase but slightly informal, it may be better to use ‘ commonly known as’ ( in what is commonly known as antiadhesive therapy). [LŠ21]If there may be more functions and mechanisms, the words should be in plural. [LŠ22]Referring to a proverb/saying/idiom can be tricky once we are approaching global audience, readers from diverse cultures may not know it and may come up with different interpretations. [LŠ23]I would avoid using personal pronouns especially where it is not crystal clear who is “our” … all researchers? Your team only? [LŠ24]We tend to avoid using ‘etc’. In academic English this is considered to be “lazy” as though the author has not got the energy to list everything out. Instead one could signpost that only some of the aspects are going to be mentioned by using the phrase ‘such as’. [LŠ25]Present perfect or past simple should be used instead of present simple. If it is research that has finished, one could use past simple. [LŠ26]‘Satisfying’ is a bit ambiguous as there is no explanation why it would be satisfying and for whom. Could we use ‘satisfactory’ which would imply the performance met required standards?