A systematic study on the chemical model of polycyclic aromatic hydrocarbons formation from nutrients (glucose, amino acids, fatty acids) in food

Polycyclic aromatic hydrocarbons (PAHs), prominent carcinogens formed during food processing, pose health risks through long-term consumption. This study focuses on 16 priority PAHs in the European Union, investigating their formation during pyrolysis. Glucose, amino acids and fatty acids are important food nutrients. To further explore whether these nutrients in food form PAHs during heating, a single chemical model method was used to heat these nutrients respectively, and GC-MS/MS was used to identify and quantify the obtained components. Glucose is the most basic nutrient in food, so the influence of water, pH, temperature and other factors on the formation of PAHs was studied in the glucose model. At the same time, the models of amino acids and fatty acids were used to assist in improving the entire nutrient research system. According to our results, some previously reported mechanisms of PAHs formation by fatty acids heating were confirmed. In addition, glucose and amino acids could also produce many PAHs after heating, and some conclusions were improved by comparing the intermediates of PAHs from three types of nutrients.

Centennial issue

The Journal of Comparative Physiology A, also known as JCPA, was founded by Karl von Frisch and Alfred Kühn in 1924, then under its German title Zeitschrift für vergleichende Physiologie. During the 100 years of its history, it became the leading international journal in comparative physiology and its daughter discipline, neuroethology. As such, it had a major impact on the development of these disciplines. In celebration of this achievement and the nearly 10,000 articles that appeared during the last 100 years, this Centennial Issue is published. Its authors reflect on the history of JCPA and the early pioneers, including women scientists, of comparative physiology; share the impact that the Journal had on their careers; discuss the benefit of the enormous taxonomic diversity of model systems used in studies published in JCPA; contrast this philosophy with the strategy of a limited number of standard biomedical model systems; review popular and trending research topics covered in JCPA; and, by interrogating the past, take a peek into the future of neuroethology.

Single and combination treatment of Toxoplasma gondii infections with a bumped kinase inhibitor and artemisone in vitro and with artemiside in experimentally infected mice

In previous studies, the artemisinin derivatives artemisone, its pro-drug artemiside and the bumped-kinase inhibitor BKI-1748 were effective against T. gondii via different modes of action. This suggests that they may act synergistically resulting in improved efficacies in vitro and in vivo. To test this hypothesis, the compounds were applied alone and in combination to T. gondii infected human fibroblast host cells in order to determine their inhibition constants and effects on cellular ultrastructure. In addition, the efficacy of either single- or combined treatments were assessed in an acute TgShSp1-oocyst infection model based on CD1 outbred mice. Whereas the IC50 of the compounds in combination (42 nM) was close to the IC50 of BKI-1748 alone (46 nM) and half of the IC50 of artemisone alone (92 nM), the IC90 of the combination was half of the values found with the single compounds (138 nM vs. ca. 270 nM). Another indication for synergistic effects in vitro were distinct alterations of the cellular ultrastructure of tachyzoites observed in combination, but not with the single compounds. These promising results could not be reproduced in vivo. There was no decrease in number of T. gondii positive brains by either treatment. However, the levels of infection in these brains, i. e. the number of tachyzoites, was significantly decreased upon BKI-1748 treatment alone, and the combination with artemiside did not produce any further decrease. The treatment with artemiside alone had no significant effects. A vertical transmission model could not be established since artemiside strongly interfered with pregnancy and caused abortion. These results show that is difficult to extrapolate from promising in vitro results to the situation in vivo.

Imagine beyond: recent breakthroughs and next challenges in mammary gland biology and breast cancer research

On 8 December 2022 the organizing committee of the European Network for Breast Development and Cancer labs (ENBDC) held its fifth annual Think Tank meeting in Amsterdam, the Netherlands. Here, we embraced the opportunity to look back to identify the most prominent breakthroughs of the past ten years and to reflect on the main challenges that lie ahead for our field in the years to come. The outcomes of these discussions are presented in this position paper, in the hope that it will serve as a summary of the current state of affairs in mammary gland biology and breast cancer research for early career researchers and other newcomers in the field, and as inspiration for scientists and clinicians to move the field forward.

Fungal volatiles have physiological properties

All fungi emit mixtures of volatile organic compounds (VOCs) during growth. The qualitative and quantitative composition of these volatile mixtures vary with the species of fungus, the age of the fungus, and the environmental parameters attending growth. In nature, fungal VOCs are found as combinations of alcohols, aldehydes, acids, ethers, esters, ketones, terpenes, thiols and their derivatives, and are responsible for the characteristic odors associated with molds, mushrooms and yeasts. One of the single most common fungal volatiles is 1-octen-3-ol also known as "mushroom alcohol" or "matsutake alcohol." Many volatiles, including 1-octen-3-ol, serve as communication agents and display biological activity as germination inhibitors, plant growth retardants or promoters, and as semiochemicals ("infochemicals") in interactions with arthropods. Volatiles are understudied and underappreciated elements of the chemical lives of fungi. This review gives a brief introduction to fungal volatiles in hopes of raising awareness of the physiological importance of these gas phase fungal metabolites to encourage mycologists and other biologists to stop "throwing away the head space."

Joint representation: Modeling a phenomenon with multiple biological systems

Biologists often study particular biological systems as models of a phenomenon of interest even if they already know that the phenomenon is produced by diverse mechanisms and hence none of those systems alone can sufficiently represent it. To understand this modeling practice, the present paper provides an account of how multiple model systems can be used to study a phenomenon that is produced by diverse mechanisms. Even if generalizability of results from a single model system is significantly limited, generalizations concerning specific aspects of mechanisms often hold across certain ranges of biological systems, which enables multiple model systems to jointly represent such a phenomenon. Comparing mechanisms that operate in different biological systems as examples of the same phenomenon also facilitates characterization and investigation of individual mechanisms. I also compare my account with two existing accounts of the use of multiple model systems and argue that my account is distinct from and complementary to them.

Approaches to benchmark and characterize in vitro human model systems

In vitro human models, such as gastruloids and organoids, are complex three-dimensional (3D) structures often consist of cells from multiple germ layers that possess some attributes of a developing embryo or organ. To use these models to interrogate human development and organogenesis, these 3D models must accurately recapitulate aspects of their in vivo counterparts. Recent advances in single-cell technologies, including sequencing and spatial approaches, have enabled efforts to better understand and directly compare organoids with native tissues. For example, single-cell genomic efforts have created cell and organ atlases that enable benchmarking of in vitro models and can also be leveraged to gain novel biological insights that can be used to further improve in vitro models. This Spotlight discusses the state of current in vitro model systems, the efforts to create large publicly available atlases of the developing human and how these data are being used to improve organoids. Limitations and perspectives on future efforts are also discussed.

Considerations for Generating Humanized Mouse Models to Test Efficacy of Antisense Oligonucleotides

Over the last decades, animal models have become increasingly important in therapeutic drug development and assessment. The use of these models, mainly mice and rats, allow evaluating drugs in the real-organism environment and context. However, several molecular therapeutic approaches are sequence-dependent, and therefore, the humanization of such models is required to assess the efficacy. The generation of genetically modified humanized mouse models is often an expensive and laborious process that may not always recapitulate the human molecular and/or physiological phenotype. In this chapter, we summarize basic aspects to consider before designing and generating humanized models, especially when they are aimed to test antisense-based therapies.

The simultaneous inhibition of histidine on 5-hydroxymethylfurfural and acrylamide in model systems and cookies

5-Hydroxymethylfurfural (HMF) and acrylamide (AA) are neoformed food contaminants. In this study, the simultaneous inhibition of HMF and AA by histidine (His) were investigated. In the asparagine (Asn)/glucose (Glc) model system, the inhibition ratios of HMF and AA were in the range of 28-58% and 0-71% when 20 mmol/L His was added. In cookies, His also exhibited excellent inhibition effects on both HMF and AA. At the His concentration of 2% (w/w), the inhibition ratios of HMF and AA reached 90% and 65%. Additionally, the sensory quality of cookies was not affected significantly. Qualitative results suggested that His inhibited the formation of AA by the competitive reaction between His and Asn for Glc, as well as directly eliminated the formed HMF and AA via the carbonyl-amine reaction and the Michael addition, respectively. This study revealed that His could be applied for the inhibition of HMF and AA in heated food.

Joan Hunt Senior award lecture: New tools to shed light on the 'black box' of pregnancy

Correct establishment of the placenta is critical to the success of a pregnancy, but many of the key events take place during or shortly after implantation and are inaccessible for study. This inaccessibility, coupled with the lack of a suitable preclinical animal model, means that knowledge of human early placental development and function is extremely limited. Hence, the first trimester is often referred to as the 'black box' of pregnancy. However, recent advances in the derivation of trophoblast stem cells and organoid cultures of the trophoblast and endometrium are opening new opportunities for basic and translational research, providing for the first time cells that faithfully replicate their tissue of origin and proliferate and differentiate in culture in a stable and reproducible manner. These cells are valuable new tools for investigating cell-lineage differentiation and maternal-fetal interactions, but become even more powerful when combined with advances in bioengineering, microfabrication and microfluidic technologies. Assembloids of the endometrium comprising various cell types as model systems to investigate events at implantation, and placentas-on-a-chip for the study of nutrient transfer or drug screening are just two examples. This is a rapidly advancing field that may usher in more personalised approaches to infertility and pregnancy complications. Many of the developments are still at the proof-of-principle phase, but with continued refinement they are likely to shed important light on events that are fundamental to our reproduction as individuals and as a species, yet for ethical reasons are hidden from view.

Microfluidic systems to study tissue barriers to immunotherapy

Immunotherapies have been heavily explored in the last decade, ranging from new treatments for cancer to allergic diseases. These therapies target the immune system, a complex organ system consisting of tissues with intricate structures and cells with a multitude of functions. To better understand immune functions and develop better therapeutics, many cellular and 2-dimensional (2D) tissue models have been developed. However, research has demonstrated that the 3-dimensional (3D) tissue structure can significantly affect cellular functions, and this is not recapitulated by more traditional 2D models. Microfluidics has been used to design 3D tissue models that allow for intricate arrangements of cells and extracellular spaces, thus allowing for more physiologically relevant in vitro model systems. Here, we summarize the multitude of microfluidic devices designed to study the immune system with the ultimate goal to improve existing and design new immunotherapies. We have included models of the different immune organs, including bone marrow and lymph node (LN), models of immunity in diseases such as cancer and inflammatory bowel disease, and therapeutic models to test or engineer new immune-modulatory treatments. We particularly emphasize research on how microfluidic devices are used to better understand different physiological states and how interactions within the immune microenvironment can influence the efficacy of immunotherapies.

Potential of 1H NMR fingerprinting and a model system approach to study non-enzymatic browning in shelf-stable orange juice during storage

For the first time, a model system approach was combined with ¹H NMR fingerprinting in studying non-enzymatic browning (NEB) of pasteurized shelf-stable orange juice during storage. Various NEB precursors were used individually or in combinations to formulate simple or complex model systems, respectively, in citric acid buffer. Based on orange juice composition, ascorbic acid, sugars (sucrose, glucose and fructose) and amino acids (proline, arginine, asparagine, aspartic acid, serine and glutamic acid) were selected as the precursors for the model systems. After pasteurization and during subsequent accelerated storage (42 °C, 16 weeks) the model systems displayed a three-phase browning development. The initial browning phase was mainly the result of ascorbic acid degradation especially in the presence of amino acids and sugars. In the later phases, the contribution of reactions of sugars and amino acids to browning became apparent. The application of ¹H NMR fingerprinting on a simple model system containing ascorbic acid revealed that its degradation pathway to intermediates such as xylonic acid, acetic acid and erythrulose was responsible for the major changes during storage. When this model system was complexed by inclusion of sugars and amino acids, the hydrolysis of sucrose to glucose and fructose was identified as the main reaction leading to differences in the samples throughout storage. These three sugars dominated the NMR spectra of the samples, overshadowing several important compounds for NEB such as ascorbic acid and its degradation products. Other more advanced NMR experiments such as two-dimensional NMR analyses should be applied in future research to identify unknown compounds from NEB reactions.

Implications of genetic variation in the complement system in age-related macular degeneration

Age-related macular degeneration (AMD) is the main cause of vision loss among the elderly in the Western world. While AMD is a multifactorial disease, the complement system was identified as one of the main pathways contributing to disease risk. The strong link between the complement system and AMD was demonstrated by genetic associations, and by elevated complement activation in local eye tissue and in the systemic circulation of AMD patients. Several complement inhibitors have been and are being explored in clinical trials, but thus far with limited success, leaving the majority of AMD patients without treatment options to date. This indicates that there is still a gap of knowledge regarding the functional implications of the complement system in AMD pathogenesis and how to bring these towards clinical translation. Many different experimental set-ups and disease models have been used to study complement activation in vivo and in vitro, and recently emerging patient-derived induced pluripotent stem cells and genome-editing techniques open new opportunities to study AMD disease mechanisms and test new therapeutic strategies in the future. In this review we provide an extensive overview of methods employed to understand the molecular processes of complement activation in AMD pathogenesis. We discuss the findings, advantages and challenges of each approach and conclude with an outlook on how recent, exciting developments can fill in current knowledge gaps and can aid in the development of effective complement-targeting therapeutic strategies in AMD.

Model systems for studying polyphosphate biology: a focus on microorganisms

Polyphosphates (polyP) are polymers of inorganic phosphates joined by high-energy bonds to form long chains. These chains are present in all forms of life but were once disregarded as 'molecular fossils'. PolyP has gained attention in recent years following new links to diverse biological roles ranging from energy storage to cell signaling. PolyP research in humans and other higher eukaryotes is limited by a lack of suitable tools and awaits the identification of enzymatic players that would enable more comprehensive studies. Therefore, many of the most important insights have come from single-cell model systems. Here, we review determinants of polyP metabolism, regulation, and function in major microbial systems, including bacteria, fungi, protozoa, and algae. We highlight key similarities and differences that may aid in our understanding of how polyP impacts cell physiology at a molecular level.

Microbial model communities: To understand complexity, harness the power of simplicity

Natural microbial communities are complex ecosystems with myriads of interactions. To deal with this complexity, we can apply lessons learned from the study of model organisms and try to find simpler systems that can shed light on the same questions. Here, microbial model communities are essential, as they can allow us to learn about the metabolic interactions, genetic mechanisms and ecological principles governing and structuring communities. A variety of microbial model communities of varying complexity have already been developed, representing different purposes, environments and phenomena. However, choosing a suitable model community for one's research question is no easy task. This review aims to be a guide in the selection process, which can help the researcher to select a sufficiently well-studied model community that also fulfills other relevant criteria. For example, a good model community should consist of species that are easy to grow, have been evaluated for community behaviors, provide simple readouts and - in some cases - be of relevance for natural ecosystems. Finally, there is a need to standardize growth conditions for microbial model communities and agree on definitions of community-specific phenomena and frameworks for community interactions. Such developments would be the key to harnessing the power of simplicity to start disentangling complex community interactions.

Non-histone protein acetylation by the evolutionarily conserved GCN5 and PCAF acetyltransferases

GCN5, conserved from yeast to humans, and the vertebrate specific PCAF, are lysine acetyltransferase enzymes found in large protein complexes. Both enzymes have well documented roles in the histone acetylation and the concomitant regulation of transcription. However, these enzymes also acetylate non-histone substrates to impact diverse aspects of cell physiology. Here, I review our current understanding of non-histone acetylation by GCN5 and PCAF across eukaryotes, from target identification to molecular mechanism and regulation. I focus mainly on budding yeast, where Gcn5 was first discovered, and mammalian systems, where the bulk of non-histone substrates have been characterized. I end the review by defining critical caveats and open questions that apply to all models.

Spawning induction, development and culturing of the solitary ascidian Polycarpa mytiligera, an emerging model for regeneration studies

BACKGROUND

Ascidians (phylum Chordata, class Ascidiacea) represent the closest living invertebrate relatives of the vertebrates and constitute an important model for studying the evolution of chordate development. The solitary ascidian Polycarpa mytiligera exhibits a robust regeneration ability, unique among solitary chordates, thus offering a promising new model for regeneration studies. Understanding its reproductive development and establishing land-based culturing methods is pivotal for utilizing this species for experimental studies. Its reproduction cycle, spawning behavior, and developmental processes were therefore studied in both the field and the lab, and methods were developed for its culture in both open and closed water systems.

RESULTS

Field surveys revealed that P. mytiligera's natural recruitment period starts in summer (June) and ends in winter (December) when seawater temperature decreases. Laboratory experiments revealed that low temperature (21 °C) has a negative effect on its fertilization and development. Although spontaneous spawning events occur only between June and December, we were able to induce spawning under controlled conditions year-round by means of gradual changes in the environmental conditions. Spawning events, followed by larval development and metamorphosis, took place in ascidians maintained in either artificial or natural seawater facilities. P. mytiligera's fast developmental process indicated its resemblance to other oviparous species, with the larvae initiating settlement and metamorphosis at about 12 h post-hatching, and reaching the juvenile stage 3 days later.

CONCLUSIONS

Polycarpa mytiligera can be induced to spawn in captivity year-round, independent of the natural reproduction season. The significant advantages of P. mytiligera as a model system for regenerative studies, combined with the detailed developmental data and culturing methods presented here, will contribute to future research addressing developmental and evolutionary questions, and promote the use of this species as an applicable model system for experimental studies.

Mechanisms of action, chemical characteristics, and model systems of obesogens

There is increasing evidence for the role of environmental endocrine disrupting contaminants, coined obesogens, in exacerbating the rising obesity epidemic. Obesogens can be found in everyday items ranging from pesticides to food packaging. Although research shows that obesogens can have effects on adipocyte size, phenotype, metabolic activity, and hormone levels, much remains unknown about these chemicals. This review will discuss what is currently known about the mechanisms of obesogens, including expression of the PPARs, hormone interference, and inflammation. Strategies for identifying obesogenic chemicals and their mechanisms through chemical characteristics and model systems will also be discussed. Ultimately, research should focus on improving models to discern precise mechanisms of obesogenic action and to test therapeutics targeting these mechanisms.

Experimental concepts for linking the biological activities of antimicrobial peptides to their molecular modes of action

The search for novel compounds to combat multi-resistant bacterial infections includes exploring the potency of antimicrobial peptides and derivatives thereof. Complementary to high-throughput screening techniques, biophysical and biochemical studies of the biological activity of these compounds enable deep insight, which can be exploited in designing antimicrobial peptides with improved efficacy. This approach requires the combination of several techniques to study the effect of such peptides on both bacterial cells and simple mimics of their cell envelope, such as lipid-only vesicles. These efforts carry the challenge of bridging results across techniques and sample systems, including the proper choice of membrane mimics. This review describes some important concepts toward the development of potent antimicrobial peptides and how they translate to frequently applied experimental techniques, along with an outline of the biophysics pertaining to the killing mechanism of antimicrobial peptides.

From blood development to disease: a paradigm for clinical translation

Translating basic research to the clinic is a primary aim of Disease Models & Mechanisms, and the recent successes in hematopoiesis research provide a blueprint of how fundamental biological research can provide solutions to important clinical problems. These advances were the main motivation for choosing hematopoiesis disorders as the focus of our inaugural meeting, 'Blood Disorders: Models, Mechanisms and Therapies', which was held in early October 2019. This Editorial discusses the reasons for and the challenges of interdisciplinary research in hematopoiesis, provides examples of how research in model systems is a key translational step towards effective treatments for blood disorders and summarizes what the community believes are the key exciting developments and challenges in this field.

Bundling the haystack to find the needle: Challenges and opportunities in modeling risk and resilience following early life stress

Various forms of early life adversity (ELA) have been linked with increased risk for negative health outcomes, including neuropsychiatric disorders. Understanding how the complex interplay between types, timing, duration, and severity of ELA, together with individual differences in genetic, socio-cultural, and physiological differences can mediate risk and resilience has proven difficult in population based studies. Use of animal models provides a powerful toolset to isolate key variables underlying risk for altered neural and behavioral maturational trajectories. However, a lack of clarity regarding the unique features of differing forms of adversity, lab differences in the implementation and reporting of methods, and the ability compare across labs and types of ELA has led to some confusion. Here, we highlight the diversity of approaches available, current challenges, and a possible ways forward to increase clarity and drive more meaningful and fruitful implementation and comparison of these approaches.

Modelling human haemoglobin switching

Genetic lesions of the β-globin gene result in haemoglobinopathies such as β-thalassemia and sickle cell disease. To discover and test new molecular medicines for β-haemoglobinopathies, cell-based and animal models are now being widely utilised. However, multiple in vitro and in vivo models are required due to the complex structure and regulatory mechanisms of the human globin gene locus, subtle species-specific differences in blood cell development, and the influence of epigenetic factors. Advances in genome sequencing, gene editing, and precision medicine have enabled the first generation of molecular therapies aimed at reactivating, repairing, or replacing silenced or damaged globin genes. Here we compare and contrast current animal and cell-based models, highlighting their complementary strengths, reflecting on how they have informed the scope and direction of the field, and describing some of the novel molecular and precision medicines currently under development or in clinical trial.

Research progress from the SCI Model Systems (SCIMS): An interactive discussion on future directions

CONTEXT/OBJECTIVE

To describe current and future directions in spinal cord injury (SCI) research.

DESIGN

The SCI Model Systems (SCIMS) programs funded by the National Institute on Disability, Independent Living, and Rehabilitation Research (NIDILRR) during the 2011 to 2016 cycle provided abstracts describing findings from current research projects. Discussion among session participants generated ideas for research opportunities.

SETTING/PARTICIPANTS

Pre-conference workshop before the 2016 American Spinal Injury Association (ASIA) annual meeting. A steering committee selected by the SCIMS directors that included the moderators of the sessions at the ASIA pre-conference workshop, researchers presenting abstracts during the session, and the audience of over 100 attending participants in the pre-conference workshop.

METHODS/RESULTS

Group discussion followed presentations in 5 thematic areas of (1) Demographics and Measurement; (2) Functional Training; (3) Psychosocial Considerations; (4) Assistive Technology; and (5) Secondary Conditions. The steering committee reviewed and summarized discussion points on future directions for research and made recommendations for research based on the discussion in each of the five areas.

CONCLUSION

Significant areas in need of research in SCI remain, the goal of which is continued improvement in the quality of life of individuals with SCI.

Current model systems for the study of preeclampsia

Preeclampsia (PE) is a pregnancy complex disease, distinguished by high blood pressure and proteinuria, diagnosed after the 20th gestation week. Depending on the values of blood pressure, urine protein concentrations, symptomatology, and onset of disease there is a wide range of phenotypes, from mild forms developing predominantly at the end of pregnancy to severe forms developing in the early stage of pregnancy. In the worst cases severe forms of PE could lead to systemic endothelial dysfunction, eclampsia, and maternal and/or fetal death. Worldwide the fetal morbidity and mortality related to PE is calculated to be around 8% of the total pregnancies. PE still being an enigma regarding its etiology and pathophysiology, in general a deficient trophoblast invasion during placentation at first stage of pregnancy, in combination with maternal conditions are accepted as a cause of endothelial dysfunction, inflammatory alterations and appearance of symptoms. Depending on the PE multifactorial origin, several in vitro, in vivo, and in silico models have been used to evaluate the PE pathophysiology as well as to identify or test biomarkers predicting, diagnosing or prognosing the syndrome. This review focuses on the most common models used for the study of PE, including those related to placental development, abnormal trophoblast invasion, uteroplacental ischemia, angiogenesis, oxygen deregulation, and immune response to maternal-fetal interactions. The advances in mathematical and computational modeling of metabolic network behavior, gene prioritization, the protein-protein interaction network, the genetics of PE, and the PE prediction/classification are discussed. Finally, the potential of these models to enable understanding of PE pathogenesis and to evaluate new preventative and therapeutic approaches in the management of PE are also highlighted. Impact statement This review is important to the field of preeclampsia (PE), because it provides a description of the principal in vitro, in vivo, and in silico models developed for the study of its principal aspects, and to test emerging therapies or biomarkers predicting the syndrome before their evaluation in clinical trials. Despite the current advance, the field still lacking of new methods and original modeling approaches that leads to new knowledge about pathophysiology. The part of in silico models described in this review has not been considered in the previous reports.

Evolution of language: Lessons from the genome

The post-genomic era is an exciting time for researchers interested in the biology of speech and language. Substantive advances in molecular methodologies have opened up entire vistas of investigation that were not previously possible, or in some cases even imagined. Speculations concerning the origins of human cognitive traits are being transformed into empirically addressable questions, generating specific hypotheses that can be explicitly tested using data collected from both the natural world and experimental settings. In this article, I discuss a number of promising lines of research in this area. For example, the field has begun to identify genes implicated in speech and language skills, including not just disorders but also the normal range of abilities. Such genes provide powerful entry points for gaining insights into neural bases and evolutionary origins, using sophisticated experimental tools from molecular neuroscience and developmental neurobiology. At the same time, sequencing of ancient hominin genomes is giving us an unprecedented view of the molecular genetic changes that have occurred during the evolution of our species. Synthesis of data from these complementary sources offers an opportunity to robustly evaluate alternative accounts of language evolution. Of course, this endeavour remains challenging on many fronts, as I also highlight in the article. Nonetheless, such an integrated approach holds great potential for untangling the complexities of the capacities that make us human.

Trends in tissue repair and regeneration

The 6th EMBO conference on the Molecular and Cellular Basis of Regeneration and Tissue Repair took place in Paestum (Italy) on the 17th-21st September, 2016. The 160 scientists who attended discussed the importance of cellular and tissue plasticity, biophysical aspects of regeneration, the diverse roles of injury-induced immune responses, strategies to reactivate regeneration in mammals, links between regeneration and ageing, and the impact of non-mammalian models on regenerative medicine.

Animal Models to Study MicroRNA Function

The discovery of the microRNAs, lin-4 and let-7 as critical mediators of normal development in Caenorhabditis elegans and their conservation throughout evolution has spearheaded research toward identifying novel roles of microRNAs in other cellular processes. To accurately elucidate these fundamental functions, especially in the context of an intact organism, various microRNA transgenic models have been generated and evaluated. Transgenic C. elegans (worms), Drosophila melanogaster (flies), Danio rerio (zebrafish), and Mus musculus (mouse) have contributed immensely toward uncovering the roles of multiple microRNAs in cellular processes such as proliferation, differentiation, and apoptosis, pathways that are severely altered in human diseases such as cancer. The simple model organisms, C. elegans, D. melanogaster, and D. rerio, do not develop cancers but have proved to be convenient systesm in microRNA research, especially in characterizing the microRNA biogenesis machinery which is often dysregulated during human tumorigenesis. The microRNA-dependent events delineated via these simple in vivo systems have been further verified in vitro, and in more complex models of cancers, such as M. musculus. The focus of this review is to provide an overview of the important contributions made in the microRNA field using model organisms. The simple model systems provided the basis for the importance of microRNAs in normal cellular physiology, while the more complex animal systems provided evidence for the role of microRNAs dysregulation in cancers. Highlights include an overview of the various strategies used to generate transgenic organisms and a review of the use of transgenic mice for evaluating preclinical efficacy of microRNA-based cancer therapeutics.

Exploiting micro-scale structural and chemical observations in real time for understanding chemical conversion: LEEM/PEEM studies over CeOx-Cu(111)

Proper consideration of length-scales is critical for elucidating active sites/phases in heterogeneous catalysis, revealing chemical function of surfaces and identifying fundamental steps of chemical reactions. Using the example of ceria thin films deposited on the Cu(111) surface, we demonstrate the benefits of multi length-scale experimental framework for understanding chemical conversion. Specifically, exploiting the tunable sampling and spatial resolution of photoemission electron microscopy, we reveal crystal defect mediated structures of inhomogeneous copper-ceria mixed phase that grow during preparation of ceria/Cu(111) model systems. The density of the microsized structures is such that they are relevant to the chemistry, but unlikely to be found during investigation at the nanoscale or with atomic level investigations. Our findings highlight the importance of accessing micro-scale when considering chemical pathways over heteroepitaxially grown model systems.

miRNAs: Nanomachines That Micromanage the Pathophysiology of Diabetes Mellitus

Diabetes mellitus (DM) refers to a combination of heterogeneous complex metabolic disorders that are associated with episodes of hyperglycemia and glucose intolerance occurring as a result of defects in insulin secretion, action, or both. The prevalence of DM is increasing at an alarming rate, and there exists a need to develop better therapeutics and prognostic markers for earlier detection and diagnosis. In this review, after giving a brief introduction of diabetes mellitus and microRNA (miRNA) biogenesis pathway, we first describe various in vitro and animal model systems that have been developed to study diabetes. Further, we elaborate on the significant roles played by miRNAs as regulators of gene expression in the context of development of diabetes and its secondary complications. The different approaches to quantify miRNAs and their potential to be used as therapeutic targets for alleviation of diabetes have also been discussed.

Influence of food intrinsic complexity on Listeria monocytogenes growth in/on vacuum-packed model systems at suboptimal temperatures

Food intrinsic factors e.g., food (micro)structure, compositional and physicochemical aspects, which are mutually dependent, influence microbial growth. While the effect of composition and physicochemical properties on microbial growth has been thoroughly assessed and characterised, the role of food (micro)structure still remains unravelled. Most studies on food (micro)structure focus on comparing planktonic growth in liquid (microbiological) media with colonial growth in/on solid-like systems or on real food surfaces. However, foods are not only liquids or solids; they can also be emulsions or gelled emulsions and have complex compositions. In this study, Listeria monocytogenes growth was studied on the whole spectrum of (micro)structure, in terms of food (model) systems. The model systems varied not only in (micro)structure, which was the target of the study, but also in compositional and physicochemical characteristics, which was an inevitable consequence of the (micro)structural variability. The compositional and physicochemical differences were mainly due to the presence or absence of fat and gelling agents. The targeted (micro)structures were: i) liquids, ii) aqueous gels, iii) emulsions and iv) gelled emulsions. Furthermore, the microbial dynamics were studied and compared in/on all these model systems, as well as on a compositionally predefined canned meat, developed in order to have equal compositional level to the gelled emulsion model system and represent a real food system. Frankfurter sausages were the targeted real foods, selected as a case study, to which the canned meat had similar compositional characteristics. All systems were vacuum packed and incubated at 4, 8 and 12°C. The most appropriate protocol for the preparation of the model systems was developed. The pH, water activity and resistance to penetration of the model systems were characterised. Results indicated that low temperature contributes to growth variations among the model systems. Additionally, the firmer the solid system, the faster L. monocytogenes grew on it. Finally, it was found that L. monocytogenes grows faster on canned meat and real Frankfurters, as found in a previous study, followed by liquids, aqueous gels, emulsions and gelled emulsions. This observation indicates that all model systems, developed in this study, underestimated L. monocytogenes growth. Despite some limitations, model systems are overall advantageous and therefore, their validation is always recommended prior to further use.

Conserved regulators of cognitive aging: From worms to humans

Cognitive decline is a major deficit that arises with age in humans. While some research on the underlying causes of these problems can be done in humans, harnessing the strengths of small model systems, particularly those with well-studied longevity mutants, such as the nematode C. elegans, will accelerate progress. Here we review the approaches being used to study cognitive decline in model organisms and show how simple model systems allow the rapid discovery of conserved molecular mechanisms, which will eventually enable the development of therapeutics to slow cognitive aging.

How Somatic Adult Tissues Develop Organizer Activity

The growth and patterning of anatomical structures from specific cellular fields in developing organisms relies on organizing centers that instruct surrounding cells to modify their behavior, namely migration, proliferation, and differentiation. We discuss here how organizers can form in adult organisms, a process of utmost interest for regenerative medicine. Animals like Hydra and planarians, which maintain their shape and fitness thanks to a highly dynamic homeostasis, offer a useful paradigm to study adult organizers in steady-state conditions. Beside the homeostatic context, these model systems also offer the possibility to study how organizers form de novo from somatic adult tissues. Both extracellular matrix remodeling and caspase activation play a key role in this transition, acting as promoters of organizer formation in the vicinity of the wound. Their respective roles and the crosstalk between them just start to be deciphered.

Enhancing metaproteomics--The value of models and defined environmental microbial systems

Metaproteomics--the large-scale characterization of the entire protein complement of environmental microbiota at a given point in time--has provided new features to study complex microbial communities in order to unravel these "black boxes." New technical challenges arose that were not an issue for classical proteome analytics before that could be tackled by the application of different model systems. Here, we review different current and future model systems for metaproteome analysis. Following a short introduction to microbial communities and metaproteomics, we introduce model systems for clinical and biotechnological research questions including acid mine drainage, anaerobic digesters, and activated sludge. Model systems are useful to evaluate the challenges encountered within (but not limited to) metaproteomics, including species complexity and coverage, biomass availability, or reliable protein extraction. The implementation of model systems can be considered as a step forward to better understand microbial community responses and ecological functions of single member organisms. In the future, improvements are necessary to fully explore complex environmental systems by metaproteomics.

Reduction of aflatoxins (B₁, B₂, G₁, and G₂) in soybean-based model systems

The effects of chemical, physical, and cooking treatments on the reduction of aflatoxin B1 (AFB1), B2, G1, and G2 in soybean matrix were investigated. A HPLC-FLD with a Kobra cell system was used for the quantitative analysis of aflatoxins (AFs). To decrease the level of AFs during the soaking process, the contaminated soybeans were submerged in organic acid solutions. The reduction rates of AFB1 in 1.0N citric acid, lactic acid, succinic acid, and tartaric acid for 18h were 94.1%, 92.7%, 62.0%, and 95.1%, respectively. In the case of pH and autoclave treatment, the level of AFB1 was significantly decreased during autoclaving process at pH 7.4, 9.0, and 11.1, compared with the non-autoclaved samples (p<0.05). In the case of physical treatment, the heating process at 100 and 150°C for 90min significantly decreased the level of AFB1 by 41.9% and 81.2%, respectively (p<0.05). The reduction rate of AFB1 after cooking was 97.9% for soybean milk and 33.6% for steamed soybeans.

Thermal oxidation of cholesterol: Preliminary evaluation of 2-methyl-6-heptanone and 3-methylbutanal as volatile oxidation markers

Cholesterol oxidation in food and model systems is usually monitored by evaluating cholesterol oxidation products, but the analysis is time-consuming and expensive. Therefore, the determination of volatile compounds deriving from cholesterol thermoxidation could be valuable to identify other possible oxidation markers. Cholesterol alone and in the presence of a triacylglycerol mixture (tripalmitin, tristearin, and triolein) were thermoxidized at 170°C for 15min. In both model systems, the total volatile compounds increased three times when oxidation time rose from 5 to 15min. The main classes of volatile compounds were aldehydes, ketones, alcohols and hydrocarbons, displaying a similar behavior in both systems. After 5min of oxidation, 2-methyl-6-heptanone was the main volatile compound, followed by 3-methylpentane, 2,3-dimethyl-1-pentene and 3-methylbutanal. To verify if 2-methyl-6-heptanone could be used as volatile marker of cholesterol oxidation, data were compared with the total cholesterol oxidation products content of each system. A significant correlation between total cholesterol oxidation products content and 2-methyl-6-heptanone amount was found when cholesterol was oxidized alone (r(2)=0.994) and in presence of triacylglycerols (r(2)=0.998). When egg yolk was thermoxidized at 80°C for 6h, 3-methylbutanal was the volatile compound that better explained the oxidative trend in this food system, showing a significant correlation with cholesterol oxidation rate (r=0.91). In conclusion, 2-methyl-6-heptanone and 3-methylbutanal could represent an easy and cheaper strategy for monitoring cholesterol oxidation in model systems and food samples, respectively; however, a deeper investigation on the amount and type of volatile compounds generated from cholesterol oxidation according to the food matrix, should be carried out.

The neuronal ceroid lipofuscinoses: Opportunities from model systems

The neuronal ceroid lipofuscinoses are a group of severe and progressive neurodegenerative disorders, generally with childhood onset. Despite the fact that these diseases remain fatal, significant breakthroughs have been made in our understanding of the genetics that underpin these conditions. This understanding has allowed the development of a broad range of models to study disease processes, and to develop new therapeutic approaches. Such models have contributed significantly to our knowledge of these conditions. In this review we will focus on the advantages of each individual model, describe some of the contributions the models have made to our understanding of the broader disease biology and highlight new techniques and approaches relevant to the study and potential treatment of the neuronal ceroid lipofuscinoses. This article is part of a Special Issue entitled: "Current Research on the Neuronal Ceroid Lipofuscinoses (Batten Disease)".

Advances in experimental systems to study hepatitis C virus in vitro and in vivo

Hepatitis C virus (HCV) represents a global health concern affecting over 185 million people worldwide. Chronic HCV infection causes liver fibrosis and cirrhosis and is the leading indication for liver transplantation. Recent advances in the field of direct-acting antiviral drugs (DAAs) promise a cure for HCV in over 90% of cases that will get access to these expensive treatments. Nevertheless, the lack of a protective vaccine and likely emergence of drug-resistant viral variants call for further studies of HCV biology. With chimpanzees being for a long time the only non-human in vivo model of HCV infection, strong efforts were put into establishing in vitro experimental systems. The initial models only enabled to study specific aspects of the HCV life cycle, such as viral replication with the subgenomic replicon and entry using HCV pseudotyped particles (HCVpp). Subsequent development of protocols to grow infectious HCV particles in cell-culture (HCVcc) ignited investigations on the full cycle of HCV infection and the virus-host interactions required for virus propagation. More recently, small animal models permissive to HCV were generated that allowed in vivo testing of novel antiviral therapies as well as vaccine candidates. This review provides an overview of the currently available in vitro and in vivo experimental systems to study HCV biology. Particular emphasis is given to how these model systems furthered our understanding of virus-host interactions, viral pathogenesis and immunological responses to HCV infection, as well as drug and vaccine development.

Advances in experimental systems to study hepatitis C virus in vitro and in vivo

Hepatitis C virus (HCV) represents a global health concern affecting over 185 million people worldwide. Chronic HCV infection causes liver fibrosis and cirrhosis and is the leading indication for liver transplantation. Recent advances in the field of direct-acting antiviral drugs (DAAs) promise a cure for HCV in over 90% of cases that will get access to these expensive treatments. Nevertheless, the lack of a protective vaccine and likely emergence of drug-resistant viral variants call for further studies of HCV biology. With chimpanzees being for a long time the only non-human in vivo model of HCV infection, strong efforts were put into establishing in vitro experimental systems. The initial models only enabled to study specific aspects of the HCV life cycle, such as viral replication with the subgenomic replicon and entry using HCV pseudotyped particles (HCVpp). Subsequent development of protocols to grow infectious HCV particles in cell-culture (HCVcc) ignited investigations on the full cycle of HCV infection and the virus-host interactions required for virus propagation. More recently, small animal models permissive to HCV were generated that allowed in vivo testing of novel antiviral therapies as well as vaccine candidates. This review provides an overview of the currently available in vitro and in vivo experimental systems to study HCV biology. Particular emphasis is given to how these model systems furthered our understanding of virus-host interactions, viral pathogenesis and immunological responses to HCV infection, as well as drug and vaccine development.