How the interplay among the tumor microenvironment and the gut microbiota influences the stemness of colorectal cancer cells

Colorectal cancer (CRC) remains the third most prevalent cancer disease and involves a multi-step process in which intestinal cells acquire malignant characteristics. It is well established that the appearance of distal metastasis in CRC patients is the cause of a poor prognosis and treatment failure. Nevertheless, in the last decades, CRC aggressiveness and progression have been attributed to a specific cell population called CRC stem cells (CCSC) with features like tumor initiation capacity, self-renewal capacity, and acquired multidrug resistance. Emerging data highlight the concept of this cell subtype as a plastic entity that has a dynamic status and can be originated from different types of cells through genetic and epigenetic changes. These alterations are modulated by complex and dynamic crosstalk with environmental factors by paracrine signaling. It is known that in the tumor niche, different cell types, structures, and biomolecules coexist and interact with cancer cells favoring cancer growth and development. Together, these components constitute the tumor microenvironment (TME). Most recently, researchers have also deepened the influence of the complex variety of microorganisms that inhabit the intestinal mucosa, collectively known as gut microbiota, on CRC. Both TME and microorganisms participate in inflammatory processes that can drive the initiation and evolution of CRC. Since in the last decade, crucial advances have been made concerning to the synergistic interaction among the TME and gut microorganisms that condition the identity of CCSC, the data exposed in this review could provide valuable insights into the biology of CRC and the development of new targeted therapies.     

Diversity and composition of cultivable gut bacteria in an endemic island bird and its mainland sister species

The study of island biodiversity has inspired many advances in evolutionary biology. However, whether patterns of microorganism diversity are influenced by insularity is poorly understood. In particular, microorganisms that live in symbiotic association, such as the microbiota that inhabit the gastrointestinal tract of bigger animals, are subjected to demographic and coevolutionary processes that may add complexity to the common expectation of impoverished diversity on oceanic islands. Here, we explore this topic by studying the cultivable gut bacteria of two sister species of birds, from São Tomé island and nearby mainland Gabon, the endemic São Tomé thrush Turdus olivaceofuscus and the African thrush Turdus pelios. We found no differences in the diversity of cultivable gut bacteria between these thrushes, suggesting that, unlike what is commonly found for macrofauna, insularity might not represent a strong constraint for gut bacterial diversity. Although further research on complete gut bacterial communities and a broader range of species and areas is needed, our initial results suggest that the cultivable gut microbial community may bypass the diversity loss associated with island colonization. This could arise from intrinsic factors such as their large population sizes within hosts and low rates of extinction. Furthermore, as gut communities are composed mainly by mutualistic bacteria, diversifying selection (against an impoverished bacterial community), may counteract the diversity loss brought about by the stochastic and demographic effects of the founder process.     

Quantifying gene expression

Identifying those genes that are expressed and at what levels is an essential part of almost any biological inquiry at the cellular level. Techniques such as Northern blot have been in existence for decades to perform this task, but advances in molecular biology and bioinstrumentation have led to the development of a variety of new techniques with a range of sensitivities, throughputs and quantitative capabilities. This review focuses on the latter issue. For several commonly used gene expression techniques, the extent and range of quantitative applicability are reviewed, and approaches for maximizing the accuracy and precision of these measurements are discussed.     

Ökosystem Darm

Ecosystem gut The analysis of the microbiome opened a new chapter in human biology. The composition of the gut microbiome was associated with a variety of human diseases. After an analytic research phase, scientists now search for possibilities of therapeutic interventions. The high complexity of the system and the relative lack of prospective studies make it difficult to differentiate causal relationships from mere associations. Targeted health-promoting modulations of the gut microbiome are still difficult.     

Intraspecies Competition for Niches in the Distal Gut Dictate Transmission during Persistent Salmonella Infection

In order to be transmitted, a pathogen must first successfully colonize and multiply within a host. Ecological principles can be applied to study host-pathogen interactions to predict transmission dynamics. Little is known about the population biology of Salmonella during persistent infection. To define Salmonella enterica serovar Typhimurium population structure in this context, 129SvJ mice were oral gavaged with a mixture of eight wild-type isogenic tagged Salmonella (WITS) strains. Distinct subpopulations arose within intestinal and systemic tissues after 35 days, and clonal expansion of the cecal and colonic subpopulation was responsible for increases in Salmonella fecal shedding. A co-infection system utilizing differentially marked isogenic strains was developed in which each mouse received one strain orally and the other systemically by intraperitoneal (IP) injection. Co-infections demonstrated that the intestinal subpopulation exerted intraspecies priority effects by excluding systemic S. Typhimurium from colonizing an extracellular niche within the cecum and colon. Importantly, the systemic strain was excluded from these distal gut sites and was not transmitted to naïve hosts. In addition, S. Typhimurium required hydrogenase, an enzyme that mediates acquisition of hydrogen from the gut microbiota, during the first week of infection to exert priority effects in the gut. Thus, early inhibitory priority effects are facilitated by the acquisition of nutrients, which allow S. Typhimurium to successfully compete for a nutritional niche in the distal gut. We also show that intraspecies colonization resistance is maintained by Salmonella Pathogenicity Islands SPI1 and SPI2 during persistent distal gut infection. Thus, important virulence effectors not only modulate interactions with host cells, but are crucial for Salmonella colonization of an extracellular intestinal niche and thereby also shape intraspecies dynamics. We conclude that priority effects and intraspecies competition for colonization niches in the distal gut control Salmonella population assembly and transmission.     

Invasive species: reality or myth?

In view of the recent debate on the future of invasion biology, we argue that species could be regarded as invasive only when after adaptation in non-native habitats they reach yet another fitness maximum. We suggest that invasion biologists need to unambiguously clarify what constitutes being “invasive” to refute those who call for an end to invasion biology.     

The histochemistry and cell biology vade mecum: a review of 2005–2006

The procurement of new knowledge and understanding in the ever expanding discipline of cell biology continues to advance at a breakneck pace. The progress in discerning the physiology of cells and tissues in health and disease has been driven to a large extent by the continued development of new probes and imaging techniques. The recent introduction of semi-conductor quantum dots as stable, specific markers for both fluorescence light microscopy and electron microscopy, as well as a virtual treasure-trove of new fluorescent proteins, has in conjunction with newly introduced spectral imaging systems, opened vistas into the seemingly unlimited possibilities for experimental design. Although it oftentimes proves difficult to predict what the future will hold with respect to advances in disciplines such as cell biology and histochemistry, it is facile to look back on what has already occurred. In this spirit, this review will highlight some advancements made in these areas in the past 2 years.     

Going viral: next-generation sequencing applied to phage populations in the human gut

Over the past decade, researchers have begun to characterize viral diversity using metagenomic methods. These studies have shown that viruses, the majority of which infect bacteria, are probably the most genetically diverse components of the biosphere. Here, we briefly review the incipient rise of a phage biology renaissance, which has been catalysed by advances in next-generation sequencing. We explore how work characterizing phage diversity and lifestyles in the human gut is changing our view of ourselves as supra-organisms. Finally, we discuss how a renewed appreciation of phage dynamics may yield new applications for phage therapies designed to manipulate the structure and functions of our gut microbiomes.     

The foundations and development of lipidomics

For over a century, the importance of lipid metabolism in biology was recognized but difficult to mechanistically understand due to the lack of sensitive and robust technologies for identification and quantification of lipid molecular species. The enabling technological breakthroughs emerged in the 1980s with the development of soft ionization methods (Electrospray Ionization and Matrix Assisted Laser Desorption/Ionization) that could identify and quantify intact individual lipid molecular species. These soft ionization technologies laid the foundations for what was to be later named the field of lipidomics. Further innovative advances in multistage fragmentation, dramatic improvements in resolution and mass accuracy, and multiplexed sample analysis fueled the early growth of lipidomics through the early 1990s. The field exponentially grew through the use of a variety of strategic approaches, which included direct infusion, chromatographic separation, and charge-switch derivatization, which facilitated access to the low abundance species of the lipidome. In this Thematic Review, we provide a broad perspective of the foundations, enabling advances, and predicted future directions of growth of the lipidomics field.     

Conceptual assessment in the biological sciences: a National Science Foundation-sponsored workshop

Twenty-one biology teachers from a variety of disciplines (genetics, ecology, physiology, biochemistry, etc.) met at the University of Colorado to begin discussions about approaches to assessing students' conceptual understanding of biology. We considered what is meant by a "concept" in biology, what the important biological concepts might be, and how to go about developing assessment items about these concepts. We also began the task of creating a community of biologists interested in facilitating meaningful learning in biology. Input from the physiology education community is essential in the process of developing conceptual assessments for physiology.     

Neurotransmitter release at central synapses

Our understanding of synaptic transmission has grown dramatically during the 15 years since the first issue of Neuron was published, a growth rate expected from the rapid progress in modern biology. As in all of biology, new techniques have led to major advances in the cell and molecular biology of synapses, and the subject has evolved in ways (like the production of genetically engineered mice) that could not even be imagined 15 years ago. My plan for this review is to summarize what we knew about neurotransmitter release when Neuron first appeared and what we recognized we did not know, and then to describe how our views have changed in the intervening decade and a half. Some things we knew about synapses--"knew" in the sense that the field had reached a consensus--are no longer accepted, but for the most part, impressive advances have led to a new consensus on many issues. What I find fascinating is that in certain ways nothing has changed--many of the old arguments persist or recur in a different guise--but in other ways the field would be unrecognizable to a neurobiologist time-transported from 1988 to 2003.     

Understanding ciliated epithelia: the power of Xenopus

Ciliated epithelia are important in a wide variety of biological contexts where they generate directed fluid flow. Here we address the fundamental advances in understanding ciliated epithelia that have been achieved using Xenopus as a model system. Xenopus embryos are covered with a ciliated epithelium that propels fluid unidirectionally across their surface. The external nature of this tissue, coupled with the molecular tools available in Xenopus and the ease of microscopic analysis on intact animals has thrust Xenopus to the forefront of ciliated epithelia biology. We discuss advances in understanding the molecular regulators of ciliated epithelia cell fate as well as basic aspects of ciliated epithelia cell biology including ciliogenesis and cell polarity.     

The study of fossil spider species

The definition of what constitutes a species has been an area of contention in biology since before the time of Darwin. Here, we discuss concepts of species in regards to the Araneae and particularly focus on diagnosing fossils. Spiders are primarily diagnosed by their copulatory organs, which may be difficult to observe in fossils due to a number of confounding factors, thus potentially hindering identification and systematic classification. However, despite potential difficulties, fossils should and must be studied alongside extant Araneae in order to garner a full understanding of the evolutionary history of this megadiverse group.     

Sex and gonadal hormones in mouse models of Alzheimer’s disease: what is relevant to the human condition?

Biologic sex and gonadal hormones matter in human aging and diseases of aging such as Alzheimer’s – and the importance of studying their influences relates directly to human health. The goal of this article is to review the literature to date on sex and hormones in mouse models of Alzheimer’s disease (AD) with an exclusive focus on interpreting the relevance of findings to the human condition. To this end, we highlight advances in AD and in sex and hormone biology, discuss what these advances mean for merging the two fields, review the current mouse model literature, raise major unresolved questions, and offer a research framework that incorporates human reproductive aging for future studies aimed at translational discoveries in this important area. Unraveling human relevant pathways in sex and hormone-based biology may ultimately pave the way to novel and urgently needed treatments for AD and other neurodegenerative diseases.     

Slowing of intestinal transit by fat depends on naloxone-blockable efferent, opioid pathway

Slowing of transit through the proximal small intestine by fat in the distal gut is termed the ileal brake. Intravenous naloxone, an opioid receptor antagonist, abolished the fat-induced ileal brake, suggesting that an endogenous opioid pathway may be involved in this response. To test the hypothesis that slowing of intestinal transit by fat in the distal half of the gut depends on an opioid pathway located on the efferent limb of this response, we compared intestinal transit in dogs equipped with duodenal and midgut fistulas while naloxone was either compartmentalized with oleate to the distal half of the gut or with buffer to the proximal half of the gut. We found that intestinal transit depended on the perfusion conditions (P<0.00001). Specifically, compared with ileal brake (marker recovery of 35.7+/-7.4%), intestinal transit was accelerated when naloxone was delivered into the proximal half of the gut (76.2+/-5.2%) (P<0.005) but not the distal half of the gut (29.4+/-5.4%). We conclude that slowing of intestinal transit by fat in the distal half of the gut depends on an opioid pathway located on the efferent limb of the ileal brake.     

Black and white and read all over: the past,present and future of giant panda genetics

Few species attract much more attention from the public and scientists than the giant panda (Ailuropoda melanoleuca), a popular, enigmatic but highly endangered species. The application of molecular genetics to its biology and conservation has facilitated surprising insights into the biology of giant pandas as well as the effectiveness of conservation efforts during the past decades. Here, we review the history of genetic advances in this species, from phylogeny, demographical history, genetic variation, population structure, noninvasive population census and adaptive evolution to reveal to what extent the current status of the giant panda is a reflection of its evolutionary legacy, as opposed to the influence of anthropogenic factors that have negatively impacted this species. In addition, we summarize the conservation implications of these genetic findings applied for the management of this high‐profile species. Finally, on the basis of these advances and predictable future changes in genetic technology, we discuss future research directions that seem promising for giant panda biology and conservation.     

How Is Meaning Grounded in the Organism?

In this paper we address the interrelated questions of why and how certain features of an organism’s environment become meaningful to it. We make the case that knowing the biology is essential to understanding the foundation of meaning-making in organisms. We employ Miguel Nicolelis et al’s seminal research on the mammalian somatosensory system to enrich our own concept of brain-objects as the neurobiological intermediary between the environment and the consequent organismic behavior. In the final section, we explain how brain-objects advance the ongoing discussion of what constitutes a biosemiotic system. In general, this paper acknowledges Marcello Barbieri’s call for biology to make room for meaning, and makes a contribution to that end.     

Adeno-associated virus vectors for gene therapy: more pros than cons?

Gene therapy vectors based on the adeno-associated virus (AAV) are being developed for a widening variety of therapeutic applications. Enthusiasm for AAV is due, not only to the relative safety of these vectors, but also to advances in understanding of the unique biology of this virus. This review examines a number of long-standing concerns regarding the utility of AAV for gene transfer in light of many new insights into the biology, immunology and production of AAV.