What do we know about the yeast strains from the Brazilian fuel ethanol industry?

The production of fuel ethanol from sugarcane-based raw materials in Brazil is a successful example of a large-scale bioprocess that delivers an advanced biofuel at competitive prices and low environmental impact. Two to three fed-batch fermentations per day, with acid treatment of the yeast cream between consecutive cycles, during 6–8 months of uninterrupted production in a nonaseptic environment are some of the features that make the Brazilian process quite peculiar. Along the past decades, some wild Saccharomyces cerevisiae strains were isolated, identified, characterized, and eventually, reintroduced into the process, enabling us to build up knowledge on these organisms. This information, combined with physiological studies in the laboratory and, more recently, genome sequencing data, has allowed us to start clarifying why and how these strains behave differently from the better known laboratory, wine, beer, and baker's strains. All these issues are covered in this minireview, which also presents a brief discussion on future directions in the field and on the perspectives of introducing genetically modified strains in this industrial process.     

Pluripotent versus totipotent plant stem cells: dependence versus autonomy?

Little is known of the mechanisms that induce the dedifferentiation of a single somatic cell into a totipotent embryogenic cell that can either be regenerated or develop into an embryo and subsequently an entire plant. In this Opinion article, we examine the cellular, physiological and molecular similarities and differences between different plant stem cell types. We propose to extend the plant stem cell concept to include single embryogenic cells as a totipotent stem cell based on their capacity to regenerate or develop into an embryo under certain conditions. Our survey suggests that differences in chromatin structure might ensure that meristem-localized stem cells have supervised freedom and are pluripotent, and that embryogenic stem cells are unsupervised, autonomous and, hence, freely totipotent.     

Strigolactone versus gibberellin signaling: reemerging concepts?

Main conclusion

In this review, we compare knowledge about the recently discovered strigolactone signaling pathway and the well established gibberellin signaling pathway to identify gaps of knowledge and putative research directions in strigolactone biology. Communication between and inside cells is integral for the vitality of living organisms. Hormonal signaling cascades form a large part of this communication and an understanding of both their complexity and interactive nature is only beginning to emerge. In plants, the strigolactone (SL) signaling pathway is the most recent addition to the classically acting group of hormones and, although fundamental insights have been made, knowledge about the nature and impact of SL signaling is still cursory. This narrow understanding is in spite of the fact that SLs influence a specific spectrum of processes, which includes shoot branching and root system architecture in response, partly, to environmental stimuli. This makes these hormones ideal tools for understanding the coordination of plant growth processes, mechanisms of long-distance communication and developmental plasticity. Here, we summarize current knowledge about SL signaling and employ the well-characterized gibberellin (GA) signaling pathway as a scaffold to highlight emerging features as well as gaps in our knowledge in this context. GA signaling is particularly suitable for this comparison because both signaling cascades share key features of hormone perception and of immediate downstream events. Therefore, our comparative view demonstrates the possible level of complexity and regulatory interfaces of SL signaling.

     

Natural alcohol exposure: is ethanol the main substrate for alcohol dehydrogenases in animals?

Alcohol dehydrogenase (ADH) activity is widely distributed in all phyla. In animals, three non-homologous NAD(P)(+)-dependent ADH protein families are reported. These arose independently throughout evolution and possess different structures and mechanisms of reaction: type I (medium-chain) ADHs are zinc-containing enzymes and comprise the most studied group in vertebrates; type II (short-chain) ADHs lack metal cofactor and have been extensively studied in Drosophila; and type III ADHs are iron-dependent/-activated enzymes that were initially identified only in microorganisms. The presence of these different ADHs in animals has been assumed to be a consequence of chronic exposure to ethanol. By far the most common natural source of ethanol is fermentation of fruit sugars by yeast, and available data support that this fruit trait evolved in concert with the characteristics of their frugivorous seed dispersers. Therefore, if the presence of ADHs in animals evolved as an adaptive response to dietary ethanol exposure, then it can be expected that the enzymogenesis of these enzymes began after the appearance of angiosperms with fleshy fruits, because substrate availability must precede enzyme selection. In this work, available evidence supporting this possibility is discussed. Phylogenetic analyses reveal that type II ADHs suffered several duplications, all of these restricted to flies (order Diptera). Induction of type II Adh by ethanol exposure, a positive correlation between ADH activity and ethanol resistance, and the fact that flies and type II Adh diversification occurred in concert with angiosperm diversification, strongly suggest that type II ADHs were recruited to allow larval flies to exploit new restricted niches with high ethanol content. In contrast, phyletic distribution of types I and III ADHs in animals showed that these appeared before angiosperms and land plants, independently of ethanol availability. Because these enzymes are not induced by ethanol exposure and possess a high affinity and/or catalytic efficiency for non-ethanol endogenous substrates, it can be concluded that the participation of types I and III ADHs in ethanol metabolism can be considered as incidental, and not adaptive.     

E-cadherin downregulation in cancer: fuel on the fire?

The development, maintenance and repair of tissue requires an exquisite balance between cell proliferation, cell adhesion and cell motility. Equally, tumour initiation and progression are characterized by not only the abnormal expression of genes involved in cell proliferation and survival but also by genes responsible for the control of cell adhesion and cell motility. Central to the process of cell-cell adhesion in epithelial tissues is E-cadherin. Loss of E-cadherin function in tumours results in the rapid progression of relatively benign adenomas to invasive, metastatic carcinomas. Germline mutation of the E-cadherin gene predisposes to diffuse, poorly differentiated gastric cancer, and its downregulation in sporadic tumours is associated with poor clinical prognosis.     

Phytotherapeutic approach to alcohol dependence: New old way?

Alcohol abuse and dependence represent a worldwide problem from both medical and social points of view. In Italy it is estimated that there are about one million alcohol-dependent subjects. The pharmacological treatment of patients with alcohol dependence plays a key role in order to achieve alcohol abstinence and prevent relapse. At present, the possible utility of the complementary medicines in the treatment of alcohol dependence is controversial. In the last years, pre-clinical and clinical data from traditional medicines suggest that novel pharmacological approaches for treatment of alcoholism and alcohol abuse may stem from natural substances. The present review summarizes the findings of the effects of phytotherapy in alcohol addiction.     

Who owns the Brazilian carbon?

Brazil is one of the major contributors to land‐use change emissions, mostly driven by agricultural expansion for food, feed, and bioenergy feedstock. Policies to avoid deforestation related to private commitments, economic incentives, and other support schemes are expected to improve the effectiveness of current command and control mechanisms increasingly. However, until recently, land tenure was unknown for much of the Brazilian territory, which has undermined the governance of native vegetation and challenged support and incentive mechanisms for avoiding deforestation. We assess the total extent of public governance mechanisms protecting aboveground carbon (AGC) stocks. We constructed a land tenure dataset for the entire nation and modeled the effects and uncertainties of major land‐use acts on protecting AGC stocks. Roughly 70% of the AGC stock in Brazil is estimated to be under legal protection, and an additional 20% is expected to be protected after areas in the Amazon with currently undesignated land undergo a tenure regularization. About 30% of the AGC stock is on private land, of which roughly two‐thirds are protected. The Cerrado, Amazon, and Caatinga biomes hold about 40%, 30%, and 20% of the unprotected AGC, respectively. Effective conservation of protected and unprotected carbon will depend on successful implementation of the Forest Act, and regularization of land tenure in the Amazon. Policy development that prioritizes unprotected AGC stocks is warranted to promote conservation of native vegetation beyond the legal requirements. However, different biomes and land tenure structures may require different policy settings considering local and regional specifics. Finally, the fate of current AGC stocks relies upon effective implementation of command and control mechanisms, considering that unprotected AGC in native vegetation on private land only accounts for 6.5% of the total AGC stock.     

East versus West: contrasts in phenological patterns?

Aim To examine whether change in the timing of a large number of phenological events and their response to temperature differs between trophic levels during the period 1988–2008. Location In the vicinity of Kazan, Tatarstan Republic, Russia (55°45′ N, 49°08′ E). Methods Observations of the dates of first events of 22 plant phases, 8 insect phases, 3 herpetofauna phases and 26 migrant bird phases were examined using regression to assess changes over time and response to temperature. Differences between trophic levels were assessed using ANOVA. Results In comparison to studies from western Europe, relatively few phenological series (15) revealed a significant advance over time, but a much larger number (37), including all the herpetofauna and nearly all the plants, showed a response to temperature. Trends in birds were, on average, twice as great as those for plants, but plants had a significantly greater temperature response. Over the study period local temperatures had not risen significantly but some phenological change was still evident. Main conclusions Phenological change has been less marked in the eastern edge of Europe than in western and central Europe. This is compatible with a lack of significant local warming during the study period. A large number of species show strong responses to temperature so will be expected to advance if/when local temperatures do increase. In contrast to results from elsewhere in Europe, early events were not the most temperature responsive, suggesting local adaptation preventing precocious behaviour and the consequent dangers of sub‐zero temperatures.     

Songs versus colours versus horns: what explains the diversity of sexually selected traits?

Papers on sexual selection often highlight the incredible diversity of sexually selected traits across animals. Yet, few studies have tried to explain why this diversity evolved. Animals use many different types of traits to attract mates and outcompete rivals, including colours, songs, and horns, but it remains unclear why, for example, some taxa have songs, others have colours, and others horns. Here, we first conduct a systematic survey of the basic diversity and distribution of different types of sexually selected signals and weapons across the animal Tree of Life. Based on this survey, we describe seven major patterns in trait diversity and distributions. We then discuss 10 unanswered questions raised by these patterns, and how they might be addressed. One major pattern is that most types of sexually selected signals and weapons are apparently absent from most animal phyla (88%), in contrast to the conventional wisdom that a diversity of sexually selected traits is present across animals. Furthermore, most trait diversity is clustered in Arthropoda and Chordata, but only within certain clades. Within these clades, many different types of traits have evolved, and many types appear to have evolved repeatedly. By contrast, other major arthropod and chordate clades appear to lack all or most trait types, and similar patterns are repeated at smaller phylogenetic scales (e.g. within insects). Although most research on sexual selection focuses on female choice, we find similar numbers of traits (among sampled species) are involved in male contests (44%) and female choice (55%). Overall, these patterns are largely unexplained and unexplored, as are many other fundamental questions about the evolution of these traits. We suggest that understanding the diversity of sexually selected traits may require a shift towards macroevolutionary studies at relatively deep timescales (e.g. tens to hundreds of millions of years ago).     

Isotopic Diversity Indices: How Sensitive to Food Web Structure?

Recently revisited, the concept of niche ecology has lead to the formalisation of functional and trophic niches using stable isotope ratios. Isotopic diversity indices (IDI) derived from a set of measures assessing the dispersion/distribution of points in the δ-space were recently suggested and increasingly used in the literature. However, three main critics emerge from the use of these IDI: 1) they fail to account for the isotopic sources overlap, 2) some indices are highly sensitive to the number of species and/or the presence of rare species, and 3) the lack of standardization prevents any spatial and temporal comparisons. Using simulations we investigated the ability of six commonly used IDI to discriminate among different trophic food web structures, with a focus on the first two critics. We tested the sensitivity of the IDI to five food web structures along a gradient of sources overlap, varying from two distinct food chains with differentiated sources to two superimposed food chains sharing two sources. For each of the food web structure we varied the number of species (from 10 to 100 species) and the type of species feeding behaviour (i.e. random or selective feeding). Values of IDI were generally larger in food webs with distinct basal sources and tended to decrease as the superimposition of the food chains increased. This was more pronounced when species displayed food preferences in comparison to food webs where species fed randomly on any prey. The number of species composing the food web also had strong effects on the metrics, including those that were supposedly less sensitive to small sample size. In all cases, computing IDI on food webs with low numbers of species always increases the uncertainty of the metrics. A threshold of ∼20 species was detected above which several metrics can be safely used.     

Discovering the Brazilian bat fauna: a task for two centuries?

• 1 Brazil is the second most bat species‐rich country in the world, but the available information on the occurrence and distribution of bat species in Brazil is still heterogeneous and fragmented.
• 2 We review the occurrence and distribution of bat species in Brazil, analyse the spatial performance of inventories conducted to date and identify knowledge gaps. We also identify the main factors contributing to the recent increase in the knowledge of the Brazilian bat fauna, and make suggestions for maintaining this momentum into the near future.
• 3 We plotted record coordinates on a map, grouped them in 0.5 degrees of latitude × 0.5 degrees of longitude grid cells, and analysed records for each of the five terrestrial biomes in Brazil, and for the 1439 priority polygons for the conservation of Brazilian biodiversity.
• 4 We identified 5502 formal bat records in Brazil, indicating that less than 10% of the country is minimally surveyed, and that for nearly 60% of Brazil there is not a single record of bat species. Record coverage varies from 79% in the Atlantic Forest to 24% in Amazonia, but none of the Brazilian biomes is well surveyed for bats. Bat species have been recorded in only 15% of the priority areas for Brazilian biodiversity conservation.
• 5 If the current rate of recording bats in empty grid cells (10% every 4 years) was maintained, it would take 33 years for all cells to have a single record. If the current rate of recording ≥20 species in a grid cell (0.8% per year) was maintained, it would take 200 years for the bat fauna of Brazil to be minimally surveyed. Alarmingly, most of the data‐poor areas are at the expansion frontiers of the agro‐business, near the surrounding deforestation fronts.
• 6 We make recommendations for scientific research on bats in Brazil, to ensure the conservation of this ecologically important taxon.