D-xylose is the second most abundant monosaccharide found in lignocellulose and is of biotechnological importance for producing second-generation ethanol and other high-value chemical compounds. D-xylose conversion to ethanol is promoted by microbial fermentation, mainly by bacteria, yeasts, or filamentous fungi. Considering yeasts, species belonging to the CTG(Ser1) or CTG(Ala) clade display a remarkable ability to ferment D-xylose to ethanol and other compounds; however, these yeasts are not employed on an industrial scale due to the poor fermentative performance compared to conventional yeasts, like Saccharomyces cerevisiae, and also due to the lack of a molecular toolbox for development of new strains tailored to fermentation stress tolerance and performance. Thus, the purpose of this review is to evaluate the major molecular tools (e.g., transformation markers and techniques, vectors, regulatory sequences, and gene editing techniques) available for the most studied yeasts of CTG(Ser1) clade, like Scheffersomyces, Spathaspora, Candida and Yamadazyma species, and the CTG(Ala) clade representative Pachysolen tannophilus. Furthermore, we synthesized the current state-of-the-art molecular developments and perspectives for D-xylose fermenting yeast strain design.

Biocontainment techniques for genetically modified yeasts (GMYs) are pivotal due to the importance of these organisms for biotechnological processes and also due to the design of new yeast strains by using synthetic biology tools and technologies. Due to the large genetic modifications that many yeast strains display, it is highly desirable to avoid the leakage of GMY cells into natural environments and, consequently, the spread of synthetic genes and circuits by horizontal or vertical gene transfer mechanisms within the microorganisms. Moreover, it is also desirable to avoid that patented yeast gene technologies spread outside the production facility. In this review, it was evaluated the different biocontainment technologies currently available for GMYs. Interestingly, uniplex-type biocontainment approaches (UTBAs), which relies on nutrient auxotrophies induced by gene mutation or deletion, or the expression of simple kill switches apparatus, are still the major biocontainment approaches still in use with GMY. While bacteria like Escherichia coli account for advanced biocontainment technologies based on synthetic biology and multiplex-type biocontainment approaches (MTBAs), GMYs are distant from this scenario due to many reasons. Thus, a comparison of different UTBAs and MTBAs applied for GMY and genetically engineered microorganisms (GEMs) was made, indicating the major advances of biocontainment techniques for GMYs.

The ability of brewing yeasts (Saccharomyces cerevisiae and Saccharomyces pastorianus) to cope with the toxic effects of ethanol during beer fermentation depends on the modulation of lipid and lipid droplets (LDs) biosynthesis, which affects membrane fluidity. However, it has been demonstrated that lipids and LDs can modulate different biological mechanisms associated to ethanol tolerance, including proteostasis and autophagy, leading to the hypothesis that lipid and LDs biosynthesis are integrative processes necessary for ethanol tolerance in yeast. Supporting this hypothesis, a transcriptome and systems biology analyses indicated the upregulation of autophagy, lipid biosynthesis, and proteostasis (ALP)-associated genes in lager yeast during beer fermentation, whose respective proteins interact in a shortest-pathway ALP network. These results indicated a cross-communication between various pathways linked to inter-organelle autophagy, lipid metabolism, and proteostasis (ALP) during lager beer fermentation, thus highlighting the importance of lipids for beer fermentation.

Yeasts from the species Saccharomyces cerevisiae (ale yeast) and Saccharomyces pastorianus (lager yeast) are the main component of beer fermentation. It is known that different beer categories depend on the use of specific ale or lager strains, where the yeast imprints its distinctive fermentative profile to the beer. Despite this, there are no studies reporting how diverse, rich, and homogeneous the beer categories are in terms of commercially available brewing yeast strains. In this work, the diversity, richness, and evenness of different beer categories and commercial yeast strains available for brewing were evaluated by applying quantitative concepts of diversity analysis in a sample of 119,189 beer recipes. For this purpose, the frequency of ale or lager and dry or liquid yeast formulations usage was accessed and its correlation with the number of yeast strains, recipes, lowest and highest values of original and final gravity, international bitter units, and alcohol by volume were analyzed. A statistical framework was applied for comparing the lowest and highest fermentation temperature as well as the attenuation percentage for ale and lager yeasts strains in both dry and liquid formulations. Additionally, the brewer's preferential use of a specific brewing yeast strain in comparison to all different yeast strains reported for a beer category was estimated. The results indicated that many beer categories are preferentially fermented with dry yeast formulations instead of liquid yeasts, despite the high number of available liquid yeast formulations. Finally, the preferential use of specific yeast formulations drives the fermentative diversity of a beer category, showing that many yeast strains are potentially and industrially underexplored.

Cell cycle alterations are among the principle hallmarks of cancer. Consequently, the study of cell cycle regulators has emerged as an important topic in cancer research, particularly in relation to environmental exposure. Particulate matter and coal dust around coal mines have the potential to induce cell cycle alterations. Therefore, in the present study, we performed chemical analyses to identify the main compounds present in two mineral coal samples from Colombian mines and performed systems chemo-biology analysis to elucidate the interactions between these chemical compounds and proteins associated with the cell cycle. Our results highlight the role of oxidative stress generated by the exposure to the residues of coal extraction, such as major inorganic oxides (MIOs), inorganic elements (IEs) and polycyclic aromatic hydrocarbons (PAH) on DNA damage and alterations in the progression of the cell cycle (blockage and/or delay), as well as structural dysfunction in several proteins. In particular, IEs such as Cr, Ni, and S and PAHs such as benzo[a]pyrene may have influential roles in the regulation of the cell cycle through DNA damage and oxidative stress. In this process, cyclins, cyclin-dependent kinases, zinc finger proteins such as TP53, and protein kinases may play a central role.

During beer production, yeast generate ethanol that is exported to the extracellular environment where it accumulates. Depending on the initial carbohydrate concentration in the wort, the amount of yeast biomass inoculated, the fermentation temperature, and the yeast attenuation capacity, a high concentration of ethanol can be achieved in beer. The increase in ethanol concentration as a consequence of the fermentation of high gravity (HG) or very high gravity (VHG) worts promotes deleterious pleiotropic effects on the yeast cells. Moderate concentrations of ethanol (5% v/v) change the enzymatic kinetics of proteins and affect biological processes, such as the cell cycle and metabolism, impacting the reuse of yeast for subsequent fermentation. However, high concentrations of ethanol (> 5% v/v) dramatically alter protein structure, leading to unfolded proteins as well as amorphous protein aggregates. It is noteworthy that the effects of elevated ethanol concentrations generated during beer fermentation resemble those of heat shock stress, with similar responses observed in both situations, such as the activation of proteostasis and protein quality control mechanisms in different cell compartments, including endoplasmic reticulum (ER), mitochondria, and cytosol. Despite the extensive published molecular and biochemical data regarding the roles of proteostasis in different organelles of yeast cells, little is known about how this mechanism impacts beer fermentation and how different proteostasis mechanisms found in ER, mitochondria, and cytosol communicate with each other during ethanol/fermentative stress. Supporting this integrative view, transcriptome data analysis was applied using publicly available information for a lager yeast strain grown under beer production conditions. The transcriptome data indicated upregulation of genes that encode chaperones, co-chaperones, unfolded protein response elements in ER and mitochondria, ubiquitin ligases, proteasome components, N-glycosylation quality control pathway proteins, and components of processing bodies (p-bodies) and stress granules (SGs) during lager beer fermentation. Thus, the main purpose of this hypothesis and theory manuscript is to provide a concise picture of how inter-organellar proteostasis mechanisms are connected with one another and with biological processes that may modulate the viability and/or vitality of yeast populations during HG/VHG beer fermentation and serial repitching.

Brewing lager yeast ( Saccharomyces pastorianus ) is exposed to stressful conditions during beer fermentation, including ethanol toxicity. In response to ethanol toxicity, various biological mechanisms are modulated, including lipid biosynthesis. It is well known that during beer fermentation, the composition of yeast membranes changes in response to ethanol toxicity, making it less fluid and permeable. Additionally, neutral lipids and lipid droplets (LDs) are produced in response to ethanol toxicity. LDs are membranous organelles that transport lipids and proteins, acting as hubs for inter-organellar communication and modulating the activity of mechanisms necessary for ethanol tolerance, such as proteostasis and autophagy. Unfortunately, little is known about the interplay between autophagy, lipid metabolism, and proteostasis (ALP) in lager cells during beer fermentation. Therefore, transcriptome analyses using publicly available DNA microarray data obtained from lager yeast cells were used to identify all the ALP-associated genes that were upregulated during beer fermentation compared to yeast biomass propagation. Thereafter, a top-down systems biology analysis was applied, involving constructing an ALP-associated shortest-pathway protein–protein interaction network (ALP network), identifying important nodes and communities within the ALP network, and identifying the overrepresented biological processes and cellular components using a Gene Ontology (GO) analysis. The transcriptome analyses indicated the upregulation of 204 non-redundant ALP-associated genes during beer fermentation, whose respective proteins interact in the shortest-pathway ALP network. Thirteen communities were selected from the ALP network, and they were associated with multiple overrepresented GO biological processes and cellular components, such as mitophagy, cytoplasm-to-vacuole transport, piecemeal microautophagy of the nucleus, endoplasmic reticulum (ER) stress, ergosterol and lipid biosynthesis, LDs, ER membrane, and phagophore assembly. These results indicate that ethanol tolerance in lager yeasts could be due to the modulation of proteostasis and various forms of autophagy by lipid biosynthesis and LDs, thus highlighting the importance of lipids for beer fermentation.### Competing Interest StatementThe authors have declared no competing interest.

Acute myelogenous leukemia (AML) is an aggressive hematological malignancy associated with high rates of mortality. This incidence is due to the complexity in which the AML cells interact with other healthy human cells. These phenomena create an environment that favors the expansion of leukemic cells, which will affect the patient's prognosis. An important aspect is the ability of AML cells to evade immune responses via targeting and signaling immune cells to suppress anti-tumor responses. Many studies have reported that associations among components in the peripheral bloodstream might modulate leukemic progression because AML survival is a fundamental step for recolonizing bone marrow after allogeneic hematopoietic stem cell (HSC) transplantation or chemotherapy. Therefore, we collected the most important data about components that circulate with leukemic blasts and contribute to their survival and proliferation. We also discuss clinical approaches that could be conducted to more effectively treat the disease.

BACKGROUND:Protein Disulfide Isomerases are thiol oxidoreductase chaperones from thioredoxin superfamily with crucial roles in endoplasmic reticulum proteostasis, implicated in many diseases. The family prototype PDIA1 is also involved in vascular redox cell signaling. PDIA1 is coded by the P4HB gene. While forced changes in P4HB gene expression promote physiological effects, little is known about endogenous P4HB gene regulation and, in particular, gene modulation by alternative splicing. This study addressed the P4HB splice variant landscape.RESULTS:Ten protein coding sequences (Ensembl) of the P4HB gene originating from alternative splicing were characterized. Structural features suggest that except for P4HB-021, other splice variants are unlikely to exert thiol isomerase activity at the endoplasmic reticulum. Extensive analyses using FANTOM5, ENCODE Consortium and GTEx project databases as RNA-seq data sources were performed. These indicated widespread expression but significant variability in the degree of isoform expression among distinct tissues and even among distinct locations of the same cell, e.g., vascular smooth muscle cells from different origins. P4HB-02, P4HB-027 and P4HB-021 were relatively more expressed across each database, the latter particularly in vascular smooth muscle. Expression of such variants was validated by qRT-PCR in some cell types. The most consistently expressed splice variant was P4HB-021 in human mammary artery vascular smooth muscle which, together with canonical P4HB gene, had its expression enhanced by serum starvation.CONCLUSIONS:Our study details the splice variant landscape of the P4HB gene, indicating their potential role to diversify the functional reach of this crucial gene. P4HB-021 splice variant deserves further investigation in vascular smooth muscle cells.

Competing endogenous RNAs (ceRNAs) are RNAs that share common miRNA binding sites and compete with each other for the miRNA association at these sites. The observation of this phenomenon in the cells altered the view of the miRNA target RNAs from molecules that are passively controlled by miRNAs to molecules that also modulate the miRNAs activity. In this review, we build a general profile of ceRNAS characteristics in order to facilitate ceRNAs identification by researchers. The information summarized here contains an actualized list of previously reported ceRNAs and classes of RNAs that can participate in this type of interaction, the expression behavior and characteristics of ceRNAs and miRNAs in the context of competition, the influence of the shared MREs/miRNAs numbers and the miRNA binding strength on the competition, reports on competition between RNAs in different subcellular localizations and the concept that ceRNAs may form a huge regulatory network in the cell.

Brettanomyces is a semi-domesticated yeast that is a crucial component of Iambic beers and is increasingly attracting the attention of the brewing industry. Brettanomyces display Saccharomyces-like features, such as a positive Crabtree effect, ethanol synthesis and tolerance to harsh environments. Additionally, Brettanomyces exhibit beta-glucosidase and esterase activities, the production of phenolic compounds and tetrahydropyridines, together with the ability to ferment dextrins and breakdown cellobiose from wooden casks. Although the importance of Brettanomyces species is documented in the production of different beer styles, the molecular and biochemical features of these species required for brewing are poorly understood. Therefore, this work reviews the current knowledge of the molecular biology and biochemistry underlying the performance of Brettanomyces in the brewing industry. (C) 2019 The Institute of Brewing & Distilling

Heat shock protein 47 (HSP47) is an important chaperone required for the correct folding and secretion of collagen. Several studies revealed that HSP47 has a role in numerous steps of collagen synthesis, preventing procollagen aggregation and inducing hydroxylation of proline and lysine residues. HSP47 is encoded by the SERPINH1 gene, which is located on chromosome 11q13.5, one of the most frequently amplified regions in human cancer. The altered expression levels of HSP47 have been correlated with several types of cancer, such as cervical, breast, pancreatic and gastric cancers. Studies have shown that HSP47 promotes tumor angiogenesis, growth, migration and metastatic capacity. In this review, we highlight the fundamental aspects of the interaction between HSP47 and collagen and the recent discoveries of the role of this chaperone in different types of malignant neoplasias. We also discuss recent treatments using HSP47 as a therapeutic target, and present evidences that HSP47 is an essential protein for cancer biology and a potential molecular target for chemotherapy.

Horizontal gene transfer (HGT) has a major impact on the evolution of prokaryotic genomes, as it allows genes evolved in different contexts to be combined in a single genome, greatly enhancing the ways evolving organisms can explore the gene content space and adapt to the environment. A systematic analysis of HGT in a large number of genomes is of key importance in understanding the impact of HGT in the evolution of prokaryotes. We developed a method for the detection of genes that potentially originated by HGT based on the comparison of BLAST scores between homologous genes to 16S rRNA-based phylogenetic distances between the involved organisms. The approach was applied to 697 prokaryote genomes and estimated that in average approximately 15% of the genes in prokaryote genomes originated by HGT, with a clear correlation between the proportion of predicted HGT genes and the size of the genome. The methodology was strongly supported by evolutionary relationships, as tested by the direct phylogenetic reconstruction of many of the HGT candidates. Studies performed with Escherichia coli W3110 genome clearly show that HGT proteins have fewer interactions when compared to those predicted as vertical inherited, an indication that the number of protein partners imposes limitations to horizontal transfer. A detailed functional classification confirms that genes related to protein translation are vertically inherited, whereas interestingly, transport and binding proteins are strongly enriched among HGT genes. Because these genes are related to the cell exchange with their environment, their transfer most likely contributed to successful adaptation throughout evolution.

Malt extract - yeast extract - peptone - glucose rich medium for yeast growth and maintenance.

BACKGROUND:Xeroderma Pigmentosum (XP) is a disease caused by mutations in the nucleotide excision repair (NER) pathway. Patients with XP exhibit a high propensity to skin cancers and some subtypes of XP can even present neurological impairments. During NER, DDB2 (XPE), in complex with DDB1 (DDB-Complex), performs the DNA lesion recognition. However, not much is known about how mutations found in XP patients affect the DDB2 structure and complex assembly. Thus, we searched for structural evidence associated with the role of three naturally occurring mutations found in XPE patients: R273H, K244E, and L350P.METHODS:Each mutant was individually constructed and submitted to multiple molecular dynamics simulations, done in triplicate for each designed system. Additionally, Dynamic Residue Interaction Networks were designed for each system and analyzed parallel with the simulations.RESULTS:DDB2 mutations promoted loss of flexibility in the overall protein structure, producing a different conformational behavior in comparison to the WT, especially in the region comprising residues 354 to 371. Furthermore, the DDB-complex containing the mutated forms of DDB2 showed distinct behaviors for each mutant: R273H displayed higher structural instability when complexed; L350P affected DDB1 protein-protein binding with DDB2; and K244E, altered the complex binding trough different ways than L350P.CONCLUSIONS:The data gathered throughout the analyses helps to enlighten the structural basis for how naturally occurring mutations found in XPE patients impact on DDB2 and DDB1 function.GENERAL SIGNIFICANCE:Our data influence not only on the knowledge of XP but on the DNA repair mechanisms of NER itself.

Cancer metastasis is defined as the dissemination of malignant cells from the primary tumor site, leading to colonization of distant organs and the establishment of a secondary tumor. Metastasis is frequently associated with chemoresistance and is the major cause of cancer-related mortality. Metastatic cells need to acquire the ability to resist to stresses provided by different environments, such as reactive oxygen species, shear stress, hemodynamic forces, stromal composition, and immune responses, to colonize other tissues. Hence, only a small population of cells has a metastasis-initiating potential. Several studies have revealed the misregulation of transcriptional variants during cancer progression, and many splice events can be used to distinguish between normal and tumoral tissue. These variants, which are abnormally expressed in malignant cells, contribute to an adaptive response of tumor cells and the success of the metastatic cascade, promoting an anomalous cell cycle, cellular adhesion, resistance to death, cell survival, migration and invasion. Understanding the different aspects of splicing regulation and the influence of transcriptional variants that control metastatic cells is critical for the development of therapeutic strategies. In this review, we describe how transcriptional variants contribute to metastatic competence and discuss how targeting specific isoforms may be a promising therapeutic strategy.

The growing of microbrewerys in Brazil has imposing an increase in the production of different supplies for brewing, iincluding yeast biomass for beer fermentation. In Brazil,only four companies produce and sell yeasts for microbreweries, and only two companies are able to attend microbreweries. Additionaly, these companies should be able to deliver yeast cells to different states and cities in Brazil. During transport, the yeast cells are exposed to thermical stress (due to the lack of temperature control) and chronological aging (due to the long period of storage and transport). When delivered to the microbreweries, those yeast cells display problems during beer fermentation as the consequence of a loweryeast vitality and viability and affecting beer’s quality. Thus, in this work a new colorimetric assay was developed to access the vitality of yeast cells by using resazurin. Resazurin is a highly dichromatic dye, showing a colorimetric change proportional to the yeast cellvitality that can be easily visualized by naked eye. To evalute the potential of resazurin to differentiate yeast cells with low and high vitality, different yeast ale and lager strains (US-05 and W34/70, respectively) were submitted to heat shock stress and their vitality was accessed by resazurin, testing different variables as concentration of work solution, cellular density and incubation time. The resazurin data, supported by acidification power test, showed a vitality decrese in cells submited to heat shock stress. Futhermore, the sensibility of the resazurin assay was explored during chronological aging of yeast cells. The assay was capable to detect differences of vitality and viability between yeast strains. In addition, the potencial of the resazurin test to predict the fermentative capacity of stressed and non-estressed yeast cells was observed in wort attenuation assays, comfirming the aplicability of resazurin in the microbrewery context.

In Brazil, bioethanol is produced by sucrose fermentation from sugarcane by Saccharomyces cerevisiae in a fed-batch process that uses high density of yeast cells (15–25 % of wet weight/v) and high sugar concentration (18–22 % of total sugars). Several research efforts have been employed to improve the efficiency of this process through the isolation of yeasts better adapted to the Brazilian fermentation conditions. Two important wild strains named CAT-1 and PE-2 were isolated during the fermentation process and were responsible for almost 60 % of the total ethanol production in Brazil. However, in the last decade the fermentative substrate composition was much modified, since new sugar cane crops were developed, the use of molasses instead of sugar cane juice increase and with the prohibition of burning of sugarcane prior harvest. As consequence, these previously isolated strains are being replaced by new wild yeasts in most of ethanol plants. In this new scenario the isolation of novel better adapted yeasts with improved fermentative characteristics is still a big challenge. Here, we discuss the main aspects of Brazilian ethanol production and the efforts for the selection, characterization and genetic modifications of new strains with important phenotypic traits such as thermotolerance.

Mutations in cancer cells frequently result in cell cycle alterations that lead to unrestricted growth compared to normal cells. Considering this phenomenon, many drugs have been developed to inhibit different cell-cycle phases. Mitotic phase targeting disturbs mitosis in tumor cells, triggers the spindle assembly checkpoint and frequently results in cell death. The first anti-mitotics to enter clinical trials aimed to target tubulin. Although these drugs improved the treatment of certain cancers, and many anti-microtubule compounds are already approved for clinical use, severe adverse events such as neuropathies were observed. Since then, efforts have been focused on the development of drugs that also target kinases, motor proteins and multi-protein complexes involved in mitosis. In this review, we summarize the major proteins involved in the mitotic phase that can also be targeted for cancer treatment. Finally, we address the activity of anti-mitotic drugs tested in clinical trials in recent years.

The growth of population in a worldwide scale and the social vulnerability of different human communities subjected to war, economy collapse, ethnical persecution and poverty impose a strong pressure to occupy multi-hazard environments, like flood plains and hill slopes subject to landslides (Sullivan-Wiley and Gianotti 2017). As human communities occupy unstable hill slope areas, activities like deforestation or irregular building sites increase the probability of landslide occurrence (Dai et al. 2002). Thus, it becomes imperative to assess the regional factors that could trigger a landslide event. The manuscript of Cerri et al. (2017) invokes a new geologic strategy to evaluate potential landslide regions in Serra do Mar based on soil fractures and foliation, and the slope geometry of the area. This method could improve the diagnostic of hazard in hill slope areas and directly impact the development of a framework for safe hill slope use for agricultural and urban purposes.