Fungal antigenic variation using mosaicism and reassortment of subtelomeric genes' repertoires.

Surface antigenic variation is crucial for major pathogens that infect humans. To escape the immune system, they exploit various mechanisms. Understanding these mechanisms is important to better prevent and fight the deadly diseases caused. Those used by the fungus Pneumocystis jirovecii that causes life-threatening pneumonia in immunocompromised individuals remain poorly understood. Here, though this fungus is currently not cultivable, our detailed analysis of the subtelomeric sequence motifs and genes encoding surface proteins suggests that the system involves the reassortment of the repertoire of ca. 80 non-expressed genes present in each strain, from which single genes are retrieved for mutually exclusive expression. Dispersion of the new repertoires, supposedly by healthy carrier individuals, appears very efficient because identical alleles are observed in patients from different countries. Our observations reveal a unique strategy of antigenic variation. They also highlight the possible role in genome rearrangements of small imperfect mirror sequences forming DNA triplexes.

Perception of cultured "meat" by Italian, Portuguese and Spanish consumers.

The aim of this study was to investigate how consumers (n = 2,171) originated from South-Western Europe (Italy, Portugal, and Spain) perceive cultured "meat" (CM) and if their demographic characteristics (origin, gender, age, education, occupation, and meat consumption) are related to their willingness to try (WTT), to regularly eat (WTE) and to pay (WTP) for CM. We found the current respondents had an initially positive attitude towards CM: 49% of them perceived CM as "promising and/or acceptable" and 23% "fun and/or intriguing" whereas 29% considered it as "absurd and/or disgusting". In addition, 66 and 25% would be willing and not willing to try CM, respectively. However, 43% had no WTE for CM and, 94% would not pay more for CM compared to conventional meat. Age and especially occupation were good indicators of consumer acceptance of CM. Respondents of 18-30 years of age had the highest acceptance. Respondents outside the meat sector had the highest WTE and people working within the meat sector had the lowest WTE, scientists (within or outside the meat sector) had the highest WTT, people not scientists but within the meat sector had the lowest WTT. Additionally, we found that men are more likely to accept CM than women, Spanish-speaking consumers had the highest WTT and WTE, people with vegan and vegetarian diets may pay more for CM but generally no more than for conventional meat. The perceptions that CM may be more eco-friendly, ethical, safe and healthy than conventional meat, and to a lower extent, the perception that current meat production causes ethical and environmental problems are likely to be major motives for the current respondents to try, regularly eat and pay for CM. On the opposite, lower perceptions of CM benefits and of conventional meat weaknesses more generally, plus emotional resistance towards CM are main barriers to accept CM.

Computational Approaches Drive Developments in Immune-Oncology Therapies for PD-1/PD-L1 Immune Checkpoint Inhibitors.

Computational approaches in immune-oncology therapies focus on using data-driven methods to identify potential immune targets and develop novel drug candidates. In particular, the search for PD-1/PD-L1 immune checkpoint inhibitors (ICIs) has enlivened the field, leveraging the use of cheminformatics and bioinformatics tools to analyze large datasets of molecules, gene expression and protein-protein interactions. Up to now, there is still an unmet clinical need for improved ICIs and reliable predictive biomarkers. In this review, we highlight the computational methodologies applied to discovering and developing PD-1/PD-L1 ICIs for improved cancer immunotherapies with a greater focus in the last five years. The use of computer-aided drug design structure- and ligand-based virtual screening processes, molecular docking, homology modeling and molecular dynamics simulations methodologies essential for successful drug discovery campaigns focusing on antibodies, peptides or small-molecule ICIs are addressed. A list of recent databases and web tools used in the context of cancer and immunotherapy has been compilated and made available, namely regarding a general scope, cancer and immunology. In summary, computational approaches have become valuable tools for discovering and developing ICIs. Despite significant progress, there is still a need for improved ICIs and biomarkers, and recent databases and web tools have been compiled to aid in this pursuit.

Cell Fusion May Be Involved in the Homothallic Mating of Pneumocystis Species.

Pneumocystis species are obligate fungal biotrophs that colonize the lungs of mammals. They cause deadly pneumonia in immunocompromised hosts. The sexual phase seems obligate during their life cycle and essential for survival because it is believed to ensure proliferation and transmission between hosts. Here, we consider if the sexual phase is initiated by the fusion of two cells or by nucleus duplication in order to generate diploid cells that can undergo meiosis. The juxtaposition of the nucleus-associated organelles of pairs of cells with fused cytoplasmic membranes demonstrated that cell fusion can occur. Nevertheless, the frequency of cell fusion remains to be determined, and it cannot be excluded that both cell fusion and nucleus duplication are used to ensure the occurrence of the essential sexual phase. In vitro culturing of these fungi is a major milestone that could clarify the issue.

Effects of partial substitution of grain by agroindustrial byproducts and sunflower seed supplementation in beef haylage-based finisher diets on growth, in vitro methane production and carcass and meat quality.

Thirty-two bulls were assigned to four total mixed biodiverse haylage-based diets to evaluate the effects of partial substitution of grains by agroindustrial byproducts, sunflower seeds (SS) supplementation and haylage level on growth, in vitro methane production and carcass and meat quality. Dietary treatments included a grain-based diet with 30% grain and haylage:concentrate ratio (H:C) of 60:40 (DM basis) (MCe); a by-product-based diet where 50% of the grain was substituted for by-products (H:C, 60:40) (MBp); a byproducts diet with 10% sunflower seed and 90% (DM) MBp (H:C, 54:46) (MBpSS); and a byproducts, SS diet with increased haylage (H:C, 67.5:32.5) (HBpSS). Dry matter intake and growth rate were lower in HBpSS, but feed conversion ratio was unaffected by diet. In vitro methane emissions were reduced by SS. Meat colour and shear force were similar among diets. Lipid oxidation in cooked meat was reduced and fatty acid composition was improved with SS. Biodiverse haylage-based diets may be a viable option for finishing bulls.

Impact of Chlorella vulgaris as feed ingredient and carbohydrases on the health status and hepatic lipid metabolism of finishing pigs.

The implication of high dietary level of Chlorella vulgaris, individually and supplemented with two carbohydrase mixtures, on pigs' health and liver metabolism was assessed in this study. Forty crossbred (Large White × Landrace sows crossed with Pietrain boars) entire male pigs were randomly allocated to the following feeding treatments (n = 10): cereal-soybean meal basal diet (control); basal diet with 5% C. vulgaris; basal diet with 5% C. vulgaris supplemented with 0.005% Rovabio® Excel AP; and basal diet with 5% C. vulgaris supplemented with 0.01% of a preselected four-CAZyme mixture. The trial lasted from 59.1 ± 5.69 kg of initial live weight to 101 ± 1.9 kg of slaughter weight. Data indicate that this high dietary level of C. vulgaris has impact on several blood parameters of finishing pigs. However, the most relevant health outcome observed was a strong immunosuppressive effect promoted by the microalga, which increases pigs' susceptibility to infection diseases. In addition, the dietary incorporation of C. vulgaris reduced the systemic antioxidant capacity of pigs. In turn, the dietary supplementation with the four-CAZyme mixture promoted a clear decrease on some blood parameters compared with the control group. Regarding hepatic lipids, pigs fed C. vulgaris diets, had an increased hepatic content of n-3 PUFA, with a consequent decrease on the n-6/n-3 ratio. In conclusion, the use of C. vulgaris as feed ingredient appears to be safe under controlled experimental conditions. However, it is imperative test it in industrial production systems, with more stressful and less hygienic environments.

Erratum: Aluwé, M. et al. Exploratory Survey on European Consumer and Stakeholder Attitudes towards Alternatives for Surgical Castration of Piglets. Animals 2020, 10, 1758.

The authors wish to make the following corrections to this paper [...].

A High Dietary Incorporation Level of Chlorella vulgaris Improves the Nutritional Value of Pork Fat without Impairing the Performance of Finishing Pigs.

The influence of a high inclusion level of Chlorella vulgaris, individually and supplemented with two carbohydrase mixtures, in finishing pig diets was assessed on zootechnical performance, carcass characteristics, pork quality traits and nutritional value of pork fat. Forty crossbred entire male pigs, sons of Large White × Landrace sows crossed with Pietrain boars, with an initial live weight of 59.1 ± 5.69 kg were used in this trial. Swines were randomly assigned to one of four dietary treatments (n = 10): cereal and soybean meal-based diet (control), control diet with 5% C. vulgaris (CV), CV diet supplemented with 0.005% Rovabio® Excel AP (CV + R) and CV diet supplemented with 0.01% of a four-CAZyme mixture (CV + M). Animals were slaughtered, after the finishing period, with a BW of 101 ± 1.9 kg. Growth performance, carcass characteristics and meat quality traits were not influenced (p > 0.05) by the incorporation of C. vulgaris in the diets. However, the inclusion of the microalga in finishing pig diets increased some lipid-soluble antioxidant pigments and n-3 PUFA, and decreased the n-6:n-3 ratio of fatty acids, thus ameliorating the nutritional value of pork fat. Moreover, the supplementation of diets with the carbohydrase mixtures did not change (p > 0.05) neither animal performance nor meat quality traits, indicating their inefficacy in the increase of digestive utilization of C. vulgaris by pigs under these experimental conditions. It is concluded that the use of C. vulgaris in finishing pig diets, at this high incorporation level, improves the nutritional value of pork fat without compromising pig performance.

Exploratory Survey on European Consumer and Stakeholder Attitudes towards Alternatives for Surgical Castration of Piglets.

Surgical castration of piglets without pain relief is still common practice in many countries. Possible alternatives for surgical castration are application of pain relief or anaesthesia or production of boars (entire males) and immunocastrates. Each of these alternatives faces advantages and disadvantages which may result in different citizen attitudes and consumers acceptability. Understanding which practice is acceptable to whom and why may further stimulate implementation. Consumer (n = 3251) and stakeholder (n = 1027) attitudes towards surgical castration without pain relief, surgical castration with anaesthesia, immunocastration, and production of boars were surveyed from April to June 2020 via an online questionnaire in 16 countries (>175 respondents per country). Surgical castration without pain relief was separated from each of the alternatives due to animal welfare and showed the lowest acceptability (32%). Within the alternatives, a further partitioning between the alternatives was based on perceived quality and food safety, with an acceptance of 85% for applying anaesthesia, 71% for immunocastration, and 49% for boar production. Differences depending on professional involvement and familiarity with agriculture could be observed, mainly for the acceptance of surgical castration without anaesthesia, immunocastration, and boars. Castration with anaesthesia was highly accepted by all types of respondents.

Effects of alfalfa particle size and starch content in diets on feeding behaviour, intake, rumen parameters, animal performance and meat quality of growing lambs.

Thirty-two crossbred Merino branco male lambs were randomly allocated to eight diets, combining two forms of alfalfa presentation (chopped or ground), with four barley grain levels (0%, 11.2%, 21.3% and 33% dry matter (DM)), balanced by low starch agro-industrial by-products (LSBP). The diets were supplemented with 6% soybean oil and included 40% of alfalfa in DM. The lambs were individually housed and the trial lasted six weeks. Intake of DM, average daily weight gain (ADG) and carcass weight were higher with ground alfalfa (P < 0.01). Replacing barley grain by LSBP reduced linearly DM intake and ADG (P < 0.001) but increased meat tenderness (P = 0.046). Regardless of the treatments, meat showed a healthy biohydrogenation fatty acid (FA) profile, with high proportions of t11-18:1, c9,t11-18:2 and a t10-18:1/t11-18:1 ratio clearly below 1. The reduction of barley in diet had a moderate positive impact on meat FA composition, decreasing t10-18:1, which was enhanced by the increase of forage particle size.

Inclusion of the aerial part and condensed tannin extract from Cistus ladanifer L. in lamb diets - Effects on growth performance, carcass and meat quality and fatty acid composition of intramuscular and subcutaneous fat.

Thirty-six lambs were used to evaluate the effect of three levels of Cistus ladanifer condensed tannins (CT; 0, 1.25 and 2.5%) and two ways of CT supply (C. ladanifer aerial parts and C. ladanifer CT extract) on lamb growth performance, carcass composition, meat quality and FA composition of intramuscular and subcutaneous fat. The basal diet was composed of dehydrated lucerne supplemented with 60 g/kg of soybean oil. The highest amount of CT (2.5%) had detrimental effects on growth performance, particularly when the aerial part of C. ladanifer was used. Conversely, 1.25% CT in diets did not affect growth performance and meat quality, and inclusion of C. ladanifer CT extract in diet at this level increased t11-18:1, but not c9,t11-18:2 content in fat. Feeding C. ladanifer CT extract might be a good approach for enhancing the nutritional value of ruminant fat, but further studies are needed to ensure upregulation of endogenous synthesis of c9,t11-18:2.

Microwave-Assisted Selective Hydrogenation of Furfural to Furfuryl Alcohol Employing a Green and Noble Metal-Free Copper Catalyst.

Green, inexpensive, and robust copper-based heterogeneous catalysts achieve 100 % conversion and 99 % selectivity in the conversion of furfural to furfuryl alcohol when using cyclopentyl-methyl ether as green solvent and microwave reactors at low H2 pressures and mild temperatures. The utilization of pressurized microwave reactors produces a 3-4 fold increase in conversion and an unexpected enhancement in selectivity as compared to the reaction carried out at the same conditions using conventional autoclave reactors. The enhancement in catalytic rate produced by microwave irradiation is temperature dependent. This work highlights that using microwave irradiation in the catalytic hydrogenation of biomass-derived compounds is a very strong tool for biomass upgrade that offers immense potential in a large number of transformations where it could be a determining factor for commercial exploitation.

Evolution of Mating Systems in Basidiomycetes and the Genetic Architecture Underlying Mating-Type Determination in the Yeast Leucosporidium scottii.

In most fungi, sexual reproduction is bipolar; that is, two alternate sets of genes at a single mating-type (MAT) locus determine two mating types. However, in the Basidiomycota, a unique (tetrapolar) reproductive system emerged in which sexual identity is governed by two unlinked MAT loci, each of which controls independent mechanisms of self/nonself recognition. Tetrapolar-to-bipolar transitions have occurred on multiple occasions in the Basidiomycota, resulting, for example, from linkage of the two MAT loci into a single inheritable unit. Nevertheless, owing to the scarcity of molecular data regarding tetrapolar systems in the earliest-branching lineage of the Basidiomycota (subphylum Pucciniomycotina), it is presently unclear if the last common ancestor was tetrapolar or bipolar. Here, we address this question, by investigating the mating system of the Pucciniomycotina yeast Leucosporidium scottii. Using whole-genome sequencing and chromoblot analysis, we discovered that sexual reproduction is governed by two physically unlinked gene clusters: a multiallelic homeodomain (HD) locus and a pheromone/receptor (P/R) locus that is biallelic, thereby dismissing the existence of a third P/R allele as proposed earlier. Allele distribution of both MAT genes in natural populations showed that the two loci were in strong linkage disequilibrium, but independent assortment of MAT alleles was observed in the meiotic progeny of a test cross. The sexual cycle produces fertile progeny with similar proportions of the four mating types, but approximately 2/3 of the progeny was found to be nonhaploid. Our study adds to others in reinforcing tetrapolarity as the ancestral state of all basidiomycetes.

Draft Genome Sequence of Sporidiobolus salmonicolor CBS 6832, a Red-Pigmented Basidiomycetous Yeast.

We report the genome sequencing and annotation of the basidiomycetous red-pigmented yeast Sporidiobolus salmonicolor strain CBS 6832. The current assembly contains 395 scaffolds, for a total size of about 20.5 Mb and a G+C content of ~61.3%. The genome annotation predicts 5,147 putative protein-coding genes.

Comparative genomics suggests primary homothallism of Pneumocystis species.

UNLABELLED: Pneumocystis species are fungal parasites of mammal lungs showing host specificity. Pneumocystis jirovecii colonizes humans and causes severe pneumonia in immunosuppressed individuals. In the absence of in vitro cultures, the life cycle of these fungi remains poorly known. Sexual reproduction probably occurs, but the system of this process and the mating type (MAT) genes involved are not characterized. In the present study, we used comparative genomics to investigate the issue in P. jirovecii and Pneumocystis carinii, the species infecting rats, as well as in their relative Taphrina deformans. We searched sex-related genes using 103 sequences from the relative Schizosaccharomyces pombe as queries. Genes homologous to several sex-related role categories were identified in all species investigated, further supporting sexuality in these organisms. Extensive in silico searches identified only three putative MAT genes in each species investigated (matMc, matMi, and matPi). In P. jirovecii, these genes clustered on the same contig, proving their contiguity in the genome. This organization seems compatible neither with heterothallism, because two different MAT loci on separate DNA molecules would have been detected, nor with secondary homothallism, because the latter involves generally more MAT genes. Consistently, we did not detect cis-acting sequences for mating type switching in secondary homothallism, and PCR revealed identical MAT genes in P. jirovecii isolates from six patients. A strong synteny of the genomic region surrounding the putative MAT genes exists between the two Pneumocystis species. Our results suggest the hypothesis that primary homothallism is the system of reproduction of Pneumocystis species and T. deformans. IMPORTANCE: Sexual reproduction among fungi can involve a single partner (homothallism) or two compatible partners (heterothallism). We investigated the issue in three pathogenic fungal relatives: Pneumocystis jirovecii, which causes severe pneumonia in immunocompromised humans; Pneumocystis carinii, which infects rats; and the plant pathogen Taphrina deformans. The nature, the number, and the organization within the genome of the genes involved in sexual reproduction were determined. The three species appeared to harbor a single genomic region gathering only three genes involved in sexual differentiation, an organization which is compatible with sexual reproduction involving a single partner. These findings illuminate the strategy adopted by fungal pathogens to infect their hosts.

Genome sequencing of the plant pathogen Taphrina deformans, the causal agent of peach leaf curl.

UNLABELLED: Taphrina deformans is a fungus responsible for peach leaf curl, an important plant disease. It is phylogenetically assigned to the Taphrinomycotina subphylum, which includes the fission yeast and the mammalian pathogens of the genus Pneumocystis. We describe here the genome of T. deformans in the light of its dual plant-saprophytic/plant-parasitic lifestyle. The 13.3-Mb genome contains few identifiable repeated elements (ca. 1.5%) and a relatively high GC content (49.5%). A total of 5,735 protein-coding genes were identified, among which 83% share similarities with other fungi. Adaptation to the plant host seems reflected in the genome, since the genome carries genes involved in plant cell wall degradation (e.g., cellulases and cutinases), secondary metabolism, the hallmark glyoxylate cycle, detoxification, and sterol biosynthesis, as well as genes involved in the biosynthesis of plant hormones. Genes involved in lipid metabolism may play a role in its virulence. Several locus candidates for putative MAT cassettes and sex-related genes akin to those of Schizosaccharomyces pombe were identified. A mating-type-switching mechanism similar to that found in ascomycetous yeasts could be in effect. Taken together, the findings are consistent with the alternate saprophytic and parasitic-pathogenic lifestyles of T. deformans. IMPORTANCE: Peach leaf curl is an important plant disease which causes significant losses of fruit production. We report here the genome sequence of the causative agent of the disease, the fungus Taphrina deformans. The genome carries characteristic genes that are important for the plant infection process. These include (i) proteases that allow degradation of the plant tissues; (ii) secondary metabolites which are products favoring interaction of the fungus with the environment, including the host; (iii) hormones that are responsible for the symptom of severely distorted leaves on the host; and (iv) drug detoxification enzymes that confer resistance to fungicides. The availability of the genome allows the design of new drug targets as well as the elaboration of specific management strategies to fight the disease.

Time-dependent endpoints as predictors of overall survival in multiple myeloma.

BACKGROUND: Supporting health care sector decisions using time-dependent endpoints (TDEs) such as time to progression (TTP), progression-free survival (PFS), and event-free survival (EFS) remains controversial. This study estimated the quantitative relationship between median TDE and median overall survival (OS) in multiple myeloma (MM) patients. METHODS: Studies (excluding allogeneic transplantation) published from 1970 to 2011 were systematically searched (PubMed). The nonparametric Spearman's rank correlation coefficient measured the association between median TDE and OS. The quantitative relationship between TDEs and OS was estimated with a two-step approach to a simultaneous Tobit model. RESULTS: We identified 153 studies: 230 treatment arms, 22,696 patients and mean study duration of 3.8 years. Mean of median TDEs was 22.5 months and median OS was 39.1 months. Correlation coefficients of median TTP, PFS, and EFS with median OS were 0.51 (P = 0.003), 0.75 (P < 0.0001), and 0.84 (P < 0.0001), respectively. We estimate a 2.5 month (95% confidence interval, 1.7-3.2) increase in median OS for each additional month reported for median TDEs. There was no evidence that this relationship differed by type of surrogate. CONCLUSION: TDEs predict OS in MM patients; this relationship may be valuable in clinical trial design, drug comparisons, and economic evaluation.

Evidence for divergent evolution of growth temperature preference in sympatric Saccharomyces species.

The genus Saccharomyces currently includes eight species in addition to the model yeast Saccharomyces cerevisiae, most of which can be consistently isolated from tree bark and soil. We recently found sympatric pairs of Saccharomyces species, composed of one cryotolerant and one thermotolerant species in oak bark samples of various geographic origins. In order to contribute to explain the occurrence in sympatry of Saccharomyces species, we screened Saccharomyces genomic data for protein divergence that might be correlated to distinct growth temperature preferences of the species, using the dN/dS ratio as a measure of protein evolution rates and pair-wise species comparisons. In addition to proteins previously implicated in growth at suboptimal temperatures, we found that glycolytic enzymes were among the proteins exhibiting higher than expected divergence when one cryotolerant and one thermotolerant species are compared. By measuring glycolytic fluxes and glycolytic enzymatic activities in different species and at different temperatures, we subsequently show that the unusual divergence of glycolytic genes may be related to divergent evolution of the glycolytic pathway aligning its performance to the growth temperature profiles of the different species. In general, our results support the view that growth temperature preference is a trait that may have undergone divergent selection in the course of ecological speciation in Saccharomyces.

BiDiBlast: comparative genomics pipeline for the PC.

Bi-directional BLAST is a simple approach to detect, annotate, and analyze candidate orthologous or paralogous sequences in a single go. This procedure is usually confined to the realm of customized Perl scripts, usually tuned for UNIX-like environments. Porting those scripts to other operating systems involves refactoring them, and also the installation of the Perl programming environment with the required libraries. To overcome these limitations, a data pipeline was implemented in Java. This application submits two batches of sequences to local versions of the NCBI BLAST tool, manages result lists, and refines both bi-directional and simple hits. GO Slim terms are attached to hits, several statistics are derived, and molecular evolution rates are estimated through PAML. The results are written to a set of delimited text tables intended for further analysis. The provided graphic user interface allows a friendly interaction with this application, which is documented and available to download at http://moodle.fct.unl.pt/course/view.php?id=2079 or https://sourceforge.net/projects/bidiblast/ under the GNU GPL license.