A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina.

The subphylum Saccharomycotina is a lineage in the fungal phylum Ascomycota that exhibits levels of genomic diversity similar to those of plants and animals. The Saccharomycotina consist of more than 1 200 known species currently divided into 16 families, one order, and one class. Species in this subphylum are ecologically and metabolically diverse and include important opportunistic human pathogens, as well as species important in biotechnological applications. Many traits of biotechnological interest are found in closely related species and often restricted to single phylogenetic clades. However, the biotechnological potential of most yeast species remains unexplored. Although the subphylum Saccharomycotina has much higher rates of genome sequence evolution than its sister subphylum, Pezizomycotina, it contains only one class compared to the 16 classes in Pezizomycotina. The third subphylum of Ascomycota, the Taphrinomycotina, consists of six classes and has approximately 10 times fewer species than the Saccharomycotina. These data indicate that the current classification of all these yeasts into a single class and a single order is an underappreciation of their diversity. Our previous genome-scale phylogenetic analyses showed that the Saccharomycotina contains 12 major and robustly supported phylogenetic clades; seven of these are current families (Lipomycetaceae, Trigonopsidaceae, Alloascoideaceae, Pichiaceae, Phaffomycetaceae, Saccharomycodaceae, and Saccharomycetaceae), one comprises two current families (Dipodascaceae and Trichomonascaceae), one represents the genus Sporopachydermia, and three represent lineages that differ in their translation of the CUG codon (CUG-Ala, CUG-Ser1, and CUG-Ser2). Using these analyses in combination with relative evolutionary divergence and genome content analyses, we propose an updated classification for the Saccharomycotina, including seven classes and 12 orders that can be diagnosed by genome content. This updated classification is consistent with the high levels of genomic diversity within this subphylum and is necessary to make the higher rank classification of the Saccharomycotina more comparable to that of other fungi, as well as to communicate efficiently on lineages that are not yet formally named. Taxonomic novelties: New classes: Alloascoideomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Dipodascomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Lipomycetes M. Groenew., Hittinger, Opulente, A. Rokas, Pichiomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Sporopachydermiomycetes M. Groenew., Hittinger, Opulente & A. Rokas, Trigonopsidomycetes M. Groenew., Hittinger, Opulente & A. Rokas. New orders: Alloascoideomycetes: Alloascoideales M. Groenew., Hittinger, Opulente & A. Rokas; Dipodascomycetes: Dipodascales M. Groenew., Hittinger, Opulente & A. Rokas; Lipomycetes: Lipomycetales M. Groenew., Hittinger, Opulente & A. Rokas; Pichiomycetes: Alaninales M. Groenew., Hittinger, Opulente & A. Rokas, Pichiales M. Groenew., Hittinger, Opulente & A. Rokas, Serinales M. Groenew., Hittinger, Opulente & A. Rokas; Saccharomycetes: Phaffomycetales M. Groenew., Hittinger, Opulente & A. Rokas, Saccharomycodales M. Groenew., Hittinger, Opulente & A. Rokas; Sporopachydermiomycetes: Sporopachydermiales M. Groenew., Hittinger, Opulente & A. Rokas; Trigonopsidomycetes: Trigonopsidales M. Groenew., Hittinger, Opulente & A. Rokas. New families: Alaninales: Pachysolenaceae M. Groenew., Hittinger, Opulente & A. Rokas; Pichiales: Pichiaceae M. Groenew., Hittinger, Opulente & A. Rokas; Sporopachydermiales: Sporopachydermiaceae M. Groenew., Hittinger, Opulente & A. Rokas. Citation: Groenewald M, Hittinger CT, Bensch K, Opulente DA, Shen X-X, Li Y, Liu C, LaBella AL, Zhou X, Limtong S, Jindamorakot S, Gonçalves P, Robert V, Wolfe KH, Rosa CA, Boekhout T, Cadez N, Péter G, Sampaio JP, Lachance M-A, Yurkov AM, Daniel H-M, Takashima M, Boundy-Mills K, Libkind D, Aoki K, Sugita T, Rokas A (2023). A genome-informed higher rank classification of the biotechnologically important fungal subphylum Saccharomycotina. Studies in Mycology 105: 1-22. doi: 10.3114/sim.2023.105.01 This study is dedicated to the memory of Cletus P. Kurtzman (1938-2017), a pioneer of yeast taxonomy.

Prevalence of attention deficit hyperactivity disorder symptoms in patients with schizophrenia.

OBJECTIVE: To investigate the frequency of childhood and adult attention deficit hyperactivity disorder (ADHD) symptoms in a cohort of patients with schizophrenia (SCZ). METHODS: A systematic review was conducted to evaluate existing evidence. Two self-report questionnaires were used to investigate adult ADHD and childhood ADHD symptoms in 126 patients with ICD-10 diagnoses of SCZ. RESULTS: Five studies were included in the systematic review, with the prevalence of childhood and adult ADHD in SCZ subjects ranging between 17-57% and 10-47% respectively. Within our cohort, 47% of patients reported positive screening for ADHD symptoms either in childhood or adulthood. 23% reported symptomatology consistent with both childhood and adult ADHD. CONCLUSIONS: We demonstrate a greater presence of ADHD symptomatology in SCZ compared to that reported for ADHD in the general population. Our findings highlight the importance of improved clinical assessment and treatment considerations in a subgroup of patients with SCZ.

Factors Associated With Reasons for Living Among Suicidal Adolescents.

OBJECTIVE: The objective of this study was to identify baseline demographic and clinical factors associated with higher scores on the Reasons for Living Inventory for Adolescents (RFL-A) at baseline and over follow-up. METHOD: Using data from a pilot clinical trial of a brief intervention for suicidal youth transitioning from inpatient to outpatient, we identified univariate associations of baseline characteristics with RFL-A and used regression to identify the most parsimonious subset of these variables. Finally, we examined to what extent changes in these characteristics over time were related to changes in RFL-A. RESULTS: Univariate analyses found that better external functional emotion regulation and social support were associated with higher RFL-A scores; more self-reported depression, internal dysfunctional emotion regulation, sleep disturbance, anxiety, and distress tolerance were associated with lower RFL-A scores. Multiple linear regression identified internal dysfunctional emotion regulation and external functional emotion regulation as the most parsimonious set of characteristics associated with RFL-A. Improvement in internal emotion regulation, sleep, and depression were related to improvements in RFL-A over time. CONCLUSION: Our findings indicate that emotion regulation-specifically maladaptive internal strategies and use of external resources-is strongly associated with RFL-A. Improvements in internal emotion regulation (r = 0.57), sleep (r = -0.45), and depression (r = -0.34) were related to increases in RFL-A.HIGHLIGHTSIn the literature, greater reasons for living are associated with lower risk for future suicidal ideation and suicide attempts.The most salient correlate of concurrent and future lower RFL-A was dysfunctional internal emotion regulation. Improved sleep and decreases in depression were correlated with increases in RFL-A.

Generation and characterization of phage-GnRH chemical conjugates for potential use in cat and dog immunocontraception.

Overpopulation of cats and dogs is a serious worldwide problem that demands novel, safe and cost-effective solutions. The objective of this study was to generate and characterize phage-peptide conjugates with gonadotropin-releasing hormone (GnRH) for potential use as an immunocontraceptive. A filamentous phage vector f5-8 with wild-type phage coat proteins was used as a carrier for construction of chemical conjugates with GnRH, a peptide that acts as a master reproductive hormone. In such conjugates, the phage body plays the role of a carrier protein, while multiple copies of GnRH peptide stimulate production of neutralizing anti-GnRH antibodies potentially leading to contraceptive effects. To generate the constructs, four different GnRH-based peptides were synthesized and conjugated to phage particles in a two-step procedure: (i) peptides were reacted with phage to form a conjugate using 1-ethyl-3-[3-dimethylaminopropyl]carbodiimide hydrochloride chemistry (EDC) and (ii) the conjugates were separated from remaining free peptides by dialysis. Formation and specificity of phage-GnRH conjugates were confirmed by three independent methods: spectrophotometry, electron microscopy and ELISA. When the conjugates were tested for interaction with sera collected from cats and dogs immunized with GnRH-based vaccines in independent studies, strong specific ELISA signals were obtained, suggesting the potential use of the conjugates for cat and dog immunosterilization. The ability of the conjugates to stimulate production of anti-GnRH antibodies in vivo was evaluated in mice. While optimization of dose, immunization route and adjuvant still requires investigation, our preliminary results demonstrated the presence of anti-GnRH antibodies in sera of mice immunized with such conjugates. Fertility trials in cats and dogs will be needed to evaluate contraceptive potentials of the phage-GnRH peptide chemical conjugates.

Evidence for a high frequency of simultaneous double-nucleotide substitutions.

Point mutations are generally assumed to involve changes of single nucleotides. Nevertheless, the nature and known mechanisms of mutation do not exclude the possibility that several adjacent nucleotides may change simultaneously in a single mutational event. Two independent approaches are used here to estimate the frequency of simultaneous double-nucleotide substitutions. The first examines switches between TCN and AGY (where N is any nucleotide and Y is a pyrimidine) codons encoding absolutely conserved serine residues in a number of proteins from diverse organisms. The second reveals double-nucleotide substitutions in primate noncoding sequences. These two complementary approaches provide similar high estimates for the rate of doublet substitutions, on the order of 0.1 per site per billion years.

Chromosomal location and evolutionary rate variation in enterobacterial genes.

The basal rate of DNA sequence evolution in enterobacteria, as seen in the extent of divergence between Escherichia coli and Salmonella typhimurium, varies greatly among genes, even when only "silent" sites are considered. The degree of divergence is clearly related to the level of gene expression, reflecting constraints on synonymous codon choice. However, where this constraint is weak, among genes not expressed at high levels, divergence is also related to the chromosomal location of the gene; it appears that genes furthest away from oriC, the origin of replication, have a mutation rate approximately two times that of genes near oriC.

Is intimal hyperplasia a marker of neuro-ophthalmic complications of giant cell arteritis?

OBJECTIVE: The ischaemic complications of giant cell arteritis (GCA) such as blindness and stroke may result from luminal narrowing of the affected arteries. This study focuses on the association between the severity of intimal proliferation on temporal artery biopsy (TAB) histology and neuro-ophthalmic complications (NOCs) of GCA. METHOD: We identified 30 cases of biopsy-proven temporal arteritis. One histopathologist (blinded to the clinical details) evaluated the TAB specimens and categorized the degree of maximum stenosis due to intimal hyperplasia into four grades: grade 1 is <50% luminal occlusion due to intimal hyperplasia, grade 2 is 50-75%, grade 3 is >75% and grade 4 is complete luminal occlusion. A second histopathologist (also blinded to the clinical details) independently evaluated the TAB specimens using the same grading system. The NOCs in these patients were noted after a case record review. RESULTS: Of the 30 patients, 12 had NOC-10 with eye complications (complete visual loss, anterior ischaemic neuropathy, visual field defects), one patient had cerebral infarcts and one had both cerebral infarcts and vision loss. There was evidence for a statistically significant trend of NOC associated with higher intimal hyperplasia scores (P = 0.001). The scores of the histopathologists agreed for 23 (77%) patients and differed by 1 category for the remaining 7 (kappa-statistic 0.88). CONCLUSIONS: Our study suggests that the degree of intimal hyperplasia on TAB histology (routinely available to all hospital units) seems to be closely associated with NOCs of GCA. The study highlights the possible prognostic as well as diagnostic role of the biopsy. We feel that intimal hyperplasia noted in biopsy specimens may help us in the risk stratification of GCA patients and targeting of appropriate and novel therapies.

Eukaryote genome duplication - where's the evidence?

Several eukaryotes, including maize, yeast and Xenopus, are degenerate polyploids formed by relatively recent whole-genome duplications. Ohno's conjecture that more ancient genome duplications occurred in an ancestor of vertebrates is probably at least partly true but the present shortage of gene sequence and map information from vertebrates makes it difficult to either prove or disprove this hypothesis. Candidate paralogous segments in mammalian genomes have been identified but the lack of statistical rigour means that many of the proposals in the literature are probably artefacts.

Ins and outs of plastid genome evolution.

Recent findings have established cracks in the straight-laced image of the plastid genome as a molecule whose sole function is photosynthesis and whose gene content is highly conserved. Genes for numerous non-photosynthetic functions have been identified. Algal plastid genomes contain many genes with no homologs in angiosperms, and the recent transfer of genes from the plastid to the nuclear genome has been described. Wholesale abandonment of genes encoding photosynthetic and gene-expression functions has occurred in the plastid genomes of a non-green plant and alga. The origins of plastid DNA, its use in phylogenetic studies, and the origins of plastid introns are also reviewed.

Yeast genome evolution in the post-genome era.

The Saccharomyces cerevisiae genome sequence, augmented by new data on gene expression and function, continues to yield new findings about eukaryote genome evolution. Analysis of the duplicate gene pairs formed by whole-genome duplication indicates that selection for increased levels of gene expression was a significant factor determining which genes were retained as duplicates and which were returned to a single-copy state, possibly in addition to selection for novel gene functions. Proteome comparisons between worm and yeast show that genes for core metabolic processes are shared among eukaryotes and unchanging in function, while comparisons between different yeast species identify 'orphan' genes as the most rapidly evolving fraction of the proteome. Natural hybridisation among yeast species is frequent, but its long-term evolutionary significance is unknown.

Yeast homologue of mammalian Ran binding protein 1.

A Saccharomyces cerevisiae gene (HTN1) that encodes a homologue of mouse Ran binding protein 1 (RanBP1, also known as HTF9A) was identified, cloned and sequenced. The two proteins are 51% identical in sequence. The HTN1 protein may interact with yeast GSP1, GSP2, and PRP20 proteins in an intracellular signalling pathway equivalent to the mammalian RanBP1-Ran/TC4-RCC1 pathway. RanBP1 homologues also exist in worms and rice.

Small single-copy region of plastid DNA in the non-photosynthetic angiosperm Epifagus virginiana contains only two genes. Differences among dicots, monocots and bryophytes in gene organization at a non-bioenergetic locus.

We have determined the nucleotide sequence of a 7 kb (1 kb = 10(3) base-pairs) region that includes the entire small single-copy region (SSC) of the plastid genome of Epifagus virginiana, a non-photosynthetic, parasitic flowering plant. The SSC (4.8 kb) is considerably smaller than those of photosynthetic plants due to the complete deletion of all photosynthetic, chlororespiratory and ribosomal protein genes. This leaves only two genes: a protein gene of 1738 codons whose product is unlikely to be involved in bioenergetic processes and a leucine tRNA gene (trn(LUAG)). Both genes span junctions between the inverted repeat and the SSC, with the consequence that the terminal 20 base-pairs of the repeat is transcribed in both directions and functions both as the 3' end of the tRNA gene and as an internal segment of orf1738. We find that the region of tobacco plastid DNA homologous to Epifagus orf1738 contains a single open reading frame (ORF) of 1901 codons rather than the three ORFs of 1244, 273 and 228 codons originally reported. However, we confirm that the equivalent region of the bryophyte Marchantia contains two genes (1068 and 464 codons) corresponding to the N and C-terminal portions of the dicot protein. In contrast, rice plastid DNA contains a severely truncated pseudogene at this locus.

A subset of conserved tRNA genes in plastid DNA of nongreen plants.

The plastid genome of the nonphotosynthetic parasitic plant Epifagus virginiana contains only 17 of the 30 tRNA genes normally found in angiosperm plastid DNA. Although this is insufficient for translation, the genome is functional, so import of cytosolic tRNAs into plastids has been suggested. This raises the question of whether the tRNA genes that remain in E. virginiana plastid DNA are active or have just fortuitously escaped deletion. We report the sequences of 20 plastid tRNA loci from Orobanche minor, which shares a nonphotosynthetic ancestor with E. virginiana. The two species have 9 intact tRNA genes in common, the others being defunct in one or both species. The intron-containing trnLUAA gene is absent from E. virginiana, but it is intact, transcribed, and spliced in O. minor. The shared intact genes are better conserved than intergenic sequences, which indicates that these genes are being maintained by natural selection and, therefore, must be functional. For the most part, the tRNA species conserved in nonphotosynthetic plastids are also those that have never been found to be imported in plant mitochondria, which suggests that the same rules may govern tRNA import in the two organelles. A small photosynthesis gene, psbI, is still intact in O. minor, and computer simulations show that some small nonessential genes have an appreciable chance of escaping deletion.

Vaginal birth after cesarean success in high-risk women: a population-based study.

OBJECTIVE: The study aim was to identify factors associated with vaginal birth after cesarean (VBAC) in high-risk women. STUDY DESIGN: This is a population-based retrospective cohort study of all births in Ohio during 2006 and 2007. High-risk patients were defined as singleton gestations in women with one previous cesarean who had ⩾1 of the following risk factors: body mass index (BMI)⩾30, hypertension, or diabetes. Multivariate logistic regression was utilized to estimate the relative influence of each factor on successful VBAC. RESULT: A total of 280 882 births were analyzed: of them, 79 084 (27.1%) were high-risk pregnancies and 8658 (10.9%) women had undergone one previous cesarean; 1433 (16.6%) underwent a trial of labor after cesarean (TOLAC). Of them, 974 (68.0%) had a successful VBAC, whereas 459 (32.0%) did not. Factors significantly associated with VBAC success were as follows: a prior vaginal delivery; pregnancy weight gain ⩽30 lbs; Caucasian race; and labor augmentation. CONCLUSION: High-risk women with one prior cesarean are unlikely to undergo a TOLAC, but have a high rate of VBAC.

Racial/ethnic differences in self-reported and biologic measures of chronic stress in pregnancy.

OBJECTIVE: Racial differences in chronic maternal stress may contribute to disparities in pregnancy outcomes. The objective is to identify racial and ethnic differences in self-reported and biologic measures of stress between non-Hispanic black (NHB) and non-Hispanic white (NHW) pregnant women. STUDY DESIGN: NHB and NHW pregnant women were enrolled before 23 weeks of gestation in this prospective cohort study. Equal numbers of women were recruited with public vs private insurance in each racial group. Self-reported stress was measured and blood samples collected in the second and third trimesters were analyzed for serum Epstein-Barr virus antibody, C-reactive protein (CRP), corticotropin-releasing hormone (CRH) and adenocorticotropic hormone (ACTH). RESULTS: One hundred and twelve women were enrolled. NHW women reported more buffers against stress (P=0.04) and neighborhood satisfaction (P=0.02). NHB women reported more discrimination (P<0.001), food insecurity (P=0.04) and had significantly higher mean CRP levels and mean ACTH levels in the second and third trimesters. CONCLUSION: Significant differences in self-reported and biologic measures of chronic stress were identified between NHB and NHW pregnant women with similar economic characteristics. Future studies should investigate mechanisms underlying these differences and their relationship to pregnancy outcomes.

Identification of functional open reading frames in chloroplast genomes.

We have used a rapid computer dot-matrix comparison method to identify all DNA regions which have been evolutionarily conserved between the completely sequenced chloroplast genomes of tobacco and a liverwort. Analysis of these regions reveals 74 homologous open reading frames (ORFs) which have been conserved as to length and amino acid sequence; these ORFs also have an excess of nucleotide substitutions at silent sites of codons. Since the nonfunctional parts of these genomes have become saturated with mutations and show no sequence similarity whatsoever, the homologous ORFs are almost certainly functional. A further four pairs of ORFs show homology limited to only a short part of their putative gene products. Amino acid sequence identities range between 50 and 99%; some chloroplast proteins are seen to be among the most slowly evolving of all known proteins. A search of the nucleotide and amino acid sequence databanks has revealed several previously unidentified genes in chloroplast sequences from other species, but no new homologies to prokaryotic genes.

Updated map of duplicated regions in the yeast genome.

We have updated the map of duplicated chromosomal segments in the Saccharomyces cerevisiae genome originally published by Wolfe and Shields in 1997 (Nature 387, 708-713). The new analysis is based on the more sensitive Smith Waterman search method instead of BLAST. The parameters used to identify duplicated chromosomal regions were optimized such as to maximize the amount of the genome placed into paired regions, under the assumption that the hypothesis that the entire genome was duplicated in a single event is correct. The core of the new map, with 52 pairs of regions containing three or more duplicated genes, is largely unchanged from our original map. 39 tRNA gene pairs and one snRNA pair have been added. To find additional pairs of genes that may have been formed by whole genome duplication, we searched through the parts of the genome that are not covered by this core map, looking for putative duplicated chromosomal regions containing only two duplicate genes instead of three, or having lower-scoring gene pairs. This approach identified a further 32 candidate paired regions, bringing the total number of protein-coding genes on the duplication map to 905 (16% of the proteome). The updated map suggests that a second copy of the ribosomal DNA array has been deleted from chromosome IV.

Molecular cloning of multiple bovine aspartyl protease genes.

Eight bovine genomic clones have been identified as members of the aspartyl protease gene family. The clones were prepared in phage vector lambda EMBL3 from Sau3AI partial digests of DNA from a single animal. Restriction maps show that seven of these clones are related and comprise at least five non-overlapping sequences. Allowing for allelic variation these probably represent three or more different genes. The nucleotide sequences show open reading frames (ORFs) corresponding closely to exons 6, 7 and 8 of human and porcine pepsin A. Comparison with other aspartyl proteases shows that these are multiple bovine pepsin A genes. The seven clones would encode at least two different but closely related forms of pepsin A. The 5' splice site at the end of exon 7 in all seven clones is the unusual sequence GC. The eighth clone contains an ORF homologous to exon 2 of the mammalian aspartyl proteases. The corresponding amino acid sequence is more closely related to bovine chymosin than to any of the other known sequences; it may be functionally homologous to chymosin but could be a novel mammalian aspartyl protease. The intron/exon boundaries seen in both this clone and in the bovine pepsin A clones are at the same positions as found in human pepsin A, bovine chymosin and human and mouse renins, further evidence that the general structure of mammalian aspartyl protease genes has been strongly conserved.

Proteinases and associated genes of parasitic helminths.

Many parasites have deployed proteinases to accomplish some of the tasks imposed by a parasitic life style, including tissue penetration, digestion of host tissue for nutrition and evasion of host immune responses. Information on proteinases from trematodes, cestodes and nematode parasites is reviewed, concentrating on those worms of major medical and economical importance. Their biochemical characterization is discussed, along with their putative biological roles and, where available, their associated genes. For example, proteinases expressed by the various stages of the schistosome life-cycle, in particular the well-characterized cercarial elastase which is involved in the penetration of the host skin and the variety of proteinases, such as cathepsin B (Sm31), cathepsin L1, cathepsin L2, cathepsin D, cathepsin C and legumain (Sm32), which are believed to be involved in the catabolism of host haemoglobin. The various endo- and exoproteinases of Fasciola hepatica, the causative agent of liver fluke disease, are reviewed, and recent reports of how these enzymes have been successfully employed in cocktail vaccines are discussed. The various proteinases of cestodes and of the diverse superfamilies of parasitic nematodes are detailed, with special attention being given to those parasites for which most is known, including species of Taenia, Echinococcus, Spirometra, Necator, Acylostoma and Haemonchus. By far the largest number of papers in the literature and entries to the sequence data bases dealing with proteinases of parasitic helminths report on enzymes belonging to the papain superfamily of cysteine proteinases. Accordingly, the final section of the review is devoted to a phylogenetic analysis of this superfamily using over 150 published sequences. This analysis shows that the papain superfamily can be divided into two major branches. Branch A contains the cathepin Bs, the cathepsin Cs and a novel family termed cathepsin Xs, while Branch B contains the cruzipains, cathepsin Ls, papain-like and aleurain/cathepsin H-like proteinases. The relationships of the helminth proteinases, and similar proteinases from protozoan parasites and other organisms, within these groups are discussed.