scholarly journals Diversification of fungal chitinases and their functional differentiation in Histoplasma capsulatum

2020 ◽  
Author(s):  
Kristie D. Goughenour ◽  
Janice Whalin ◽  
Jason C. Slot ◽  
Chad A. Rappleye
Keyword(s):  
Large Scale ◽  
Histoplasma Capsulatum ◽  
Phylogenetic Analyses ◽  
Domain Architecture ◽  
Functional Differentiation ◽  
Chitinase Activity ◽  
Glycoside Hydrolase Family ◽  
Dimorphic Fungus ◽  
Preferential Expression ◽  
Fungal Chitinases

ABSTRACTChitinases enzymatically hydrolyze chitin, a highly abundant biomolecule with many potential industrial and medical uses in addition to their natural biological roles. Fungi are a rich source of chitinases, however the phylogenetic and functional diversity of fungal chitinases are not well understood. We surveyed fungal chitinases from 373 publicly available genomes, characterized domain architecture, and conducted phylogenetic analyses of the glycoside hydrolase family 18 (GH18) domain. This large-scale analysis does not support the previous division of fungal chitinases into three major clades (A, B, C). The chitinases previously assigned to the “C” clade are not resolved as distinct from the “A” clade in this larger phylogenetic analysis. Fungal chitinase diversity was partly shaped by horizontal gene transfer, and at least one clade of bacterial origin occurs among chitinases previously assigned to the “B” clade. Furthermore, chitin binding domains (CBD) including the LysM domain do not define specific clades but instead are found more broadly across clades of chitinase enzymes. To gain insight into biological function diversity, we characterized all eight chitinases (Cts) from the thermally dimorphic fungus, Histoplasma capsulatum: six A clade (3 A-V, 1 A-IV, and two A-II), one B clade (B-I), and one formerly classified C clade (C-I) chitinases. Expression analyses showed variable induction of chitinase genes in the presence of chitin but preferential expression of CTS3 in the mycelial stage. Activity assays demonstrated that Cts1 (B-I), Cts2 (A-V), Cts3 (A-V), Cts4 (A-V) have endochitinase activities with varying degrees of chitobiosidase function. Cts6 (C-I) has activity consistent with N-acetyl-glucosaminidase exochitinase function and Cts8 (A-II) has chitobiase activity. This suggests chitinase activity is variable even within sub-clades and that predictions of functionality require more sophisticated models.

scholarly journals Diversification of Fungal Chitinases and Their Functional Differentiation in Histoplasma capsulatum

2020 ◽  
Author(s):  
Kristie D Goughenour ◽  
Janice Whalin ◽  
Jason C Slot ◽  
Chad A Rappleye
Keyword(s):  
Large Scale ◽  
Histoplasma Capsulatum ◽  
Phylogenetic Analyses ◽  
Domain Architecture ◽  
Functional Differentiation ◽  
Chitinase Activity ◽  
Dimorphic Fungus ◽  
Preferential Expression ◽  
Chitinase Genes ◽  
Fungal Chitinases

Abstract Chitinases enzymatically hydrolyze chitin, a highly abundant and utilized polymer of N-acetyl-glucosamine. Fungi are a rich source of chitinases; however, the phylogenetic and functional diversity of fungal chitinases are not well understood. We surveyed fungal chitinases from 373 publicly available genomes, characterized domain architecture, and conducted phylogenetic analyses of the glycoside hydrolase (GH18) domain. This large-scale analysis does not support the previous division of fungal chitinases into three major clades (A, B, C) as chitinases previously assigned to the “C” clade are not resolved as distinct from the “A” clade. Fungal chitinase diversity was partly shaped by horizontal gene transfer, and at least one clade of bacterial origin occurs among chitinases previously assigned to the “B” clade. Furthermore, chitin-binding domains (including the LysM domain) do not define specific clades, but instead are found more broadly across clades of chitinases. To gain insight into biological function diversity, we characterized all eight chitinases (Cts) from the thermally dimorphic fungus, Histoplasma capsulatum: six A clade, one B clade, and one formerly classified C clade chitinases. Expression analyses showed variable induction of chitinase genes in the presence of chitin but preferential expression of CTS3 in the mycelial stage. Activity assays demonstrated that Cts1 (B-I), Cts2 (A-V), Cts3 (A-V), Cts4 (A-V) have endochitinase activities with varying degrees of chitobiosidase function. Cts6 (C-I) has activity consistent with N-acetyl-glucosaminidase exochitinase function and Cts8 (A-II) has chitobiase activity. These results suggest chitinase activity is variable even within subclades and that predictions of functionality require more sophisticated models.

scholarly journals Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

Science ◽  
2021 ◽  
pp. eabf2946
Author(s):  
Louis du Plessis ◽  
John T. McCrone ◽  
Alexander E. Zarebski ◽  
Verity Hill ◽  
Christopher Ruis ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Transmission Dynamics ◽  
Genetic Lineage ◽  
Size Dependent ◽  
Spatio Temporal ◽  
The Uk ◽  
Lineage Structure ◽  
And Control ◽  
Lineage Diversity

The UK’s COVID-19 epidemic during early 2020 was one of world’s largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 SARS-CoV-2 genomes, including 26,181 from the UK sampled throughout the country’s first wave of infection. Using large-scale phylogenetic analyses, combined with epidemiological and travel data, we quantify the size, spatio-temporal origins and persistence of genetically-distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, while lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

scholarly journals Role of cysteine in regulating morphogenesis and mitochondrial activity in the dimorphic fungus Histoplasma capsulatum.

1981 ◽  
Vol 78 (7) ◽  
pp. 4596-4600 ◽  
Author(s):  
B. Maresca ◽  
A. M. Lambowitz ◽  
V. B. Kumar ◽  
G. A. Grant ◽  
G. S. Kobayashi ◽  
...  
Keyword(s):  
Histoplasma Capsulatum ◽  
Mitochondrial Activity ◽  
Dimorphic Fungus

Genetic and morphological diversity of the cosmopolitan chaetognath Pseudosagitta maxima (Conant, 1896) in the Atlantic Ocean and its relationship with the congeneric species

2017 ◽  
Vol 74 (7) ◽  
pp. 1875-1884 ◽  
Author(s):  
Dmitry N. Kulagin ◽  
Tatiana V. Neretina
Keyword(s):  
Atlantic Ocean ◽  
Large Scale ◽  
Phylogenetic Analyses ◽  
Morphological Diversity ◽  
Maturity Stage ◽  
Congeneric Species ◽  
Morphological Examination ◽  
Posterior Teeth ◽  
Biogeographic Patterns ◽  
True Diversity

Abstract Until recently many oceanic zooplankton species have been considered as cosmopolitan organisms. At present it became evident that some of them comprise many distinct molecular operational taxonomic units (MOTUs) that often are regarded as cryptic species. As they can significantly change our perceptions of large-scale biogeographic patterns, it is important to characterize the true diversity within common and ecologically important groups. We have analysed the molecular and morphological diversity of the cosmopolitan mesopelagic chaetognath Pseudosagitta maxima throughout the Atlantic Ocean from 60° S to 85° N and its position within the genus Pseudosagitta. Three distinct mitochondrial clades within P. maxima were revealed with phylogenetic analyses (Maximum Likelihood, Bayesian Inference) and were geographically separated. The subsequent analyses of nuclear markers (H3, ITS1) have shown that P. maxima most likely comprises two distinct MOTUs, tropical and bipolar, that also have some morphological differences. The latter MOTU consists of two genetically slightly divergent populations: southern and northern. The morphological examination allowed the determination of a character (type of hook coloration) that accurately distinguishes juveniles of the P. maxima complex from the other congeneric species. Molecular data have shown that evolutionary P. lyra and P. gazellae are more closely related to each other than to P. maxima. Number of hooks, number of anterior and posterior teeth and the arrangement of ova in the ovary were proposed to be the most useful morphological characters to distinguish between tropical and bipolar MOTUs within the P. maxima complex. The first three characters should be determined for each maturity stage separately.

scholarly journals Identification and functional characterization of two bamboo FD gene homologs having contrasting effects on shoot growth and flowering

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Smritikana Dutta ◽  
Anwesha Deb ◽  
Prasun Biswas ◽  
Sukanya Chakraborty ◽  
Suman Guha ◽  
...  
Keyword(s):  
Large Scale ◽  
Forest Ecology ◽  
Phylogenetic Analyses ◽  
Functional Characterization ◽  
Constitutive Expression ◽  
Transcript Level ◽  
In Planta ◽  
Mobility Shift ◽  
Vegetative Development ◽  
Sequence Comparisons

AbstractBamboos, member of the family Poaceae, represent many interesting features with respect to their fast and extended vegetative growth, unusual, yet divergent flowering time across species, and impact of sudden, large scale flowering on forest ecology. However, not many studies have been conducted at the molecular level to characterize important genes that regulate vegetative and flowering habit in bamboo. In this study, two bamboo FD genes, BtFD1 and BtFD2, which are members of the florigen activation complex (FAC) have been identified by sequence and phylogenetic analyses. Sequence comparisons identified one important amino acid, which was located in the DNA-binding basic region and was altered between BtFD1 and BtFD2 (Ala146 of BtFD1 vs. Leu100 of BtFD2). Electrophoretic mobility shift assay revealed that this alteration had resulted into ten times higher binding efficiency of BtFD1 than BtFD2 to its target ACGT motif present at the promoter of the APETALA1 gene. Expression analyses in different tissues and seasons indicated the involvement of BtFD1 in flower and vegetative development, while BtFD2 was very lowly expressed throughout all the tissues and conditions studied. Finally, a tenfold increase of the AtAP1 transcript level by p35S::BtFD1 Arabidopsis plants compared to wild type confirms a positively regulatory role of BtFD1 towards flowering. However, constitutive expression of BtFD1 had led to dwarfisms and apparent reduction in the length of flowering stalk and numbers of flowers/plant, whereas no visible phenotype was observed for BtFD2 overexpression. This signifies that timely expression of BtFD1 may be critical to perform its programmed developmental role in planta.

Expression of alpha- and beta-tubulin genes during dimorphic-phase transitions of Histoplasma capsulatum

1989 ◽  
Vol 9 (5) ◽  
pp. 2042-2049
Author(s):  
G S Harris ◽  
E J Keath ◽  
J Medoff
Keyword(s):  
Phase Transitions ◽  
Histoplasma Capsulatum ◽  
Blot Hybridization ◽  
Dot Blot ◽  
Dimorphic Fungus ◽  
Tubulin Gene ◽  
Beta Tubulin ◽  
Two Dimensional Gel Electrophoresis ◽  
Western Blots ◽  
Alpha Tubulin

Recent investigations have confirmed the presence of one alpha-tubulin gene (TUB1) and one beta-tubulin gene (TUB2) in the dimorphic fungus Histoplasma capsulatum. In the present study, Northern blot (RNA blot) analyses revealed multiple alpha-tubulin transcripts and a single beta-tubulin transcript in the yeast and mycelial phases of the high-virulence 217B strain and low-virulence Downs strain. S1 nuclease protection assays demonstrated one initiation start site and two major stop sites for the TUB1 transcripts, suggesting that variations in 3' processing generate the alpha-tubulin messages of 2.5 and 2.0 kilobases. Dot blot hybridization experiments indicated that tubulin gene expression is developmentally regulated during the dimorphic phase transitions. alpha- and beta-tubulin mRNAs increased six- to eightfold during the yeast-to-mycelium conversion and decreased two- to threefold during the reverse transition. These changes in tubulin mRNA content coincided with major morphological events associated with H. capsulatum development. Western blots (immunoblots) of H. capsulatum yeast-specific proteins resolved by two-dimensional gel electrophoresis demonstrated a single alpha- and a single beta-tubulin isoform. Multiple tubulin polypeptides expressed in mycelia are probably products of posttranslational modifications.

Design of a Bio-Inspired Embryonic Cellular Array Based on Bus Structure

2019 ◽  
Vol 29 (06) ◽  
pp. 2050099
Author(s):  
Tao Wang ◽  
Jinyan Cai ◽  
Yafeng Meng ◽  
Meng Lv ◽  
Zexi Li
Keyword(s):  
Large Scale ◽  
Evaluation Model ◽  
Functional Differentiation ◽  
Digital Circuit ◽  
Resource Consumption ◽  
Internal Communication ◽  
Oxide Semiconductor ◽  
Cellular Array ◽  
Hardware Resource ◽  
Bus Structure

There are some shortcomings, such as huge hardware resource consumption, functional differentiation is difficult and limited fault detection coverage, when embryonic cellular array (ECA) is used to design large-scale circuit. In this paper, the structure characteristics and communication method of multicellular organism are analyzed briefly, and a new bio-inspired ECA based on bus structure (BECA) is proposed, besides that the corresponding self-repairing strategy is designed. First, the functional decomposition has been applied in BECA, which uses bus structure to realize internal communication. BECA consists of bus and electronic tissues (ET), which can be used to realize large-scale circuit. C17 circuit in ISCAS85 circuit library is chosen as experiment subject, and experiment simulation results indicate that BECA based on bus structure is suitable for large-scale circuit, and the faults occurred in ET can be repaired effectively. In order to research BECA from the mathematical point of view, the reliability evaluation model of BECA is established, which is based on [Formula: see text]-out-of-[Formula: see text] system reliability model. In addition, the hardware resource consumption model of BECA is established by analyzing the number of metal oxide semiconductor (MOS) transistors that ECA consumed. Based on BECA reliability and hardware resource consumption evaluation model, comparative experiment is studied, and the results indicate that the proposed ECA can improve the reliability of circuit and reduce hardware resource consumption effectively. Therefore, the BECA presented will play an important role in designing large-scale digital circuit with self-repairing ability.

scholarly journals Disseminated histoplasmosis in a renal transplant recipient – a fatal case report

2011 ◽  
Vol 12 (2) ◽  
pp. 163-165
Author(s):  
Tânia Mara L.B. Araújo ◽  
Geraldo B. Silva Junior ◽  
Orivaldo A. Barbosa ◽  
Rafael S.A. Lima ◽  
Elizabeth F. Daher
Keyword(s):  
Renal Transplant ◽  
Transplant Recipient ◽  
Renal Transplant Recipient ◽  
Histoplasma Capsulatum ◽  
Fatal Case ◽  
Tracheal Aspirate ◽  
Respiratory Pattern ◽  
Vasoactive Drugs ◽  
Dimorphic Fungus ◽  
Disseminated Histoplasmosis

Histoplasmosis is an infectious disease caused by the dimorphic fungus Histoplasma capsulatum.. The disseminated form is usually found in immunocompromised patients. A 53 year-old man, renal transplant recipient, was admitted with fever, dyspnea, productive cough, adynamia and weight loss. He was septic, but hemodynamically stable. The tracheal aspirate found intracellular fungi and the peripheral blood exam was compatible with histoplasmosis. The patient presented a progressive worsening of respiratory pattern and needed mechanical ventilation, vasoactive drugs and hemodialysis. A large spectrum antimicrobial therapy was started, including amphotericin B, but the patient died. Keyword: Disseminated histoplasmosis. Kidney transplantation. Immunosuppression DOI: http://dx.doi.org/10.3329/jom.v12i2.7125 JOM 2011; 12(2): 163-165

scholarly journals Cystine reductase in the dimorphic fungus Histoplasma capsulatum.

1978 ◽  
Vol 135 (3) ◽  
pp. 987-992 ◽  
Author(s):  
B Maresca ◽  
E Jacobson ◽  
G Medoff ◽  
G Kobayashi
Keyword(s):  
Histoplasma Capsulatum ◽  
Dimorphic Fungus

scholarly journals Cooperation between HNF-1α, Cdx2, and GATA-4 in initiating an enterocytic differentiation program in a normal human intestinal epithelial progenitor cell line

2010 ◽  
Vol 298 (4) ◽  
pp. G504-G517 ◽  
Author(s):  
Yannick D. Benoit ◽  
Fréderic Paré ◽  
Caroline Francoeur ◽  
Dominique Jean ◽  
Eric Tremblay ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Cell Line ◽  
Large Scale ◽  
Morphological Changes ◽  
Ectopic Expression ◽  
Functional Differentiation ◽  
Stem Cell Markers ◽  
Intestinal Epithelial ◽  
Differentiation Markers ◽  
Functional Features

In the intestinal epithelium, the Cdx, GATA, and HNF transcription factor families are responsible for the expression of differentiation markers such as sucrase-isomaltase. Although previous studies have shown that Cdx2 can induce differentiation in rat intestinal IEC-6 cells, no data are available concerning the direct implication of transcription factors on differentiation in human normal intestinal epithelial cell types. We investigated the role of Cdx2, GATA-4, and HNF-1α using the undifferentiated human intestinal epithelial crypt cell line HIEC. These transcription factors were tested on proliferation and expression of polarization and differentiation markers. Ectopic expression of Cdx2 or HNF-1α, alone or in combination, altered cell proliferation abilities through the regulation of cyclin D1 and p27 expression. HNF-1α and GATA-4 together induced morphological modifications of the cells toward polarization, resulting in the appearance of functional features such as microvilli. HNF-1α was also sufficient to induce the expression of cadherins and dipeptidylpeptidase, whereas in combination with Cdx2 it allowed the expression of the late differentiation marker sucrase-isomaltase. Large-scale analysis of gene expression confirmed the cooperative effect of these factors. Finally, although DcamKL1 and Musashi-1 expression were downregulated in differentiated HIEC, other intestinal stem cell markers, such as Bmi1, were unaffected. These observations show that, in cooperation with Cdx2, HNF-1α acts as a key factor on human intestinal cells to trigger the onset of their functional differentiation program whereas GATA-4 appears to promote morphological changes.

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