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Drowned organ donors can be exposed to environmental molds through the aspiration of water; transplantation of exposed organs can cause invasive mold infections in recipients. We describe 4 rapidly fatal cases of potentially donor-derived invasive mold infections in the United States, highlighting the importance of maintaining clinical suspicion for these infections in transplant recipients.

(1) Background: Bacillus velezensis and Bacillus amyloliquefaciens are closely related members of the "operational group B. amyloliquefaciens ", a taxonomical unit above species level within the " Bacillus subtilis species complex". They have similar morphological, physiological, biochemical, phenotypic, and phylogenetic characteristics. Thus, separating these two taxa from each another has proven to be difficult to implement and could not be pushed easily into the line of routine analyses. (2) Methods: The aim of this study was to determine whether whole FAME profiling could be used to distinguish between these two species, using both type strains and environmental isolates. Initially, the classification was determined by partial sequences of the gyrA and rpoB genes and the classified isolates and type strains were considered as samples to develop the identification method, based on FAME profiles. (3) Results: The dissimilarities in 16:0, 17:0 iso, and 17:0 FA components have drawn a distinction between the two species and minor differences in FA 14:0, 15:0 iso, and 16:0 iso were also visible. The statistical analysis of the FA profiles confirmed that the two taxa can be distinguished into two separate groups, where the isolates are identified without misreading. (4) Conclusions: Our study proposes that the developed easy and fast-automated identification tool based on cellular FA profiles can be routinely applied to distinguish B. velezensis and B. amyloliquefaciens .

Asperelines are short-sequence peptaibol molecules, and these peptides composed of 10 residues were isolated from the Trichoderma asperellum. In our study, a detailed structural characterization was performed on the asperelines by means of molecular dynamics methods. For the aspereline peptides, the occurrence of various secondary structural elements (i.e. β-turns and helical structures) was investigated along their entire sequences. The results derived from the simulated annealing calculations led to the observations that in the case of asperelines, the types I, III and III' β-turn structures, as well as their stabilizing i ← i+3 H-bonds appeared. However, beside the different β-turns, shorter or longer helical structures were also detected. Based on the results obtained by the molecular dynamics simulations, it was concluded that the three-dimensional structure of aspereline peptides could be characterized by helical conformations (i.e. 3 10 - and α-helix). Nevertheless, on the basis of individual molecular dynamics trajectories, it was observed that the asperelines could adopt not only the right-handed, but also the left-handed helical structures., (© 2021 John Wiley & Sons A/S.)

Background: The coronavirus disease 2019 (COVID-19) pandemic continues to produce substantial morbidity and mortality. To understand the reasons for the wide-spectrum complications and severe outcomes of COVID-19, we aimed to identify cellular targets of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) tropism and replication in various tissues., Methods: We evaluated RNA extracted from formalin-fixed, paraffin-embedded autopsy tissues from 64 case patients (age range, 1 month to 84 years; 21 COVID-19 confirmed, 43 suspected COVID-19) by SARS-CoV-2 reverse-transcription polymerase chain reaction (RT-PCR). For cellular localization of SARS-CoV-2 RNA and viral characterization, we performed in situ hybridization (ISH), subgenomic RNA RT-PCR, and whole-genome sequencing., Results: SARS-CoV-2 was identified by RT-PCR in 32 case patients (21 COVID-19 confirmed, 11 suspected). ISH was positive in 20 and subgenomic RNA RT-PCR was positive in 17 of 32 RT-PCR-positive case patients. SARS-CoV-2 RNA was localized by ISH in hyaline membranes, pneumocytes, and macrophages of lungs; epithelial cells of airways; and endothelial cells and vessel walls of brain stem, leptomeninges, lung, heart, liver, kidney, and pancreas. The D614G variant was detected in 9 RT-PCR-positive case patients., Conclusions: We identified cellular targets of SARS-CoV-2 tropism and replication in the lungs and airways and demonstrated its direct infection in vascular endothelium. This work provides important insights into COVID-19 pathogenesis and mechanisms of severe outcomes., (Published by Oxford University Press for the Infectious Diseases Society of America 2021.)

We report a case of Rickettsia honei infection in a US tourist returning from India and the Himalayas. This case highlights a need for awareness of various Rickettsia species endemic to India and the importance for physicians to consider rickettsial diseases in returning travelers with eschar or rash-associated febrile illnesses., (Published by Oxford University Press on behalf of Infectious Diseases Society of America 2020.)

Since February 12, 2020, approximately 6.5 million cases of SARS-CoV-2 infection, the cause of coronavirus disease 2019 (COVID-19), and 190,000 SARS-CoV-2-associated deaths have been reported in the United States (1,2). Symptoms associated with SARS-CoV-2 infection are milder in children compared with adults (3). Persons aged <21 years constitute 26% of the U.S. population (4), and this report describes characteristics of U.S. persons in that population who died in association with SARS-CoV-2 infection, as reported by public health jurisdictions. Among 121 SARS-CoV-2-associated deaths reported to CDC among persons aged <21 years in the United States during February 12-July 31, 2020, 63% occurred in males, 10% of decedents were aged <1 year, 20% were aged 1-9 years, 70% were aged 10-20 years, 45% were Hispanic persons, 29% were non-Hispanic Black (Black) persons, and 4% were non-Hispanic American Indian or Alaska Native (AI/AN) persons. Among these 121 decedents, 91 (75%) had an underlying medical condition,* 79 (65%) died after admission to a hospital, and 39 (32%) died at home or in the emergency department (ED). † These data show that nearly three quarters of SARS-CoV-2-associated deaths among infants, children, adolescents, and young adults have occurred in persons aged 10-20 years, with a disproportionate percentage among young adults aged 18-20 years and among Hispanics, Blacks, AI/ANs, and persons with underlying medical conditions. Careful monitoring of SARS-CoV-2 infections, deaths, and other severe outcomes among persons aged <21 years remains particularly important as schools reopen in the United States. Ongoing evaluation of effectiveness of prevention and control strategies will also be important to inform public health guidance for schools and parents and other caregivers., Competing Interests: All authors have completed and submitted the International Committee of Medical Journal Editors form for disclosure of potential conflicts of interest. No potential conflicts of interest were disclosed.

During January 1, 2020-May 18, 2020, approximately 1.3 million cases of coronavirus disease 2019 (COVID-19) and 83,000 COVID-19-associated deaths were reported in the United States (1). Understanding the demographic and clinical characteristics of decedents could inform medical and public health interventions focused on preventing COVID-19-associated mortality. This report describes decedents with laboratory-confirmed infection with SARS-CoV-2, the virus that causes COVID-19, using data from 1) the standardized CDC case-report form (case-based surveillance) (https://www.cdc.gov/coronavirus/2019-ncov/php/reporting-pui.html) and 2) supplementary data (supplemental surveillance), such as underlying medical conditions and location of death, obtained through collaboration between CDC and 16 public health jurisdictions (15 states and New York City).

Certain Trichoderma species are causing serious losses in mushroom production worldwide. Trichoderma aggressivum and Trichoderma pleuroti are among the major causal agents of the green mould diseases affecting Agaricus bisporus and Pleurotus ostreatus, respectively. The genus Trichoderma is well-known for the production of bioactive secondary metabolites, including peptaibols, which are short, linear peptides containing unusual amino acid residues and being synthesised via non-ribosomal peptide synthetases (NRPSs). The aim of this study was to get more insight into the peptaibol production of T. aggressivum and T. pleuroti. HPLC/MS-based methods revealed the production of peptaibols closely related to hypomurocins B by T. aggressivum, while tripleurins representing a new group of 18-residue peptaibols were identified in T. pleuroti. Putative NRPS genes enabling the biosynthesis of the detected peptaibols could be found in the genomes of both Trichoderma species. In vitro experiments revealed that peptaibols are potential growth inhibitors of mushroom mycelia, and that the host mushrooms may have an influence on the peptaibol profiles of green mould agents., (© 2017 Wiley-VHCA AG, Zurich, Switzerland.)

We studied the folding processes of long-sequence hypomurocin (HM) peptides and their analogs by means of molecular dynamics methods, focusing on the formation of various helical structures and intramolecular H-bonds. The evolution of different helical conformations, such as the 310 -, α-, and left-handed α-helices, was examined, taking into account the entire sequence and each amino acid of peptides. The results indicated that the HM peptides and their analogs possessed a propensity to adopt helical conformations, and they showed a preference for the 310 -helical structure over the α-helical one. The evolution of a variety of the intramolecular H-bonds, including local and non-local interactions, was also investigated. The results pointed out that on the one hand, the appearance of local, helix-stabilizing H-bonds correlated with the presence of helical conformations, and on the other hand, the non-local H-bonds did not affect significantly the formation of helical structures. Additionally, comparing the structural and folding features of HM peptides and their analogs, our study led to the observation that the L-D isomerism of isovaline amino acid induced effects on the folding processes of these long-sequence peptaibol molecules. Accordingly, the HM peptides and their analogs could be characterized by typical structural and folding properties. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 645-657, 2016., (© 2016 Wiley Periodicals, Inc.)

In this theoretical study, the folding processes of long-sequence trichobrachin peptides (i.e., TB IIb peptides) were investigated by molecular dynamics methods. The formation of various helical structures (i.e., 310 -, α-, and left-handed α-helices) was studied with regard to the entire sequence of peptides, as well as to each amino acid. The results pointed out that TB IIb molecules showed a propensity to form helical conformations, and they could be characterized by 310 -helical structure rather than by α-helical structure. The formation of local (i.e., i←i+3 and i←i+4) as well as of non-local (i.e., i←i+n, where n>4; and all i→i+n) H-bonds was also examined. The results revealed that the occurrence of local, helix-stabilizing H-bonds was in agreement with the appearance of helical conformations, and the non-local H-bonds did not produce relevant effects on the evolution of helical structures. Based on the data obtained by our structural investigation, differences were observed between the TB IIb peptides, according to the type of amino acid located in the 17th position of their sequences. In summary, the folding processes were explored for TB IIb molecules, and our theoretical study led to the conclusion that these long-sequence peptaibols showed characteristic structural and folding features., (Copyright © 2015 Verlag Helvetica Chimica Acta AG, Zürich.)

In this theoretical study, a conformational analysis was performed on short-sequence hypomurocin A peptides, in order to identify their characteristic structural properties. For each hypomurocin A molecule, not only the backbone conformations, but also the side-chain conformations were examined. The results indicated that certain tetrapeptide units could be characterized by types I and III β-turn structures, and considering the helical conformations, it could be concluded that the hypomurocin A peptides showed a preference for the 310-helical structure over the α-helical structure. Beside the backbone conformations, the side-chain conformations were investigated, and the preferred rotamer states of the side-chains of amino acids were determined. Furthermore, the occurrence of i ← i + 3 and i ← i + 4 intramolecular H-bonds was studied, which could play a role in the structural stabilization of β-turns and helical conformations. On the whole, our theoretical study supplied a comprehensive characterization of the three-dimensional structure of short-sequence hypomurocin A peptides.

We performed molecular dynamics simulations on the tryptophane-cage miniprotein using a nonpolarizable force field, in order to model the effect of concentrated water solutions of neutral salts on protein conformation, which is a manifestation of Hofmeister effects. From the equilibrium values and the fluctuations of the solvent accessible surface area of the miniprotein, the salt-induced changes of the mean value of protein-water interfacial tension were determined. At 300 K, the chaotropic ClO4(-) and NO3(-) decreased the interfacial tension according to their position in the Hofmeister series (by approximately 5 and 2.7 mN/m, respectively), while the kosmotropic F(-) increased it (by 1 mN/m). These values were compared to those obtained from the Gibbs equation using the excess surface adsorption calculated from the probability distribution of the water molecules and ions around the miniprotein, and the two sets were found to be very close to each other. Our results present a direct evidence for the central role of interfacial tension and fluctuations at the protein-water interface in Hofmeister phenomena, and provide a computational method for the determination of the protein-water interfacial tension, establishing a link between the phenomenological and microscopic description of protein-water interfaces.

A structural characterization was carried out by molecular-dynamics methods for eight trichobrachin peptides, to identify the conformational features of these short peptaibols. For all peptides, the backbone and side-chain conformations were investigated, different secondary structures, such as type-I and -III β-turns as well as β-bend ribbon spirals, were determined in certain tetrapeptide units of the molecules, and the preferred rotamers of the side chains of amino acids were identified. Furthermore, the end-to-end and residueresidue distances were examined, as well as the fluctuations of backbone atoms were studied. Based on these results, the peptides were compared to one another. Our theoretical study indicated that trichobrachins could be characterized by typical structural properties, and both conformational similarities and dissimilarities were observed between these peptaibols. In summary, this structural investigation supplied a characterization of the various conformational features of eight trichobrachin peptides., (Copyright © 2013 Verlag Helvetica Chimica Acta AG, Zürich.)

Phytochromes (PHYs) are photoreceptors of the red (R ~660 nm) and far-red (FR ~730 nm) light, and they control a wide range of responses affecting crucial aspects of plant life. There are five genes PHYA-PHYE encoding for phytochromes of different but overlapping function. One of these, PHYA has the unique function controlling specific responses in high irradiance far-red, as well as in very weak light. Appropriate PHYA functioning requires not only the photoreversibility of molecule but also the proper nuclear localization and degradation of receptor. Recently, we identified and described a mutant PHYA allele (phyA-5) in Arabidopsis thaliana, which showed reduced binding affinity to FHY1/FHL, the proteins regulating its nuclear transport, resulting in impaired nuclear localization and altered signaling under certain conditions. We present here a hypothesis to explain how the identified amino acid substitution may lead to structural changes manifested as altered signaling and phenotype displayed by the phyA-5 mutant.

In this study, taking into account both the l-d and cis-trans isomerisms, a comprehensive structural characterization and a comparative conformational analysis were performed on the 32 stereoisomeric forms of opioid tetrapeptide, endomorphin-2. For all stereoisomers, the Φ-Ψ and χ conformational spaces were explored, in the course of which the conformational distributions, as well as the rotamer states of aromatic side chains were characterized in detail. Furthermore, the typical β- and γ-turn structures, as well as the characteristic intramolecular interactions (i.e., H-bonds, aromatic-aromatic and proline-aromatic interplays) were determined. The afore-mentioned structural and conformational features identified for each stereoisomeric form were compared with one another, considering all 32 stereoisomers. The results obtained from this comparative study indicated that both similarities and dissimilarities could be observed between the stereoisomeric forms, with regard to their structural and conformational properties. This theoretical work supplied several valuable observations concerning the effects of both l-d and cis-trans isomerisms on the three-dimensional structure of parent peptide and its stereoisomers. Nevertheless, in the course of this structural investigation, it was clarified how the structural and conformational features of stereoisomeric forms differed from one another., (© 2011 John Wiley & Sons A/S.)

In this study, molecular dynamics simulations were carried out on Lys- and Arg-containing Ala-based peptides (i.e. Ace-(AAAAK)(n)A-NH(2) and Ace-(AAAAR)(n)A-NH(2), where n=1-4), in order to explore and characterize their folding processes. For the oligopeptides, the evolution of α-helical structure with regard to the whole conformation, as well as to each residue was investigated, and the helix-forming propensities were characterized. On the basis of the helicity curves, representing the alteration of average helicity as a function of time, the typical time values describing the folding processes and subprocesses were identified. In the case of each peptide, the evolution and role of helix-stabilizing, non-local and side-chain-to-backbone H-bonds were examined. The appearing i←i+4 H-bonds pointed out the role of these interactions in the stabilization of α-helical conformations, while the occurring i←i+3 H-bonds indicated the presence of β-turn or 3(10)-helical structures. Studying the formation and role of non-local and side-chain-to-backbone H-bonds led to the observation that these types of interactions produced an effect on the evolution of helical conformations, as well as on the folding processes., (Copyright © 2011 Elsevier Ltd. All rights reserved.)

Arg-conopressin-S and Lys-conopressin-G are cyclic disulphide-bridged nonapeptides isolated from the venom of cone snails. We performed a comprehensive conformational analysis for the cis and trans isomers of these conopeptides, in order to identify their characteristic structural and conformational features. In the course of our theoretical study, the Phi-Psi and chi(1) conformational spaces were explored in detail and the conformational distributions were compared to each other. For both cis and trans isomers of conopressins, the characteristic secondary structural elements and intramolecular H-bonds were identified. Our results pointed out that various turn structures stabilized by typical intramolecular H-bonds could be observed in the conformers of these conopeptides. Comparing the different conformational features of the cis and trans isomers of conopressins disclosed that several of them could be found for both isomers, however, structural properties characteristic for only the cis or trans isomer were also identified. Altogether, our comprehensive conformational study provided a detailed description of the three-dimensional (3D) structure of both conopressins.

Poly-(Ala) and poly-(Gln) peptides have important biological effects, and can cause various human illnesses and neurodegenerative diseases. Conformational analysis of these homo-oligopeptides (HOPs) was carried out by simulated annealing in order to identify their structural properties regarding secondary structures and intramolecular H-bonding patterns. Poly-(Ala) and poly-(Gln) peptides composed of 7, 10, 14 or 20 amino acids were modelled in both charged and terminally blocked forms. In the case of conformers derived from simulated annealing calculations, the presence of various secondary structural elements (different types of beta-turns, alpha-helix, 3(10)-helix, poly-proline II helix, parallel and antiparallel beta-strands) was investigated. Moreover, the intramolecular H-bonding patterns formed either between the backbone atoms for both HOPs or between the backbone and side-chain atoms for the poly-(Gln) peptides were examined. Our results showed that different secondary structural elements (type I and type III beta-turns, alpha-helix, 3(10)-helix, antiparallel beta-strand) could be observed in both poly-(Ala) and poly-(Gln) peptides and, according to their presence, characteristic H-bonding patterns formed mainly by i<--i+3 and i<--i+4 H-bonds could be found.

A total of 36 UV-induced mutants with altered colony morphology were isolated from strain Trichoderma harzianum T334, a potential biocontrol agent against plant pathogenic fungi with the ability to produce constitutively low levels of chitinases. The level of constitutive beta-1,4-N-acetyl-glucosaminidase production in standing and shaken cultures under non-inductive conditions was tested in mutants and compared to that of the parental strain. About 30% of the mutants showed significantly increased levels of enzyme production, with strain T334 col26a being the best producer. This mutant and the parental strain were subjected to in vitro confrontation assays with plant pathogenic Fusarium culmorum, Pythium debaryanum and Rhizoctonia solani strains. The mutant derivative could be characterized by significantly higher biocontrol index values than the parental strain in each experiment, suggesting, that mutants with improved constitutive extracellular chitinase secretion could be applied for biocontrol purposes against fungal plant pathogens.

A novel method is proposed for the accurate evaluation of in vitro antagonism. Based on the measurement of areas of the fungal colonies, biocontrol indices were calculated, which are characteristic to the antagonistic Trichoderma strains. These indices provide a useful tool to describe the biocontrol abilities of fungi.

We investigated the aromatic-aromatic and proline-aromatic interactions in endomorphin-1 and endomorphin-2, and different types of these interactions were observed. For all the interacting pairs, the preferred geometric orientations were identified. We examined these interactions in the preferred secondary structures, which are different types of beta-turns and gamma-turns. These results revealed that the majority of the turn structures contained one of the interacting aromatic-aromatic or proline-aromatic pairs. On the basis of our results, it can be assumed that these interactions may be important in the determination and stabilization of the structures of endomorphins. Furthermore, our observations suggest that a conformation stabilized by an aromatic-aromatic or proline-aromatic interaction can play an important role in the association with the receptor.

In this study we compared the steric structures of the bioactive part of substance P (SP[6-11]) and its analogs (NY3460 and pHOPA-SP5). The molecular dynamics-simulated annealing method was used to explore the conformational space, and the structural differences and similarities of these molecules were identified. For the three peptides, the conformational distributions were represented in Ramachandran density plots. The occurring secondary structural elements of the investigated molecules were identified, namely alpha-Helix, type III beta-Turn, gamma-Turn, and inverse gamma-Turn. For SP[6-11] and its two analogs, different intramolecular interactions (H-bonds between the main-chain atoms, aromatic-aromatic interactions, and amino-aromatic interactions) that can stabilize the various conformations of the three peptides were investigated. Detailed examination of these intramolecular interactions revealed that H-bonds between the main-chain atoms are relevant in the determination and stabilization of the conformer structures of the peptides, while the aromatic-aromatic interactions do not play an important stabilizing role. Furthermore, in the conformers of NY3460 and pHOPA-SP5, different types of amino-aromatic interactions were identified that contribute to the formation of the various structures of these peptides. For all three molecules, the orientations of the side chains were investigated and the rotamer populations were determined.

Endomorphin-2 (EM2, H-Tyr-Pro-Phe-Phe-NH(2)) is a highly potent and selective mu-opioid receptor agonist. A conformational analysis of EM2 was carried out by simulated annealing (SA) and molecular dynamics (MD) methods. Molecular modeling was conducted on both neutral (N-terminal NH(2)) and charged (N-terminal NH(3) (+)) molecules. Based on the results of NMR investigations showing an equilibrium mixture of cis and trans Tyr(1)-Pro(2) peptide bonds for EM2 in solution, simulations were performed with restrained cis-Pro and trans-Pro peptide bonds, too. A separate SA study with unrestrained Pro peptide bonds was also conducted. Preferred conformational states are presented in Ramachandran plots. The g(+), g(-), and trans populations of the aromatic amino acid residue side chains were determined in chi(1) space. The distances between the N-terminal N atom and the other backbone N and O atoms, and the distances between the centers of the aromatic rings and the Pro(2) ring, were determined. The energy distribution of the structures obtained by SA was calculated. The preferred secondary structural elements were different kinds of beta-turns, an inverse gamma-turn located in the N-terminal region, and regular and inverse gamma-turns located in the C-terminal region. These turns were stabilized by intramolecular H-bonds and bifurcated H-bonds., (Copyright 2003 Wiley Periodicals, Inc.)