Amycolatopsis mediterranei: A Sixty-Year Journey from Strain Isolation to Unlocking Its Potential of Rifamycin Analogue Production by Combinatorial Biosynthesis

Ever since the isolation of Amycolatopsis mediterranei in 1957, this strain has been the focus of research worldwide. In the last 60 years or more, our understanding of the taxonomy, development of cloning vectors and conjugation system, physiology, genetics, genomics, and biosynthetic pathway of rifamycin B production in A. mediterranei has substantially increased. In particular, the development of cloning vectors, transformation system, characterization of the rifamycin biosynthetic gene cluster, and the regulation of rifamycin B production by the pioneering work of Heinz Floss have made the rifamycin polyketide biosynthetic gene cluster (PKS) an attractive target for extensive genetic manipulations to produce rifamycin B analogues which could be effective against multi-drug-resistant tuberculosis. Additionally, a better understanding of the regulation of rifamycin B production and the application of newer genomics tools, including CRISPR-assisted genome editing systems, might prove useful to overcome the limitations associated with low production of rifamycin analogues.

Broad Tricyclic Ring Inhibitors Block SARS-CoV-2 Spike Function Required for Viral Entry

The entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into host cells requires binding of the viral spike glycoprotein to the angiotensin-converting enzyme 2 (ACE2) receptor, which triggers subsequent conformational changes to facilitate viral and cellular fusion at the plasma membrane or following endocytosis. Here, we experimentally identified selective and broad inhibitors of SARS-CoV-2 entry that share a tricyclic ring (or similar) structure. The inhibitory effect was restricted to early steps during infection and the entry inhibitors interacted with the receptor binding domain of the SARS-CoV-2 spike but did not significantly interfere with receptor (ACE2) binding. Instead, some of these compounds induced conformational changes or affected spike assembly and blocked SARS-CoV-2 spike cell-cell fusion activity. The broad inhibitors define a highly conserved binding pocket that is present on the spikes of SARS-CoV-1, SARS-CoV-2, and all circulating SARS-CoV-2 variants tested and block SARS-CoV spike activity required for mediating viral entry. These compounds provide new insights into the SARS-CoV-2 spike topography, as well as into critical steps on the entry pathway, and can serve as lead candidates for the development of broad-range entry inhibitors against SARS-CoVs.

Recurrence quantification analysis of resting state EEG signals in autism spectrum disorder - a systematic methodological exploration of technical and demographic confounders in the search for biomarkers

BACKGROUND

Autism spectrum disorder (ASD) is a neurodevelopmental disorder with a worldwide prevalence of 1-2%. In low-resource environments, in particular, early identification and diagnosis is a significant challenge. Therefore, there is a great demand for 'language-free, culturally fair' low-cost screening tools for ASD that do not require highly trained professionals. Electroencephalography (EEG) has seen growing interest as an investigational tool for biomarker development in ASD and neurodevelopmental disorders. One of the key challenges is the identification of appropriate multivariate, next-generation analytical methodologies that can characterise the complex, nonlinear dynamics of neural networks in the brain, mindful of technical and demographic confounders that may influence biomarker findings. The aim of this study was to evaluate the robustness of recurrence quantification analysis (RQA) as a potential biomarker for ASD using a systematic methodological exploration of a range of potential technical and demographic confounders.

METHODS

RQA feature extraction was performed on continuous 5-second segments of resting state EEG (rsEEG) data and linear and nonlinear classifiers were tested. Data analysis progressed from a full sample of 16 ASD and 46 typically developing (TD) individuals (age 0-18 years, 4802 EEG segments), to a subsample of 16 ASD and 19 TD children (age 0-6 years, 1874 segments), to an age-matched sample of 7 ASD and 7 TD children (age 2-6 years, 666 segments) to prevent sample bias and to avoid misinterpretation of the classification results attributable to technical and demographic confounders. A clinical scenario of diagnosing an unseen subject was simulated using a leave-one-subject-out classification approach.

RESULTS

In the age-matched sample, leave-one-subject-out classification with a nonlinear support vector machine classifier showed 92.9% accuracy, 100% sensitivity and 85.7% specificity in differentiating ASD from TD. Age, sex, intellectual ability and the number of training and test segments per group were identified as possible demographic and technical confounders. Consistent repeatability, i.e. the correct identification of all segments per subject, was found to be a challenge.

CONCLUSIONS

RQA of rsEEG was an accurate classifier of ASD in an age-matched sample, suggesting the potential of this approach for global screening in ASD. However, this study also showed experimentally how a range of technical challenges and demographic confounders can skew results, and highlights the importance of probing for these in future studies. We recommend validation of this methodology in a large and well-matched sample of infants and children, preferably in a low- and middle-income setting.

Mycobacterium tuberculosis IMPDH in Complexes with Substrates, Products and Antitubercular Compounds

Tuberculosis (TB) remains a worldwide problem and the need for new drugs is increasingly more urgent with the emergence of multidrug- and extensively-drug resistant TB. Inosine 5’-monophosphate dehydrogenase 2 (IMPDH2) from Mycobacterium tuberculosis (Mtb) is an attractive drug target. The enzyme catalyzes the conversion of inosine 5’-monophosphate into xanthosine 5’-monophosphate with the concomitant reduction of NAD⁺ to NADH. This reaction controls flux into the guanine nucleotide pool. We report seventeen selective IMPDH inhibitors with antitubercular activity. The crystal structures of a deletion mutant of MtbIMPDH2 in the apo form and in complex with the product XMP and substrate NAD⁺ are determined. We also report the structures of complexes with IMP and three structurally distinct inhibitors, including two with antitubercular activity. These structures will greatly facilitate the development of MtbIMPDH2-targeted antibiotics.

Selective inhibition of nicotinamide adenine dinucleotide kinases by dinucleoside disulfide mimics of nicotinamide adenine dinucleotide analogues

Diadenosine disulfide (5) was reported to inhibit NAD kinase from Listeria monocytogenes and the crystal structure of the enzyme-inhibitor complex has been solved. We have synthesized tiazofurin adenosine disulfide (4) and the disulfide 5, and found that these compounds were moderate inhibitors of human NAD kinase (IC(50)=110 microM and IC(50)=87 microM, respectively) and Mycobacterium tuberculosis NAD kinase (IC(50)=80 microM and IC(50)=45 microM, respectively). We also found that NAD mimics with a short disulfide (-S-S-) moiety were able to bind in the folded (compact) conformation but not in the common extended conformation, which requires the presence of a longer pyrophosphate (-O-P-O-P-O-) linkage. Since majority of NAD-dependent enzymes bind NAD in the extended conformation, selective inhibition of NAD kinases by disulfide analogues has been observed. Introduction of bromine at the C8 of the adenine ring restricted the adenosine moiety of diadenosine disulfides to the syn conformation making it even more compact. The 8-bromoadenosine adenosine disulfide (14) and its di(8-bromoadenosine) analogue (15) were found to be the most potent inhibitors of human (IC(50)=6 microM) and mycobacterium NAD kinase (IC(50)=14-19 microM reported so far. None of the disulfide analogues showed inhibition of lactate-, and inosine monophosphate-dehydrogenase (IMPDH), enzymes that bind NAD in the extended conformation.

Biosorption of heavy metals from aqueous solutions with tobacco dust

A typical lignocellulosic agricultural residue, namely tobacco dust, was investigated for its heavy metal binding efficiency. The tobacco dust exhibited a strong capacity for heavy metals, such as Pb(II), Cu(II), Cd(II), Zn(II) and Ni(II), with respective equilibrium loadings of 39.6, 36.0, 29.6, 25.1 and 24.5mg of metal per g of sorbent. Moreover, the heavy metals loaded onto the biosorbent could be released easily with a dilute HCl solution. Zeta potential and surface acidity measurements showed that the tobacco dust was negatively charged over a wide pH range (pH>2), with a strong surface acidity and a high OH(-) adsorption capacity. Changes in the surface morphology of the tobacco dust as visualized by atomic force microscopy suggested that the sorption of heavy metal ions on the tobacco could be associated with changes in the surface properties of the dust particles. These surface changes appeared to have resulted from a loss of some of the structures on the surface of the particles, owing to leaching in the acid metal ion solution. However, Fourier transform infrared spectroscopy (FTIR) showed no substantial change in the chemical structure of the tobacco dust subjected to biosorption. The heavy metal uptake by the tobacco dust may be interpreted as metal-H ion exchange or metal ion surface complexation adsorption or both.

New methodology for hazardous waste classification using fuzzy set theory Part II. Intelligent decision support system

In part 1 of this paper, factors that influence hazards and eco/toxicity in composite hazardous wastes were described. In part 2, a computer-aided decision support tool based on fuzzy set theory is proposed to support the classification of composite wastes. Given the chemical properties, the nature of microorganisms that may be present, the behaviour of chemicals in humans and ecosystems, and the quantities of wastes, the computer-aided tool automatically classifies the waste as benign, partially hazardous, hazardous or highly hazardous. The functionality of the computer-aided decision tool is demonstrated through nine worked examples and the results are discussed in detail.

New methodology for hazardous waste classification using fuzzy set theory Part I. Knowledge acquisition

In the literature on hazardous waste classification, the criteria used are mostly based on physical properties, such as quantity (weight), form (solids, liquid, aqueous or gaseous), the type of processes generating them, or a set of predefined lists. Such classification criteria are inherently inadequate to account for the influence of toxic and hazard characteristics of the constituent chemicals in the wastes, as well as their exposure potency in multimedia environments, terrestrial mammals and other biota. Second, none of these algorithms in the literature has explicitly presented waste classification by examining the contribution of individual constituent components of the composite wastes. In this two-part paper, we propose a new automated algorithm for waste classification that takes into account physicochemical and toxicity effects of the constituent chemicals to humans and ecosystems, in addition, to the exposure potency and waste quantity. In part I, available data on the physicochemical and toxicity properties of individual chemicals in humans and ecosystems, their exposure potency in environmental systems and the effect of waste quantity are described, because they fundamentally contribute to the final waste ranking. Knowledge acquisition in this study was accomplished through the extensive review of published and specialized literature to establish facts necessary for the development of fuzzy rule-bases. Owing to the uncertainty and imprecision of various forms of data (both quantitative and qualitative) essential for waste classification, and the complexity resulting from knowledge incompleteness, the use of fuzzy set theory for the aggregation and computation of waste classification ranking index is proposed. A computer-aided intelligent decision tool is described in part II of this paper and the functionality of the fuzzy waste classification algorithm is illustrated through nine worked examples.

An aggregate fuzzy hazardous index for composite wastes

In this paper, a fuzzy waste index for evaluating the hazard posed by composite wastes generated from industrial processes is proposed. Within this methodology, a fuzzy index as a measure of hazardousness of a given composite waste is derived from the crisp inputs of its component's flammability, corrosivity, toxicity and reactivity attributes based on the National Fire Protection Association (NFPA) hazard rankings. The novelty of this work lies in establishing an integrated fuzzy hazardous waste index (FHWI) which provides a single-value representing the hazard ranking of a composite waste. This is contrary to current techniques which do not provide a final aggregated hazard index. The efficacy of the new proposed approach is illustrated through several worked examples. The results demonstrate that the fuzzy algorithm can be useful in aiding policy and decision-makers in conducting comprehensive initial evaluation of the status of waste hazardous status without the need for costly laboratory experiments. As such, the approach offers a robust and transparent decision-making methodology.

Synthesis of GTP-derived Ras ligands

A practical and convenient method for the synthesis of acid- and base-sensitive GTP analogues carrying a further substituent at the terminal phosphate has been developed. Key to the successful synthesis of these potential ligands of the Ras protein is the use of Pd0-sensitive allyl protecting groups in a one-pot synthesis that avoids evaporation steps. Initial biochemical analysis of a representative compound revealed that such GTP analogues can bind to Ras and might open up the possibility of developing small molecules that can act as deactivators of oncogenic Ras.

Embedding of multidimensional time-dependent observations

A method is proposed to reconstruct dynamic attractors by embedding of multivariate observations of dynamic nonlinear processes. The Takens embedding theory is combined with independent component analysis to transform the embedding into a vector space of linearly independent vectors (phase variables). The method is successfully tested against prediction of the unembedded state vector in two case studies of simulated chaotic processes.

A null mutation in HLA-G is not associated with preeclampsia or intrauterine growth retardation

Modulation of the expression of genes of the major histocompatibility complex (MHC) in tissues at the maternal-fetal interface almost certainly plays a role in successful development of the semi-allogeneic fetus. While expression of the classical class I genes (HLA-A, B, C) is low to non-existent at this site, the non-classical molecule, HLA-G, is expressed uniquely in fetal cells at the maternal-fetal interface. The recent demonstration that homozygotes for a deletion mutation in exon 3 (1597DeltaC) of HLA-G do not express the full-length HLA-G1 isoforms indicates a potential reduction in expression of this isoform in heterozygotes. If the full-length isoform of HLA-G (i.e. HLA-G1) contributes to proper invasion of maternal spiral arteries by extravillous cytotrophoblast, then 1597DeltaC heterozygotes could be at increased risk for disorders of trophoblast invasion. Two populations, infants with intrauterine growth retardation (IUGR) and infants of preeclamptic (PE) mothers, were genotyped for the 1597DeltaC polymorphism. The frequency of 1597DeltaC in these samples was not significantly different from healthy controls, suggesting that heterozygotes for this deletion mutation are not at significantly increased risk for PE or IUGR (P = 0.727 and 0.803, respectively).

Apoptosis and regeneration of hepatocytes during recovery from transient hepadnavirus infections

It is well known that hepatitis B virus infections can be transient or chronic, but the basis for this dichotomy is not known. To gain insight into the mechanism responsible for the clearance of hepadnavirus infections, we have performed a molecular and histologic analysis of liver tissues obtained from transiently infected woodchucks during the critical phase of the recovery period. We found as expected that clearance from transient infections occurred subsequent to the appearance of CD4(+) and CD8(+) T cells and the production of interferon gamma and tumor necrosis factor alpha in the infected liver. These events were accompanied by a significant increase in apoptosis and regeneration of hepatocytes. Surprisingly, however, accumulation of virus-free hepatocytes was delayed for several weeks following this initial influx of lymphocytes. In addition, we observed that chronically infected animals can exhibit levels of T-cell accumulation, cytokine expression, and apoptosis that are comparable with those observed during the initial phase of transient infections. Our results are most consistent with a model for recovery predicting replacement of infected hepatocytes with regenerated cells, which by unknown mechanisms remain protected from reinfection in animals that can be cured.

Aberrant expression of a cytokeratin in a subset of hepatocytes during chronic WHV infection

Chronic infection of woodchucks with woodchuck hepatitis virus (WHV) invariably leads, within 2-4 years, to the appearance of hepatocellular carcinoma (HCC). HCC is preceded by an extended period of chronic liver damage, probably resulting from the immune response to viral antigens. It may be that infection itself also induces changes in the hepatocyte population. To begin to identify some of the changes in the liver prior to the appearance of HCC, monoclonal antibodies (MAbs) were generated from mice immunized with hepatocytes from a woodchuck chronically infected with WHV or with a tumor lysate. Immunofluorescence microscopy was used to select MAbs that reacted with host markers whose patterns of expression would distinguish chronically infected from uninfected liver or from liver tumors. One of these MAbs (2F2) reacted strongly with a subset of hepatocytes in chronically infected liver; a similar staining pattern was not detected in uninfected or transiently infected liver. Evidence is presented that this strong staining reaction reflects the overexpression or accumulation of the hepatocyte-specific intermediate filament protein, cytokeratin K18, a protein previously implicated in cryptogenic cirrhosis of the liver in humans (Ku, N. O. , Wright, T. L., Terrault, N. A., Gish, R., and Omary, M. B. J. Clin. Invest. 99: 19-23, 1997). Double immunofluorescent staining with antibodies to K18 and M-envelope protein of WHV suggested that strong reactivity to K18 was limited to cells expressing high levels of one or both of the large viral-envelope proteins, M and L; however, high expression of these viral proteins was not always associated with a strong K18 staining reaction.

HLA-G1 protein expression is not essential for fetal survival

HLA-G is a nonclassical, class I HLA gene that is primarily expressed by fetal cells at the maternal-fetal interface and is thought to play a key role in the induction of tolerance in pregnancy. This paper reports the identification of a single base pair deletion at position 1597 (1597delC) in exon 3 (encoding the alpha2-domain) of HLA-G on 20 of 272 (7.4 per cent) African American chromosomes, three of 102 (2.9 per cent) Hispanic chromosomes, and none of 134 Caucasian chromosomes. This relatively common frameshift mutation results in amino acid substitutions in all of the residues in the second half of exon 3 including the conserved cysteine at codon 164. An adult individual was identified who was homozygous for this 'null' allele, and a first trimester placenta that was homozygous for 1597delC had no detectable HLA-G1 protein. These data indicate that expression of HLA-G1 protein is not essential for fetal survival.