Large Repertoire Research Articles

Monoclonal Antibodies Targeting Surface-Exposed and Secreted Proteins from Staphylococci.

Staphylococci (specifically Staphylococcus aureus and Staphylococcus epidermidis) are the causative agents of diseases ranging from superficial skin and soft tissue infections to severe conditions such as fatal pneumonia, bacteremia, sepsis and endocarditis. The widespread and indiscriminate use of antibiotics has led to serious problems of resistance to staphylococcal disease and has generated a renewed interest in alternative therapeutic agents such as vaccines and antibodies. Staphylococci express a large repertoire of surface and secreted virulence factors, which provide mechanisms (adhesion, invasion and biofilm development among others) for both bacterial survival in the host and evasion from innate and adaptive immunity. Consequently, the development of antibodies that target specific antigens would provide an effective protective strategy against staphylococcal infections. In this review, we report an update on efforts to develop anti-staphylococci monoclonal antibodies (and their derivatives: minibodies, antibody–antibiotic conjugates) and the mechanism by which such antibodies can help fight infections. We also provide an overview of mAbs used in clinical trials and highlight their therapeutic potential in various infectious contexts.

Gene Families With Stochastic Exclusive Gene Choice Underlie Cell Adhesion in Mammalian Cells.

Exclusive stochastic gene choice combines precision with diversity. This regulation enables most T-cells to express exactly one T-cell receptor isoform chosen from a large repertoire, and to react precisely against diverse antigens. Some cells express two receptor isoforms, revealing the stochastic nature of this process. A similar regulation of odorant receptors and protocadherins enable cells to recognize odors and confer individuality to cells in neuronal interaction networks, respectively. We explored whether genes in other families are expressed exclusively by analyzing single-cell RNA-seq data with a simple metric. This metric can detect exclusivity independently of the mean value and the monoallelic nature of gene expression. Chromosomal segments and gene families are more likely to express genes concurrently than exclusively, possibly due to the evolutionary and biophysical aspects of shared regulation. Nonetheless, gene families with exclusive gene choice were detected in multiple cell types, most of them are membrane proteins involved in ion transport and cell adhesion, suggesting the coordination of these two functions. Thus, stochastic exclusive expression extends beyond the prototypical families, permitting precision in gene choice to be combined with the diversity of intercellular interactions.

Multiple sub-repertoires and singing patterns of Red-eyed Vireos (Vireo olivaceus)

Some songbirds produce only one or a few song types, but others sing large repertoires with many different song types. Birds with large repertoires can arrange these songs in a variety of distinct singing patterns that add a layer of complexity to their vocal production. Both large repertoires and singing patterns may communicate important information to conspecific males and females. Previous estimates of repertoire size of Red-eyed Vireos (Vireo olivaceus) range from 39 to 59. These estimates were based on a small number of recorded phrases per individual, and on single recordings of most individuals. I have made lengthy, multiple recordings over periods of days and weeks of 46 Red-eyed Vireos to revisit the question of their repertoire size. Repertoire size estimated for the birds I recorded varied between 17 and 341 phrase types, with a mean of 91. Fourteen birds for which I recorded at least 1,000 phrases had a mean repertoire of 154 phrase types. Previous estimates may have been low by a factor of 2–3 because of limited sampling. Plotting of phrase type vs. phrases sung for each bird showed a variety of singing patterns. Six birds sang a single limited repertoire of 17–47 phrase types. Nineteen birds sang a single repertoire, but new phrases continued to be added as more recordings were made, so these repertoires had no clear size limits. Twenty birds sang multiple groups or sub-repertoires of phrase types at different times, often changing between sub-repertoires during a single continuous bout of singing. Five birds sang frequent repetitions of a small number of phrase types selected from larger repertoires. The mean singing rate of the birds studied climbed from a low of 33 phrases/min at the beginning of the breeding season to a high of 46 phrases/min at the peak, and declined to 34 phrases/ min at the end of the breeding season. My study shows that Red-eyed Vireo repertoires are significantly larger than previously estimated, that singing patterns vary widely among individual birds, and that many birds group phrase types into multiple sub-repertoires, sung at different times.

Gut Bacteria of Rattus rattus (Rat) Produce Broad-Spectrum Antibacterial Lipopeptides.

Among several animals, Rattus rattus (rat) lives in polluted environments and feeds on organic waste/small invertebrates, suggesting the presence of inherent mechanisms to thwart infections. In this study, we isolated gut bacteria of rats for their antibacterial activities. Using antibacterial assays, the findings showed that the conditioned media from selected bacteria exhibited bactericidal activities against Gram-negative (Escherichia coli K1, Klebsiella pneumoniae, Pseudomonas aeruginosa, Serratia marcescens, and Salmonella enterica) and Gram-positive (Bacillus cereus, methicillin-resistant Staphylococcus aureus, and Streptococcus pyogenes) pathogenic bacteria. The conditioned media retained their antibacterial properties upon heat treatment at boiling temperature for 10 min. Using MTT assays, the conditioned media showed minimal cytotoxic effects against human keratinocyte cells. Active conditioned media were subjected to tandem mass spectrometry, and the results showed that conditioned media from Bacillus subtilis produced a large repertoire of surfactin and iturin A (lipopeptides) molecules. To our knowledge, this is the first report of isolation of lipopeptides from bacteria isolated from the rat gut. In short, these findings are important and provide a platform to develop effective antibacterial drugs.

Genomic characterization of a polyvalent hydrocarbonoclastic bacterium Pseudomonas sp. strain BUN14

Bioremediation offers a viable alternative for the reduction of contaminants from the environment, particularly petroleum and its recalcitrant derivatives. In this study, the ability of a strain of Pseudomonas BUN14 to degrade crude oil, pristane and dioxin compounds, and to produce biosurfactants, was investigated. BUN14 is a halotolerant strain isolated from polluted sediment recovered from the refinery harbor on the Bizerte coast, north Tunisia and capable of producing surfactants. The strain BUN14 was assembled into 22 contigs of 4,898,053 bp with a mean GC content of 62.4%. Whole genome phylogeny and comparative genome analyses showed that strain BUN14 could be affiliated with two validly described Pseudomonas Type Strains, P. kunmingensis DSM 25974T and P. chloritidismutans AW-1T. The current study, however, revealed that the two Type Strains are probably conspecific and, given the priority of the latter, we proposed that P. kunmingensis DSM 25974 is a heteronym of P. chloritidismutans AW-1T. Using GC-FID analysis, we determined that BUN14 was able to use a range of hydrocarbons (crude oil, pristane, dibenzofuran, dibenzothiophene, naphthalene) as a sole carbon source. Genome analysis of BUN14 revealed the presence of a large repertoire of proteins (154) related to xenobiotic biodegradation and metabolism. Thus, 44 proteins were linked to the pathways for complete degradation of benzoate and naphthalene. The annotation of conserved functional domains led to the detection of putative genes encoding enzymes of the rhamnolipid biosynthesis pathway. Overall, the polyvalent hydrocarbon degradation capacity of BUN14 makes it a promising candidate for application in the bioremediation of polluted saline environments.

IgA Antibodies and IgA Deficiency in SARS-CoV-2 Infection.

A large repertoire of IgA is produced by B lymphocytes with T-independent and T-dependent mechanisms useful in defense against pathogenic microorganisms and to reduce immune activation. IgA is active against several pathogens, including rotavirus, poliovirus, influenza virus, and SARS-CoV-2. It protects the epithelial barriers from pathogens and modulates excessive immune responses in inflammatory diseases. An early SARS-CoV-2 specific humoral response is dominated by IgA antibodies responses greatly contributing to virus neutralization. The lack of anti-SARS-Cov-2 IgA and secretory IgA (sIgA) might represent a possible cause of COVID-19 severity, vaccine failure, and possible cause of prolonged viral shedding in patients with Primary Antibody Deficiencies, including patients with Selective IgA Deficiency. Differently from other primary antibody deficiency entities, Selective IgA Deficiency occurs in the vast majority of patients as an asymptomatic condition, and it is often an unrecognized, Studies are needed to clarify the open questions raised by possible consequences of a lack of an IgA response to SARS-CoV-2.

No evidence for a role of trills in male response to territorial intrusion in a complex singer, the Thrush Nightingale

Among the broad diversity of songbird vocalisations, song can serve a wide range of different functions depending on the species and context. In many species, aggressive motivation has often been linked with the use of fast repeated series of elements typically referred to as trills. However, only a few studies explored the role of this specific component in species with a large repertoire and high song complexity. Here, we investigate the potential role of trills in the territorial vocal response of males Thrush Nightingale (Luscinia luscinia), a species with complex songs characterised by the frequent use and diversity of their trills. We performed playback experiments simulating territorial intrusion to test if trills signal aggressive motivation in this species. If so, we expected tested males to respond by changing their trill rate or frequency of trill use in songs, and/or using different trill types than before the stimulation. Contrary to our expectation, males did not modify their trill rate or differed in trill type use before, during or after playback. There was a tendency for decrease in trill duration and the number of elements in the trills during the playback stimulation, reflecting to some extent the overall use of shorter songs by males during that stage of the experiment. Altogether, our study does not support the role of trills as motivation signals for territory defence in Thrush Nightingales, but advocates for more research on their potential roles in signalling other information.

Genomes of Thaumarchaeota from deep sea sediments reveal specific adaptations of three independently evolved lineages

Marine sediments represent a vast habitat for complex microbiomes. Among these, ammonia oxidizing archaea (AOA) of the phylum Thaumarchaeota are one of the most common, yet little explored, inhabitants, which seem extraordinarily well adapted to the harsh conditions of the subsurface biosphere. We present 11 metagenome-assembled genomes of the most abundant AOA clades from sediment cores obtained from the Atlantic Mid-Ocean ridge flanks and Pacific abyssal plains. Their phylogenomic placement reveals three independently evolved clades within the order Nitrosopumilales, of which no cultured representative is known yet. In addition to the gene sets for ammonia oxidation and carbon fixation known from other AOA, all genomes encode an extended capacity for the conversion of fermentation products that can be channeled into the central carbon metabolism, as well as uptake of amino acids probably for protein maintenance or as an ammonia source. Two lineages encode an additional (V-type) ATPase and a large repertoire of DNA repair systems that may allow to overcome the challenges of high hydrostatic pressure. We suggest that the adaptive radiation of AOA into marine sediments occurred more than once in evolution and resulted in three distinct lineages with particular adaptations to this extremely energy-limiting and high-pressure environment.

Filling in the gaps: Acoustic gradation increases in the vocal ontogeny of chimpanzees (Pan troglodytes).

Human vocal ontogeny is considered to be a process whereby a large repertoire of discrete sounds seemingly emerges from a smaller number of acoustically graded vocalizations. While adult chimpanzee vocal behavior is highly graded, its developmental trajectory is poorly understood. In the present study, we therefore examined the size and structure of the chimpanzee vocal repertoire at different stages of ontogeny. Audio recordings were collected on infant (N = 13) and juvenile (N = 13) semi-wild chimpanzees at Chimfunshi Wildlife Orphanage, Zambia, using focal and ad libitum sampling. All observed call types were acoustically measured. These were predominantly grunts, whimpers, laughs, screams, hoos, and barks and squeaks. A range of spectral and temporal acoustic parameters were extracted, and fuzzy c-means clustering was used to quantify the size and structure of the repertoire. The infant and juvenile vocal repertoires were both best described with the same number of clusters. However, compared to infants, juvenile call clusters were less distinct from one another and could be extracted only when a low level of overlap between call clusters was permitted. Moreover, the acoustic overlap between call clusters was significantly higher for juveniles. Overall, this pattern shows greater acoustic overlap in juvenile vocalizations compared to infants, suggesting a trend toward increased acoustic gradation in chimpanzee vocal ontogeny. This may imply in contrast to humans, chimpanzees become increasingly proficient in using graded signals effectively rather than developing a larger repertoire of more discrete sounds in ontogeny.

Long, Noncoding RNA Dysregulation in Glioblastoma.

Simple SummaryDeveloping effective therapies for glioblastoma (GBM), the most common primary brain cancer, remains challenging due to the heterogeneity within tumors and therapeutic resistance that drives recurrence. Noncoding RNAs are transcribed from a large proportion of the genome and remain largely unexplored in their contribution to the evolution of GBM tumors. Here, we will review the general mechanisms of long, noncoding RNAs and the current knowledge of how these impact heterogeneity and therapeutic resistance in GBM. A better understanding of the molecular drivers required for these aggressive tumors is necessary to improve the management and outcomes of this challenging disease.Transcription occurs across more than 70% of the human genome and more than half of currently annotated genes produce functional noncoding RNAs. Of these transcripts, the majority—long, noncoding RNAs (lncRNAs)—are greater than 200 nucleotides in length and are necessary for various roles in the cell. It is increasingly appreciated that these lncRNAs are relevant in both health and disease states, with the brain expressing the largest number of lncRNAs compared to other organs. Glioblastoma (GBM) is an aggressive, fatal brain tumor that demonstrates remarkable intratumoral heterogeneity, which has made the development of effective therapies challenging. The cooperation between genetic and epigenetic alterations drives rapid adaptation that allows therapeutic evasion and recurrence. Given the large repertoire of lncRNAs in normal brain tissue and the well-described roles of lncRNAs in molecular and cellular processes, these transcripts are important to consider in the context of GBM heterogeneity and treatment resistance. Herein, we review the general mechanisms and biological roles of lncRNAs, with a focus on GBM, as well as RNA-based therapeutics currently in development.

One norm to rule them all? Corpus-derived norms in learner corpus research and foreign language teaching

AbstractThis paper considers the issue of the norm in the context of learner corpus research and its implications for foreign language teaching. It seeks to answer three main questions: Does learner corpus research require a native norm? What corpus-derived norms are available and how do we choose? What do we do with these norms in the classroom? The first two questions are more research-oriented, reviewing the types of reference corpora that can be used in the analysis of learner corpora, whereas the third one looks into the pedagogical use of corpus-derived norms. It is shown that, while studies in learner corpus research can dispense with a native norm, they usually rely on one, and that a wide range of native and non-native norms are available, from which choosing the most appropriate one(s) is of crucial importance. This large repertoire of corpus-derived norms is then reconsidered in view of the reality of the foreign language classroom.

Dromedary camels as a natural source of neutralizing nanobodies against SARS-CoV-2.

The development of prophylactic and therapeutic agents for coronavirus disease 2019 (COVID-19) is a current global health priority. Here, we investigated the presence of cross-neutralizing antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in dromedary camels that were Middle East respiratory syndrome coronavirus (MERS-CoV) seropositive but MERS-CoV free. The tested 229 dromedaries had anti–MERS-CoV camel antibodies with variable cross-reactivity patterns against SARS-CoV-2 proteins, including the S trimer and M, N, and E proteins. Using SARS-CoV-2 competitive immunofluorescence immunoassays and pseudovirus neutralization assays, we found medium-to-high titers of cross-neutralizing antibodies against SARS-CoV-2 in these animals. Through linear B cell epitope mapping using phage immunoprecipitation sequencing and a SARS-CoV-2 peptide/proteome microarray, we identified a large repertoire of Betacoronavirus cross-reactive antibody specificities in these dromedaries and demonstrated that the SARS-CoV-2–specific VHH antibody repertoire is qualitatively diverse. This analysis revealed not only several SARS-CoV-2 epitopes that are highly immunogenic in humans, including a neutralizing epitope, but also epitopes exclusively targeted by camel antibodies. The identified SARS-CoV-2 cross-neutralizing camel antibodies are not proposed as a potential treatment for COVID-19. Rather, their presence in nonimmunized camels supports the development of SARS-CoV-2 hyperimmune camels, which could be a prominent source of therapeutic agents for the prevention and treatment of COVID-19.

DIVERSIFY: A Fungal Multispecies Gene Expression Platform.

Recent sequencing of numerous fungal species revealed large repertoires of putative biotechnologically relevant genes and secondary metabolite gene clusters. However, often the commercial potential of these species is impeded by difficulties to predict host physiological and metabolic compatibility with a given product, and lack of adequate genetic tools. Consequently, most heterologous production is performed in standard hosts where genetic tools and experience are in place. However, these species may not be suitable for all products. To increase chances of successful heterologous production, we have created a flexible platform, DIVERSIFY, for multispecies heterologous gene expression. This reduces the workload to construction of a single gene expression cassette, used to transform all DIVERSIFY strains in order to identify the optimal cell factory host. As proof of principle of the DIVERSIFY concept, we present the first version of our platform, DIVERSIFY 1.0, which we have successfully used for the production of three proteins and a metabolite in four different Aspergilli species, and for the identification of the best producer for each of the products. Moreover, we show that DIVERSIFY 1.0 is compatible with marker-free gene targeting induced by the CRISPR nucleases Cas9 and MAD7.

Curcumin promotes oligodendrocyte differentiation and their protection against TNF-\u03b1 through the activation of the nuclear receptor PPAR-\u03b3

Curcumin is a compound found in the rhizome of Curcuma longa (turmeric) with a large repertoire of pharmacological properties, including anti-inflammatory and neuroprotective activities. The current study aims to assess the effects of this natural compound on oligodendrocyte progenitor (OP) differentiation, particularly in inflammatory conditions. We found that curcumin can promote the differentiation of OPs and to counteract the maturation arrest of OPs induced by TNF-α by a mechanism involving PPAR-γ (peroxisome proliferator activated receptor), a ligand-activated transcription factor with neuroprotective and anti-inflammatory capabilities. Furthermore, curcumin induces the phosphorylation of the protein kinase ERK1/2 known to regulate the transition from OPs to immature oligodendrocytes (OLs), by a mechanism only partially dependent on PPAR-γ. Curcumin is also able to raise the levels of the co-factor PGC1-α and of the cytochrome c oxidase core protein COX1, even when OPs are exposed to TNF-α, through a PPAR-γ-mediated mechanism, in line with the known ability of PPAR-γ to promote mitochondrial integrity and functions, which are crucial for OL differentiation to occur. Altogether, this study provides evidence for a further mechanism of action of curcumin besides its well-known anti-inflammatory properties and supports the suggested therapeutic potential of this nutraceutical in demyelinating diseases.

Transcending Time (Feels)

Over the past fifteen years, much of the music-theoretical scholarship on heavy metal has addressed metric processes (Lucas 2019, Capuzzo 2018, Hannan 2018, Lucas 2018, Lennard 2016, Smialek 2008, Pieslak 2007) and the use of the voice (Smialek 2017, Young 2018). A significant portion of the literature deals with the band Meshuggah, but the music of countless artists scattered across manifold subgenres remains unexplored. Widening the focus on such a large repertoire not only helps remedy this issue, but serves to inform one recent music-theoretical topic that relies on a broad stylistic understanding: time feels. To date, scholars have mainly limited the discussion of time feels to the kick and snare drums (e.g., de Clercq 2016), and indeed, these instruments ultimately determine a feel. I argue, however, that different uses of guitar, bass, and cymbals can reinforce, clarify, or contradict the feel laid down by the kick and snare. In this article, I describe several categories of guitar and bass riff types and timekeeping cymbals. I then discuss how their associations with certain time-feel contexts inform further analyses. To this end, I draw from post-millennial metal music in various subgenres including black metal, death metal, doom metal, grindcore, metalcore, progressive metal, sludge metal, and thrash metal.

Attacins: A Promising Class of Insect Antimicrobial Peptides.

Insects produce a large repertoire of antimicrobial peptides (AMPs) as the first line of defense against bacteria, viruses, fungi or parasites. These peptides are produced from a large precursor that contains a signal domain, which is cleaved in vivo to produce the mature protein with antimicrobial activity. At present, AMPs from insects include several families which can be classified as cecropins, ponericins, defensins, lebocins, drosocin, Metchnikowin, gloverins, diptericins and attacins according to their structure and/or function. This short review is focused on attacins, a class of glycine-rich peptides/proteins that have been first discovered in the cecropia moth (Hyalophora cecropia). They are a rather heterogeneous group of immunity-related proteins that exhibit an antimicrobial effect mainly against Gram-negative bacteria. Here, we discuss different attacin and attacin-like AMPs that have been discovered so far and analyze their structure and phylogeny. Special focus is given to the physiological importance and mechanism of action of attacins against microbial pathogens together with their potential pharmacological applications, emphasizing their roles as antimicrobials.

First-in-Class Selective HDAC6 Inhibitor (ACY-1215) Has a Highly Favorable Safety Profile in Patients with Relapsed and Refractory Lymphoma.

Oral selective HDAC6 inhibitors could allow for decreased toxicity compared to pan-class inhibitors, and increased ease of use. ACY-1215 is well tolerated and led to disease stabilization in 50% of patients treated on a twice-daily dosing schedule. Rational drug combinations with ACY-1215 improve efficacy in patients with lymphoma. Biomarkers such as XBP-1 level or HDAC6-score may improve patient selection. ACY-1215, ricolinostat, is an oral, first-in-class isoform-selective HDAC6 inhibitor. HDAC6 is a class IIb deacetylase and plays a critical role in protein homeostasis via the unfolded protein response (UPR). Lymphocytes generate a large repertoire of antibodies and depend on an activated UPR to maintain proteostasis. Lymphomas utilize this biology to evade programmed cell death. In preclinical models of lymphoma, ACY-1215 disrupted proteostasis, triggering apoptosis. We translated these findings into a multi-institution, open-label, dose-escalation phase Ib/II study aimed to determine the safety and efficacy in patients with relapsed and refractory lymphoma. Twenty-one patients with heavily pretreated lymphoma were accrued. Patients in the phase Ib portion were enrolled on one of two dose cohorts [Arm A: 160 mg daily (n = 3) or Arm B: 160 mg twice daily (n = 10)]. ACY-1215 was well tolerated. There were no dose limiting toxicities. Most adverse events were grade 1-2, including diarrhea (57%), nausea (57%), and fatigue (43%). Grade 3-4 toxicities were rare and included anemia (9.5%) and hypercalcemia (9.5%). An additional 8 patients were enrolled on the phase II portion, at 160 mg twice daily. Sixteen patients were evaluable for response. ACY-1215 did not result in any complete or partial responses in patients treated. Eight patients had stable disease (50%) lasting a median duration of 4.5 months, all of whom were treated twice daily. Disease progressed in eight patients (50%) at cycle 2. Five patients were not evaluable due to disease progression prior to cycle 2. The median PFS was 56 days. ACY-1215 is an oral selective HDAC6 inhibitor that was safe in patients with relapsed and refractory lymphoid malignancies and led to disease stabilization in half of the evaluable patients.

Osteogenic Mechanisms of Basal Ganglia Calcification and its ex vivo Model in the Hypoparathyroid Milieu.

Basal-ganglia calcification (BGC) is common (70%) in patients with chronic hypoparathyroidism. Interestingly, cortical gray matter is spared from calcification. The mechanism of BGC, role of hyperphosphatemia, and modulation of osteogenic molecules by parathyroid hormone (PTH) in its pathogenesis is not clear. We assessed the expression of a large repertoire of molecules with proosteogenic or antiosteogenic effects, including neuroprogenitor cells in caudate, dentate, and cortical gray matter from normal autopsy tissues. The effect of high phosphate and PTH was assessed in an ex vivo model of BGC using striatum tissue culture of the Sprague-Dawley rat. The messenger RNA and protein expression of 39 molecules involved in multiple osteogenic pathways were assessed in 25 autopsy tissues using reverse-transcriptase polymerase chain reaction, Western blot, and immunofluorescence. The striatal culture was maintained in a hypoparathyroid milieu for 24 days with and without (a) high phosphate (10-mm β-glycerophosphate) and (b) PTH(1-34) (50 ng/mL Dulbecco's modified Eagle's medium-F12 media) for their effect on striatal calcification and osteogenic molecules. Procalcification molecules (osteonectin, β-catenin, klotho, FZD4, NT5E, LRP5, WNT3A, collagen-1α, and SOX2-positive neuroprogenitor stem cells) had significantly higher expression in the caudate than gray matter. Caudate nuclei also had higher expression of antiosteogenic molecules (osteopontin, carbonic anhydrase-II [CA-II], MGP, sclerostin, ISG15, ENPP1, and USP18). In an ex vivo model, striatum culture showed an increased propensity for calcified nodules with mineral deposition similar to that of bone tissue on Fourier-transformed infrared spectroscopy, alizarin, and von Kossa stain. Mineralization in striatal culture was enhanced by high phosphate and decreased by exogenous PTH through increased expression of CA-II. This study provides a conceptual advance on the molecular mechanisms of BGC and the possibility of PTH therapy to prevent this complication in a hypoparathyroid milieu.

Tuning of a Membrane-Perforating Antimicrobial Peptide to Selectively Target Membranes of Different Lipid Composition.

The use of designed antimicrobial peptides as drugs has been impeded by the absence of simple sequence-structure-function relationships and design rules. The likely cause is that many of these peptides permeabilize membranes via highly disordered, heterogeneous mechanisms, forming aggregates without well-defined tertiary or secondary structure. We suggest that the combination of high-throughput library screening with atomistic computer simulations can successfully address this challenge by tuning a previously developed general pore-forming peptide into a selective pore-former for different lipid types. A library of 2916 peptides was designed based on the LDKA template. The library peptides were synthesized and screened using a high-throughput orthogonal vesicle leakage assay. Dyes of different sizes were entrapped inside vesicles with varying lipid composition to simultaneously screen for both pore size and affinity for negatively charged and neutral lipid membranes. From this screen, nine different LDKA variants that have unique activity were selected, sequenced, synthesized, and characterized. Despite the minor sequence changes, each of these peptides has unique functional properties, forming either small or large pores and being selective for either neutral or anionic lipid bilayers. Long-scale, unbiased atomistic molecular dynamics (MD) simulations directly reveal that rather than rigid, well-defined pores, these peptides can form a large repertoire of functional dynamic and heterogeneous aggregates, strongly affected by single mutations. Predicting the propensity to aggregate and assemble in a given environment from sequence alone holds the key to functional prediction of membrane permeabilization.

Biosynthesis of sulfonamide and sulfamate antibiotics in actinomycete

Sulfonamides and sulfamates are a group of organosulfur compounds that contain the signature sulfamoyl structural motif. These compounds were initially only known as synthetic antibacterial drugs but were later also discovered as natural products. Eight highly potent examples have been isolated from actinomycetes to date, illustrating the large biosynthetic repertoire of this bacterial genus. For the biosynthesis of these compounds, several distinct and unique biosynthetic machineries have been discovered, capable to generate the unique S–N bond. For the creation of novel, second generation natural products by biosynthetic engineering efforts, a detailed understanding of the underlying enzyme machinery toward potent structural motifs is crucial. In this review, we aim to summarize the current state of knowledge on sulfonamide and sulfamate biosynthesis. A detailed discussion for the secondary sulfamate ascamycin, the tertiary sulfonamide sulfadixiamycin A, and the secondary sulfonamide SB-203208 is provided and their bioactivities and mode of actions are discussed.