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We have recently reported the synthesis and application of boron–nitrogen dihydroindeno[1,2-b]fluorene derivatives as acceptors in organic photovoltaic devices. Their modest observed efficiencies may be related to the properties of their reduced congeners. In this work, we report two new members of this family of compounds prepared via the electrophilic borylation of 2,5-di- p-tolylpyrazine followed by an arylation of the boron center with ZnAr2 reagents. Two derivatives, 1 (Ar = 2,4,6-F3C6H2) and 2 (Ar = C6F5) were synthesized, and their radical anions, 1•− and 2•−, were formed via chemical reductions with CoCp*2 and CoCp2, respectively. Through comparison of structural parameters, as well as spectroscopic and computational data, the unpaired electron in the radical anions is localized in the planar core of the molecule, and dimerization is disfavored as a result. However, unlike the neutral starting materials, 1•− and 2•− are reactive toward ambient atmosphere. These observations suggest that the reduced compounds are stable toward intrinsic degradation pathways but subject to extrinsic degradation in device operation.

Series of BODIPY dyads featuring both through-space and through-bond electronic coupling is reported. The degree of electronic interactions depends on the linker used and the strongest one is achieved for diethynylmaleimide linker.

The triplet nature of the genetic code is considered a universal feature of known organisms. However, frequent stop codons at internal mRNA positions in Euplotes ciliates ultimately specify ribosomal frameshifting by one or two nucleotides depending on the context, thus posing a nontriplet feature of the genetic code of these organisms. Here, we sequenced transcriptomes of eight Euplotes species and assessed evolutionary patterns arising at frameshift sites. We show that frameshift sites are currently accumulating more rapidly by genetic drift than they are removed by weak selection. The time needed to reach the mutational equilibrium is several times longer than the age of Euplotes and is expected to occur after a several-fold increase in the frequency of frameshift sites. This suggests that Euplotes are at an early stage of the spread of frameshifting in expression of their genome. In addition, we find the net fitness burden of frameshift sites to be noncritical for the survival of Euplotes . Our results suggest that fundamental genome-wide changes such as a violation of the triplet character of genetic code can be introduced and maintained solely by neutral evolution.

Background Data are limited regarding use of piperacillin/tazobactam for ESBL urinary tract infections (UTIs). The objective of this study was to compare clinical outcomes of patients treated empirically with piperacillin/tazobactam versus carbapenems for ESBL UTIs. Methods This retrospective, observational, propensity score-matched study evaluated adults with an ESBL on urine culture. Patients who had UTI symptoms or leukocytosis, and who received a carbapenem or piperacillin/tazobactam empirically for at least 48 h were included. The primary outcome was clinical success within 48 h, defined as resolution of temperature (36–38°C), resolution of symptoms or leukocytosis (WBC Results Overall, 223 patients were included in the full cohort and 200 patients in the matched cohort (piperacillin/tazobactam = 100, carbapenem = 100). Baseline characteristics were similar between the groups. There was no difference in the primary outcome of clinical success between the carbapenem and piperacillin/tazobactam groups (58% versus 56%, respectively; P = 0.76). Additionally, there was no difference in median (IQR) time to clinical resolution [38.9 h (21.5, 50.9 h) versus 40.3 h (27.4, 57.5 h); P = 0.37], in-hospital all-cause mortality (3% versus 3%; P = 1.00), or 30 day all-cause mortality (4% versus 2%; P = 0.68) between the carbapenem and piperacillin/tazobactam groups, respectively. Conclusions There was no significant difference in clinical success for patients treated empirically with piperacillin/tazobactam compared with carbapenems for ESBL UTIs.

Most bacterial genomes have a single chromosome that may be supplemented by smaller, dispensable plasmids. However, to date, approximately 10% of bacteria with completely sequenced genomes, mostly pathogens and plant symbionts, have more than one stable large replicon. Some secondary replicons are species-specific, carrying pathogenicity or symbiotic factors. Other replicons are common on at least the genus level, carry house-keeping genes, and may have a size of several million base pairs.We analyzed the abundance and sizes of large secondary replicons in different groups of bacteria and identified two patterns in the evolution of multipartite genomes. In nine genera of four families,Pseudoalteromonadaceae,Burkholderiaceae,Vibrionaceae, andBrucellaceae,we observed a positive correlation between the sizes of the chromosome and the secondary replicon with the slope in the range of 0.6–1.2. This indicates that in these genera the replicons evolve in a coordinated manner, with comparable rates of gene gain/loss, hence supporting classification of such secondary replicons as ‘chromids’. The second, more common pattern, features gene gains and losses mainly occurring in the primary replicon, yielding a stable size of the secondary replicon. Moreover, such secondary replicons are usually present in only a low fraction of the genus’ species. Hence, such replicons behave as ‘megaplasmids’. A mixed behavior was observed in symbiotic genera from theRhizobiaceaefamily (Rhizobium, Agrobacterium,Azospirillum, and Ensifer) with large, essential secondary replicons of stable size. These results may provide a general framework for understanding the evolution of genome complexity in prokaryotes.Data summaryThe datasets supporting the conclusions of this article are available athttps://github.com/zaryanichka/MultipleReplicons

While mutational processes operating in theEscherichia coligenome have been revealed by multiple laboratory experiments, the contribution of these processes to accumulation of bacterial polymorphism and evolution in natural environments is unknown. To address this question, we reconstruct signatures of distinct mutational processes from experimental data onE. colihypermutators, and ask how these processes contribute to differences between naturally occurringE. colistrains. We show that both mutations accumulated in the course of evolution of wild type strains in nature and in the lab-grown non-mutator laboratory strains are explained predominantly by the low fidelity of DNA polymerases II and III. By contrast, contributions specific to disruption of DNA repair systems cannot be detected, suggesting that temporary accelerations of mutagenesis associated with such disruptions are unimportant for within-species evolution. These observations demonstrate that accumulation of diversity in bacterial strains in nature is predominantly associated with errors of DNA polymerases.

Eukaryotic chromosomes are spatially segregated into topologically associating domains (TADs). Some TADs are attached to the nuclear lamina (NL) through lamina-associated domains (LADs). Here, we identified LADs and TADs at two stages of Drosophila spermatogenesis – in bamΔ86 mutant testes which is the commonly used model of spermatogonia (SpG) and in larval testes mainly filled with spermatocytes (SpCs). We found that initiation of SpC-specific transcription correlates with promoters’ detachment from the NL and with local spatial insulation of adjacent regions. However, this insulation does not result in the partitioning of inactive TADs into sub-TADs. We also revealed an increased contact frequency between SpC-specific genes in SpCs implying their de novo gathering into transcription factories. In addition, we uncovered the specific X chromosome organization in the male germline. In SpG and SpCs, a single X chromosome is stronger associated with the NL than autosomes. Nevertheless, active chromatin regions in the X chromosome interact with each other more frequently than in autosomes. Moreover, despite the absence of dosage compensation complex in the male germline, randomly inserted SpG-specific reporter is expressed higher in the X chromosome than in autosomes, thus evidencing that non-canonical dosage compensation operates in SpG.

Group 7 tris(carbonyl) bipyridine complexes have been well explored as important CO2 reduction reaction (CO2RR) electrocatalysts and now represent an excellent platform for catalyst design.

Pyrazoles are ubiquitous structures in medicinal chemistry. We report the first regioselective route to C3-hydroxyarylated pyrazoles obtained through reaction of pyrazole

Microporous metal-phosphonate materials can offer greater stability but are challenging to crystallize. Here, a novel orthogonalized aryl-phosphonate linker, 1,3,5-tris(4'-phosphono-2',6'-dimethylphenyl) benzene (H6L3) is used to direct formation of open frameworks. The peripheral aryl rings of H6L3 are orthogonalized relative to the central aromatic ring giving a tri-cleft conformation of the linker in which aromatic molecules can nest. When coordinated to magnesium ions, a series of porous crystalline metal-organic, and hydrogen-bonded metal-organic frameworks (MOFs, HMOFs) are formed (CALF-41 (Mg), HCALF-42 (Mg), -43 (Mg)). While most MOFs are tailored based on choice of metal and linker, here, the network structures are highly dependent on the inclusion and structure of the guest compounds. Larger guests, and a higher stoichiometry of metal, result in increased solvation of the metal ion, resulting in networks with connectivities increasingly involving H-bonds rather than direct phosphonate coordination. Upon thermal activation, the materials exhibit surface areas ranging from 400-600 m2/g. Self-assembly in the absence of aromatic guests yields mixtures of phases, frequently co-producing a dense structure (1). Interestingly, a series of both more porous (525-900 m2/g), and more robust solids is formed by complexing with trivalent metal ions (Al, Ga, In) with aromatic guest; however, these are only attainable as microcrystalline powders. The polyprotic nature of phosphonates enables structural analogy to the divalent CALF-41 analogues. Finally, insights to the structural transformations during metal ion desolvation are gained by considering structurally related Co materials, whose hydrogen-bonded (HCALF-44 (Co)) and desolvated (CALF-44 (Co)) coordination networks were structurally characterized.

The chromatin interaction assays, particularly Hi-C, enable detailed studies of genome architecture in multiple organisms and model systems, resulting in a deeper understanding of gene expression regulation mechanisms mediated by epigenetics. However, the analysis and interpretation of Hi-C data remain challenging due to technical biases, limiting direct comparisons of datasets obtained in different experiments and laboratories. As a result, removing biases from Hi-C-generated chromatin contact matrices is a critical data analysis step. Our novel approach, HiConfidence, eliminates biases from the Hi-C data by weighing chromatin contacts according to their consistency between replicates so that low-quality replicates do not substantially influence the result. The algorithm is effective for the analysis of global changes in chromatin structures such as compartments and topologically associating domains. We apply the HiConfidence approach to several Hi-C datasets with significant technical biases, that could not be analyzed effectively using existing methods, and obtain meaningful biological conclusions. In particular, HiConfidence aids in the study of how changes in histone acetylation pattern affect chromatin organization in Drosophila melanogaster S2 cells. The method is freely available at GitHub: https://github.com/victorykobets/HiConfidence.

Background Intravenous (IV) fluid manufacturers report an acceptable volume of overfill range for a 250 mL bag of normal saline from 265-285 mL. This overfill can contribute to residual drug that is not administered to patients. Frequent instances of incomplete eravacycline infusions were noticed by infectious disease providers. Residual Eravacycline Volume Following IV Infusion Methods This single-center, retrospective, quasi-experimental study evaluated residual volume after the completion of IV eravacycline infusion in patients admitted during the pre-intervention period (July 1 – 30, 2021) vs. post-intervention period (November 1 – 30, 2021). The intervention (August 1 – October 31, 2021), consisted of updating drug labels to add the drug diluent to total volume and a comment in the administration section to “infuse at current rate until bag is empty.” Nursing education was provided to encourage administration of the entire drug volume. The primary outcome compared residual antibiotic volume before and after implementation of the intervention. The secondary outcomes evaluated amount of drug lost (total mg and percent of total dose) in the pre- and post-intervention periods and cost of facility drug waste. Nursing Education Distributed During Intervention Period Results There was an average residual volume of 38.0 mL (range 6 – 85 mL) for pre-intervention (n=9, total of 46 doses) vs. 12.2 mL (range 0 – 37 mL) for the post-intervention (n=7, total of 21 doses) population (p< 0.0001). Residual volume accounted for an average of 15.2% of the total bag volume compared to 4.7% for the pre- and post-intervention groups, respectively (p< 0.0001). The pre-intervention residual volume contained an average of 13.5 mg (15.3% of total dose) of eravacycline, versus 4.7 mg (4.7% of total dose) in the post-intervention (p< 0.0001). Cost analysis used average wholesale price for 50 mg vials. Residual volume in the pre-intervention period estimated $893.45 ($10,721.40 annualized) vs. $161.04 ($1,932.48 annualized) in the post-intervention period. Pre- and Post-Intervention Comparison Clinical Analysis of Residual Antibiotic Volume Facility Waste Conclusion Average residual volume and amount of discarded drug was significantly reduced after the interventions. Following the results of this study, interventions were expanded to all admixed antimicrobials. Further studies are needed to determine the potential clinical impact when patients do not receive the complete antibiotic infusion due to residual volume. Disclosures Kerry O. Cleveland, MD, AbbVie: Honoraria|Cumberland: Honoraria|Merck: Honoraria|Pfizer: Honoraria Michael S. Gelfand, MD, AbbVie: Expert Testimony|La Jolla: Expert Testimony.

Background While literature supports use of carbapenems over piperacillin-tazobactam (TZP) for extended spectrum beta-lactamase (ESBL) bacteremia, data is limited regarding the use of TZP for ESBL urinary tract infections (UTIs). The objective of this study is to determine if patients have similar clinical outcomes when empirically treated with TZP versus carbapenems for ESBL UTIs. Methods This IRB-approved, retrospective, non-inferiority study evaluated adult patients admitted to a 5-facility healthcare system from January 1, 2016 to June 30, 2021. Patients who received a carbapenem or TZP empirically for at least 48 hours with a urine culture positive for an ESBL, urinary symptoms or leukocytosis, and isolate susceptibility to the empiric antibiotic of choice were included. The primary outcome was clinical success within 48 hours defined as resolution of temperature (36-38 °C), resolution of symptoms or leukocytosis (WBC < 12 x103/μL) in the absence of symptoms, and the absence of readmission for an ESBL UTI within 6 months. Secondary outcomes included time to clinical success, hospital length of stay (LOS), and 30-day all-cause mortality. Results A total of 223 patients were included with 123 (55%) patients receiving TZP and 100 (45%) patients receiving a carbapenem. Patients were predominantly female (65%) and Caucasian (52%) with a median (IQR) age of 70 (58, 81) years. Baseline characteristics were similar between the groups with no difference in complicated cystitis (60%), pyelonephritis (27%), or concomitant bacteremia (25%) (Table 1). There was no difference in the primary outcome of clinical success between the carbapenem and TZP group (60% vs 59%, respectively; p=0.92). Additionally, there was no difference in median (IQR) time to clinical success [39 (21, 52) vs 40 (25, 57) hrs, p=0.53], median hospital LOS [7.0 (5.1, 10.6) vs 6.8 (4.7, 9.2) days, p=0.12], or 30-day all-cause mortality (4% vs 2%, p=0.72) between the carbapenem and TZP groups, respectively (Table 2). Conclusion In this large, multi-center study, we found no difference in clinical outcomes in patients with UTIs caused by ESBL-producing organisms treated empirically with TZP versus carbapenems. Clinicians could consider using TZP in patients with ESBL UTIs susceptible to TZP. Disclosures Michael S. Gelfand, MD, AbbVie: Expert Testimony|La Jolla: Expert Testimony Kerry O. Cleveland, MD, AbbVie: Honoraria|Cumberland: Honoraria|Merck: Honoraria|Pfizer: Honoraria.

We report the design, synthesis, and characterization of four N-annulated perylene diimide (NPDI) functionalized rhenium bipyridine [Re(bpy)] supramolecular dyads. The Re(bpy) scaffold was connected to the NPDI chromophore either directly [Re(py-C0-NPDI)] or via an ethyl [Re(bpy-C2-NPDI)], butyl [Re(bpy-C4-NPDI)], or hexyl [Re(bpy-C6-NPDI)] alkyl-chain spacer. Upon electrochemical reduction in the presence of CO2 and a proton source, Re(bpy-C2/4/6-NPDI) all exhibited significant current enhancement effects, while Re(py-C0-NPDI) did not. During controlled potential electrolysis (CPE) experiments at Eappl = -1.8 V vs Fc+/0, Re(bpy-C2/4/6-NPDI) all achieved comparable activity (TONco ∼ 25) and Faradaic efficiency (FEco ∼ 94%). Under identical CPE conditions, the standard catalyst Re(dmbpy) was inactive for electrocatalytic CO2 reduction; only at Eappl = -2.1 V vs Fc+/0 could Re(dmbpy) achieve the same catalytic performance, representing a 300 mV lowering in overpotential for Re(bpy-C2/4/6-NPDI). At higher overpotentials, Re(bpy-C4/6-NPDI) both outperformed Re(bpy-C2-NPDI), indicating the possibility of coinciding electrocatalytic CO2 reduction mechanisms that are dictated by tether-length and overpotential. Using UV-vis-nearIR spectroelectrochemistry (SEC), FTIR SEC, and chemical reduction experiments, it was shown that the NPDI-moiety served as an electron-reservoir for Re(bpy), thereby allowing catalytic activity at lower overpotentials. Density functional theory studies probing the optimized geometries and frontier molecular orbitals of various catalytic intermediates revealed that the geometric configuration of NPDI relative to the Re(bpy)-moiety plays a critical role in accessing electrons from the electron-reservoir. The improved performance of Re(bpy-C2/4/6-NPDI)dyads at lower overpotentials, relative to Re(dmbpy), highlights the utility of chromophore electron-reservoirs as a method for lowering the overpotential for CO2 conversion.

During attempts to prepare spirodithiaselenuranes as GPx mimetics, a series of unexpected dimeric macrocycles was obtained, each containing two selenide and two disulfide moieties in rings ranging from 18- to 26-membered. The products showed potent GPx-like activity in an NMR assay based on their ability to catalyze the reduction of hydrogen peroxide with benzyl thiol. The high catalytic activity was attributed to transannular effects during selenide to selenoxide oxidation. This redox process was also characterized by an induction period that indicated autocatalysis in the formation of an intermediate selenoxide from the oxidation of the corresponding selenide.

Group 7 tris(carbonyl) bipyridine complexes have been well explored as important CO

Although several variants of the standard genetic code are known, its triplet character is universal with an exception in ciliatesEuplotes, where stop codons at internal mRNA positions specify ribosomal frameshifting. How didEuplotesspp. evolved and maintained such an unusual genetic code remains a mystery. To investigate these questions, we explored the evolution of frameshifting occurrence in Euplotes genes. We sequenced and analyzed several transcriptomes from differentEuplotesspp to characterize the gain-and-loss dynamics of frameshift sites. Surprisingly, we found a sharp asymmetry between frameshift gain and frameshift loss events with the former exceeding the latter by about 10 folds. Further analysis of mutation rates in protein-coding and non-coding regions revealed that this asymmetry is expected based on single nucleotide mutation rates and does not require positive selection for frameshifting. We found that the number of frameshift sites inEuplotesspp is increasing and is far from the steady state. The steady equilibrium state is expected in about 0.1 to 1 billion years leading to about a 10 fold increase in the number of frameshift sites in Euplotes genes.

The synthesis of aryl selenonic acids was achieved from diverse aryl bromides via a one-pot method involving metalation, selenation, and oxidation with hydrogen peroxide followed by ion exchange to afford the pure products in 77-90% yield. An o-hydroxymethyl derivative was found to dehydrate readily, affording the first example of a cyclic selenonic ester, while two minor byproducts were isolated and shown by X-ray crystallography to be mixed salts of aryl selenonic acids with either the corresponding aryl seleninic or selenious acid.

Dosage compensation equalizes gene expression in a single male X chromosome with that in the pairs of autosomes and female X chromosomes. In the fruit fly

Background The histidine metabolism and transport (his) genes are controlled by a variety of RNA-dependent regulatory systems among diverse taxonomic groups of bacteria including T-box riboswitches in Firmicutes and Actinobacteria and RNA attenuators in Proteobacteria. Using a comparative genomic approach, we previously identified a novel DNA-binding transcription factor (named HisR) that controls the histidine metabolism genes in diverse Gram-positive bacteria from the Firmicutes phylum. Results Here we report the identification of HisR-binding sites within the regulatory regions of the histidine metabolism and transport genes in 395 genomes representing the Bacilli, Clostridia, Negativicutes, and Tissierellia classes of Firmicutes, as well as in 97 other HisR-encoding genomes from the Actinobacteria, Proteobacteria, and Synergistetes phyla. HisR belongs to the TrpR family of transcription factors, and their predicted DNA binding motifs have a similar 20-bp palindromic structure but distinct lineage-specific consensus sequences. The predicted HisR-binding motif was validated in vitro using DNA binding assays with purified protein from the human gut bacterium Ruminococcus gnavus. To fill a knowledge gap in the regulation of histidine metabolism genes in Firmicutes genomes that lack a hisR repressor gene, we systematically searched their upstream regions for potential RNA regulatory elements. As result, we identified 158 T-box riboswitches preceding the histidine biosynthesis and/or transport genes in 129 Firmicutes genomes. Finally, novel candidate RNA attenuators were identified upstream of the histidine biosynthesis operons in six species from the Bacillus cereus group, as well as in five Eubacteriales and six Erysipelotrichales species. Conclusions The obtained distribution of the HisR transcription factor and two RNA-mediated regulatory mechanisms for histidine metabolism genes across over 600 species of Firmicutes is discussed from functional and evolutionary points of view.

Tricarbonyl Group 7 complexes have a longstanding history as efficacious CO

ExuR and UxuR are paralogous proteins belonging to the GntR family of transcriptional regulators. Both are known to control hexuronic acid metabolism in a variety of Gammaproteobacteria but the relative impact of each of them is still unclear. Here, we apply 2D difference electrophoresis followed by mass-spectrometry to characterise the changes in the Escherichia coli proteome in response to the uxuR or exuR deletion. Our data clearly show that the effects are different: deletion of uxuR resulted in significantly enhanced expression of D-mannonate dehydratase UxuA and flagellar protein FliC, and inhibition of outer membrane porin OmpF, while the absence of ExuR did not significantly alter the spectrum of detected proteins.This suggests that the roles of proteins predicted as homologs are far from identical. Effects of uxuR deletion were largely dependent on the cultivation conditions: during growth with glucose, UxuA and FliC were dramatically altered, while during growth with glucuronate activation of both was not so prominent. During growth on glucose, the maximal activation was detected for FliC. This was further confirmed by expression analysis and physiological tests thus suggesting involvement of UxuR in the regulation of bacterial motility and biofilm formation.

ExuR and UxuR are paralogous proteins belonging to the GntR family of transcriptional regulators. Both are known to control hexuronic acid metabolism in a variety of Gammaproteobacteria but the relative impact of each of them is still unclear. Here, we apply 2D difference electrophoresis followed by mass-spectrometry to characterise the changes in the

Fascinating progress in understanding our world at the smallest scales moves us to the border of a new technological revolution governed by quantum physics. By taking advantage of quantum phenomena, quantum computing devices allow a speedup in solving diverse tasks. In this Perspective, we discuss the potential impact of quantum computing on computational biology. Bearing in mind the limitations of existing quantum computing devices, we attempt to indicate promising directions for further research in the emerging area of quantum computational biology. Quantum computing has the potential to assist with myriad tasks in science. In this Perspective, the applicability and promising directions of quantum computing in computational biology, genetics and bioinformatics is evaluated and discussed.

We report the use of electron rich iron complexes supported by a dianionic diborate pentadentate ligand system, B2Pz4Py, for the coordination and activation of ammonia (NH3) and hydrazine (NH2NH2). For ammonia, coordination to neutral (B2Pz4Py)Fe(ii) or cationic [(B2Pz4Py)Fe(iii)]+ platforms leads to well characterized ammine complexes from which hydrogen atoms or protons can be removed to generate, fleetingly, a proposed (B2Pz4Py)Fe(iii)–NH2 complex (3Ar-NH2). DFT computations suggest a high degree of spin density on the amido ligand, giving it significant aminyl radical character. It rapidly traps the H atom abstracting agent 2,4,6-tri-tert-butylphenoxy radical (ArO˙) to form a C–N bond in a fully characterized product (2Ar), or scavenges hydrogen atoms to return to the ammonia complex (B2Pz4Py)Fe(ii)–NH3 (1Ar-NH3). Interestingly, when (B2Pz4Py)Fe(ii) is reacted with NH2NH2, a hydrazine bridged dimer, (B2Pz4Py)Fe(ii)–NH2NH2–Fe(ii)(B2Pz4Py) ((1Ar)2-NH2NH2), is observed at −78 °C and converts to a fully characterized bridging diazene complex, 4Ar, along with ammonia adduct 1Ar-NH3 as it is allowed to warm to room temperature. Experimental and computational evidence is presented to suggest that (B2Pz4Py)Fe(ii) induces reductive cleavage of the N–N bond in hydrazine to produce the Fe(iii)–NH2 complex 3Ar-NH2, which abstracts H˙ atoms from (1Ar)2-NH2NH2 to generate the observed products. All of these transformations are relevant to proposed steps in the ammonia oxidation reaction, an important process for the use of nitrogen-based fuels enabled by abundant first row transition metals., Synopsis: a highly reactive Fe(iii)–NH2 complex is generated via activation of ammonia or hydrazine in reactions of relevance to fundamental steps in ammonia oxidation processes mediated by an abundant, first row transition metal.

The synthesis and characterization of six new N-annulated perylene diimide (N-PDI) molecules consisting of different alkyl-based heteroatom and waxy infused sidechains is reported. Amino, urea, quaternary methyl ammonium, iminopyridine, hexadecyl and pyridine moieties were all appended to the pyrrolic N-position of N-annulated PDI. These N-PDI derivatives have been synthesized using facile SN2 chemistry resulting in high yields and without the need for purification via column chromatography. To further demonstrate the functional diversification offered by N-PDI we appended a cyano group to the 6,7-bay positions opposite the N-annulation and tested its capability for use in organic field effect transistor devices. Complete characterization of these N-PDI derivatives was completed using UV-Vis spectroscopy, cyclic voltammetry and solubility determination to observe how the appended sidechains have affected the structure-properties relationships of N-PDI derivatives.

Current methods for the preparation of heterobifunctional pomalidomide-conjugates rely on methods that are often low yielding and produce intractable byproducts. Herein we describe our strategy for the reliable and succinct preparation of pomalidomide-linkers which is essential to the formation of these conjugates. We present the preparation of 18 pomalidomide-linkers in high yield compared to current literature methods. Our findings show that secondary amines consistently afford greater yields than their primary counterparts, a trend that we were able to exploit in the synthesis of several new pomalidomide homo-dimers in enhanced yields compared to similar literature syntheses. This trend was further utilised to develop the first one-pot synthesis of JQ1-pomalidomide conjugates in yields up to 62%, providing a method that is suited to rapid preparation of conjugate libraries as is frequently required for the development of new protein degraders., Current methods for the preparation of heterobifunctional pomalidomide-conjugates rely on methods that are often low yielding and produce intractable byproducts. Herein we describe our strategy for the succinct preparation of pomalidomide-linkers.

First triplets of mRNA coding region affect the yield of translation. We have applied the flowseq method to analyze >30 000 variants of the codons 2–11 of the fluorescent protein reporter to identify factors affecting the protein synthesis. While the negative influence of mRNA secondary structure on translation has been confirmed, a positive role of rare codons at the beginning of a coding sequence for gene expression has not been observed. The identity of triplets proximal to the start codon contributes more to the protein yield then more distant ones. Additional in-frame start codons enhance translation, while Shine–Dalgarno-like motifs downstream the initiation codon are inhibitory. The metabolic cost of amino acids affects the yield of protein in the poor medium. The most efficient translation was observed for variants with features resembling those of native Escherichia coli genes.

Summary Translation efficiency contributes several orders of magnitude difference in the overall yield of exogenous gene expression in bacteria. In diverse bacteria, the translation initiation site, whose sequence is the primary determinant of the translation performance, is comprised of the start codon and the Shine–Dalgarno box located upstream. Here, we have examined how the sequence of a spacer between these main components of the translation initiation site contributes to the yield of synthesized protein. We have created a library of reporter constructs with the randomized spacer region, performed fluorescently activated cell sorting and applied next‐generation sequencing analysis (the FlowSeq protocol). As a result, we have identified sequence motifs for the spacer region between the Shine–Dalgarno box and AUG start codon that may modulate the translation efficiency in a 100‐fold range., Understanding the principles that determine mRNA translation efficiency is of primary value for deciphering translational control of gene expression and for optimization of protein synthesis in biotechnology. In this work we combined Flowseq method with randomization of a region within the spacer between the Shine‐Dalgarno box and AUG start codon to decipher an influence of this mRNA part on translation efficiency.

Isomeric bis(aldiminium) salts with a 1,4-cyclohexylene framework were synthesized. The first isolable bis(CAAC) was prepared from the

Until recently, Shigella and enteroinvasive Escherichia coli were thought to be primate-restricted pathogens. The base of their pathogenicity is the type 3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates host cell invasion and subsequent proliferation. A large family of T3SS effectors, E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella pathogenicity through the modulation of cellular ubiquitination that degrades host proteins. However, recent genomic studies identified ipaH genes in the genomes of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted from fecal samples of bovine calves, suggesting that non-human hosts may also be infected by these strains, potentially pathogenic to humans. We performed a comparative genomic study of the functional repertoires in the ipaH gene family in Shigella and enteroinvasive Escherichia from human and predicted non-human hosts. We found that fewer than half of Shigella genomes had a complete set of ipaH genes, with frequent gene losses and duplications that were not consistent with the species tree and nomenclature. Non-human host IpaH proteins had a diverse set of substrate-binding domains and, in contrast to the Shigella proteins, two variants of the NEL C-terminal domain. Inconsistencies between strains phylogeny and composition of effectors indicate horizontal gene transfer between E. coli adapted to different hosts. These results provide a framework for understanding of ipaH-mediated host-pathogens interactions and suggest a need for a genomic study of fecal samples from diseased animals.

The coordinative pliancy of the phosphonate functional group means that metal-phosphonate materials often self-assemble as well-packed structures with minimal porosity, as efficient inter-ligand packing is enabled. Here, we report a multistep synthesis of a novel aryl-phosphonate linker with an orthogonalized ligand core, 1,3,5-tris(4'-phosphonophenyl)-2,4,6-trimethylbenzene (H

Intravenous (IV) drugs are administered through infusion pumps and IV administration sets for patients who are seen in healthcare settings. There are multiple areas of the medication administration process that can influence the amount of a drug a patient receives. For example, IV administration sets that deliver a drug from an infusion bag to a patient vary in terms of length and bore. In addition, fluid manufacturers report that the total acceptable volume range for a 250 mL bag of normal saline can be anywhere from 265 to 285 mL. At the institution chosen for our study, each 50 mg vial of eravacycline is reconstituted using 5 mL of diluent, and the total dose is administered as a 250 mL admixture. This single-center, retrospective, quasi-experimental study evaluated the residual medication volume after the completion of an IV eravacycline infusion in patients admitted during the pre-intervention study period compared to those in the post-intervention study period. The primary outcome of the study was to compare the residual antibiotic volume remaining in the bags following IV infusions of eravacycline before and after the implementation of interventions. The secondary outcomes included the following: comparing the amount of the drug lost in the pre- and post-intervention periods, determining whether the amount of residual volume was affected by nursing shifts (day versus night), and lastly assessing the cost of facility drug waste. On average, approximately 15% of the total bag volume was not infused during the pre-intervention period, which was reduced to less than 5% in the post-intervention period. Clinically, the average estimated amount of eravacycline discarded decreased from 13.5 mg to 4.7 mg in the pre- and post-intervention periods, respectively. Following the statistically significant results of this study, the interventions were expanded at this facility to include all admixed antimicrobials. Further studies are needed to determine the potential clinical impact when patients do not receive complete antibiotic infusions.

While somatic mutations are known to be enriched in genome regions with non-canonical DNA secondary structure, the impact of particular mutagens still needs to be elucidated. Here, we demonstrate that in human cancers, the APOBEC mutagenesis is not enriched in direct repeats, mirror repeats, short tandem repeats, and G-quadruplexes, and even decreased below its level in B-DNA for cancer samples with very high APOBEC activity. In contrast, we observe that the APOBEC-induced mutational density is positively associated with APOBEC activity in inverted repeats (cruciform structures), where the impact of cytosine at the 3'-end of the hairpin loop is substantial. Surprisingly, the APOBEC-signature mutation density per TC motif in the single-stranded DNA of a G-quadruplex (G4) is lower than in the four-stranded part of G4 and in B-DNA. The APOBEC mutagenesis, as well as the UV-mutagenesis in melanoma samples, are absent in Z-DNA regions, owing to the depletion of their mutational signature motifs.

Deep learning is a class of machine learning techniques capable of creating internal representation of data without explicit preprogramming. Hence, in addition to practical applications, it is of interest to analyze what features of biological data may be learned by such models. Here, we describe PredPair, a deep learning neural network trained to predict base pairs in RNA structure from sequence alone, without any incorporated prior knowledge, such as the stacking energies or possible spatial structures. PredPair learned the Watson-Crick and wobble base-pairing rules and created an internal representation of the stacking energies and helices. Application to independent experimental (DMS-Seq) data on nucleotide accessibility in mRNA showed that the nucleotides predicted as paired indeed tend to be involved in the RNA structure. The performance of the constructed model was comparable with the state-of-the-art method based on the thermodynamic approach, but with a higher false positives rate. On the other hand, it successfully predicted pseudoknots. t-SNE clusters of embeddings of RNA sequences created by PredPair tend to contain embeddings from particular Rfam families, supporting the predictions of PredPair being in line with biological classification.

Enterotypes of the human gut microbiome have been proposed to be a powerful prognostic tool to evaluate the correlation between lifestyle, nutrition, and disease. However, the number of enterotypes suggested in the literature ranged from two to four. The growth of available metagenome data and the use of exact, non-linear methods of data analysis challenges the very concept of clusters in the multidimensional space of bacterial microbiomes. Using several published human gut microbiome datasets, we demonstrate the presence of a lower-dimensional structure in the microbiome space, with high-dimensional data concentrated near a low-dimensional non-linear submanifold, but the absence of distinct and stable clusters that could represent enterotypes. This observation is robust with regard to diverse combinations of dimensionality reduction techniques and clustering algorithms.

Until recently, Shigella and enteroinvasive Escherichia coli were thought to be primate-restricted pathogens. The base of their pathogenicity is the type 3 secretion system (T3SS) encoded by the pINV virulence plasmid, which facilitates host cell invasion and subsequent proliferation. A large family of T3SS effectors, E3 ubiquitin-ligases encoded by the ipaH genes, have a key role in the Shigella pathogenicity through the modulation of cellular ubiquitination that degrades host proteins. However, recent genomic studies identified ipaH genes in the genomes of Escherichia marmotae, a potential marmot pathogen, and an E. coli extracted from fecal samples of bovine calves, suggesting that non-human hosts may also be infected by these strains, potentially pathogenic to humans.We performed a comparative genomic study of the functional repertoires in the ipaH gene family in Shigella and enteroinvasive Escherichia from human and predicted non-human hosts. We found that fewer than half of Shigella genomes had a complete set of ipaH genes, with frequent gene losses and duplications that were not consistent with the species tree and nomenclature. Non-human host IpaH proteins had a diverse set of substrate-binding domains and, in contrast to the Shigella proteins, two different types of the NEL C-terminal domain. Only the ipaH9.8 gene was found in Escherichia derived from both human and non-human hosts. These results provide a framework for understanding of ipaH-mediated host-pathogens interactions and suggest a need for a genomic study of fecal samples from diseased animals.

Cobalt(I) complexes supported by a series of PCcarbeneP pincer ligands of varying donicity, differing in the aryl group linking the phosphine arms with the anchoring carbon donor, are described. Addition of the proligands to cobalt bromide results in the formation of a series of cobalt(II) tetrahedral complexes, Ln-1, which serve as excellent precur-sors to the corresponding PCalkylP and PCcarbeneP complexes. Square planar cobalt PCcarbeneP complexes, L2R-3-X (X = Cl, Br), are readily synthesized by addition of a bulky aryloxide radical to the corresponding PCalkylP complex, L1-2-Br or via addition of L2R to ClCo(PPh3)3 in the presence of trityl radical or by addition of NaHBEt3 and trityl radical to iso-lated L2R-1. For the L2NMe2 PCcarbeneP complexes, salt metathesis reactions with either CsOH·H2O, LiCH2TMS, or LiNH2 result in the corresponding hydroxo, alkyl, and amine complexes, L2NMe2-3-R (R = OH, CH2TMS, NH2). Reaction of L2NMe2-3-OH with benzoic acid affords the 2-O2CPh derivative The nature of the carbene bond in either ligand plat-form as well as the effects of the X-type capping ligand on the Co=C bond are explored computationally and show that triplet structures are relatively more stable in for the less electron donating ligand L1 while singlet Co(I) carbenes dominate for the more electron rich L2 derivatives. For L2NMe2 complexes, the effect of the trans ligand X was also probed. Pi donors imbue the carbene with singlet character while the strongly  donating alkyl derivative exhibits significant triplet character.

While somatic mutations are known to be enriched in genome regions with non-canonical DNA secondary structure, the impact of particular mutagens still needs to be elucidated. Here, we demonstrate that in human cancers, the APOBEC mutagenesis is not enriched in direct repeats, mirror repeats, short tandem repeats, and G-quadruplexes, and even decreased below its level in B-DNA for cancer samples with very high APOBEC activity. In contrast, we observe that the APOBEC-induced mutational density is positively associated with APOBEC activity in inverted repeats (cruciform structures), where the impact of cytosine at the 3’-end of the hairpin loop is substantial. Surprisingly, the APOBEC-signature mutation density per TC motif in the single-stranded DNA of a G-quadruplex (G4) is lower than in the four-stranded part of G4 and in B-DNA. The APOBEC mutagenesis, as well as the UV-mutagenesis in melanoma samples are absent in Z-DNA regions, due to depletion of their mutational signature motifs.

The purpose of this work is to adapt and apply Next Generation Sequencing methods in oil and gas well field studies. Relatively recent NGS methods provide a description of a geological formation by analyzing millions of DNA sequences and represent an entirely new way to obtain information about oil and gas reservoirs and the composition of their fluids, which could significantly change the approach to exploration and field development. We present the results of pilot work to determine the inflow profile in a horizontal well based on DNA markers. The technology is based on the comparison of bacterial DNA from drill cuttings obtained while drilling with DNA from microorganisms of fluids obtained during production at the wellhead. Because of their high selectivity, individual microbes live only under certain conditions (salinity, oil saturation, temperature) and can be used as unique natural biomarkers. The comparison of DNA samples of drilling cutting and produced fluid allows for identification of the segment of the horizontal well from which the main flow comes, as well as identifying the type of incoming fluid (water, oil, gas) without stopping the operation process and without conducting expensive downhole operations. As a result of these studies, the microbial communities of the oil-bearing sands and formation fluids of the Cretaceous deposits (group BS) in Western Siberia were identified, and the relative numerical ratio of microorganisms in the formations was determined. It was shown that the microbiome diversity changes with depth, and depends on the lithological composition, and sequencing data obtained from cuttings samples correlate with data from wellhead samples of produced fluid. Thus, the practical applicability of DNA sequencing for solving field problems in oil and gas field development, in particular for determining the inflow profile in horizontal wells, was confirmed.

We report the design, synthesis, and characterization of four N-annulated perylene diimide (NPDI) functionalized rhenium bipyridine [Re(bpy)] supramolecular dyads. The Re(bpy) scaffold was connected to the NPDI chromophore either directly [

Benzeneperoxyseleninic acid has been proposed as the key intermediate in the widely used epoxidation of alkenes with benzeneseleninic acid and hydrogen peroxide. However, it reacts sluggishly with cyclooctene and instead rapidly decomposes in solution to a mixed selenonium-selenonate salt that was identified by X-ray absorption and 77 Se NMR spectroscopy, as well as by single crystal X-ray diffraction. This process includes a selenoxide elimination of the peroxyseleninic acid with liberation of oxygen and additional redox steps. The salt is relatively stable in the solid state, but generates the corresponding selenonic acid in the presence of hydrogen peroxide. The selenonic acid is inert towards cyclooctene on its own; however, rapid epoxidation occurs when hydrogen peroxide is added. This shows that the selenonic acid must first be activated through further oxidation, presumably to the heretofore unknown benzeneperoxyselenonic acid. The latter is the principal oxidant in this epoxidation.

Unusual 6,7-bis-nitrated N-annulated perylene diimides are reported which have stabilized frontier molecular orbitals making them highly electron deficient. Radical anion formation under ambient conditions is readily feasible. A crowded NO2 substitution pattern significantly alters the perylene core geometry. Varied functionalization at the pyrrolic N-position allows for crystal engineering.

The synthesis of a new perylene diimide organic semiconductor via the use of an acid-catalyzed condensation reaction is presented. The strategy involves the incorporation of an N–H moiety into the molecular design which can be polarized to facilitate green solvent processing. Compared to the parent chromophore, onset of optical absorption in solution is redshifted by 180 nm. Utility as an electron transporting semiconductor in organic field effect transistors is demonstrated.