Degradation Kinetics of Disulfide Cross-Linked Microgels: Real-Time Monitoring by Confocal Microscopy.

Although biodegradable microgels represent a useful drug delivery system, questions remain regarding the kinetics of gel degradation and subsequent drug release. Spherical microgels (~Ø10-300 µm) were synthesized using an inverse suspension polymerization method. Specifically, acrylamide and acrylonitrile monomers were thermally co-polymerized with N,N'-bis(acryloyl)cystamine as a cross-linker with disulfide bridges. The kinetics and mechanism of degradation of these cross-linked, degradable, fluorescently labeled microgels (PAAm-AN-BAC-FA) were quantitatively studied under confocal microscopy at various concentrations of glutathione (reducing agent) ranging from 0.06 to 91.8 mM. It was found that polymer network degradation via the cleavage of disulfide bonds was accompanied by two overlapping processes: diffusion-driven swelling and dissolution-driven erosion. A slow increase in microgel size (swelling) resulted from partial de-cross-linking in the bulk of the microgel, whereas a faster decrease in fluorescence intensity (erosion) resulted from the complete cleavage of disulfide bonds and the release of uncleaved polymeric chains from the microgel immediate surface into the solution. Swelling and erosion exhibited distinct kinetics and characteristic times. Importantly, the dependence of kinetics on glutathione concentration for both swelling and erosion suggests that degradation would occur faster in cancer cells (higher concentration of reductants) than in normal cells (lower concentration of reductants), such that drug release profiles would be correspondingly different. A greater comprehension of microgel degradation kinetics would help in (i) predicting the drug release profiles for novel multifunctional drug delivery systems and (ii) using redox-sensitive degradable hydrogel particles to determine the concentrations of reducing agents either in vitro or in vivo.

Structure-Activity Relationships and Transcriptomic Analysis of Hypoxia-Inducible Factor Prolyl Hydroxylase Inhibitors.

To evaluate the differences in action of commercially available 2-oxoglutarate mimetics and "branched-tail" oxyquinoline inhibitors of hypoxia-inducible factor prolyl hydroxylase (HIF PHD), the inhibitors' IC50 values in the activation of HIF1 ODD-luciferase reporter were selected for comparative transcriptomics. Structure-activity relationship and computer modeling for the oxyquinoline series of inhibitors led to the identification of novel inhibitors, which were an order of magnitude more active in the reporter assay than roxadustat and vadadustat. Unexpectedly, 2-methyl-substitution in the oxyquinoline core of the best HIF PHD inhibitor was found to be active in the reporter assay and almost equally effective in the pretreatment paradigm of the oxygen-glucose deprivation in vitro model. Comparative transcriptomic analysis of the signaling pathways induced by HIF PHD inhibitors showed high potency of the two novel oxyquinoline inhibitors (#4896-3249 and #5704-0720) at 2 µM concentrations matching the effect of 30 µM roxadustat and 500 µM dimethyl oxalyl glycine in inducing HIF1 and HIF2-linked pathways. The two oxyquinoline inhibitors exerted the same activation of HIF-triggered glycolytic pathways but opposite effects on signaling pathways linked to alternative substrates of HIF PHD 1 and 3, such as p53, NF-κB, and ATF4. This finding can be interpreted as the specificity of the 2-methyl-substitute variant for HIF PHD2.

Probable Mechanisms of Doxorubicin Antitumor Activity Enhancement by Ginsenoside Rh2.

Ginsenoside Rh2 increases the efficacy of doxorubicin (DOX) treatment in murine models of solid and ascites Ehrlich's adenocarcinoma. In a solid tumor model (treatment commencing 7 days after inoculation), DOX + Rh2 co-treatment was significantly more efficacious than DOX alone. If treatment was started 24 h after inoculation, the inhibition of tumor growth of a solid tumor for the DOX + Rh2 co-treatment group was complete. Furthermore, survival in the ascites model was dramatically higher for the DOX + Rh2 co-treatment group than for DOX alone. Mechanisms underlying the combined DOX and Rh2 effects were studied in primary Ehrlich's adenocarcinoma-derived cells and healthy mice's splenocytes. Despite the previously established Rh2 pro-oxidant activity, DOX + Rh2 co-treatment revealed no increase in ROS compared to DOX treatment alone. However, DOX + Rh2 treatment was more effective in suppressing Ehrlich adenocarcinoma cell adhesion than either treatment alone. We hypothesize that the benefits of DOX + Rh2 combination treatment are due to the suppression of tumor cell attachment/invasion that might be effective in preventing metastatic spread of tumor cells. Ginsenoside Rh2 was found to be a modest activator in a Neh2-luc reporter assay, suggesting that Rh2 can activate the Nrf2-driven antioxidant program. Rh2-induced direct activation of Nrf2 might provide additional benefits by minimizing DOX toxicity towards non-cancerous cells.

Nickel - p-block metal mixed chalcogenides based on AuCu3-type fragments: iodine-assisted synthesis as a way of obtaining new structures.

Two new mixed nickel-gallium chalcogenides, Ni9.39Ga2S2 and Ni5.80GaTe2, and a new mixed nickel-indium telluride, Ni5.78InTe2, have been synthesized by a high-temperature ampoule route with the addition of iodine, and characterized from single-crystal or powder diffraction data. They belong to the relatively uncommon Ni7-xMQ2/Ni10-xM2Q2 type of structures (M = Ge, Sn, Sb, In), and are built from p-block metal-centered nickel cuboctahedra, alternating along the c axis with defective Cu2Sb-type nickel-chalcogen ones. Both tellurium-containing compounds show a small degree of orthorhombic distortion with respect to the idealized tetragonal structure, only detectable in the powder diffraction data. No phase transition to the tetragonal structure was detected for Ni5.80GaTe2 by the in situ powder diffraction measurements from room temperature to 550 °C. DFT calculations show close relationships of electronic structures of these ternary compounds to their parent intermetallics, Ni3M (M = Ga, In). Metallic conductivity and paramagnetic properties are predicted for all three with the latter confirmed by magnetic measurements. The bonding patterns, investigated via the ELF topological analysis, show multi-centered nickel - p-block metal bonds in the AuCu3-type fragments and pairwise covalent interactions in the nickel-chalcogen fragments. Both Ni7-xMTe2 compounds showed no structural or compositional changes upon high-temperature mid-pressure hydrogenation.

HIF Prolyl Hydroxylase Inhibitors for COVID-19 Treatment: Pros and Cons.

The review analyzes the potential advantages and problems associated with using HIF prolyl hydroxylase inhibitors as a treatment for COVID-19. HIF prolyl hydroxylase inhibitors are known to boost endogenous erythropoietin (Epo) and activate erythropoiesis by stabilizing and activating the hypoxia inducible factor (HIF). Recombinant Epo treatment has anti-inflammatory and healing properties, and thus, very likely, will be beneficial for moderate to severe cases of COVID-19. However, HIF PHD inhibition may have a significantly broader effect, in addition to stimulating the endogenous Epo production. The analysis of HIF target genes reveals that some HIF-targets, such as furin, could play a negative role with respect to viral entry. On the other hand, HIF prolyl hydroxylase inhibitors counteract ferroptosis, the process recently implicated in vessel damage during the later stages of COVID-19. Therefore, HIF prolyl hydroxylase inhibitors may serve as a promising treatment of COVID-19 complications, but they are unlikely to aid in the prevention of the initial stages of infection.

Targeted sequencing analysis of ACVR2A gene identifies novel risk variants associated with preeclampsia.

Background: Preeclampsia (PE) is the most common complication of pregnancy that remains to be a major cause of maternal and fetal mortality. Prediction and early diagnosis of PE would allow for timely initiation of preventive therapy. According to recent studies of ACVR2A gene polymorphism is associated with PE, but it is still unclear whether these findings reflect specific pathogenetic mechanisms of this disease. Methods: We performed targeted next-generation sequencing (NGS) sequencing of ACVR2A gene by means of Ion Torrent Personal Genome machine (PGM) Sequencer. A genetic analysis of patients with PE and control group was performed. Bioinformatics analysis using Polyphen2 (Boston, MA), SIFT (La Jolla, CA), and SnpSift software were used. To select genetic markers in PE patients two additive models and score analysis were applied. Results: Based on the score analysis, we detected two substitutions (rs145399059 and rs17692648) and one insertion insAA at position 148642724 that were associated with PE in our cohorts. We also detected a variant rs17742573 that can be considered as protective against preeclampsia. Conclusions: Our data suggest that some variants in ACVR2A gene are associated with PE. But more studies are required to reveal the role of ACVR2A gene in the pathogenesis of this disease during pregnancy.

De novo mutations in FLNC leading to early-onset restrictive cardiomyopathy and congenital myopathy.

Mutations in FLNC for a long time are known in connection to neuromuscular disorders and only recently were described in association with various cardiomyopathies. Here, we report a new clinical phenotype of filaminopathy in four unrelated patients with early-onset restrictive cardiomyopathy (RCM) in combination with congenital myopathy due to FLNC mutations (NM_001458.4:c.3557C>T, p.A1186V, rs1114167361 in three probands and c.[3547G>C; 3548C>T], p.A1183L, rs1131692185 in one proband). In all cases, concurrent myopathy was confirmed by neurological examination, electromyography, and morphological studies. Three of the patients also presented with arthrogryposis. The pathogenicity of the described missense variants was verified by cellular and morphological studies and by in vivo modeling in zebrafish. Combination of in silico and experimental approaches revealed that FLNC missense variants localized in Ig-loop segments often lead to development of RCM. The described FLNC mutations associated with early-onset RCMP extend cardiac spectrum of filaminopathies and facilitate the differential diagnosis of restrictive cardiac phenotype associated with neuromuscular involvement in children.

Draft Genome Sequence of Coxiella burnetii Historical Strain Leningrad-2, Isolated from Blood of a Patient with Acute Q Fever in Saint Petersburg, Russia.

This is the announcement of a draft genome sequence of Coxiella burnetii strain Leningrad-2, phase I. The strain, which is mildly virulent in infected guinea pigs, was isolated in 1957 from the blood of a patient with acute Q fever in Leningrad (now Saint Petersburg), Russia.

Hydrogel Micro-/Nanosphere Coated by a Lipid Bilayer: Preparation and Microscopic Probing.

The result of polymeric nanogels and lipid vesicles interaction-lipobeads-can be considered as multipurpose containers for future therapeutic applications, such as targeted anticancer chemotherapy with superior tumor response and minimum side effects. In this work, micrometer sized lipobeads were synthesized by two methods: (i) mixing separately prepared microgels made of poly(N-isopropylacrylamide) (PNIPA) and phospholipid vesicles of micrometer or nanometer size and (ii) polymerization within the lipid vesicles. For the first time, a high vacuum scanning electron microscopy was shown to be suitable for a quick validation of the structural organization of wet lipobeads and their constituents without special sample preparation. In particular, the structural difference of microgels prepared by thermal and UV-polymerization in different solvents was revealed and three types of giant liposomes were recognized under high vacuum in conjunction with their size, composition, and method of preparation. Importantly, the substructure of the hydrogel core and multi- and unilamellar constructions of the peripheral lipid part were explicitly distinguished on the SEM images of lipobeads, justifying the spontaneous formation of a lipid bilayer on the surface of microgels and evidencing an energetically favorable structural organization of the hydrogel/lipid bilayer assembly. This key property can facilitate lipobeads' preparation and decrease technological expenses on their scaled production. The comparison of the SEM imaging with the scanning confocal and atomic force microscopies data are also presented in the discussion.

Structural and Thermodynamic Stability of the "1111" Structure Type: A Case Study of the EuFZnPn Series.

Two new compounds with the LaOAgS structure, EuFZnAs (1) and EuFZnSb (2), were obtained via solid state reaction. Both compounds are tetragonal (P4/nmm) with the cell parameters a = 4.1000(1) Šand c = 9.0811(1) Šfor 1 and a = 4.2852(1)Šand c = 9.4238(1)Šfor 2. The absence of their phosphide analog can be explained based on crystal chemical considerations as well as on quantum-chemical estimates of their thermodynamic stability with respect to EuF2 and EuZn2Pn2. The magnetic response of 1 and 2 is ascribed to the presence of Eu2+ ions. Both compounds are paramagnetic down to low temperatures, where they order antiferromagnetically at ∼5 K and ∼3 K, respectively. They are narrow-gap semiconductors, and EuFZnSb demonstrates a relatively high value of the Seebeck coefficient.

MetaFast: fast reference-free graph-based comparison of shotgun metagenomic data.

MOTIVATION: High-throughput metagenomic sequencing has revolutionized our view on the structure and metabolic potential of microbial communities. However, analysis of metagenomic composition is often complicated by the high complexity of the community and the lack of related reference genomic sequences. As a start point for comparative metagenomic analysis, the researchers require efficient means for assessing pairwise similarity of the metagenomes (beta-diversity). A number of approaches were used to address this task, however, most of them have inherent disadvantages that limit their scope of applicability. For instance, the reference-based methods poorly perform on metagenomes from previously unstudied niches, while composition-based methods appear to be too abstract for straightforward interpretation and do not allow to identify the differentially abundant features. RESULTS: We developed MetaFast, an approach that allows to represent a shotgun metagenome from an arbitrary environment as a modified de Bruijn graph consisting of simplified components. For multiple metagenomes, the resulting representation is used to obtain a pairwise similarity matrix. The dimensional structure of the metagenomic components preserved in our algorithm reflects the inherent subspecies-level diversity of microbiota. The method is computationally efficient and especially promising for an analysis of metagenomes from novel environmental niches. AVAILABILITY AND IMPLEMENTATION: Source code and binaries are freely available for download at https://github.com/ctlab/metafast The code is written in Java and is platform independent (tested on Linux and Windows x86_64). CONTACT: ulyantsev@rain.ifmo.ru SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Liposome-Nanogel Structures for Future Pharmaceutical Applications: An Updated Review.

Nature uses combination of lipid bilayers and cross-linked macromolecular networks to achieve workability, multifunctionality, and dynamism in living cells of different types. Despite the concept of liposome-nanogel structures (lipobeads) is known for about 30 years, lipobead-based drug delivery systems are still largely experimental. The data available on nano- and giant lipobeads are reviewed to demonstrate technological achievability of lipobeads and to support the expectations that additional expenses on their production will be reimbursed by the potential advantages of their use. Indeed, lipobeads exhibit the properties attractive for the next generation of drug delivery systems: (i) retaining all the important benefits of polymeric and liposomal drug carriers, the hydrogel core brings mechanical stability and environmental responsiveness to the formulation in one construct, (ii) lipobeaddelivered combination therapy shows no toxicity on intravenously administered mice, accumulation of drug-loaded lipobeads both in the area surrounding tumor and within the tumor itself outside the vasculature, high therapeutic activity at the targeted site, and drastically increased survival, (iii) bipartite structure of lipobeads can provide a number of novel and unique options (e.g., consecutive multistep triggering and combined drug delivery systems). In addition, some ideas on the conceptually new drug delivery systems, new mechanisms of lipobead internalization into the cell and new schemes of drug release regulated by specific signaling are discussed.

Bioactive Flavonoids and Catechols as Hif1 and Nrf2 Protein Stabilizers - Implications for Parkinson's Disease.

Flavonoids are known to trigger the intrinsic genetic adaptive programs to hypoxic or oxidative stress via estrogen receptor engagement or upstream kinase activation. To reveal specific structural requirements for direct stabilization of the transcription factors responsible for triggering the antihypoxic and antioxidant programs, we studied flavones, isoflavones and catechols including dihydroxybenzoate, didox, levodopa, and nordihydroguaiaretic acid (NDGA), using novel luciferase-based reporters specific for the first step in HIF1 or Nrf2 protein stabilization. Distinct structural requirements for either transcription factor stabilization have been found: as expected, these requirements for activation of HIF ODD-luc reporter correlate with in silico binding to HIF prolyl hydroxylase. By contrast, stabilization of Nrf2 requires the presence of 3,4-dihydroxy- (catechol) groups. Thus, only some but not all flavonoids are direct activators of the hypoxic and antioxidant genetic programs. NDGA from the Creosote bush resembles the best flavonoids in their ability to directly stabilize HIF1 and Nrf2 and is superior with respect to LOX inhibition thus favoring this compound over others. Given much higher bioavailability and stability of NDGA than any flavonoid, NDGA has been tested in a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-animal model of Parkinson's Disease and demonstrated neuroprotective effects.

Effect of Transition Metal Substitution on the Structure and Properties of a Clathrate-Like Compound Eu7Cu44As23.

A series of substitutional solid solutions-Eu7Cu44-xTxAs23 (T = Fe, Co, Ni)-based on a recently discovered clathrate-like compound (Eu7Cu44As23) were synthesized from the elements at 800 °C. Almost up to 50% of Cu can be substituted by Ni, resulting in a linear decrease of the cubic unit cell parameter from a = 16.6707(1) Å for the ternary compound to a = 16.3719(1) Å for the sample with the nominal composition Eu7Cu24Ni20As23. In contrast, Co and Fe can only substitute less than 20% of Cu. Crystal structures of six samples of different composition were refined from powder diffraction data. Despite very small differences in scattering powers of Cu, Ni, Co, and Fe, we were able to propose a reasonable model of dopant distribution over copper sites based on the trends in interatomic distances as well as on Mössbauer spectra for the iron-substituted compound Eu7Cu36Fe8As23. Ni doping increases the Curie temperature to 25 K with respect to the parent compound, which is ferromagnetically ordered below 17.5 K, whereas Fe doping suppresses the ferromagnetic ordering in the Eu sublattice.

Synthesis and cation distribution in the new bismuth oxyhalides with the Sillén-Aurivillius intergrowth structures.

About 20 new compounds with the Sillén-Aurivillius intergrowth structure, Me(1)Me(2)Bi3Nb2O11X (Me(1) = Pb, Sr, Ba; Me(2) = Ca, Sr, Ba; X = Cl, Br, I), have been prepared. They are composed of stacking of [ANb2O7] perovskite blocks, fluorite-type [M2O2] blocks and halogen sheets. The cation distribution between the fluorite and perovskite layers has been studied for Ba2Bi3Nb2O11I, Ca1.25Sr0.75Bi3Nb2O11Cl, BaCaBi3Nb2O11Br and Sr2Bi3Nb2O11Cl. The smaller Me cations tend to reside in the perovskite block while the larger ones are situated in the fluorite-type block. The distribution of the elements was confirmed for BaCaBi3Nb2O11Br using energy dispersive X-ray analysis combined with scanning transmission electron microscopy (STEM-EDX). An electron diffraction study of this compound reveals a local symmetry lowering caused by weakly correlated rotation of NbO6 octahedra. Based on our findings, we suggest a new stability criterion for mixed-layer structures, which is that net charges of any two consecutive layers do not compensate for each other and only the whole layer sequence is electroneutral.

High-quality draft genome sequence of a new phytase-producing microorganism Pantoea sp. 3.5.1.

Strain 3.5.1 was isolated from soils of the Republic of Tatarstan, Russia, on the basis of presence of a high phytate-degrading activity. Strains with such activities attract special interest because of its potential use as feed additives and natural manures. Strain 3.5.1 harbors a 99 % 16S rRNA nucleotide sequence similarity to different Pantoea species (P. vagans, P. ananatis, P. agglomerans, P. anthophila and Pantoea sp.) and exhibits unique biochemical properties that do not allow strain identification up to species. Moreover, the strain 3.5.1 shows a low ANI and MALDI-TOF Mass Spectrometry scores. Thus, it is likely that the strain 3.5.1 represents a new Pantoea species. Here, we present the genome sequence of Pantoea sp. strain 3.5.1. The 4,964,649 bp draft genome consists of 23 contigs with 4,556 protein-coding and 143 RNA genes. Genome sequencing and annotation revealed two phytase genes and putative regulatory genes controlling its activity.

Draft Genome Sequence of Bacillus ginsengihumi Strain M2.11 with Phytase Activity.

This paper announces the genome sequence of Bacillus ginsengihumi strain M2.11, which has been characterized as a strain which produces the enzyme with the ability to degrade phytase. The genome of the strain M2.11 is 3.7 Mb and harbors 3,082 coding sequences.

Targeted next-generation sequencing (NGS) of nine candidate genes with custom AmpliSeq in patients and a cardiomyopathy risk group.

BACKGROUND: Hypertrophic cardiomyopathy is a common genetic cardiac disease. Prevention and early diagnosis of this disease are very important. Because of the large number of causative genes and the high rate of mutations involved in the pathogenesis of this disease, traditional methods of early diagnosis are ineffective. METHODS: We developed a custom AmpliSeq panel for NGS sequencing of the coding sequences of ACTC1, MYBPC3, MYH7, MYL2, MYL3, TNNI3, TNNT2, TPM1, and CASQ2. A genetic analysis of student cohorts (with and without cardiomyopathy risk in their medical histories) and patients with cardiomyopathies was performed. For the statistical and bioinformatics analysis, Polyphen2, SIFT, SnpSift and PLINK software were used. To select genetic markers in the patients with cardiomyopathy and in the students of the high risk group, four additive models were applied. RESULTS: Our AmpliSeq custom panel allowed us to efficiently explore targeted sequences. Based on the score analysis, we detected three substitutions in the MYBPC3 and CASQ2 genes and six combinations between loci in the MYBPC3, MYH7 and CASQ2 genes that were responsible for cardiomyopathy risk in our cohorts. We also detected substitutions in the TNNT2 gene that can be considered as protective against cardiomyopathy. CONCLUSION: We used NGS with AmpliSeq libraries and Ion PGM sequencing to develop improved predictive information for patients at risk of cardiomyopathy.

Two new arsenides, Eu7Cu44As23 and Sr7Cu44As23, with a new filled variety of the BaHg11 structure.

Two new ternary arsenides, namely, Eu7Cu44As23 and Sr7Cu44As23, were synthesized from elements at 800 °C. Their crystal structure represents a new filled version of the BaHg11 motif with cubic voids alternately occupied by Eu(Sr) and As atoms, resulting in a 2 × 2 × 2 superstructure of the aristotype: space group Fm3̅m, a = 16.6707(2) Å and 16.7467(2) Å, respectively. The Eu derivative exhibits ferromagnetic ordering below 17.5 K. In agreement with band structure calculations both compounds are metals, exhibiting relatively low thermopower, but high electrical and low thermal conductivity.

Draft Genome Sequence of Serratia grimesii Strain A2.

We report the first draft genome assembly of Serratia grimesii strain A2, previously identified as Escherichia coli strain A2, which produces protease ECP32 with a high specificity toward actin. S. grimesii strain A2 has multidrug resistance associated with a number of efflux pump genes.