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Introduction: Tumor budding (TB) is considered to be a morphological and prognostic factor relevant to colon cancer (CC). The aim of our study is to assess the TB and to evaluate its relationship to clinicopathological findings within stage II and III CC patients as a single center experience.

Many optimization algorithm benchmarking platforms allow users to share their experimental data to promote reproducible and reusable research. However, different platforms use different data models and formats, which drastically complicates the identification of relevant datasets, their interpretation, and their interoperability. Therefore, a semantically rich, ontology-based, machine-readable data model that can be used by different platforms is highly desirable. In this article, we report on the development of such an ontology, which we call OPTION (OPTImization algorithm benchmarking ONtology). Our ontology provides the vocabulary needed for semantic annotation of the core entities involved in the benchmarking process, such as algorithms, problems, and evaluation measures. It also provides means for automatic data integration, improved interoperability, and powerful querying capabilities, thereby increasing the value of the benchmarking data. We demonstrate the utility of OPTION, by annotating and querying a corpus of benchmark performance data from the BBOB collection of the COCO framework and yet another black-box optimization benchmark (YABBOB) family of the Nevergrad environment. In addition, we integrate features of the BBOB functional performance landscape into the OPTION knowledge base (KB) using publicly available datasets with exploratory landscape analysis. Finally, we integrate the OPTION KB into the IOHprofiler environment and provide users with the ability to perform a meta-analysis of performance data.

Peritoneal dialysis (PD) is one of the options for renal replacement therapy (RRT) in the end stage renal disease (ESRD) patients. Compared to hemodialysis (HD), patients on PD experience a greater sense of well-being, an improved steady state in terms of extracellular fluid volume shifts and hemodynamics and it is preferred method for patients with problematic vascular access, bleeding tendencies, heart failure and elderly patients.

Median arcuate ligament syndrome (MALS) is a rare condition that is often overlooked as a result of its nonspecific symptoms. It is usually presented with nausea, bloating, abdominal postprandial pain, and weight loss. The diagnosis of MALS is usually delayed and made by excluding other causes for the symptoms. The diagnosis of this syndrome is based on clinical presentation and radiological findings on computer tomography angiography (CTA) or magnetic resonance angiography (MRA). Surgery is treatment of choice, with promising results from laparoscopic surgery.

Neutralizing agents against SARS-CoV-2 are urgently needed for the treatment and prophylaxis of COVID-19. Here, we present a strategy to rapidly identify and assemble synthetic human variable heavy (VH) domains toward neutralizing epitopes. We constructed a VH-phage library and targeted the angiotensin-converting enzyme 2 (ACE2) binding interface of the SARS-CoV-2 Spike receptor-binding domain (Spike-RBD). Using a masked selection approach, we identified VH binders to two non-overlapping epitopes and further assembled these into multivalent and bi-paratopic formats. These VH constructs showed increased affinity to Spike (up to 600-fold) and neutralization potency (up to 1,400-fold) on pseudotyped SARS-CoV-2 virus when compared to standalone VH domains. The most potent binder, a trivalent VH, neutralized authentic SARS-CoV-2 with a half-maximal inhibitory concentration (IC50) of 4.0?nM (180?ng?ml-1). A cryo-EM structure of the trivalent VH bound to Spike shows each VH domain engaging an RBD at the ACE2 binding site, confirming our original design strategy.

Nanotechnology presents a modern field of science that in the last twenty-five years plays a dominant role in the biomedicine. Different analytical methods are used for evaluation of the physico-chemical properties of nanoparticles including chromatography, electrophoresis, X-ray scattering, spectroscopy, mass spectrometry, zeta potential measurement and microscopy on which this article will focus.

Heterozygous somatic mutations affecting the spliceosome gene SF3B1 drive age-related clonal hematopoiesis, myelodysplastic syndromes (MDS) and other neoplasms. To study their role in such disorders, we generated knock-in mice with hematopoietic-specific expression of Sf3b1-K700E, the commonest type of SF3B1 mutation in MDS. Sf3b1K700E/+animals had impaired erythropoiesis and progressive anemia without ringed sideroblasts, as well as reduced hematopoietic stem cell numbers and host-repopulating fitness. To understand the molecular basis of these observations, we analyzed global RNA splicing in Sf3b1K700E/+hematopoietic cells. Aberrant splicing was associated with the usage of cryptic 3′ splice and branchpoint sites, as described for human SF3B1 mutants. However, we found a little overlap between aberrantly spliced mRNAs in mouse versus human, suggesting that anemia may be a consequence of globally disrupted splicing. Furthermore, the murine orthologues of genes associated with ring sideroblasts in human MDS, including Abcb7 and Tmem14c, were not aberrantly spliced in Sf3b1K700E/+mice. Our findings demonstrate that, despite significant differences in affected transcripts, there is overlap in the phenotypes associated with SF3B1-K700E between human and mouse. Future studies should focus on understanding the basis of these similarities and differences as a means of deciphering the consequences of spliceosome gene mutations in MDS.

ABSTRACTIntraerythrocytic development of the human malaria parasite Plasmodium falciparumappears as a continuous flow through growth and proliferation. To develop a greater understanding of the critical regulatory events, we utilized piggyBacinsertional mutagenesis to randomly disrupt genes. Screening a collection of piggyBacmutants for slow growth, we isolated the attenuated parasite C9, which carried a single insertion disrupting the open reading frame (ORF) of PF3D7_1305500. This gene encodes a protein structurally similar to a mitogen-activated protein kinase (MAPK) phosphatase, except for two notable characteristics that alter the signature motif of the dual-specificity phosphatase domain, suggesting that it may be a low-activity phosphatase or pseudophosphatase. C9 parasites demonstrated a significantly lower growth rate with delayed entry into the S/M phase of the cell cycle, which follows the stage of maximum PF3D7_1305500 expression in intact parasites. Genetic complementation with the full-length PF3D7_1305500 rescued the wild-type phenotype of C9, validating the importance of the putative protein phosphatase PF3D7_1305500 as a regulator of pre-S-phase cell cycle progression in P. falciparum.

Coordinated regulation of gene expression is a hallmark of the Plasmodium falciparum asexual blood-stage development cycle. We report that carbon catabolite repressor protein 4 (CCR4)-associated factor 1 (CAF1) is critical in regulating more than 1,000 genes during malaria parasites' intraerythrocytic stages, especially egress and invasion proteins. CAF1 knockout results in mistimed expression, aberrant accumulation and localization of proteins involved in parasite egress, and invasion of new host cells, leading to premature release of predominantly half-finished merozoites, drastically reducing the intraerythrocytic growth rate of the parasite. This study demonstrates that CAF1 of the CCR4-Not complex is a significant gene regulatory mechanism needed for Plasmodium development within the human host.

ABSTRACTCoordinated regulation of gene expression is a hallmark of the Plasmodium falciparumasexual blood-stage development cycle. We report that carbon catabolite repressor protein 4 (CCR4)-associated factor 1 (CAF1) is critical in regulating more than 1,000 genes during malaria parasites' intraerythrocytic stages, especially egress and invasion proteins. CAF1 knockout results in mistimed expression, aberrant accumulation and localization of proteins involved in parasite egress, and invasion of new host cells, leading to premature release of predominantly half-finished merozoites, drastically reducing the intraerythrocytic growth rate of the parasite. This study demonstrates that CAF1 of the CCR4-Not complex is a significant gene regulatory mechanism needed for Plasmodiumdevelopment within the human host.

The family of AZARYPHOS (aza–aryl–phosphane) phosphane ligands, containing a phosphine unit and sterically shielded nitrogen lone pairs in the ligand periphery, is introduced as a tool for developing ambifunctional catalysis by the metal center and nitrogen lone pairs in the ligand sphere. General synthetic strategies have been developed to synthesize over 25 examples of structurally diverse (6‐aryl‐2‐pyridyl)phosphanes (ARPYPHOS), (6‐alkyl‐2‐pyridyl)phosphanes (ALPYPHOS), 4,6‐disubsituted 1,3‐diazin‐2‐ylphosphanes or 1,3,5‐triazin‐2‐ylphosphanes, quinazolinylphosphanes, quinolinylphosphanes, and others. The scalable syntheses proceed in a few steps. The incorporation of AZARYPHOS ligands (L) into complexes [RuCp(L)2(MeCN)][PF6] (Cp=cyclopentadienyl) gives catalysts for the anti‐Markovnikov hydration of terminal alkynes of the highest known activities. Electronic and steric ligand effects modulate the reaction kinetics over a range of two orders of magnitude. These results highlight the importance of using structurally diverse ligand families in the process of developing cooperative ambifunctional catalysis by a metal and its ligand.

AbstractSome of the most valuable frescoes in the world can be found in the churches and monasteries in the Republic of Macedonia. Painted mostly in the Byzantine (eleventh to fifteenth centuries) and post-Byzantine periods (fifteenth to eighteenth centuries), these frescoes are now under threat, presumably due to the fact that the original roofs covering the churches were replaced by modern ones. The new roofs, made of aggressive materials such as cement mortar and reinforced concrete, have very low air permeability and do not allow sufficient drying of the fresco layers during the humid periods in winter and cause over-drying of the fresco layers during the hot and dry summer periods. This phenomenon is believed to be the main cause for the frescoes' degradation.This study examines some recent interventions to Macedonian church buildings and what appears to be consequential damage to the fresco paintings, which in some cases is already irreversible. It also proposes possible approaches which could help to save this important element of world heritage and preserve it for posterity.

Unlike other types of cancer, tumors of the breast are greatly influenced by steroid hormones. The effect of estrogen and progesterone depends on the presence of their specific receptors and these constitute important parameters in determining the aggressiveness of the tumor, the feasibility of certain therapies and the prediction of relapse. The molecular mechanisms of steroid hormone action have not been fully elucidated but recent findings implicate the nitric oxide (NO) pathway in some of these effects. Both hormones can regulate the nitric oxide synthases (NOS) and, in turn, the NO produced has profound consequences on tumor cell homeostasis. On one hand, estrogen increases the activity of endothelial NOS (eNOS or NOSIII), while progesterone activates inducible NOS (iNOS or NOSII) expression. The data presented suggest that the low levels of NO produced by NOSIII mediate the proliferative effect of estrogen. On the other hand, the increase in apoptosis in response to progesterone could implicate the high levels of NO produced by induction of NOSII expression. Understanding of the mechanisms and interactions of steroid hormones with the NO pathway could lead to the development of new approaches and strategies for the effective treatment of breast cancer.

Electrical excitability in neurons depends on the expression and activity of voltage-gated sodium channels in the neuronal plasma membrane. The ion-conducting α-subunit of the channel is associated with auxiliary β-subunits of which there are four known types. In the present study, we describe the first detailed structure/function analysis of the β3-subunit. We correlate the effect of point mutations and deletions in β3 with the functional properties of the sodium channel and its membrane-targeting behaviour. We show that the extracellular domain influences sodium channel gating properties, but is not required for the delivery of β3 to the plasma membrane when expressed with the α-subunit. In contrast, the intracellular domain is essential for correct subunit targeting. Our results reveal the crucial importance of the Cys21–Cys96 disulphide bond in maintaining the functionally correct β3 structure and establish a role for a second putative disulphide bond (Cys2–Cys24) in modulating channel inactivation kinetics. Surprisingly, our results imply that the wild-type β3 molecule can traverse the secretory pathway independently of the α-subunit.

Abstract: The crystal structure of tripotassium trisaccharinate dihydrate, K3(C7H4NO3S)32H2O, is triclic, space group $$P \bar 1, Z = 2$$ . It consists of three crystallographically independent potassium and saccharinato ions as well as two structurally different water molecules. Potassium coordination polyhedra are irregular, with K1 and K3 six-coordinated and the third one K2 seven-coordinated. The K-O distances range from 2.652(9) to 3.100(2) (mean: 2.790 ) whereas the K-N distance is 3.025(3) . The water molecules W2 is disordered over three positions with occupancies of approximately 0.6, 0.2 and 0.2. The hydrogen atom (H1W1) of the ordered water molecule (O1W) is hydrogen bonded to the sulfonyl oxygen atom (O11) (R(O...O)=2.976(3) ), whereas the other hydrogen atom (H2W1) is bifurcated to the carbonyl oxygen atom (O13) (R(O...O)=2.851(3) ) and the disordered water molecules (O23W) (R(O...O)=3.067(12) ). The carbonyl oxygens (O13, O23 and O33) and one of the disordered water molecules (O22W) are involved in C-H...O hydrogen bonds (R(C-H...O)=3.027(4)–3.304(9) ). Structural characteristics of the studied compound are compared with the analogous trisodium trisaccharinate dihydrate and dipotassium sodium trisaccharinate monohydrate. Infrared and Raman spectra of the title compound have been analyzed in relation to the structure, and compared with the spectra of trisodium trisaccharinate dihydrate.

The structures of saccharinates retrieved from the Cambridge Structural Database were used to discuss the coordination propcrties of deprotonated saccharin. The series of the first-row metal(II) saccharinato isomorphs and of tnphenylstannyl sacchainates were analyzed within the bond valence model (BVM). The "relative radius" parameter of the saccharinato ligand for the M(Ow)4(Nsac)2 type of coordination was estimated (1.424 Å) from correlation of the metal-N(saccharinato) distances with the Shannon-Prewitt ionic radii.Making use of the exponential bond distance-bond order (BDBO) relation of Pauling within the BVM, ligand-specific mean bond order sums (MBOS) were recently derived for several ligands. Coupled with the coordination number (CN), they are predictive for the metal-ligand bond lengths. Using parameterized power function instead of the exponential form of the BDBO relation, a new set of MBOS's is derived here: isothiocyanate 2.56 ± 0.06; pyridine 1.84 ± 0.16; imidazole 2.02 ± 0.12; chloride 2.05 ± 0.10; water 1.54 ± 0.03. The two sets of MBOS values can be used to predict the metal-ligand distances nearly equally well, showing that the distances are solely predetermined by the MBOS and CN values, independently of the particular form of BDBO relation used.

We report the first observation of bound-state proximity resonances in coupled dielectric resonators. The proximity resonances arise from the combined action of symmetry and dissipation. We argue that the large ratio between the widths is a distinctive signature of the multidimensional nature of the system. Our experiments shed light on the properties of 2D tunneling in the presence of a dissipative environment.

ABSTRACTNumerous neutralizing antibodies that target SARS-CoV-2 have been reported, and most directly block binding of the viral Spike receptor-binding domain (RBD) to angiotensin-converting enzyme II (ACE2). Here, we deliberately exploit non-neutralizing RBD antibodies, showing they can dramatically assist in neutralization when linked to neutralizing binders. We identified antigen-binding fragments (Fabs) by phage display that bind RBD, but do not block ACE2 or neutralize virus as IgGs. When these non-neutralizing Fabs were assembled into bispecific VH/Fab IgGs with a neutralizing VH domain, we observed a ~ 25-fold potency improvement in neutralizing SARS-CoV-2 compared to the mono-specific bi-valent VH-Fc alone or the cocktail of the VH-Fc and IgG. This effect was epitope-dependent, reflecting the unique geometry of the bispecific antibody toward Spike. Our results show that a bispecific antibody that combines both neutralizing and non-neutralizing epitopes on Spike-RBD is a promising and rapid engineering strategy to improve the potency of SARS-CoV-2 antibodies.

The human inducible nitric oxide synthase (iNOS or NOSII) gene is regulated through an extended and complex promoter. In this study, the transcriptional regulation of human NOSII is investigated in the human colon cell line HCT‐8R. Stimulation with a cytokine mix (interferon‐γ, interleukin 1‐β, and tumor necrosis factor α) induces NOSII mRNA accumulation, as well as promoter activity in these cells. Several random deletions were performed within the proximal 7 kb of the promoter, which led to the identification of a region, whose deletion provokes a marked increase in transcriptional activity upon cytokine stimulation. Furthermore, this region is shown to repress a viral‐driven luciferase construct, mainly at basal levels. An AP‐1‐like sequence present in this region that is specifically recognized by nuclear proteins is shown to be involved in the repressive effect. This element is capable of repressing a viral promoter, and its deletion augments cytokine‐stimulated transcription. These findings are confirmed in various cell lines and suggest a general mechanism for the control of basal levels of NOSII expression, to avoid unnecessary toxicity under normal conditions.

There is considerable interest in determining the conditions leading to enhanced inducible nitric oxide synthase (iNOS) gene expression and nitric oxide (NO) biosynthesis. Using in vivofootprinting, we demonstrate that heat shock of murine macrophages concurrent with lipopolysaccharide (LPS) treatment stimulated changes in guanine methylation sensitivity at ‐898/9, at a putative partial heat shock element (HSE) and at ‐893/4, a site bordering an E‐box, within the iNOS gene enhancer, suggesting inducible occupation by transcription factors at these regions. LPS treatment accompanied by heat shock provoked increased iNOS gene transcription, increased levels of iNOS protein, and increased production of NO compared with LPS treatment alone. Electrophoretic mobility shift analysis revealed low constitutive levels of specific binding to an E‐box and a partial HSE within the iNOS enhancer. Binding to the E‐box was increased by LPS treatment or by heat shock, achieving a greater increase by a combination of both treatments. The proteins occupying this site were identified as belonging to the USF family of transcription factors. Heat shock or LPS increased binding to the HSE, and the factor responsible for this interaction was identified as heat shock factor‐1 (HSF‐1). Mutations at the HSE revealed the importance of HSF‐1 in the induction of iNOS by LPS. Thus, our data reveal two novel regulatory sites in the murine iNOS gene, one of which is implicated in enhancing iNOS expression via LPS stimulation, and provide the first evidence that heat shock enhances transcription of the iNOS gene. These results could have implications in the host response mechanism to fever‐associated gram‐negative infection.

The title compound, C10H9NO2Se, crystallizes as flat mol­ecules linked by selenium–oxy­gen interactions [Se⃛O = 3.189 (4) Å] into a linear chain along the aaxis of the triclinic cell. The bond dimensions that are derived from ab initiogeometry optimization calculations are similar to those determined from the diffraction measurements.

This month’s Genome Watch explores the genetic variability of the anti-malaria vaccine protein and discusses its significance for an efficacious intervention.

This month’s Genome Watch highlights discoveries of high variability in the genes underlying cytoplasmic incompatibility among Wolbachiastrains that help identify the best strains to use for the control of vector-borne diseases such as Zika virus and malaria.

In the title compound (5‐fluoro­isatin), C8H4FNO2, the N atom of one mol­ecule is linked to the amido‐O atom of an adjacent mol­ecule across a center of symmetry by a cyclic hydrogen bond [N⃛O = 2.888 (4) Å].

In the title compound, [Ni(C2H3O)2(C3H4N2)4], the Ni atom is coordinated centrosymmetrically by four N and two O atoms in an octahedral coordination [Ni—N = 1.986 (3) and 2.054 (3) Å; Ni—O = 2.697 (3) Å]. The O atoms of the acetate anions form hydrogen bonds to adjacent imidazole moieties, with the free O atom forming a somewhat shorter bond [N⃛O = 2.679 (3) and 2.870 (4) Å]. The hydrogen bonds give rise to a two‐dimensional layer structure.

Bis(N,N‐di­methyl­thio­carbamoyl­thio)­acetic acid, [(CH3)2NC(=S)S]2CHC(=O)OH or C8H14N2O2S4, exists as a centrosymmetric hydrogen‐bonded dimer [O⋯O 2.661 (3) Å].

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.

ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.