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N Kalkkinen

Publications and source records attributed to N Kalkkinen.

At least 37 records · Page 2Linked to original sources

matB, a common fimbrillin gene of Escherichia coli, expressed in a genetically conserved, virulent clonal group.

A novel fimbrial type in Escherichia coli was identified and characterized. The expression of the fimbria was associated with the O18acK1H7 clonal group of E. coli, which cause newborn meningitis and septicemia when grown at low temperature; hence, it was named the Mat (meningitis associated and temperature regulated) fimbria. The fimbriae were purified from a fimA::cat sfaA::Gm fliC::St derivative of the O18K1H7 isolate E. coli IHE 3034. The purified Mat fimbrillin had an apparent molecular mass of 18 kDa and did not serologically cross-react with the type 1 or S fimbria of the same strain. The matB gene encoding the major fimbrillin was cloned from the genomic DNA of the fimA::cat sfaA::Gm fliC::St derivative of IHE 3034. The predicted MatB sequence was of 195 amino acids, contained a signal sequence of 22 residues, and did not show significant homology to any of the previously characterized fimbrial proteins. The DNA sequence of matB was 97.8% identical to a region from nucleotides 17882 to 18469 in the 6- to 8-min region of the E. coli K-12 chromosome, reported to encode a hypothetical protein. The 7-kb DNA fragment containing matB of IHE 3034 was found by restriction mapping and partial DNA sequencing to be highly similar to the corresponding region in the K-12 chromosome. Trans complementation of the matB::cat mutation in the IHE 3034 chromosome showed that matB in combination with matA or matC restored surface expression of the Mat fimbria. A total of 27 isolates representing K-12 strains and the major pathogroups of E. coli were analyzed for the presence of a matB homolog as well as for expression of the Mat fimbria. A conserved matB homolog was found in 25 isolates; however, expression of the Mat fimbriae was detected only in the O18acK1H7 isolates. Expression of the Mat fimbria was temperature regulated, with no or a very small amount of fimbriae or intracellular MatB fimbrillin being detected in cells cultivated at 37(o)C. Reverse transcriptase PCR and complementation assays with mat genes controlled by the inducible trc promoter indicated that regulation of Mat fimbria expression involved both transcriptional and posttranscriptional events.

Amino Acid Sequence↗

The gaf fimbrial gene cluster of Escherichia coli expresses a full-size and a truncated soluble adhesin protein.

The GafD lectin of the G (F17) fimbriae of diarrhea-associated Escherichia coli was overexpressed and purified from the periplasm of E. coli by affinity chromatography on GlcNAc-agarose. The predicted mature GafD peptide comprises 321 amino acids, but the predominant form of GafD recovered from the periplasm was 19,092 Da in size and corresponded to the 178 N-terminal amino acid residues, as judged by mass spectrometry and amino acid sequencing, and was named DeltaGafD. Expression of gafD from the cloned gaf gene cluster in DegP-, Lon-, and OmpT-deficient recombinant strains did not significantly decrease the formation of DeltaGafD. The peptide was also detected in the periplasm of the wild-type E. coli strain from which the gaf gene cluster originally was cloned. We expressed gafD fragments encoding C-terminally truncated peptides. Peptides GafD1-252, GafD1-224, GafD1-189, and the GafD1-178, isolated from the periplasm by affinity chromatography, had apparent sizes closely similar to that of DeltaGafD. Only trace amounts of truncated forms with expected molecular sizes were detected in spheroplasts. In contrast, the shorter GafD1-157 peptide was detected in spheroplasts but not in the periplasm, indicating that it was poorly translocated or was degraded by periplasmic proteases. Pulse-chase assays using gafD indicated that DeltaGafD was processed from GafD and is not a primary translation product. The DeltaGafD peptide was soluble by biochemical criteria and exhibited specific binding to GlcNAc-agarose. Inhibition assays with mono- and oligosaccharides gave a similar inhibition pattern in the hemagglutination by the G-fimbria-expressing recombinant E. coli strain and in the binding of [(14)C]DeltaGafD to GlcNAc-agarose. DeltaGafD bound specifically to laminin, a previously described tissue target for the G fimbria. Our results show that a soluble, protease-resistant subdomain of GafD exhibits receptor-binding specificity similar to that for intact G fimbriae and that it is formed when gafD is expressed alone or from the gaf gene cluster.

Acetylglucosamine↗

Increased levels of IgA antibodies against desmin in children with coeliac disease.

BACKGROUND: In addition to IgA anti-endomysial antibodies, IgA anti-smooth muscle antibodies have been observed in a number of patients with coeliac disease (CoD), but only limited data exist on the frequency and antigen specificity of IgA against cytoskeletal proteins in CoD. METHODS: We evaluated the sera of 42 untreated CoD patients, follow-up sera of 26 CoD patients after treatment, and 116 control sera for IgA reactivity to cytoskeletal proteins from the human umbilical cord (HUC) by immunoblotting, and compared the results with anti-tissue transglutaminase IgA (anti-tTG IgA) ELISA and immunofluorescence results. RESULTS: Serum IgA from CoD patients most frequently recognized a 57-kD antigen in HUC cytoskeletal extract, identified as desmin using mass spectrometry and internal peptide sequencing. Increased IgA reactivity to the human desmin band was detected in 22 children with untreated CoD (52.4%), in 4 treated CoD patients (15.4%), and in 12 control subjects (10.3%) (p < 0.01); similar results were obtained with anti-chicken desmin IgA ELISA. Anti-tTG IgA levels (increased in 71.4% of untreated CoD patients) correlated significantly with anti-desmin IgA levels in untreated CoD, and both autoantibody reactivities decreased in response to a gluten-free diet. Pre-adsorption experiments and affinity purification of anti-desmin IgA antibodies further confirmed that desmin is an IgA autoantigen in CoD and is recognized by antibodies which are not cross-reactive with tTG. CONCLUSIONS: Anti-desmin IgA antibodies are frequently occurring if not the predominant cytoskeletal antibodies in children with untreated CoD and could be related to the disease process in the small intestine.

Adolescent↗

In mouse alpha -methylacyl-CoA racemase, the same gene product is simultaneously located in mitochondria and peroxisomes.

alpha-Methylacyl-CoA racemase, an enzyme of the bile acid biosynthesis and branched chain fatty acid degradation pathway, was studied at the protein, cDNA, and genomic levels in mouse liver. Immunoelectron microscopy and subcellular fractionation located racemase to mitochondria and peroxisomes. The enzymes were purified from both organelles with immunoaffinity chromatography. The isolated proteins were of the same size, with identical N-terminal amino acid sequences, and the existence of additional proteins with alpha-methylacyl-CoA racemase activity was excluded. A racemase gene of about 15 kilobases was isolated. Southern blot analysis and chromosomal localization showed that only one racemase gene is present, on chromosome 15, region 15B1. The putative initial ATG in the racemase gene was preceded by a functional promotor as shown with the luciferase reporter gene assay. The corresponding cDNAs were isolated from rat and mouse liver. The recombinant rat protein was overexpressed in active form in Pichia pastoris. The presented data suggest that the polypeptide encoded by the racemase gene can alternatively be targeted to peroxisomes or mitochondria without modifications. It is concluded that the noncleavable N-terminal sequence of the polypeptide acts as a weak mitochondrial and that the C-terminal sequence acts as a peroxisomal targeting signal.

Amino Acid Sequence↗

IgE reactivity to patatin-like latex allergen, Hev b 7, and to patatin of potato tuber, Sol t 1, in adults and children allergic to natural rubber latex.

BACKGROUND: Patients allergic to natural rubber latex (NRL) frequently show positive skin prick tests (SPT) and hypersensitivity reactions to various fruits, such as avocado, banana, and kiwi, as well as to vegetables such as potato. METHODS: Hev b 7 was purified from NRL "C-serum" and Sol t 1 from potato extract, and they were detected by immunoblotting. IgE antibodies to Hev b 7 and Sol t 1 were measured with ELISA in sera from 35 adults and 35 children allergic to NRL. ELISA inhibition and immunoblotting were used to study allergen cross-reactivity. The in vivo reactivity of Hev b 7 and Sol t 1 were demonstrated in the SPT. RESULTS: Seventeen (49%) of the 35 NRL-allergic adults had IgE antibodies to Hev b 7, in contrast to only one of the 35 NRL-allergic children. Fifteen (43%) of the NRL-allergic adults and 29 (83%) of the NRL-allergic children had IgE antibodies to Sol t 1. Ten (29%) of the adult sera showed IgE binding to both Sol t 1 and Hev b 7, and crosswise inhibition tests with pooled sera revealed marked cross-reactivity. In the SPT, both natural Hev b 7 and Sol t 1 were able to produce a wheal and flare reaction. CONCLUSIONS: One-half of the NRL-allergic adults, but only one of the NRL-allergic children, had IgE antibodies to natural Hev b 7. These results suggest that Hev b 7 is an important NRL allergen for adults, but not for children. Elucidation of the clinical importance of the observed cross-reactivity between Hev b 7 and Sol t 1 requires further studies.

Adolescent↗

Endoxylanase II from Trichoderma reesei has several isoforms with different isoelectric points.

Two minor xylanases present in Trichoderma reesei Rut C30 cultivation broth were purified as a mixture using ion-exchange, hydrophobic-interaction and gel chromatography. The purified enzyme preparation contained two active xylanases with pI values of 7.1 and 8.1. Both components had a molecular mass of 20 kDa. The purified xylanase preparation exhibited properties very similar to those of the previously isolated XYL II (pI 9.0) of T. reesei Rut C30. The activity and stability properties, apparent kinetic parameters as well as the titration curve forms were similar. The major difference in enzymic properties was the significantly lower specific activity of the pI-7.1+8.1 xylanase mixture (3350 nkat/mg) compared with the specific activity of XYL II (13500 nkat/mg). Amino acid sequences of tryptic peptides (34% of the total amino acid sequence was determined) were identical to the amino acid sequence of XYL II. Furthermore, in vitro modification of the pI-9.0 form of XYL II to pI-8.1 and pI-7.1 forms was demonstrated. Thus the purified xylanase preparation most probably contained two modified forms of XYL II. The primary amino acid sequence of XYL II contains 28 glutamine and asparagine residues and theoretically deamination of one of them lowers the pI to 8.06 and deamination of two amino acids lowers the pI to 7.02.

Amino Acid Sequence↗

Proteome analysis reveals ubiquitin-conjugating enzymes to be a new family of interferon-alpha-regulated genes.

Interferon (IFN)-alpha is a cytokine with antiviral, antiproliferative, and immunomodulatory properties, the functions of which are mediated via IFN-induced protein products. We used metabolic labeling and two-dimensional gel electrophoresis followed by MS and database searches to identify potentially new IFN-alpha-induced proteins in human T cells. By this analysis, we showed that IFN-alpha induces the expression of ubiquitin cross-reactive protein (ISG15) and two ubiquitin-conjugating enzymes, UbcH5 and UbcH8. Northern-blot analysis showed that IFN-alpha rapidly enhances mRNA expression of UbcH5, UbcH6 and UbcH8 in T cells. In addition, these genes were induced in macrophages in response to IFN-alpha or IFN-gamma stimulation or influenza A or Sendai virus infections. Similarly, IFNs enhanced UbcH8 mRNA expression in A549 lung epithelial cells, HepG2 hepatoma cells, and NK-92 cells. Cycloheximide, a protein synthesis inhibitor, did not block IFN-induced upregulation of UbcH8 mRNA expression, suggesting that UbcH8 is the primary target gene for IFN-alpha and IFN-gamma. Ubiquitin conjugation is a rate-limiting step in antigen presentation and therefore the upregulation of UbcHs by IFNs may contribute to the enhanced antigen presentation by macrophages. Our results show that proteome analysis of cells is a suitable method for identifying previously unrecognized cytokine-inducible genes.

Cells, Cultured↗

Identification of foetal brain proteins by two-dimensional gel electrophoresis and mass spectrometry comparison of samples from individuals with or without chromosome 21 trisomy.

Protein expression in foetal brain with or without chromosome 21 trisomy (Down's syndrome) was analyzed by two-dimensional gel electrophoresis and mass spectrometry. Data generated by in-gel digestion and matrix-assisted laser desorption/ionization mass spectrometry allowed identification of 40 proteins. Most of these are common to syndrome and healthy subjects and represent different types of protein. However, a few proteins, identified as truncated structural proteins (tubulin, actin), were present in part of the trisomy samples but absent from the controls. This is interpreted to indicate increased proteolysis in the syndrome samples but could also reflect some altered expression or processing. Independent of the apparently increased proteolysis in the syndrome samples, and in spite of the use of total brain tissues, the results show that two-dimensional protein separation patterns are largely similar between the syndrome and control samples upon silver-staining, but that differences associated with structural components can be detected and identified.

Brain↗

Molecular epidemiology of coxsackievirus B4 and disclosure of the correct VP1/2A(pro) cleavage site: evidence for high genomic diversity and long-term endemicity of distinct genotypes.

Genetic diversity among 107 coxsackievirus B4 field isolates has been studied. These isolates included clinical and environmental isolates originating from Finland, the Netherlands and France, and also from several other countries, including the USA. Three genomic regions were used for phylogenetic analyses: the VP1/2A junction, the entire VP1 and the VP4/VP2 region. Alignment of the deduced amino acid sequence in the VP1/2A junction revealed extensive sequence variation at the previously proposed cleavage site. MS analysis of proteolytic fragments from VP1 revealed that the exact cleavage site is situated between amino acid residues Thr-849 and Gly-850. At least seven distinct genetic lineages, or genotypes, had been circulating in Europe during the period 1959-1998. Two genotypes were endemic in the Netherlands during most of the investigated period. Genetically closely related strains could be found in different countries, and different genotypes co-circulated at the same time in a given country. Clustering patterns were identical in the three genomic intervals. In the VP4/VP2 region, the intraserotypic variation approached interserotype variation. Sequence comparisons of the entire VP1 gene gave a reliable genetic identification of enterovirus serotype. It is suggested that, for genotype classification of previously serotyped coxsackievirus B4 isolates, comparison of VP1/2A sequences is sufficient, but for more detailed investigation of genetic relationships, and for 'genetic serotyping', the entire VP1 gene should be used. The VP4/VP2 region is less reliable for genetic serotyping and genotyping, although the primers are able to amplify many different serotypes.

Amino Acid Sequence↗

Characterization of the collagen-binding S-layer protein CbsA of Lactobacillus crispatus.

The cbsA gene of Lactobacillus crispatus strain JCM 5810, encoding a protein that mediates adhesiveness to collagens, was characterized and expressed in Escherichia coli. The cbsA open reading frame encoded a signal sequence of 30 amino acids and a mature polypeptide of 410 amino acids with typical features of a bacterial S-layer protein. The cbsA gene product was expressed as a His tag fusion protein, purified by affinity chromatography, and shown to bind solubilized as well as immobilized type I and IV collagens. Three other Lactobacillus S-layer proteins, SlpA, CbsB, and SlpnB, bound collagens only weakly, and sequence comparisons of CbsA with these S-layer proteins were used to select sites in cbsA where deletions and mutations were introduced. In addition, hybrid S-layer proteins that contained the N or the C terminus from CbsA, SlpA, or SlpnB as well as N- and C-terminally truncated peptides from CbsA were constructed by gene fusion. Analysis of these molecules revealed the major collagen-binding region within the N-terminal 287 residues and a weaker type I collagen-binding region in the C terminus of the CbsA molecule. The mutated or hybrid CbsA molecules and peptides that failed to polymerize into a periodic S-layer did not bind collagens, suggesting that the crystal structure with a regular array is optimal for expression of collagen binding by CbsA. Strain JCM 5810 was found to contain another S-layer gene termed cbsB that was 44% identical in sequence to cbsA. RNA analysis showed that cbsA, but not cbsB, was transcribed under laboratory conditions. S-layer-protein-expressing cells of strain JCM 5810 adhered to collagen-containing regions in the chicken colon, suggesting that CbsA-mediated collagen binding represents a true tissue adherence property of L. crispatus.

Amino Acid Sequence↗

A novel function for a ubiquitous plant enzyme pectin methylesterase: the host-cell receptor for the tobacco mosaic virus movement protein.

Plant virus-encoded movement proteins promote viral spread between plant cells via plasmodesmata. The movement is assumed to require a plasmodesmata targeting signal to interact with still unidentified host factors presumably located on plasmodesmata and cell walls. The present work indicates that a ubiquitous cell wall-associated plant enzyme pectin methylesterase of Nicotiana tabacum L. specifically binds to the movement protein encoded by tobacco mosaic virus. We also show that pectin methylesterase is an RNA binding protein. These data suggest that pectin methylesterase is a host cell receptor involved in cell-to-cell movement of tobacco mosaic virus.

Base Sequence↗

Purification and protein composition of PM2, the first lipid-containing bacterial virus to be isolated.

The marine, icosahedral bacteriophage PM2 was isolated in the late 1960s. It was the first phage for which lipids were firmly demonstrated to be part of the virion structure and it has been classified as the type organism of the Corticoviridae family. The host, Pseudoalteromonas espejiana BAL-31, belongs to a common group of marine bacteria. We developed a purification method producing virions with specific infectivity approximately as high as that of the lipid-containing phages PRD1 and &phi;6. The sensitivity of the virus to normally used purification media such as those containing sucrose is demonstrated. We also present an alternative host, a pseudoalteromonad, that allows enhanced purification of the virus under reduced salt conditions. We show, using N-terminal amino acid sequencing and comparison with the genomic sequence, that there are at least eight structural proteins in the infectious virus.

Amino Acid Sequence↗

Matrix metalloproteinases-3, -7, and -12, but not -9, reduce high density lipoprotein-induced cholesterol efflux from human macrophage foam cells by truncation of the carboxyl terminus of apolipoprotein A-I. Parallel losses of pre-beta particles and the high affinity component of efflux.

Matrix metalloproteinases (MMPs) have been suggested to function in remodeling of the arterial wall, but no information is available on their possible role in early atherogenesis, when cholesterol accumulates in the cells of the arterial intima, forming foam cells. Here, we incubated the major component responsible for efflux of cholesterol from foam cells, high density lipoprotein 3 (HDL(3)), with MMP-1, -3, -7, -9, or -12 at 37 degrees C before adding it to cholesterol-loaded human monocyte-derived macrophages. After incubation with MMP-3, -7, or -12, the ability of HDL(3) to induce the high affinity component of cholesterol efflux from the macrophage foam cells was strongly reduced, whereas preincubation with MMP-1 reduced cholesterol efflux only slightly and preincubation with MMP-9 had no effect. These differential effects of the various MMPs were reflected in their differential abilities to degrade the small pre-beta migrating particles present in the HDL(3) fraction. NH(2)-terminal sequence and mass spectrometric analyses of the apolipoprotein (apo) A-I fragments generated by MMPs revealed that those MMPs that strongly reduced cholesterol efflux (MMPs-3, -7, and -12) cleaved the COOH-terminal region of apoA-I and produced a major fragment of about 22 kDa, whereas MMPs-1 and -9, which had little and no effect on cholesterol efflux, degraded apoA-I only slightly and not at all, respectively. These results show, for the first time, that some members of the MMP family can degrade the apoA-I of HDL(3), so blocking cholesterol efflux from macrophage foam cells. This expansion of the substrate repertoire of MMPs to include apoA suggests that these proteinases are directly involved in the accumulation of cholesterol in atherosclerotic lesions.

Apolipoprotein A-I↗

Analysis of the multimeric state of proteins by matrix assisted laser desorption/ionization mass spectrometry after cross-linking with glutaraldehyde.

We have undertaken a systematic study on the suitability of matrix-assisted laser desorption/ionization mass spectrometry to analyze and determine the multimericity of several proteins after cross-linking with glutaraldehyde. Using both commercially available proteins and others of viral origin currently being characterized in our laboratory, we studied the range of concentrations of cross-linker and protein for optimal analysis. Under the conditions developed during this study, we confirmed the multimeric states of three phage PRD1 structural proteins with monomeric masses ranging from 13.5 to 63 kDa. In addition, we addressed the question of the general applicability of the method by using it successfully to confirm the stoichiometry of the heptameric chaperonin GroEL, a bacterial protein with a mass well over 450 kDa.

Animals↗

Avidin is a promising tag for fusion proteins produced in baculovirus-infected insect cells.

The baculovirus expression vector system (BEVS) has become one of the most versatile and powerful eukaryotic systems for recombinant protein expression. We have constructed a novel baculovirus transfer vector (pbacAVs+C) which allows for the efficient production, detection, and single-step purification of the desired molecule as a secretion-compatible avidin fusion protein in insect cells. It also enables fast construction of the baculoviruses by site-specific transposition in Escherichia coli. To demonstrate the power of this vector, we report here on the production of immunologically intact hevein, a major cysteine-rich latex allergen, as avidin fusion protein. Our results indicate that avidin is a stable and versatile tag in the BEVS. It retains its extraordinarily high biotin-binding activity and also enables independent folding of the fusion partner. The versatility with which avidin fusion proteins can be detected, purified, and immobilized is the basis for the use of our system as a useful alternative in eukaryotic fusion protein production.

Amino Acid Sequence↗

Increased allergen production in turnip (Brassica rapa) by treatments activating defense mechanisms.

BACKGROUND: Practical applications to enhance the productivity of agriculture by using plants with improved resistance to pathogens are expected to increase in the near future. Defense proteins play an important role in pathogen resistance, and some defense-related proteins are significant cross-reacting allergens. For example, cross-allergies are common among patients allergic to natural rubber latex (NRL), which contains many defense-related proteins. OBJECTIVE: Using a model plant (ie, turnip), we studied whether allergen contents increase after treatments activating defense mechanisms of the plants. METHODS: Whole or wounded turnips treated with salicylic acid, ethephon, or water were incubated for 2, 4, or 8 days. Allergen content was investigated by IgE immunoblotting with sera from patients allergic to NRL. An induced protein that bound IgE most intensively was purified and further characterized by mass analysis, amino acid sequencing, IgE-ELISA, and skin prick tests. RESULTS: In immunoblotting, clear IgE-binding bands were discernible only in samples from chemically treated plants. IgE was bound most intensively to a protein with an apparent molecular weight of 25 kd in SDS-PAGE and with a determined molecular weight of 18.7 kd. Sequenced peptides of the 18.7-kd protein showed over 70% homology to prohevein, a major allergen of NRL, and to many other prohevein-like defense proteins. In ELISA, sera from 30 of 34 (88%) adults and 21 of 26 (81%) children previously shown to have IgE against prohevein bound to the purified protein. In skin prick testing with the protein, 4 of 6 patients allergic to NRL had positive reactions. CONCLUSION: These results demonstrate that activating defense mechanisms of plants may considerably increase their allergen content.

Adult↗

A novel wheat gliadin as a cause of exercise-induced anaphylaxis.

BACKGROUND: Food-dependent, exercise-induced anaphylaxis is a severe form of allergy; the reaction is caused by ingestion of a specific food before exercise. This disorder often escapes diagnosis because neither the ingested food nor the exercise alone induces the symptoms. OBJECTIVE: The aim of the study was to characterize the allergens involved in wheat-dependent, exercise-induced anaphylaxis and to describe the clinical outcome in a series of 18 adult patients. METHODS: All 18 patients had experienced recurrent episodes of generalized urticaria during exercise, 17 patients in association with collapse and 15 patients with an anaphylactic reaction. The symptoms appeared only when the patients had eaten food containing wheat before exercise. Wheat allergens were detected by immunoblotting, purified by gel filtration and reversed-phase chromatography, and subjected to N-terminal sequencing. The IgE-binding ability of the purified proteins was studied by ELISA, and their in vivo reactivity was studied by skin prick testing. RESULTS: IgE antibodies from pooled patient sera were bound to 65-kd and 40-kd wheat proteins in immunoblotting. The 65-kd allergen was a previously undescribed wheat protein, showing 61% sequence identity to gamma-gliadin, whereas the 40-kd allergen had 100% identity to alpha-gliadin. In ELISA, all 18 patients showed elevated IgE levels to the novel gamma-like gliadin, and 13 of the patients showed elevated IgE levels to the alpha-gliadin. None of the 54 control subjects with wheat allergy, urticaria, or coeliac disease had IgE antibodies to the gamma-like gliadin. The in vivo reactivity of the gamma-like gliadin was verified by positive skin prick test responses in all of the 15 patients who were tested. During the follow-up on a gluten-free or wheat-free diet, 3 patients experienced reactions after having unknowingly eaten wheat before exercise, but all the other patients who were adhering to the diet remained symptom-free. CONCLUSION: This study shows that wheat is a frequent cause of food-dependent, exercise-induced anaphylaxis and suggests that the major allergen is a previously undescribed gamma-like gliadin. For screening of this life-threatening allergy, we recommend skin prick testing with crude gliadin and we recommend a gluten-free diet for treatment.

Adolescent↗