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At least 163 records · Page 9Linked to original sources

Molecular mapping of genes for resistance to the bean pod weevil (Apion godmani Wagner) in common bean.

The bean pod weevil (Apion godmani Wagner) is a serious insect pest of common beans (Phaseolus vulgaris L.) grown in Mexico and Central America that is best controlled by host-plant resistance available in Durango or Jalisco genotypes such as J-117. Given unreliable infestation by the insect, the use of marker-assisted selection is desirable. In the present study, we developed a set of nine molecular markers for Apion resistance and mapped them to loci on chromosomes 2, 3, 4 and 6 (linkage groups b01, b08, b07 and b11, respectively) based on genetic analysis of an F (5:10) susceptible x resistant recombinant inbred line population (Jamapa x J-117) and two reference mapping populations (DOR364 x G19833 and BAT93 x JaloEEP558) for which chromosome and linkage group designations are known. All the markers were derived from randomly amplified polymorphic DNA (RAPD) bands that were identified through bulked segregant analysis and cloned for conversion to sequence tagged site (STS) markers. One of the markers was dominant while four detected polymorphism upon digestion with restriction enzymes. The other markers were mapped as RAPD fragments. Phenotypic data for the population was based on the evaluation of percentage seed damage in replicated trials conducted over four seasons in Mexico. In single point regression analysis, individual markers explained from 3.5 to 22.5% of the variance for the resistance trait with the most significant markers overall being F10-500S, U1-1400R, R20-1200S, W9-1300S and Z4-800S, all markers that mapped to chromosome 2 (b01). Two additional significant markers, B1-1400R and W6-800R, were mapped to chromosome 6 (b11) and explained from 4.3 to 10.2% of variance depending on the season. The latter of these markers was a dominant STS marker that may find immediate utility in marker-assisted selection. The association of these two loci with the Agr and Agm genes is discussed as well as the possibility of additional resistance genes on chromosome 4 (b07) and chromosome 3 (b08). These are among the first specific markers developed for tagging insect resistance in common bean and are expected to be useful for evaluating the mechanism of resistance to A. godmani.

Animals↗

Analysis of the nucleotide sequence of bean pod mottle virus middle component RNA.

The complete nucleotide sequence of the middle component RNA (M RNA) of the comovirus bean pod mottle virus (BPMV) has been determined. The sequence consists of 3662 nucleotides and contains a single long open reading frame sufficient to code for a protein of 113,353 Da. The proteolytic processing sites within this protein have been identified by comparison with the known three-dimensional structure of the virion and cleavage at these sites would lead to a range of products consistent with those observed during processing of the M RNA-encoded polyproteins in vitro. We have performed computer-aided searches for reiterated sequences within BPMV M RNA which might explain why ordered RNA is visible in the electron density map of BPMV middle component particles (Chen, Z., Stauffacher, C. V., Li, Y., Schmidt, T., Bomu, W., Kamer, G., Shanks, M., Lomonossoff, G., and Johnson, J. E., 1989, Science 245, 154-159). These searches revealed both the presence of overrepresented pentameric sequences and a consensus sequence which was repeated 15 times within the RNA sequence.

Amino Acid Sequence↗

Optimization of blends of synthetic pheromone components for trapping male limabean pod borers (Etiella zinckenella Tr.) (Lepidoptera: Phycitidae): preliminary evidence on geographical differences.

From the five previously identified pheromone components of the limabean pod borer (Etiella zinckenella Tr.) (Lepidoptera: Phycitidae), the 100:3 mixture of (Z)-11-tetradecenyl acetate and (Z)-9-tetradecenyl acetate was necessary for maximal attraction of males into traps in tests performed in Hungary. The addition of (E)-11-tetradecenyl acetate in percentages higher than 10-30% generally had an adverse effect on catches, while the addition of the other two compounds present in pheromone extracts had no influence on catches. In contrast to the results in Hungary, none of the traps baited with combinations of the above compounds captured any moths in tests performed in Taiwan, suggesting possible geographical differences in pheromonal response of European and Eastern Asian populations of E. zinckenella.

Animals↗

PAMPA--a drug absorption in vitro model. 5. Unstirred water layer in iso-pH mapping assays and pKa(flux)--optimized design (pOD-PAMPA).

Iso-pH mapping unstirred parallel artificial membrane permeability assay (PAMPA) was used to measure the effective permeability, P(e), as a function of pH from 3 to 10, of five weak monoprotic acids (ibuprofen, naproxen, ketoprofen, salicylic acid, benzoic acid), an ampholyte (piroxicam), five monoprotic weak bases (imipramine, verapamil, propranolol, phenazopyridine, metoprolol), and a diprotic weak base (quinine). The intrinsic permeability, P(o), the unstirred water layer (UWL) permeability, P(u), and the apparent pK(a) (pK(a)(flux)) were determined from the pH dependence of logP(e). The underlying permeability-pH equations were derived for multiprotic weak acids, weak bases and ampholytes. The average thickness of the unstirred water layer on each side of the membrane was estimated to be nearly 2000 microm, somewhat larger than that found in Caco-2 permeability assays (unstirred). Since the UWL thickness in the human intestine is believed to be about forty times smaller, it is critical to correct the in vitro permeability data for the effect of the UWL. Without such correction, the in vitro permeability coefficient of lipophilic molecules would be indicative only of the property of water. In single-pH PAMPA (e.g. pH 7.4), the uncertainty of the UWL contribution can be minimized if a specially-selected pH (possibly different from 7.4) were used in the assay. From the analysis of the shapes of the log P(e)-pH plots, a method to improve the selection of the assay pH, called pK(a)(flux)-optimized design (pOD-PAMPA), was described and tested. From an optimally-selected assay pH, it is possible to estimate P(o), as well as the entire membrane permeability-pH profile.

Algorithms↗

Distribution of total mercury, methyl mercury and selenium in pod of killer whales (Orcinus Orca) stranded in the northern area of Japan: comparison of mature females with calves.

Total mercury (T-Hg) and selenium (Se) concentrations in liver, kidney and muscle from a pod of killer whales including five mature females and three calves stranded in the northern area of Japan were analyzed. In the mature female, contamination level of T-Hg in the liver sample (62.2+/-21.9 microg/wet g) was markedly higher than that in kidney sample and muscle sample. The molar ratio of T-Hg to Se in the liver sample was approximately 1, and those in the kidney and muscle samples were markedly lower than 1. These results suggest that the formation of HgSe compound increases the hepatic accumulation of mercury (Hg). In contrast, contamination level of T-Hg in the calf organs was much lower than that in the mature female organs. These results suggest that the transfer of Hg from the mother to the fetus via placenta and/or to calf via milk is trace.

Aging↗

Immunological adjuvant activities of saponin extracts from the pods of Acacia concinna.

Pods of Acacia concinna (Leguminosae) contain several saponins. In this study, four saponin fractions which were acetone fraction (AAC), aqueous fraction (WAC), hydromethanolic fraction (HAC) and methanolic fraction (MAC) were generated and their haemolytic activities and surface activities were determined in comparison with quillaja saponin (QS). There were no significant differences between the haemolytic activities of MAC and QS. However, the surface tensions of MAC was significantly lower than QS (p < 0.001). Furthermore, the immunomodulatory effect and the adjuvant potential of MAC on the cellular and humoral immune response of BALB/c mice against ovalbumin were investigated. The splenocyte proliferations induced by MAC were significantly higher than QS at the concentrations of 200, 400, 800 and 1000 microg/ml (p < 0.05). BALB/c mice were immunized subcutaneously either with OVA 20 microg alone or with OVA 20 microg combining with QS (10 microg) or MAC (10 and 40 microg). Ten days after the second immunization, concanavalin A (Con A)-, pokeweed mitogen (PWM)-, and OVA-stimulated splenocyte proliferation and OVA-specific antibodies in serum were measured. The results suggested that MAC (40 microg) could activate T and B cells. In addition, OVA-specific IgG, IgG1 IgG2a and IgG2b antibody levels in serum were significantly enhanced by MAC (40 microg) as compared with OVA control group (p < 0.001). This finding suggested that MAC might be effect on Th1 and Th2 helper T cells. In conclusion, the results indicated that MAC at a dose of 40 microg could be used as vaccine adjuvant to increase immune responses.

Acacia↗

Erythrinaline alkaloids from the flowers and pods of Erythrina lysistemon and their DPPH radical scavenging properties.

Fourteen different erythrinaline alkaloids have been isolated from the flowers and pods of Erythrina lysistemon with four being reported for the first time in nature and five for the first time in this species and the rest having been re-isolated. The new compounds are (+)-11beta-hydroxyerysotramidine (1), (+)-11beta-methoxyerysotramidine (2), (+)-11beta-hydroxyerysotrine N-oxide (4) and (+)-11beta-hydroxyerysotrine (8). (+)-11alpha-Hydroxyerysotrine N-oxide (3), earlier misidentified as erythrartine N-oxide (beta-hydroxyerysotrine N-oxide 4), was also re-isolated along with four other alkaloids. Correct identification of compounds 4 and 8 was aided by the fact that the two sets of C-11 epimers 3, 4 and 8, 9 were both isolated in this study thus making it easier to identify and assign the individual epimers. (+)-Erythristemine (14) was found distributed in most of the plant parts investigated. Preliminary work on the crude chloroform/methanol (1:1) showed moderate toxicity to brine shrimp (LC50 23 ppm) and moderate (IC50 86 microg/ml) radical scavenging properties against stable 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical. The DPPH radical scavenging properties of the isolated compounds were assessed using TLC autographic and spectrophotometric assays whereupon only compounds 11 (1 microg; 90 microg/ml) and 12 (0.1 microg; 160 microg/ml) showed any notable activity. It appears the two compounds are slow reacting and do not reach steady state conditions within the standard half an hour time frame but only seemed to have reached steady state conditions after 4 h.

Alkaloids↗

Flavonoids from the pods of Millettia erythrocalyx.

From the pods of Millettia erythrocalyx, 2'-hydroxy-3,4-dimethoxy-[2'',3'':4',3']-furanochalcone, 2',3-dihydroxy-4-methoxy-4'-gamma,gamma-dimethylallyloxychalcone, (-)-(2S)-6,3',4'-trimethoxy-[2'',3'':7,8]-furanoflavanone, 3',4'-methylenedioxy-[2'',3'':7,8]-furanoflavonol and 6,3'-dimethoxy-[2'',3'':7,8]-furanoflavone were isolated, along with six other known flavonoids. Their structures were elucidated through analysis of their spectroscopic data.

Flavonoids↗

The Bean pod mottle virus proteinase cofactor and putative helicase are symptom severity determinants.

Full-length infectious cDNA clones were constructed from the genomic RNAs of three distinct strains (K-G7, K-Ha1 and K-Ho1) of the comovirus Bean pod mottle virus (BPMV). Whereas K-G7, a subgroup I strain, and K-Ha1, a subgroup II strain produce mild mottling, the reassortant strain K-Ho1 (RNA1(I) + RNA2(II)) induces necrotic primary lesions on inoculated leaves of soybean and severe systemic leaf mottling and blistering. Pseudorecombinants of all possible combinations of transcripts were generated and tested for symptom production. Only soybean plants inoculated with combinations having RNA1 derived from the severe strain K-Ho1, regardless of the origin of RNA2, induced severe symptoms, indicating that symptom severity maps to RNA1. Experiments with chimeric RNA1 constructs indicated that the coding regions of the protease co-factor (Co-pro) and the C-terminal half of the putative helicase (Hel) are determinants of symptom severity. Symptom severity correlated well with higher accumulation of viral RNA, but neither the Co-pro nor Hel protein could be demonstrated as a suppressor of RNA silencing.

Base Sequence↗

Development of Bean pod mottle virus-based vectors for stable protein expression and sequence-specific virus-induced gene silencing in soybean.

Plant virus-based vectors provide valuable tools for expression of foreign proteins in plants and for gene function studies. None of the presently available virus vectors is suitable for use in soybean. In the present study, we produced Bean pod mottle virus (BPMV)-based vectors that are appropriate for gene expression and virus-induced gene silencing (VIGS) in soybean. The genes of interest were inserted into the RNA2-encoded polyprotein open reading frame between the movement protein (MP) and the large coat protein (L-CP) coding regions. Additional proteinase cleavage sites were created to flank the foreign protein by duplicating the MP/L-CP cleavage site. To minimize the chances of homologous recombination and thus insert instability, we took advantage of the genetic code degeneracy and altered the nucleotide sequence of the duplicated regions without affecting amino acid sequences. The recombinant BPMV constructs were stable following several serial passages in soybean and relatively high levels of protein expression were attained. Successful expression of several proteins with different biological activities was demonstrated from the BPMV vector. These included the reporter proteins GFP and DsRed, phosphinothricin acetyltransferase (encoded by the herbicide resistance bar gene), and the RNA silencing suppressors encoded by Tomato bushy stunt virus, Turnip crinkle virus, Tobacco etch virus, and Soybean mosaic virus. The possible use of BPMV as a VIGS vector to study gene function in soybean was also demonstrated with the phytoene desaturase gene. Our results suggest that the BPMV-based vectors are suitable for expression of foreign proteins in soybean and for functional genomics applications.

Amino Acid Sequence↗

Concurrent validity of the BOD POD and dual energy x-ray absorptiometry techniques for assessing body composition in young women.

The purpose of this study was to determine the concurrent validity of the BOD POD (BP) (Life Measurement Instruments) and Dual Energy X-Ray Absorptiometry (DXA) Elite 4500A (Hologic, Inc.) techniques for assessing the body fat percentage of young women. The participants were forty-three white college-aged women (19.4 +/- 1.4 years) with a BMI of 23.4 +/- 2.3. Both body composition analyses were completed on the same day and were taken within 10 minutes of each other. Body fat percentage was estimated to be 24.3 (SE = 1.1) and 23.8 (SE = 0.8) using the BP and DXA techniques, respectively. Exact matches, in terms of body fat percentage, were obtained for 10 of the 43 participants (23.3%). In conclusion, our data supports the concurrent validity of the BP and DXA techniques for assessing body fat in young women.

Absorptiometry, Photon↗

Raman dynamic probe of hydrogen exchange in bean pod mottle virus: base-specific retardation of exchange in packaged ssRNA.

We describe a novel approach to investigating exchange kinetics in biological assemblies. The method makes use of a Raman multichannel analyzer coupled with a dialysis flow cell. We employ this methodology to determine exchange rates of labile hydrogens in both the packaged RNA genome and protein subunits of bean pod mottle virus (BPMV). In the BPMV assembly, which is similar to human picornaviruses, the x-ray structure indicates that about 20% of the ssRNA chain is ordered at the threefold vertices of the icosahedral capsid, although the nucleotide bases in the ordered segments are not known (Chen et al., 1989). Here, we compare exchange profiles of the native virus with those of the empty capsid, model nucleic acids and aqueous solvent to reveal the following exchange characteristics of BPMV RNA and protein: (i) Base-specific retardation of exchange is observed in the packaged RNA. (ii) Retardation is greatest for uracil residues, for which the first-order exchange rate constant (kU = 0.18 +/- 0.02 min-1) is 40% lower than that of either the H2O solvent or adenine or cytosine groups of RNA (ksolv approximately kA approximately kC = 0.30 +/- 0.02 min-1). (iii) Retardation of exchange is also observed for the guanine residues of packaged RNA. (iv) No appreciable exchange of amide NH groups of capsid subunits occurs within the time of complete exchange (t approximately 10 min) of packaged RNA or bulk solvent. Thus, the present results identify sites in both the protein subunits (amide NH) and RNA nucleotides (amino NH2 and imino NH) which are resistant to solvent-catalyzed hydrogen exchange. We propose that retardation of exchange of labile sites of the RNA nucleotides is a consequence of the organization of the RNA chromosome within the virion. Our findings support a model for BPMV in which surface and buried domains of capsid subunits are extensively and rigidly hydrogen-bonded, and in which uracil and guanine exocyclic donor groups of packaged RNA are the principal targets for subunit interaction at the threefold vertices of the capsid.

Biophysical Phenomena↗

Clerodane-type diterpenes from the seed pods of Hymenaea courbaril var. stilbocarpa.

Three known and two new diterpenes were isolated from the ethyl acetate extract of Hymenaea courbaril var. stilbocarpa seed pods. One of the compounds was elucidated as (5R*,8S*,9S*,10R*)-cleroda-3,13E-dien-15-oic acid and the other was elucidated, after treatment with diazomethane, as methyl (5S*,8S*,9S*,10R*)-cleroda-3,13E-dien-15-oate. The known diterpenes were identified as (-)-ozic acid, (-)-isoozic acid and (-)-kovalenic acid which were characterized as their methyl ester derivatives.

Diterpenes↗

The African yam bean seed lectin affects the development of the cowpea weevil but does not affect the development of larvae of the legume pod borer.

Artificial feeding assays were used to study the effect of purified galactose-specific lectins from African yam beans (Sphenostylis stenocarpa) on development of larvae of the cowpea weevil, Callosobruchus maculatus (Coleoptera : Bruchidae) and the legume pod-borer, Maruca vitrata (Lepidoptera : Pyrialidae). Inhibition of development of C. maculatus was observed when larvae were fed on artificial cowpea seeds containing 0.2%, 2.0% and 5.0% (wt/wt) of dietary lectin. Larval mortality was between 30% and 88%, while delays in total developmental time ranged between 7 and 13 days. The lectin had no effect on development of larvae of M. vitrala, when tested through topical artificial diet incorporation assays, except at the extremely high dose of 35% dietary level.

Animals↗

Molecular characterization of vitellogenin and its receptor with CRISPR-based sgRNA validation in the legume pod borer, Maruca vitrata (Geyer) (Lepidoptera: Crambidae).

Maruca vitrata, the legume pod borer, causes yield losses of up to 80% in grain legumes. Increasing insecticide resistance and environmental concerns necessitate sustainable pest management alternatives. In the present study, the complete vitellogenin (Vg) coding sequence (CDS), a key reproductive gene involved in oogenesis and embryonic development, was cloned and molecularly characterised from M. vitrata. The assembled Vg CDS (&#x223c;5.3 kb) shared 99.04% sequence identity with the reported M. vitrata Vg sequence (MG799570.1). Phylogenetic analysis demonstrated close evolutionary association with related Lepidopteran species, while protein domain analysis identified three conserved domains, namely LPD_N, DUF1943, and VWD. Among these, the single exon-encoded LPD_N domain was selected as the target region for CRISPR/Cas9-mediated editing. Homology models of Vg and vitellogenin receptor (VgR) (Global Model Quality Estimation (GMQE): 0.58 and 0.51) showed a favourable interaction by protein-protein docking (score: -295.66). Three single-guide RNAs (sgRNAs) were designed, synthesised through in-vitro transcription, and evaluated using in vitro cleavage assays. sgRNA1 targeting the LPD_N domain and sgRNA2 targeting the signal peptide region exhibited efficient site-specific cleavage activity, whereas sgRNA3 failed to induce cleavage because of an unfavourable secondary structure that likely impaired Cas9-sgRNA complex formation. Overall, this study provides the first CRISPR-oriented functional characterisation and sgRNA validation of the M. vitrata Vg gene, together with structural characterisation of VgR and Vg-VgR interaction analysis, providing preliminary molecular resources for future CRISPR/Cas9 studies and supporting future embryo microinjection and heritable&#xa0;genome editing for sustainable management of M. vitrata.

CRISPR/Cas9↗

NEP1 orthologs encoding necrosis and ethylene inducing proteins exist as a multigene family in Phytophthora megakarya, causal agent of black pod disease on cacao.

Phvytophthora megakarya is a devastating oomycete pathogen that causes black pod disease in cacao. Phytophthora species produce a protein that has a similar sequence to the necrosis and ethylene inducing protein (Nep1) of Fusarium oxysporum. Multiple copies of NEP1 orthologs (PmegNEP) have been identified in P. megakarya and four other Phytophthora species (P. citrophthora, P. capsici, P. palmivora, and P. sojae). Genome database searches confirmed the existence of multiple copies of NEP1 orthologs in P. sojae and P. ramorum. In this study, nine different PmegNEP orthologs from P. megakarya strain Mk-1 were identified and analyzed. Of these nine orthologs, six were expressed in mycelium and in P. megakarya zoospore-infected cacao leaf tissue. The remaining two clones are either regulated differently, or are nonfunctional genes. Sequence analysis revealed that six PmegNEP orthologs were organized in two clusters of three orthologs each in the P. megakarya genome. Evidence is presented for the instability in the P. megakarya genome resulting from duplications, inversions, and fused genes resulting in multiple NEP1 orthologs. Traits characteristic of the Phytophthora genome, such as the clustering of NEP1 orthologs, the lack of CATT and TATA boxes, the lack of introns, and the short distance between ORFs were also observed.

Amino Acid Sequence↗

Conformations, interactions, and thermostabilities of RNA and proteins in bean pod mottle virus: investigation of solution and crystal structures by laser Raman spectroscopy.

We report and interpret laser Raman spectra of the three virion components of bean pod mottle virus (BPMV). The top component of BPMV is an empty capsid; middle and bottom components package the RNA2 and RNA1 genome segments, respectively. All components were investigated as both single crystals and aqueous solutions, the latter over wide ranges of temperature and ionic strength. The isolated RNA2 molecule of BPMV middle component was also investigated in both H2O and D2O solutions. The results permit assessment of RNA and protein structures, their mutual interactions in the virions, and their conformational thermostabilities and comparison of these structural characteristics for solution and crystal states of the particles. The principal findings of this study are (i) The extent of ordered A-form backbone (74%) and of base pairing (38% AU + 22% GC) in unpackaged (aqueous) RNA2 are significantly altered by packaging. The A-form secondary structure of RNA2 is increased by 12 +/- 4%, and guanine base interactions are also substantially increased with packaging. (ii) The thermostability of Raman-monitored secondary structure of unpackaged RNA2 (Tm approximately 43 degrees C) is greatly increased in the packaged state (Tm approximately 53 degrees C). This increase corresponds to a stabilization of the A-form backbone geometry in 15 +/- 5% of genome nucleotides. (iii) Packaging of RNA2 in the middle component stabilizes subunit-subunit interactions of the capsid, as evidenced by a thermal denaturation temperature Td approximately 65 degrees C for the virion, compared with Td approximately 55 degrees C for the empty capsid. (iv) Raman marker-band shifts implicate the purine 7N sites of RNA2 and aromatic side chains of subunits as the principal targets for RNA-subunit interaction. (v) At the conditions of the present experiments (8 degrees C, pH approximately 7, moderate ionic strength), the subunit secondary structures observed for solutions of the top, middle, and bottom components are indistinguishable by Raman spectroscopy from secondary structures observed for corresponding crystalline samples. (vi) On the other hand, side chains of subunits in the top component (empty capsid) yield significantly different Raman intensities in crystalline and solution states. These differences are interpreted as the result of changes in a small number of side-chain environments between crystal and solution. (vii) Similarly, small differences exist between RNA Raman markers of crystalline and aqueous virions, which are attributed to altered environments of nucleotide residues and to a small increase in the amount of A-form backbone geometry upon going from the crystal to the solution.(ABSTRACT TRUNCATED AT 400 WORDS)

Base Composition↗

Structural studies of bean pod mottle virus, capsid, and RNA in crystal and solution states by laser Raman spectroscopy.

Structures of protein and RNA components of bean pod mottle virus (BPMV) have been investigated by use of laser Raman spectroscopy. Raman spectra were collected from both aqueous solutions and single crystals of BPMV capsids (top component) and virions (middle and bottom components, which package, respectively, small and large RNA molecules). Analysis of the data permits the assignment of conformation-sensitive Raman bands to viral protein and RNA constituents and observation of structural similarities and differences between solution and crystalline states of BPMV components. The Raman results show that the protein subunits of the empty capsid contain between 45% and 55% beta-strand and beta-turn secondary structure, in agreement with the recently determined X-ray crystal structure, and that this total beta-strand content undergoes a small increase (approximately 5%) with packaging of RNA. The subunits are relatively deficient in alpha-helix secondary structure, estimated at less than 25%, and therefore must contain extensive amounts (greater than 20%) of loops and irregular chain conformations. The Raman spectra also show the following: (1) The molecular environments of as many as four tryptophan residues per subunit are altered upon packaging RNA, resulting in stronger 1N-H hydrogen bonding for two Trp residues and more hydrophobic environments for two indole rings. (2) Hydrogen-bonding states of the seven Tyr residues per subunit do not change detectably when RNA is packaged. At least five tyrosine OH groups are involved exclusively as strong hydrogen bond donors to protein acceptor groups, which suggests restricted access of solvent H2O molecules to these parahydroxyls.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acids↗