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PubMed1980

Antihypertensive activity of 16, 16-dimethyl-oxa-alkyl-prostaglandins of the PGA2, PGE2 and trans-delta 2-11-deoxy-PGE1 series: structure-activity relationships.

Utilizing Corey's synthesis, a variety of prostaglandins (PGs) with a modified omega-side chain were prepared. The 16, 16-dimethyl-oxa-alkyl analogues of PGA2 had potent antihypertensive activity. HR 466 (16, 16-dimethyl-18-oxa-PGA2), the best compound out of this series was active for 5-6 hours after oral administration of 0, 1 mg/kg to conscious renal hypertensive dogs. The corresponding analogues of PGE2 were also potent anti-hypertensive compounds, but were much more spasmogenic. Structural variations within the trans-delta 2-11-deoxy-PGE1-series, in both side chains, gave HR 601 (trans-delta2-15alpha-acetoxy-16, 16-dimethyl-18-oxa-11-deoxy-PGE1-methylester) which was orally active in the hypertensive dog with similar activity to HR 466.

16,16-Dimethylprostaglandin E2↗
PubMed2005

Application of phosphoramidate pronucleotide technology to abacavir leads to a significant enhancement of antiviral potency.

We report the first application of pronucleotide (ProTide) technology to the antiviral agent abacavir (Ziagen), used for the treatment of HIV infection. The phenylmethoxyalaninyl phosphoramidate of abacavir was prepared in good yield in one step. Also prepared was the corresponding phosphoramidate of the guanine nucleoside analogue "carbovir". The antiviral profile of each of the parent nucleosides was compared to that of the phosphoramidate ProTides. A significant (28- to 60-fold) increase in anti-HIV potency was noted for the ProTide of abacavir but not for that of carbovir. These findings were in agreement with the markedly higher (ca. 37-fold) levels of carbovir triphosphate that are formed in CEM cells upon response to the abacavir ProTide compared with the parent abacavir compound. In contrast the anti-HBV potency of both abacavir and carbovir were improved (10- and 20-fold, respectively) by ProTide formation. As in CEM cells, the abacavir ProTide provided significantly enhanced carbovir triphosphate levels in HepG2 2.2.15 cells over that of the parent nucleoside. On the basis of these data, a series of phosphoramidate analogues with structural variation in the ester and amino acid regions were prepared and their antiviral profiles described. In addition, the pharmacokinetic disposition of the abacavir phenylethoxyalaninyl phosphoramidate was evaluated in Cynomolgus monkeys.

Administration, Oral↗
PubMed1998

Parabolic Relationship between the Basicity of the Nucleophile and pi-Face Selection in Addition of the Substituted Acetylide Ions to Cyclohexanone and Cyclohexanethione.

Energy changes, structural variation, and electron density shifts during nucleophilic addition to cyclohexanone and cyclohexanethione were examined by means of the ab initio calculations at the HF/6-31G level. The atomic charge on the carbonyl C was found to become more positive upon approach of the nucleophile; the density deformation maps suggest that the charge polarization occurs to a large extent in the pi bond. Since this effect is not compensated for by charge transfer until in the late stage of addition, the reaction site is considerably electron deficient (more so than the carbonyl C in the substrate) for most of the reaction path, and its interactions with the ligands are dominated by hyperconjugation with the vicinal C-H and C-C bonds. Relative stabilities of the axial and equatorial transition-state structures were examined in the series HN=C, ON&tbd1;C(-), N&tbd1;C(-), FC&tbd1;C(-), HC&tbd1;C(-), SBeC&tbd1;C(2-), O(3)SC&tbd1;C(2-), H(3)AlC&tbd1;C(2-), SC&tbd1;C(2-), H(3)BC&tbd1;C(2-), and C&tbd1;C(2-) and found to depend on polarization of the electrophiles, C=O vs C=S, and basicity of the nucleophiles. The latter dependence is parabolic: the axial preference reaches a maximum for the moderately basic anions, and it is diminished or even reversed for the most and least basic nucleophiles, i.e., in the case of reactions proceeding through the very early or very late transition states. Thus, the stereoelectronic effect is largest in the region of the reaction coordinate where the electron deficiency at the reaction site reaches a maximum. These findings corroborate the premises of the hypothesis of hyperconjugative assistance to bond formation and are consistent with major trends in the experimental data if the stereochemistry of alkylation of 4-tert-butylcyclohexanone is correlated with Pauling electronegativity of metals in the case of methylmetals, methylmetal ate complexes, allylmetals and arylmetals, and with the pK(a) of conjugated acids in the case of sulfur-, carbonyl-, and nitrile-stabilized carbanions.

Journal Article↗
PubMed2005

Genetic basis of variation in adenoma multiplicity in ApcMin/+ Mom1S mice.

Apc(Min) mice have provided an example of a locus (Modifier of Min1; Mom1) modifying adenoma numbers in the intestines of inbred strains. Linkage analysis located Mom1 on chromosome 4, and further investigation identified secretory phospholipase A2 (Pla2g2a) as a candidate gene. Because of unknown variation introduced by a single founding male mouse, our Min stock, although Pla2g2a(Mom1-s), was not on a pure C57BL/6J background and exhibited several polymorphic loci, including a region on chromosome 18 distal to Apc. Through selective breeding for homozygosity for distal chromosome 18 markers, six recombinant lines that presented with limited intraline variation in adenoma numbers were established. One line (V) showed a particularly severe phenotype (mean adenoma number +/- SEM, 370 +/- 21) compared with the other lines that recorded significantly lower means (3- to 5-fold; P < 10(-3), t test). Intercrosses between lines I and V showed suppression of the severe phenotype in the N1 generation. In N2 (and subsequent) backcrosses, tumor multiplicity depended on the origins of the WT and Min Apc alleles. Mice carrying both alleles from line V had a severe phenotype; others had mild disease very similar to line I (likelihood ratio statistic > 49.0; likelihood of odds > 10; P < 10(-5)). Frequency of allele loss at Apc was increased significantly in adenomas of mice with more severe disease. We propose that a modifier gene close to Apc or structural variation on chromosome 18 modifies polyp numbers in our mice, possibly by altering the frequency of WT Apc allele loss.

Adenoma↗
PubMed2006

ASPIC: a web resource for alternative splicing prediction and transcript isoforms characterization.

Alternative splicing (AS) is now emerging as a major mechanism contributing to the expansion of the transcriptome and proteome complexity of multicellular organisms. The fact that a single gene locus may give rise to multiple mRNAs and protein isoforms, showing both major and subtle structural variations, is an exceptionally versatile tool in the optimization of the coding capacity of the eukaryotic genome. The huge and continuously increasing number of genome and transcript sequences provides an essential information source for the computational detection of genes AS pattern. However, much of this information is not optimally or comprehensively used in gene annotation by current genome annotation pipelines. We present here a web resource implementing the ASPIC algorithm which we developed previously for the investigation of AS of user submitted genes, based on comparative analysis of available transcript and genome data from a variety of species. The ASPIC web resource provides graphical and tabular views of the splicing patterns of all full-length mRNA isoforms compatible with the detected splice sites of genes under investigation as well as relevant structural and functional annotation. The ASPIC web resource-available at http://www.caspur.it/ASPIC/--is dynamically interconnected with the Ensembl and Unigene databases and also implements an upload facility.

Algorithms↗
PubMed1972

Ceramide-like synthetic amides that inhibit cerebroside galactosidase.

Amides resembling ceramide (fatty acyl sphingosine) were synthesized and tested for their effects on rat brain cerebrosidase (galactosyl ceramide beta-galactosidase). The best inhibitor was N-decanoyl dl-erythro-3-phenyl-2-aminopro-panediol, which exhibited a K(i) of 0.4 mm. A Lineweaver-Burk plot indicated that the amide acted as a noncompetitive inhibitor, presumably by attachment to a site other than the substrate-active site. Preincubation did not affect the degree of inhibition, and inhibition was independent of incubation duration; these observations suggest that the inhibitor does not combine with the enzyme irreversibly. Structural variations produced decreased inhibitory activity: loss of one of the hydroxyl groups, replacement of the aromatic side chain with an aliphatic or substituted phenyl group, or isomeric inversion of the 3-hydroxyl group. It appears that the best activity is obtained with a substance most closely resembling natural ceramide. The cerebrosidases of rat spleen, kidney, and liver are also inhibited by the same amide.

Acylation↗
PubMed2001

Electrospray ionization mass spectrometry of tetrodotoxin and its analogs: liquid chromatography/mass spectrometry, tandem mass spectrometry, and liquid chromatography/tandem mass spectrometry.

Tetrodotoxin (TTX), a powerful sodium channel blocker, usually exists as a mixture of its analogs (TTXs) in natural sources. Due to the structural variation, some analogs are difficult to detect using the postcolumn liquid chromatography-fluorescent detection (LC-FLD) system. Liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) analysis of TTXs can be achieved by a combination of chromatography on a reversed-phase column with long carbon chains (C30) and the mobile phase containing an ion pair reagent (ammonium heptafluorobutyrate). The relationship between the amount of applied standard TTX and its peak area on the mass chromatogram (m/z 320) showed good linearity over a range of 50-1000 pmol. The detection limit for TTX in the selected ion monitoring (SIM) mode was estimated to be 0.7 pmol (signal to noise ratio: 2). The tandem mass spectrometry (MS/MS) scan for the fragment ions of eight TTXs arising from the molecular ions provided characteristic spectra, and the structures of the origins of the prominent fragment ions were proposed. The intense fragment ions of TTX and 11-deoxyTTX were applicable to LC/MS/MS operated in the selected reaction monitoring mode. This method might be useful for further identification of TTXs.

Animals↗
PubMed1985

Close linkage between mouse genes determining the two forms of complement component C6 and component C7, and cis action of a C6 regulatory gene.

Two forms of mouse complement component C6, with molecular weights (Mrs) of 90 and 100 kilodaltons (kd), are present in the sera from certain inbred strains such as the CBA strain; other strains, such as the BALB/c and DBA/2 strains, have only the 90 kd C6A form. The present work was undertaken to determine whether the two Mr forms were the products of genes coding at separate loci. We screened sera from mice from a number of inbred strains by isoelectric focusing and found one strain, AKR, exhibiting allotypic structural variations of C6 forms. To distinguish the various types, we designated the 90 kd types from CBA and AKR mice C6A1 and C6A2, respectively, and the corresponding 100 kd types C6B1 and C6B2, respectively. Mice possessing only one Mr form were all typed as C6A1. Results of breeding experiments strongly suggested that the two Mr forms of C6 are coded for at two closely linked loci. Sera from a number of inbred strains were also screened for a complement C7 polymorphism by means of isoelectric focusing and functional overlay. C7 from all strains, excepting the AKR strain, produced identical C7 band patterns. AKR C7 produced a unique band pattern, and results of breeding experiments with AKR and BALB/c mice showed the C6 and C7 loci to be closely linked. In addition, we identified a regulatory gene for C6 production. The gene apparently requires androgen to facilitate C6 production in the majority of strains. In these strains C6 activity is virtually absent from female sera. However, we observed moderate levels of C6 activity in sera from IS/Cam females, indicating that, in this strain, male physiological androgen levels are not necessary for C6 production. IS/Cam possess one form of circulating C6 which appears identical with BALB/c C6A1, and therefore IS/Cam mice differ from AKR mice at both the C6 structural and regulatory loci. These two strains were thus suitable for use in breeding experiments to determine the manner of action of the regulatory gene. Results showed that it acted in a cis manner.

Animals↗
PubMed2002

Diazabicyclononanones, a potent class of kappa opioid analgesics.

The 1,5-dimethyl 3,7-diaza-3,7-dimethyl-9-oxo-2,4-di-2-pyridine-bicyclo[3.3.1]nonane-1,5-dicarboxylate, HZ2, has a high and selective affinity for the kappa opioid receptor and an antinociceptive activity comparable to morphine. In addition, it is characterized by a long duration of action and a high oral bioavailability. QSAR studies within series of kappa agonists revealed a chair-boat conformation of a double protonated HZ2 characterized by an almost parallel orientation of the C9 carbonyl group and the N7-H group and at least one aromatic ring to be the pharmacophoric arrangement. Structural variations showed that the pyridine rings in 2 and 4 position can be replaced with p-methoxy-, m-hydroxy- and m-fluoro-substituted phenyl rings. However, all other substituents have to be kept the same for a high affinity to the kappa receptor.

3,4-Dichloro-N-methyl-N-(2-(1-pyrrolidinyl)-cycloh↗
PubMed2003

Age-related changes in cyclic voltammetry and potentiodynamic studies of normal human dentine.

Impedance spectroscopy is one of the non-destructive techniques used by researchers to measure electrical resistance of biological tissues and ceramics. The purpose of this study is to investigate the voltage-current (V-I) characteristics of sound human dentine from young and old teeth, using cyclic voltammetry and potentiodynamic techniques. Dentine samples were prepared from freshly extracted sound third molars. After electrical measurements, dentine samples were characterized using scanning electron microscopy (SEM). Cyclic voltammetric measurements showed that variation of current through sample as a function of applied voltage is linear for dry samples of both age groups. However, for wet samples V-I characteristic were found to be different. The resistivity of dry young dentine is greater than that of old dentine in dry environment, whereas, it was found to be opposite for wet dentine samples. Using the same voltage sweep in potentiodynamic measurements dry samples display similar traces to controls suggesting that the dry dentine acts as an insulator. The number of dentinal tubules and their diameter has been found to decrease with increasing age. We propose that these changes determine the changes in electrical characteristics of sound human dentine. In spite of increasing use of electrical techniques to understand electrical properties of teeth, it is clear from this study that local structural variations and environment have a marked influence. Therefore, this baseline data needs to be considered in any future study or clinical application.

Journal Article↗
PubMed2003

Elaborate manifold of short hydrogen bond arrays mediating binding of active site-directed serine protease inhibitors.

An extensive structural manifold of short hydrogen bond-mediated, active site-directed, serine protease inhibition motifs is revealed in a set of over 300 crystal structures involving a large suite of small molecule inhibitors (2-(2-phenol)-indoles and 2-(2-phenol)-benzimidazoles) determined over a wide range of pH (3.5-11.4). The active site hydrogen-bonding mode was found to vary markedly with pH, with the steric and electronic properties of the inhibitor, and with the type of protease (trypsin, thrombin or urokinase type plasminogen activator (uPA)). The pH dependence of the active site hydrogen-bonding motif is often intricate, constituting a distinct fingerprint of each complex. Isosteric replacements or minor substitutions within the inhibitor that modulate the pK(a) of the phenol hydroxyl involved in short hydrogen bonding, or that affect steric interactions distal to the active site, can significantly shift the pH-dependent structural profile characteristic of the parent scaffold, or produce active site-binding motifs unique to the bound analog. Ionization equilibria at the active site associated with inhibitor binding are probed in a series of the protease-inhibitor complexes through analysis of the pH dependence of the structure and environment of the active site-binding groups involved in short hydrogen bond arrays. Structures determined at high pH (>11), suggest that the pK(a) of His57 is dramatically elevated, to a value as high as approximately 11 in certain complexes. K(i) values involving uPA and trypsin determined as a function of pH for a set of inhibitors show pronounced parabolic pH dependence, the pH for optimal inhibition governed by the pK(a) of the inhibitor phenol involved in short hydrogen bonds. Comparison of structures of trypsin, thrombin and uPA, each bound by the same inhibitor, highlights important structural variations in the S1 and active sites accessible for engineering notable selectivity into remarkably small molecules with low nanomolar K(i) values.

Animals↗
PubMed1987

Substrate-derived two-protonic-state electrophiles as sensitive kinetic specificity probes for cysteine proteinases. Activation of 2-pyridyl disulphides by hydrogen-bonding.

1. 2-(N'-Acetyl-L-phenylalanylamino)ethyl 2'-pyridyl disulphide [compound (III)] and 2-(acetamido)ethyl 2'-pyridyl disulphide [compound (IV)] were synthesized by acylation of the common intermediate, 2-aminoethyl 2'-pyridyl disulphide, to provide examples of chromogenic thiol-specific substrate-derived two-protonic-state electrophilic probe reagents. These two reagents, together with n-propyl 2-pyridyl disulphide [compound (II)], provide structural variation in the non-pyridyl part of the molecule from a simple hydrocarbon side chain in compound (II) to a P1-P2 amide bond in compound (IV) and further to both a P1-P2 amide bond and a hydrophobic side chain (of phenylalanine) at P2 as a potential occupant of S2 subsites. 2. These disulphides were used as reactivity probes to investigate specificity and binding-site-catalytic-site signalling in a number of cysteine proteinases by determining (a) the reactivity at pH 6.0 at 25 degrees C at I 0.1 of compound (III) (a close analogue of a good papain substrate) towards 2-mercaptoethanol, benzimidazol-2-ylmethanethiol [compound (V), as a minimal catalytic-site model], chymopapains B1-B3, chymopapain A, papaya proteinase omega, actinidin, cathepsin B and papain, (b) the effect of changing the structure of the probe as indicated above on the reactivities of compound (V) and of the last five of these enzymes, and (c) the forms of pH-dependence of the reactivities of papain and actinidin towards compound (III). 3. The kinetic data suggest that reagents of the type investigated may be sensitive probes of molecular recognition features in this family of enzymes and are capable not only of detecting differences in binding ability of the various enzymes but also of identifying enzyme-ligand contacts that provide for binding-site-catalytic-site signalling mechanisms. 4. The particular value of this class of probe appears to derive from the possibility of activating the 2-mercaptopyridine leaving group not only by formal protonation, as was recognized previously [see Brocklehurst (1982) Methods Enzymol. 87C, 427-469], but also by hydrogen-bonding to the pyridyl nitrogen atom when the appropriate geometry in the catalytic site is provided by enzyme-ligand contacts involving the non-pyridyl part of the molecule.(ABSTRACT TRUNCATED AT 400 WORDS)

2,2'-Dipyridyl↗
PubMed2024

Strategic targeting of Cas9 nickase induces large segmental duplications.

Gene/segmental duplications play crucial roles in genome evolution and variation. Here, we introduce paired nicking-induced amplification (PNAmp) for their experimental induction. PNAmp strategically places two Cas9 nickases upstream and downstream of a replication origin on opposite strands. This configuration directs the sister replication forks initiated from the origin to break at the nicks, generating a pair of one-ended double-strand breaks. If homologous sequences flank the two break sites, then end resection converts them to single-stranded DNAs that readily anneal to drive duplication of the region bounded by the homologous sequences. PNAmp induces duplication of segments as large as &#x223c;1 Mb with efficiencies exceeding 10% in the budding yeast Saccharomyces cerevisiae. Furthermore, appropriate splint DNAs allow PNAmp to duplicate/multiplicate even segments not bounded by homologous sequences. We also provide evidence for PNAmp in mammalian cells. Therefore, PNAmp provides a prototype method to induce structural variations by manipulating replication fork progression.

Saccharomyces cerevisiae↗
PubMed2000

Conformational changes in the PBX homeodomain and C-terminal extension upon binding DNA and HOX-derived YPWM peptides.

PBX is a member of the three amino acid loop extension (TALE) class of homeodomains. PBX binds DNA cooperatively with HOX homeodomain proteins that contain a conserved YPWM motif. The amino acids immediately C-terminal to the PBX homeodomain increase the affinity of the homeodomain for its DNA site and HOX proteins. We have determined the structure of the free PBX homeodomain using NMR spectroscopy. Both the PBX homeodomain and the extended PBX homeodomain make identical contacts with a 5'-TGAT-3' DNA site and a YPWM peptide. A fourth alpha-helix, which forms upon binding to DNA, stabilizes the extended PBX structure. Variations in DNA sequence selectivity of heterodimeric PBX-HOX complexes depend on the HOX partner; however, a comparison of five different HOX-derived YPWM peptides showed that each bound to PBX in the same way, differing only in the strength of the association.

Amino Acid Motifs↗
PubMed1998

Some structural characteristics of the inguinal region in the northern Croatia.

In studying anatomical samples of both inguinal hernia patients and healthy controls with no changes observable in the inguinal region, the authors aimed at investigating the constitution of the inguinal region in relation to the formation of inguinal hernia. The morphological investigation of 68 anatomical samples and 44 inguinal regions at autopsy, revealed that the length of the interspinal line, independent of sex, varies from 180 to 310 mm and is 63 to 132 mm removed from the pubic tubercle (the height of the anterior pelvic arch). Thus, in 35% of male and 22% of female subjects the height of the anterior pelvic arch exceeded 75 mm indicating a low position of the groin. The research carried out in 640 inguinal hernia patients and 186 controls indicated a shift towards higher values in the interspinal line in inguinal hernia patients as compared with the controls. In addition, the height of the anterior pelvic arch in patients with inguinal hernia conspicuously exceeded that observed in the controls. The present study undoubtedly shows that the number of muscle and connective structure variations of the inguinal region depends upon the position of the groin in relation to the interspinal plane. The authors therefore agree with the classification of these relationships to high, medial and low groin position. The high position of the pubic tubercles up to 75 mm removed from the interspinal spine is accompanied with the firm constitution of the entire inguinal region. Moreover, the medical position of pubic tubercles 75 to 90 mm removed from the interspinal line does not indicate the risk of developing inguinal hernia. On the other hand, the low position of the pubic tubercles more than 90 mm removed from the interspinal line is often due to the inferior constitution of the inguinal region. This group is regularly at higher risk of developing inguinal hernia, particularly with other risk factors being added as well. The identification of structural characteristics of the inguinal region therefore enables the selection of the most appropriate operation procedure, i.e. between the classic hernia repair and endoscopic approach for prosthetic mesh implantation.

Female↗
PubMed1993

Genetic variation in thymidylate synthase confers resistance to 5-fluorodeoxyuridine.

The human colorectal tumor cell line HCT 116 was resident to the cytotoxic effects of 5-fluorodeoxyuridine (FdUrd). The response to FdUrd was increased only slightly by the presence of 10 microM folinic acid (CF). HCT 116 formed FdUMP and CH2H4PteGlu polyglutamates after exposure to FdUrd and CF. The sensitivity to FdUrd correlated well with the extent of TS inhibition. The role of TS in the resistance of the cells to FdUrd was examined. HCT 116 expresses two TS enzymes, which differ in pI. The more basic TS has been detected in only HCT 116 cells. The other TS is identical in pI to the enzymes detected in other human cells. The variant TS differs from the common by His replacement of Tyr at residue 33. The variant TS exhibited a 3-fold lower affinity for FdUMP than the common TS. The enzymes co-expressed in HCT 116 exhibited an FdUMP binding constant similar to that of the variant TS. TS-deficient cells were transfected with cDNAs encoding the two TS polypeptides. Transfectants expressing the variant TS were more resistant to FdUrd cytotoxicity than cells expressing the common TS. Thus, the structural variation in TS reduced enzyme affinity for FdUMP and conferred resistance to FdUrd.

Colorectal Neoplasms↗
PubMed2006

How the headpiece hinge angle is opened: New insights into the dynamics of integrin activation.

How the integrin head transitions to the high-affinity conformation is debated. Although experiments link activation with the opening of the hinge angle between the betaA and hybrid domains in the ligand-binding headpiece, this hinge is closed in the liganded alpha(v)beta3 integrin crystal structure. We replaced the RGD peptide ligand of this structure with the 10th type III fibronectin module (FnIII10) and discovered through molecular dynamics (MD) equilibrations that when the conformational constraints of the leg domains are lifted, the betaA/hybrid hinge opens spontaneously. Together with additional equilibrations on the same nanosecond timescale in which small structural variations impeded hinge-angle opening, these simulations allowed us to identify the allosteric pathway along which ligand-induced strain propagates via elastic distortions of the alpha1 helix to the betaA/hybrid domain hinge. Finally, we show with steered MD how force accelerates hinge-angle opening along the same allosteric pathway. Together with available experimental data, these predictions provide a novel framework for understanding integrin activation.

Allosteric Regulation↗
PubMed1999

Isoprenoid quinones as biomarkers of microbial populations in the environment.

Isoprenoid quinones are lipid molecules present in all species of respiratory and photosynthetic microorganisms and exhibit marked structural variations depending upon the microbial taxon. Taking advantage of this, quinones have been used not only as chemotaxonomic markers in microbial systematics but also as good measures of microbial populations in the environment in terms of quantity, quality, and activity. Basically, this biomarker approach, called the quinone profile method, is applicable to all environmental samples from which an absolute amount of microbial biomass > or =10(9) cells can be collected. The quinone profile method allows good measurement of both fundamental and applied aspects of ecological and environmental microbiology. In particular, numerical cluster analyses of quinone profiles are useful for monitoring microbial population shifts in an ecosystem which is not amenable to conventional culture methods and molecular techniques. The combined use of molecular techniques and the quinone profile method in this research area should provide more accurate and reliable data regarding population dynamics and community structures.

Journal Article↗