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Biomedical subjects

J Ding

Publications and source records attributed to J Ding.

At least 199 records · Page 11Linked to original sources

Crystal structure of the human adenovirus proteinase with its 11 amino acid cofactor.

The three-dimensional structure of the human adenovirus-2 proteinase complexed with its 11 amino acid cofactor, pVIc, was determined at 2.6 A resolution by X-ray crystallographic analysis. The fold of this protein has not been seen before. However, it represents an example of either subtly divergent or powerfully convergent evolution, because the active site contains a Cys-His-Glu triplet and oxyanion hole in an arrangement similar to that in papain. Thus, the adenovirus proteinase represents a new, fifth group of enzymes that contain catalytic triads. pVIc, which extends a beta-sheet in the main chain, is distant from the active site, yet its binding increases the catalytic rate constant 300-fold for substrate hydrolysis. The structure reveals several potential targets for antiviral therapy.

Adenoviruses, Human↗

The importance of patient preference in the decision to screen for prostate cancer. Prostate Patient Outcomes Research Team.

OBJECTIVE: Routine screening for prostate cancer is controversial because of frequent false-positive results, the potential for slow, non-life-threatening growth of untreated cancer, the uncertainty regarding whether treatment can extend life, and the potential for treatment complications. This study examines how information about prostate-specific antigen (PSA) testing and the uncertain benefits of treating prostate cancer affects patients' desire for PSA testing. DESIGN: An educational videotape designed to inform men about the uncertainty surrounding PSA screening and the treatment of early-stage prostate cancer was presented to two groups of male patients 50 years of age or older. SETTING: Dartmouth-Hitchcock Medical Center. PATIENTS/PARTICIPANTS: For study 1, men seeking a free prostate cancer screening were preassigned to view the educational videotape (N = 184) or another videotape (N = 185). For study 2, men scheduled to visit a general internal medicine clinic viewed either the educational videotape (N = 103) or no videotape (N = 93). MEASUREMENTS AND MAIN RESULTS: The men's information and preferences about prostate cancer screening and treatment and actual choice of PSA test at the next test opportunity were measured. Men who viewed the educational videotape were: better informed about PSA tests, prostate cancer, and its treatment; preferred no active treatment if cancer were found; and preferred not to be screened (all significant at p < or = .002 in both studies). Men viewing the educational video were less likely to have a PSA test (p = .041, study 2). This tendency was not significant at the free-PSA clinic (p = .079). CONCLUSIONS: Preference regarding cancer screening and treatment is greatly affected by information about medical uncertainties. Because informed patient choices vary. PSA screening decisions should incorporate individual preferences.

Case-Control Studies↗

In vitro fertilization of in vitro matured pig oocytes: effects of boar and ejaculate fraction.

Ejaculates from 3 young boars were collected on 4 occasions as a series of separate 15-ml fractions. The contribution of different fractions of these ejaculates to observed variability in the quality of the semen when used for IVF was then determined. On the basis of sperm concentration, 3 fractions representing the first peak concentration (Fraction 1), the lowest sperm concentration after Fraction 1 (Fraction 2), and the second peak concentration (Fraction 3) were selected for analysis in vitro. Oocyte-cumulus-granulosa cell complexes were obtained by dissection from slaughterhouse ovaries. In vitro matured oocytes were randomly assigned for fertilization by the 3 semen samples from each boar. Sperm concentration was the same in all the samples during prefertilization incubation, while the final concentration for fertilization was 5 x 10(5) sperm/ml. Data were analysed using ANOVA for a split-plot design. In the presence of fraction effects, Student-Newman-Keuls (SNK) test was used for multiple comparison of treatment means. Oocyte penetration rates differed among fractions (P = 0.001) and varied from 69 to 100% (mean 95.7%) for Fraction 1, from 0 to 100% (mean 53.3%) for Fraction 2, and from 50to 100% (mean 89.9%) for Fraction 3. There were also differences in male pronuclear formation rate (P = 0.028; mean 27.6, 9.3 and 16.4% for Fractions 1, 2 and 3, respectively); in the rate of polyspermy (P = 0.0001; mean 92.3, 31.9 and 76.3% for Fractions 1, 2 and 3, respectively); and in the number of penetrated spermatozoa per oocyte P = 0.002; mean 5.58, 1.94 and 4.07 for Fractions 1, 2, and 3, respectively). The first peak concentration of semen (Fraction 1) showed superiority in fertilizing ability and less variability in penetration rate from replicate to replicate compared with the other 2 fractions. By multiple comparison, Boar 1 showed higher rates of penetration (P < 0.05), male pronuclear formation (P < 0.05) and polyspermy (P < 0.05) than the other 2 boars. There was no fraction-by-boar interaction. The IVM-IVF system adopted proved to be a promising method for boar semen evaluation.

Journal Article↗

Response properties of units in the dorsal cochlear nucleus of unanesthetized decerebrate gerbil.

1. The electrophysiological responses of single units in the dorsal cochlear nucleus of unanesthetized decerebrate Mongolian gerbil (Meriones unguiculatus) were recorded. Units were classified according to the response map scheme of Evans and Nelson as modified by Young and Brownell, Young and Voigt, and Shofner and Young. Type II units have a V-shaped excitatory response map similar to typical auditory nerve tuning curves but little or no spontaneous activity (SpAc < 2.5 spikes/s) and little or no response to noise. Type I/III units also have a V-shaped excitatory map and SpAc < 2.5 spikes/s, but have an excitatory response to noise. Type III units have a V-shaped excitatory map with inhibitory sidebands, SpAc > 2.5 spikes/s, and an excitatory response to noise. Type IV-T units typically also have a V-shaped excitatory map with inhibitory sidebands, but have a highly nonmonotonic rate versus level response to best frequency (BF) tones like type IV units, SpAc > 2.5 spikes/s, and an excitatory response to noise. Type IV units have a predominantly inhibitory response map above an island of excitation of BF, SpAc > 2.5 spikes/s, and an excitatory response to noise. We present results for 133 units recorded with glass micropipette electrodes. The purpose of this study was to establish a normative response map data base in this species for ongoing structure/function and correlation studies. 2. The major types of units (type II, type I/III, type III, type IV-T, and type IV) found in decerebrate cat are found in decerebrate gerbil. However, the percentage of type II (7.5%) and type IV (11.3%) units encountered are smaller and the percentage of type III (62.4%) units is larger in decerebrate gerbil than in decerebrate cat. In comparison, Shofner and Young found 18.5% type II units, 30.6% type IV units, and 23.1% type III units using metal electrodes. 3. Two new unit subtypes are described in gerbil: type III-i and type IV-i units. Type III-i units are similar to type III units except that type III-i units are inhibited by low levels of noise and excited by high levels of noise whereas type III units have strictly excitatory responses to noise. Type IV-i units are similar to type IV units except that type IV-i units are excited by low levels of noise and become inhibited by high levels of noise whereas type IV units have strictly excitatory responses to noise. Type III-i units are approximately 30% of the type III population and type IV-i units are approximately 50% of the type IV population. 4. On the basis of the paucity of classic type II units and the reciprocal responses to broadband noise of type III-i and type IV-i units, we postulate that some gerbil type III-i units are the same cell type and have similar synaptic connections as cat type II units. 5. Type II and type I/III units are distinguished from one another on the basis of both their relative noise response, rho, and the normalized slope of the BF tone rate versus level functions beyond the first maximum. Previously, type II units were defined to be those nonspontaneously active units with rho values < 0.3 where rho is defined as the ratio of the maximum noise response minus spontaneous rate to the maximum BF tone response minus spontaneous rate. In the gerbil, the average rho value for type II units is 0.25, although a few values are > 0.3, and the rate-level curves are consistently nonmonotonic with normalized slopes steeper than than -0.007/dB. The average rho value for type I/III units is 0.54, although a few values are < 0.3, and the rate-level curves tend to saturate with slopes shallower than -0.006/dB. In general, the response properties of type II units recorded in gerbil are similar to those recorded in decerebrate cat. 6. In comparison to decerebrate cat, the lower percentage of type IV units recorded in decerebrate gerbil may be due to a species difference (a reduced number of type II units in gerbil) or an electrode bias.

Animals↗

Analysis of multiple conductance states observed in Ca2+ release channel of sarcoplasmic reticulum.

Both slowly and rapidly fluctuating currents were observed after incorporating a heavy sarcoplasmic reticulum (HSR) vesicle or a purified ryanodine receptor (RyR) of rabbit skeletal muscle into a lipid bilayer. The responses to the cis side Ca2+, ruthenium red and ryanodine confirmed that both were the currents through one Ca2+ release channel. From the analysis of conductance states, RyR is supposed to have two different configurations. The current through one configuration has a high reversal potential (HRP) (-18 mV) and that through another one has a low reversal potential (LRP) (-11 mV). The current with HRP fluctuates rapidly but the current with LRP always fluctuates slowly. From the analysis of both rapidly and slowly fluctuating currents, it was shown that there are four pores in RyR. Among the conductance states of the slowly fluctuating current with LRP, the conductance of the 4OP (four opened pores) state was smaller than four times that of 1OP (one opened pore). To explain this fact, we proposed a model of the channel, a large central pore in series with four small parallel pores. The calculation according to the model has a good fit with the bilayer measurement.

Animals↗

Molecular replacement study on form-B monoclinic crystal of insulin.

The form-B monoclinic insulin crystal was obtained from the sodium citrate buffer with 1% zinc chloride, keeping phenolic content between 0.76% and 1.25%. Its space group is P2(1), cell constants are: a = 4.924 nm, b = 6.094 nm, c = 4.818 nm, beta = 95.8 degrees. There are 6 insulin molecules which form a hexamer. The initial phase was obtained by using rotation function program of X-PLOR program package and molecular packing program of our laboratory. The molecular model was chosen from 4 zinc bovine insulin hexamer. After the preliminary refinement by using the macromolecular rigid body refinement technique, the molecular model was further refined and adjusted by using the energy-minimizing stereochemically restrained least-squared refinement on the difference Fourier maps. The final R-factor is 22.4% at 0.3 nm resolution, the r.m.s. deviations from standard bond length and bond angle are 0.0022 nm and 4.7 degrees, respectively.

Crystallography↗

Targeting HIV reverse transcriptase for anti-AIDS drug design: structural and biological considerations for chemotherapeutic strategies.

The reverse transcriptase of HIV is a key target for the antiviral treatment of AIDS. Numerous potent inhibitors of RT have been described including all of the drugs that have been currently licensed for the treatment of AIDS, but their efficacy has been limited by the emergence of drug-resistant HIV variants. Extensive biochemical, genetic, and clinical data about HIV RT enzymatic mechanisms, inhibition, and drug resistance have been reported. This information, taken together with structural data from crystallographic studies of HIV-1 RT, has set the stage for structure-based design of improved inhibitors of this essential viral enzyme. Comparisons of the different crystal structures of HIV-1 RT shows that the enzyme has great conformational flexibility, providing additional possibilities for drug targeting. Recent clinical and virological data suggest that HIV-1 RT enzymes that carry drug-resistance mutations can be substantially impaired and that combinations of RT inhibitors can produce significant clinical benefit in the treatment of AIDS. An immediate goal is to use the available information to design specific inhibitors or combination therapies that will select for relatively less fit HIV variants.

Binding Sites↗

Construction of a stable expression vector carrying sop genes [ZJ1].

Mini-F, the fifth fragment of F plasmid from EcoRI digestion, is known to carry an efficient partitioning function. Two pBR322 plasmid derivatives, pDMC32 and pDMC311, have been constructed from this fragment. The plasmid pDMC32 carries all the relative genes for plasmid stability, ccd, repD, and sop genes (sopA, sopB, and sopC), along with oriS and oriV, while pDMC311 carries only sop genes (sopA, sopB, and sopC). The plasmid maintenance proportions for pDMC32 and pDMC311 in E. coli were 93% and 100%, respectively, after 100 generations continuous cultivation of cells harboring the derivatives, MI32 (pDMC32) and MI311 (pDMC311), in a phosphate-limited basal medium. As a control, the maintenance proportion of plasmid pBR322 dropped down to a low of 10% at generation 55 of continuous cultivation of E. coli MIR322 (pBR322) in the same medium. In order to make a stable expression vector that carries only sop genes, plasmid pDMC40 was constructed by adding a trp promoter from pDR720 to pBR322. The stable expression vector pDMC48 was then derived from pDMC40 by inserting sop genes into it from pDMC311. The maintenance proportion of plasmid pDMC48 in E. coli was still 100% after 100 generations of continuous cultivation of cells harboring the plasmid in phosphate-limited basal medium.

Ampicillin↗

[Lung carcinosarcoma--a report of 15 cases].

Lung carcinosarcoma is a rare pulmonary mixed malignant tumor. From November 1979 to Sept. 1992, among 4251 cases of pulmonary malignant tumor operated in our department 15 were lung carcinosarcoma (0.35%). Pneumonectomy was done in 6 patients, lobectomy in 8, thoacotomy in 1. Pathologically, squamous carcinoma with fibrosarcoma was observed in 4, squamous carcinoma with chondrosarcoma in 1, squamous carcinoma with pleomorphic sarcoma in 1, adenocarcinomma with fibrosarcoma in 7, adenocarcinoma with chondrosarcoma in 1, and small-cell carcinoma with chondrosarcoma in 1. There was no operation death. Upon follow up, the 1-, 3-, 5-, and 7-year survival rates were 66.7%, 53.3%, 42.9% and 2/7, respectively. The longest survival was 97 months. The histologica origin, the relationship between pathological findings and clinical features and the diagnosis, treatment and prognosis are discussed.

Adult↗

Preparation of monoclonal antibodies against chicken liver 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase and their effects on enzyme activities.

The effects of the monoclonal antibodies (McAbs) directed against chicken liver 6-phosphofructo-2-kinase/fructose-2, 6-bisphosphatase (6PF-2-K/Fru-2, 6-P2ase) on the structure and function of the enzyme were studied. Using chicken liver 6PF-2-K/Fru-2, 6-P2ase as antigen, 7 clones of monoclonal antibodies specifically binding with the antigen were obtained. The epitopes of the antigen recognized by the 6 McAbs localized on the fructose-2, 6-bisphosphatase domain of chicken liver 6PF-2-K/Fru-2, 6-P2ase, and the other (H2) are on the 6-phosphofructo-2-kinase domain. All of the 7 McAbs could activate the kinase activity of the bifunctional enzyme by twofold and had a similar effect on the bisphosphatase activity of the bifunctional enzyme which resulted in a fourfold increase of the bisphosphatase activity of the bifunctional enzyme. However, the McAbs did not affect the activity of the separated fructose-2, 6-bisphosphatase domain. The results suggested that the Fru-2, 6-P2ases in the bifunctional enzyme and in the separated bisphosphatase domain were in two different conformation and activity states.

Animals↗

Naphthalenesulphonamides block neutrophil superoxide production by intact cells and in a cell-free system: is myosin light chain kinase responsible for these effects?

Selective antagonists of myosin light chain kinase (MLCK) [e.g. ML-7; 1-(5-iodonaphthalene-1-sulphonyl)-1H-hexahydro-1,4-diazepine hydrochloride] were found to inhibit superoxide (O2-) release from stimulated neutrophils. The concentrations of ML-7 that were inhibitory were substantially lower than those reported for a selective antagonist of protein kinase C [i.e. H-7; 1-(5-isoquinolinesulphonyl)-2-methylpiperazine dihydrochloride]. ML-7 also reduced the phosphorylation of the 47 kDa subunit of the NADPH-oxidase system (p47-phox) and blocked translocation of this protein to the Triton X-100-insoluble fraction in stimulated cells. Interestingly, ML-7 also inhibited O2- production in a cell-free system derived from neutrophils at concentrations similar to those that were effective in vivo. This cell-free system does not require ATP and is insensitive to all other inhibitors of protein kinases tested, including some highly effective against MLCK (i.e. staurosporine). Thus, the data suggest that ML-7 does not block O2- release by inhibiting a protein kinase but instead may interact directly with a subunit of the oxidase. The binding site for ML-7 may provide a valuable target for inhibiting the inflammatory properties of phagocytic leucocytes by naphthalenesulphonamides designed to lack activity against protein kinases.

1-(5-Isoquinolinesulfonyl)-2-Methylpiperazine↗

Antagonists of phosphatidylinositol 3-kinase block activation of several novel protein kinases in neutrophils.

Several novel protein kinases are known to be rapidly activated in neutrophils stimulated with the chemoattractant fMet-Leu-Phe (fMLP). These kinases include a histone H4 protein kinase and several renaturable kinases with molecular masses of about 69, 63, 49, and 40 kDa. The renaturable kinases can catalyze the phosphorylation of a peptide that corresponds to residues 297-331 of the 47-kDa subunit of the NADPH-oxidase system (p47-phox). Previous studies have indicated that the activation of all of these protein kinases involves an uncharacterized stimulatory pathway and/or novel second messenger. The studies reported herein were undertaken to determine if phosphatidylinositol 3-kinase (PI3-K) is a component of this pathway. We report that certain chromosome derivatives (e.g. 2-(4-morpholinyl)-8-phenylchromone (LY294002)) and wortmannin, which inhibit PI3-K by distinct mechanisms, blocked activation of all of these novel kinases. These antagonists also inhibited the phosphorylation of p47-phox (about 50%) and O2.- release (about 80%) in cells stimulated with fMLP, but not with 4 beta-phorbol 12-myristate 13-acetate. A strong correlation exists between the amounts of these antagonists required to produce 50% inhibition of PI3-K in vitro and O2.- release in vivo. In contrast, a single atom substitution of LY294002 produced a compound (LY303511) that did not inhibit PI3-K. Compound LY303511 did not appreciably inhibit the activation of the novel protein kinases or O2.- generation. These data strongly suggest that PI3-K is involved in the activation of several novel protein kinases in neutrophils, one or more of which may be involved in O2.- release.

Androstadienes↗

Insights into DNA polymerization mechanisms from structure and function analysis of HIV-1 reverse transcriptase.

When the single-stranded RNA genome of HIV-1 is copied into double-stranded DNA, the viral enzyme reverse transcriptase (RT) catalyzes the addition of approximately 20,000 nucleotides; however, the precise mechanism of nucleotide addition is unknown. In this study, we attempt to integrate the genetic data and biochemical mechanism of DNA polymerization with the structure of HIV-1 RT complexed with a dsDNA template-primer. The first step of polymerization involves the physical association of a polymerase with its nucleic acid substrate. A comparison of the structures of HIV-1 RT in the presence and absence of DNA indicates that the tip of the p66 thumb moves approximately 30 A upon DNA binding. This conformational change permits numerous interactions between residues of alpha-helices H and I in the thumb subdomain and the DNA. Measurements of DNA binding affinity for nucleic acids with double-stranded DNAs that have an increasing number of bases in the template overhang and molecular modeling suggest that portions of beta 3 and beta 4 within the fingers subdomain bind single-stranded regions of the template. Measurements of nucleotide incorporation efficiency (kcat/Km) show that the binding and incorporation of the next complementary nucleotide are not dependent on the length of the template overhang. Molecular modeling of an incoming nucleotide triphosphate (dTTP), based in part on the position of mercury atoms in a RT/DNA/Hg-UTP/Fab structure, suggests that portions of secondary structural elements alpha C-beta 6, alpha E, beta 11b, and beta 9-beta 10 determine the topology of the dNTP-binding site. These results also suggest that nucleotide incorporation is accompanied by a protein conformational change that positions the dNTP for nucleophilic attack. Nucleophilic attack by the oxygen atom of the 3'-OH group of the primer strand could be metal-mediated, and Asp185 may be directly involved in stabilizing the transition state. The translocation step may be characterized by rotational as well as translational motions of HIV-1 RT relative to the DNA double helix. Some of the energy required for translocation could be provided by dNTP hydrolysis and could be coupled with conformational changes within the nucleic acid. A structural comparison of HIV-1 RT, Klenow fragment, and T7 RNA polymerase identified regions within T7 RNA polymerase which are not present in the other two polymerases that might help this polymerase to remain bound with nucleic acids and contribute to the ability of the T7 RNA polymerase to polymerize processively.

Amino Acid Sequence↗

Structure of HIV-1 reverse transcriptase in a complex with the non-nucleoside inhibitor alpha-APA R 95845 at 2.8 A resolution.

BACKGROUND: HIV-1 reverse transcriptase (RT) is a multifunctional enzyme that copies the RNA genome of HIV-1 into DNA. It is a heterodimer composed of a 66 kDa (p66) and a 51 kDa (p51) subunit. HIV-1 RT is a crucial target for structure-based drug design, and potent inhibitors have been identified, whose efficacy, however, is limited by drug resistance. RESULTS: The crystal structure of HIV-1 RT in complex with the non-nucleoside inhibitor alpha-anilinophenyl-acetamide (alpha-APA) R95845 has been determined at 2.8 A resolution. The inhibitor binds in a hydrophobic pocket near the polymerase active site. The pocket contains five aromatic amino acid residues and the interactions of the side chains of these residues with the aromatic rings of non-nucleoside inhibitors appear to be important for inhibitor binding. Most of the amino acid residues where mutations have been correlated with high levels of resistance to non-nucleoside inhibitors of HIV-1 RT are located close to alpha-APA. The overall fold of HIV-1 RT in complex with alpha-APA is similar to that found when in complex with nevirapine, another non-nucleoside inhibitor, but there are significant conformational changes relative to an HIV-1 RT/DNA/Fab complex. CONCLUSIONS: The non-nucleoside inhibitor-binding pocket has a flexible structure whose mobility may be required for effective polymerization, and may be part of a hinge that permits relative movements of two subdomains of the p66 subunit denoted the 'palm' and 'thumb'. An understanding of the structure of the inhibitor-binding pocket, of the interactions between HIV-1 RT and alpha-APA, and of the locations of mutations that confer resistance to inhibitors provides a basis for structure-based design of chemotherapeutic agents for the treatment of AIDS.

Acetamides↗

Farnesyl thiotriazole, a potent neutrophil agonist and structurally novel activator of protein kinase C.

Farnesylcysteine derivatives can initiate or inhibit superoxide (O2-) release in neutrophils. The mechanism by which one of these derivatives, farnesyl thiotriazole (FTT), initiates O2- release in neutrophils is the subject of this paper. Treatment of guinea pig neutrophils with FTT results in the rapid release of O2- by a route shown to be independent of the chemotactic peptide N-formyl-Met-Leu-Phe (fMLP) receptor. The signal transduction pathway utilized by the chemoattractant fMLP is generally accepted as the paradigm for receptor-mediated stimulation of O2- production. Antagonists of fMLP had no effect on FTT-induced O2- release, and pretreatment of neutrophils with fMLP had no effect on the ability of FTT to trigger further O2- generation. In fact, FTT behaves like a typical protein kinase C (PKC) activator. It promotes phosphorylation of the 47-kDa subunit of the NADH oxidase complex (p47-phox) in neutrophils, and this phosphorylation is specifically blocked by 1-(5-isoquinolinylsulfonyl)-2-methylpiperazine (H-7), an antagonist of PKC. FTT is also shown to activate PKC in vitro in a specific and saturable fashion. FTT is approximately equipotent with (S)-diolein, a physiologically relevant activator of this kinase. FTT represents a new, and quite novel, structure for a PKC activator. PKC activators include diglycerides and the structurally diverse tumor promoters.

Animals↗

Synthesis of phospholipid-based detergents and their effects on the Ca(2+)-ATPase of sarcoplasmic reticulum.

Phospholipid molecules containing a cholate or hemisuccinylcholate moiety at the 2-position were synthesized as possible detergents for solubilization of membrane proteins. 1-Myristoleoyl-2-cholyl-sn-glycero-3- phosphatidylcholine ((C14:1,cholyl)PC) was found to solubilize sarcoplasmic reticulum vesicles at concentrations above its cmc of ca. 4 micrograms/ml. Effects of (C14:1,cholyl)PC on the activity of the Ca(2+)-ATPase of sarcoplasmic reticulum were complex, as for other detergents. High concentrations (0.2 mg/ml) of (C14:1,cholyl)PC were able to displace phospholipids from the lipid/protein interface of the ATPase. Although under these conditions the activity of the ATPase was low, the ATPase was not denatured since activity could be regained by displacement of (C14:1,cholyl)PC with the detergent C12E8. 1-oleoyl-2-cholyl-sn-glycero-3-phosphatidylcholine ((C18:1,cholyl)PC) was found to have a very low water solubility, but this could be increased by the introduction of a hemisuccinyl group to give 1-oleoyl-2-(3 alpha-hemisuccinyl)cholyl-sn-glycero-3-phosphatidylcholine ((C18:1,cholylCOOH)PC). This was able to solubilize and delipidate the Ca(2+)-ATPase; the ATPase was stable in (C18:1,cholylCOOH)PC for long periods of time.

Animals↗