Lipari–Szabo mapping: A graphical approach to Lipari–Szabo analysis of NMR relaxation data using reduced spectral density mapping

In this paper, we explore connections between the Lipari–Szabo formalism and reduced spectral density mapping, and show how spectral density estimates can be associated with Lipari–Szabo parameters via a simple geometric construction which we call Lipari–Szabo mapping. This relationship can be used to estimate Lipari–Szabo parameters from spectral density estimates without the need for nonlinear optimization, and to perform `model selection' in a graphical manner. The Lipari–Szabo map also provides insight into the Lipari–Szabo model, and allows us to determine when a given set of experimental spectral densities are inconsistent with the Lipari–Szabo formalism. Practical applications of Lipari–Szabo mapping in conjunction with more traditional analysis methods are discussed.     

Observations on species of Discocriconemella De Grisse & Loof, 1965 and Macroposthonia de Man, 1880 (Nematoda: Tylenchida: Criconematidae) from Ecuador, with the proposal of M. napoensis n. sp. and M. planilobata n. sp.

Macroposthonia napoensis n. sp. and M. planilobata n. sp. from Ecuador are described and illustrated. Differential characters of M. napoensis are: first annule with four enlarged submedian lobes but not giving the lip region a disc–like appearance , vagina sigmoid, none or very few anastomoses, a poorly–developed spermatheca, L = 0.33–0.42 mm, V = 89–93, stylet = 55–74 µ and R = 73–79. M. planilobata n. sp. can be distinguished by the four large and anteriorly flattened submedian lobes which give the lip region a disc–like appearance, a sigmoid vagina, a conoid–rounded tail with coarse annules, L = 0.41–0.49 mm, a = 11.3–13.3, V = 90–94, stylet = 66.5–78.5 µ and R = 75–84. Measurements from populations of Discocriconemella limitanea and M. surinamensis from Ecuador are also provided. D. repleta is accepted as a junior synonym of D. limitanea, and D. heynsi Van den Berg & Marais, 1995 is proposed as a junior synonym of M. surinamensis.     

Secondary Rhythms of Cardiac Activity in Rat Ontogeny

Endogenous periodic oscillations of the heart beat rate are described in rat pups aged 3–4, 7–8, 10–11, 13–14, 21–22 days and 1.5 month after birth. These oscillations have all characteristic features established earlier for the secondary rhythms of endogenous contractile activity in the wall of various regions of the gastrointestinal tract and for bursts of spontaneous somatomotor excitation in the early postnatal ontogeny of rats: a multi-stage organization, inconstancy, irregularity of components. In frequency spectra of secondary oscillations of the heart rate obtained by means of fast Fourier transform of R–R intervals of the periodogram, age-related changes of the spectral frequency power are demonstrated in 4 ranges, 0.01–0.03, 0.03–0.1, 0.1–1.0, and 1.0–2.5 Hz, which correspond to the about-one-minute, decasecond, and about-one-second waves of the heart rhythm oscillations and to sinus arrhythmia. It is shown that the dominating frequencies of the secondary rhythms in each range do not have regular age-related changes, which is characteristic of all endogenous secondary rhythms.     

Role of cation-pi interactions in single chain 'all-alpha' proteins

Cation–π interactions are known to be important contributors to protein stability and ligand–protein interactions. In this study, we have analyzed the influence of cation–π interactions in single chain ‘all-alpha’ proteins. We observed 135 cation–π interactions in a data set of 75 proteins. No significant correlation was observed between the total number of amino acid residues and number of cation–π interactions. These interactions are mainly formed by long-range contacts and there is preference of Arg over Lys in these interactions. Arg–Phe interactions are predominant among the various pairs analyzed. Despite the scarcity of interactions involving Trp, the average energy for Trp–cation interactions, was quite high. This information implies that the cation–π interactions involving Trp, maybe of high relevance to the proteins. Secondary structure analysis reveals that cation–π interactions are formed preferrably between residues, in which at least one of them, is in the secondary structure of alpha-helical segments. Among the various types of folds of ‘all-alpha’ proteins considered for the analysis, proteins belonging to alpha–alpha superhelix fold have the highest number of cation–π interaction forming residues.     

Dry matter and nutrient inputs through litter fall in a dry tropical forest of India

The present paper elucidates the pattern of leaf and non-leaf fall and quantifies of the total annual input of litter in a dry tropical forest of India. In addition, concentration of selected nutrients in various litter species and their annual return to the forest floor are examined. Total annual input of litter measured in litter traps ranged between 488.0–671.0 g m^-2 of which 65–72% was leaf litter fall and 28–35% wood litter fall. 73–81% leaves fall during the winter season. Herbaceous litter fall ranged between 80.0–110.0 g m^-2 yr^-1. The annual nutrient return through litter fall amounted (kg ha^-1): 51.6–69.6 N, 3.1–4.3 P, 31.0–40.0 Ca, 14.0–19.0 K and 3.7–5.0 Na, of which 71–77% and 23–29% were contributed by leaf and wood litter fall, respectively for different nutrients. Input of nutrients through herbaceous litter was: 13.0–16.6 for N, 1.0–1.4 for P, 4.0–5.0 for Ca, 7.9–10.5 for K and 0.8–1.0 kg ha^-1 yr^-1 for Na.     

Efficient double-stranded DNA cleavage by artificial zinc-finger nucleases composed of one zinc-finger protein and a single-chain FokI dimer

Zinc-finger–FokI nucleases (ZFNs) are useful for manipulating genomic DNA, but two ZFNs are required to cleave one site of double-stranded DNA (dsDNA), which limits the choice of targets. To refine ZFN technology, we constructed artificial zinc-finger nucleases containing an artificial zinc-finger protein (AZP) and a single-chain FokI dimer with nine different peptide linkers between two FokI molecules (designated AZP–scFokI). DNA cleavage assays revealed that the AZP–scFokI variant possessing the longest peptide linker cleaved dsDNA with equal or greater reactivity than the corresponding AZP–FokI dimer. The DNA cleavage pattern of AZP–scFokI suggests that the enhanced dsDNA cleavage was due to increased formation of FokI dimer in AZP–scFokI. Furthermore, we demonstrated that AZP–scFokI site-specifically cleaved its target DNA due to the AZP moiety discriminating one base pair difference. Thus, a single AZP–scFokI molecule is able to cleave dsDNA efficiently and site-specifically, and enhances the usefulness of the ZFN approach.     

The Disulfide Bond Arrangement in the Extracellular Domain of the Activin Type II Receptor

The initial step in the signaling cascade of the growth factor activin involves its binding to the extracellular domain of the activin type II receptor. This receptor domain contains 10 cysteine residues which are engaged in intramolecular disulfide bonds. To elucidate the structural framework of this domain we have characterized its disulfide-bonding pattern using an extracellular fragment of the receptor which binds activin A with high affinity. By combining proteolysis with mass spectroscopy and chemical sequence analysis, the disulfide connectivity was determined to be as follows: C1–C3, C2–C4, C5–C8, C6–C7, and C9–C10. A similar disulfide arrangement occurs in a family of snake toxins for which the three-dimensional structure is known.     

Inhibition in the fish olfactory bulb

Inhibition in the olfactory bulb of the carp was studied by recording potentials from secondary neurons intracellularly. Three types of inhibition — trace, early, and late — can arise in neurons of the olfactory bulb. Trace inhibition corresponds to hyperpolarization about 20 msec in duration, which is closely connected with the spike, but it is not after-hyperpolarization but an IPSP. Early and late inhibition correspond to IPSPs of different parameters. The first has a latency of 0–50 msec (relative to the spike) and a duration of 60–400 msec; the corresponding values for the second are 100–400 msec and 0.5–3 sec. The possible mechanisms of these types of inhibition are discussed.M. V. Lomonosov Moscow State University. Translated from Neirofiziologiya, Vol. 3, No. 6, pp. 650–656, November–December, 1971.     

Different strategies for the chemical synthesis of lignans

This paper summarises the results of three projects. The first is concerned with developing general routes for the synthesis of lignans. In particular, two routes involving tandem conjugate addition reactions and Diels Alder reactions respectively that have been used to synthesise podophyllotoxin derivatives are described. The second project is concerned with the asymmetric synthesis of lignans and involves the application of these reactions, with the introduction of a menthyloxy group as a chiral auxiliary, to achieve the asymmetric synthesis of podophyllotoxin derivatives. The third project is concerned with the attempted biomimetic syntheses of podophyllotoxin derivatives using oxidative coupling reactions. Attention is focussed primarily on the use of hypervalent iodine reagents, which yield stegane and isostegane derivatives rather than podophyllotoxin derivatives. Other examples of biaryl coupling leading to stegane and isostegane derivatives are included, and other examples of lignan synthesis involving hypervalent iodine reagents are also described. Abbreviations: DDQ – 2,3-dichloro-5,6-dicyano-1,4-benzoquinone; DMAD – dimethyl acetylenedicarboxylate (dimethyl butynedioate); PIDA – phenyliodonium diacetate, iodobenzene diacetate; PIFA – phenyliodonium bis(trifluoroacetate), [bis(trifluoroacetoxy) iodobenzene]; Ra-Ni – Raney nickel; TBAF – tetrabutylammonium fluoride; TBDMS –t-butyldimethylsilyl; TFA – trifluoroacetic acid; TFAA – trifluoroacetic anhydride; TFE – 2,2,2-trifluoroethanol; TTFA – thallium(III) trifluoroacetate.     

Trophic roles of particle feeders and detritus in a mangrove island prop root ecosystem

Swarms of Dioithona oculata, shoals of Mysidium columbiae, and schools of planktivorous fish were observed among mangrove prop roots on a lagoonal island. Detritus covering epiphytic and benthic macroalgae and invertebrates was a probable food source for pelagic mysids, and copepods, as well as benthic oysters and sponges. Open water blooms of dinoflagellate Amphidinium klebsii were probably only accessible to the swarming dioithonans which spend the night away from the mangrove prop roots. Dominant species were analyzed for stable carbon isotopic composition (expressed as ¹³C%.) to elucidate the origin and fate of detritus. Detrital components (–23.6 to –19.1%.), which included floating detritus, marine snow, prop root detritus, and detritus below prop roots, probably originated from the dominant subtidal macroalgal species (–24.2 to –14.6%.) and A. klebsii (–25.8 to –21.2%.), although other sources which are end-members could theoretically contribute since detrital isotopic ratios are half way between end-members. These other sources include the intertidal red algal Bostrychia spp. (–30.9 to –29.6%.), red mangrove Rhizophora mangle leaves (–28.2 to –27.0%.), and turtle grass Thalassia testudinum (–12.3 to –11.1%.). Particle feeders such as mangrove oysters, sponges, mysids, and dioithonans were usually enriched with ¹³C (–21.0 to –16.2%.) compared to their probable food sources, detritus and A. klebsii. At Anchovy Bay, adult mysids and planktivorous fish were more ¹³C enriched (1–3%.) than their probable prey, the dioithonans. Turtle grass may have a minor role in food webs, since dioithonans and mysids from Outer Twin and Anchovy Bays where turtle grass beds were abundant were consistently more ¹³C enriched (2–7%.) than in the Lair Channel where turtle grass beds were sparse.