Fast and reliable analysis of molecular motion using proximity relations and dimensionality reduction

The analysis of molecular motion starting from extensive sampling of molecular configurations remains an important and challenging task in computational biology. Existing methods require a significant amount of time to extract the most relevant motion information from such data sets. In this work, we provide a practical tool for molecular motion analysis. The proposed method builds upon the recent ScIMAP (Scalable Isomap) method, which, by using proximity relations and dimensionality reduction, has been shown to reliably extract from simulation data a few parameters that capture the main, linear and/or nonlinear, modes of motion of a molecular system. The results we present in the context of protein folding reveal that the proposed method characterizes the folding process essentially as well as ScIMAP. At the same time, by projecting the simulation data and computing proximity relations in a low-dimensional Euclidean space, it renders such analysis computationally practical. In many instances, the proposed method reduces the computational cost from several CPU months to just a few CPU hours, making it possible to analyze extensive simulation data in a matter of a few hours using only a single processor. These results establish the proposed method as a reliable and practical tool for analyzing motions of considerably large molecular systems and proteins with complex folding mechanisms.     

A procedure for quantification of cytokinins as free bases involving scintillation proximity immunoassay

Cytokinins occur in a diversity of forms and determination of their individual levels requires extensive purification. However, determination of the total level of each major base in free, riboside and nucleotide forms would often be adequate. Hence, a methanolysis procedure which releases cytokinin bases from 9-ribosyl derivatives was developed and applied to plant extracts. A simple procedure, involving low pressure column chromatography, for purification of the cytokinin bases in treated extracts, and a scintillation proximity immunoassay for their quantification, were developed. The total level of each cytokinin base [N⁶-(2-isopentenyl)adenine, zeatin and dihydrozeatin] in free and ribosylated forms determined by these methods is reported for several plant tissues and the results are compared with those obtained after additional purification by HPLC. Values for zeatin were not changed by HPLC but isopentenyl-adenine and dihydrozeatin levels were usually reduced indicating the presence of unknown compounds which cross-react in the immunoassay. Modifications to the above purification method to quantify O-glucosyl cytokinins are also described.
The methods described facilitate the quantification of the total amount of each cytokinin base in forms closely associated with cytokinin action, and the detection of cytokinin biosynthesis by labelled precursor incorporation.     

Self-assembly of proximity probes for flexible and modular proximity ligation assays

Proximity ligation assay (PLA) is a recently developed strategy for protein analysis in which antibody-based detection of a target protein via a DNA ligation reaction of oligonucleotides linked to the antibodies results in the formation of an amplifiable DNA strand suitable for analysis. Here we describe a faster and more cost-effective strategy to construct the antibody-based proximity ligation probes used in PLA that is based on the noncovalent interaction of biotinylated oligonucleotides with streptavidin followed by the interaction of this complex with biotinylated antibodies.     

Isolation and characterization of a second molybdopterin dinucleotide: molybdopterin cytosine dinucleotide

The pterin cofactor (bactopterin) in the molybdoenzyme CO dehydrogenase isolated from Pseudomonas carboxydoflava has previously been shown to differ from molybdopterin in molecular mass, phosphate content, stability, and other properties, implying a novel structure. The structure of the CO dehydrogenase pterin has been investigated in the present studies by alkylation and isolation of the carboxamidomethyl derivative. The alkylated pterin was identified as [di-(carboxamidomethyl)]molybdopterin cytosine dinucleotide on the basis of its absorption properties and by degradation with nucleotide pyrophosphatase yielding carboxamidomethylmolybdopterin and CMP. Further treatment of these products with alkaline phosphatase produced species with absorption and chromatographic properties identical to those of the corresponding dephospho compounds. Molybdopterin cytosine dinucleotide is the second molybdopterin variant to be structurally characterized. The fact that molybdopterin cytosine dinucleotide and molybdopterin guanine dinucleotide contain molybdopterin in their structure shows that the pterin moiety, with its unique dithiolene-containing sidechain, is a structural element which is common to the organic portion of the molybdenum cofactors of many molybdoenzymes.     

DNA sequence specificity of 4,5',8-trimethylpsoralen cross-linking. Effect of neighboring bases on cross-linking the 5'-TA dinucleotide

The DNA sequence specificity for 4,5',8-trimethylpsoralen cross-linking of DNA has been examined using chemically synthesized DNA fragments containing all possible pyrimidine and purine base pair combinations. We confirm our previous findings that the 5'-TA dinucleotide represents a preferred cross-link site. Other dinucleotides that form cross-links are 5'-AT much greater than 5'-TG greater than 5'-GT. Although 5'-TA represents a preferred cross-link site, the rate of cross-linking can vary 3-4-fold depending on the base composition flanking the cross-linkable 5'-TA dinucleotide. In some cases, changes in DNA sequence 3 base pairs (bp) away from 5'-TA resulted in significant changes in the rate of cross-linking. We also see evidence for a long-range sequence context effect on the rate of cross-linking. A 30-bp fragment cross-linked at a relative rate of 2.9 compared to the rate of cross-linking of a 20-bp fragment when cloned contiguously in plasmid DNA. When cross-linked as separate fragments, the 30-bp fragment cross-linked at a relative rate of 1.9 compared to the 20-bp fragment. The results suggest that the reactivity of DNA to psoralens, and perhaps other intercalating drugs, is dependent on the dinucleotide sequence, the bases flanking the dinucleotide, and the long-range sequence context of the DNA.     

Effects of spatial proximity and alliances on dominance relations among female ring-tailed lemurs (Lemur catta) at Berenty Reserve, Madagascar

In the present study, we describe a change in the dominance rank of the top-ranking female in a wild troop of ring-tailed lemurs (Lemur catta) at Berenty Reserve, Madagascar. After the top-ranking female fell to the bottom-ranking position, she was able to outrank a low-ranking female with the support of her adult daughter or an unrelated high-ranking female. These results indicate that, as in cercopithecine monkeys such as macaques and baboons, close proximity and alliances influence dominance relations among adult females in a wild troop of ring-tailed lemurs.     

Light-induced conversion of nicotinamide adenine dinucleotide to nicotinamide adenine dinucleotide phosphate in higher plant leaves

Light-induced conversion of NAD to NADP was investigated in higher plants. Upon illumination, conversion of NAD to NADP was observed in intact leaves of wheat and pea following incubation in the dark. This conversion was also observed in mesophyll protoplasts of wheat leaves when they were isolated in the dark or isolated in light and then preincubated in the dark. Chloroplasts isolated from wheat protoplasts prepared in the dark carried out the conversion. The conversion in the mechanically isolated spinach chloroplasts was observed only when they were isolated in the dark from leaves preincubated in darkness.     

Reciprocal host-parasite relations as exemplified byChrysomphalus aonidum [Homoptera: Diaspididae] andPteroptrix smithi [Hymenoptera: Aphelinidae]

The parasitePteroptrix smithi (Compere) prefers to oviposit in hosts (Chrysomphalus aonidum L.) that are at least 5 weeks old. Parasitization of two week old hosts is possible, but only few parasites reach maturity, and the developmental duration is lengthened by about one third. The sex ratio with both large and small hosts was usually 1∶2, whereas the average number of emerging parasites varied from 1.9 for 2 week old hosts to 3–4 for 5 week old ones. Non-ovipositing scales that are attacked by the parasite will fail to reproduce and ovipositing ones will only produce part of their potential progeny. Other externally observable changes in the young parasitized host include the formation of a thinner scale cover that differs in coloration and size from the normal one.     

Reciprocal altruism in bats and other mammals

In this paper five conditions are specified which must be met before reciprocal altruism, rather than kin selection, should be invoked. Four purported mammalian examples— social grooming in coati, cluster position in roosting pallid bats, information exchange among greater spear-nosed bats, and blood regurgitation among vampire bats—are examined to determine if reciprocal altruism is necessary to plausibly explain each situation. Results from a computer simulation which apportions the relative selective advantage of vampire bat food sharing to kin selection and reciprocal altruism are then presented. The results demonstrate that the increase in individual survivorship due to reciprocal food sharing events in this species provides a greater increase in inclusive fitness than can be attributed to aiding relatives. This analysis suggests that reciprocal altruism can be selectively more important than kin selection when altruistic behaviors in a relatively large social group occur frequently and provide a major fitness benefit to the recipient even when that recipient is related to the donor.