Does secondary structure determine tertiary structure in proteins?

Is highly approximate knowledge of a protein's backbone structure sufficient to successfully identify its family, superfamily, and tertiary fold? To explore this question, backbone dihedral angles were extracted from the known three‐dimensional structure of 2,439 proteins and mapped into 36 labeled, 60° × 60° bins, called mesostates. Using this coarse‐grained mapping, protein conformation can be approximated by a linear sequence of mesostates. These linear strings can then be aligned and assessed by conventional sequence‐comparison methods. We report that the mesostate sequence is sufficient to recognize a protein's family, superfamily, and fold with good fidelity. Proteins 2005. © 2005 Wiley‐Liss, Inc.     

Generation of reactive intermediates

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:173–174, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20072     

Biomarkers of effects: the immune system

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:177–179, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20075     

The Agricultural Health Study biomarker workshop on cancer etiology. Introduction: overview of study design, results, and goals of workshop

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:169–171, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20070     

Toxicology of AHS important chemicals

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:180–181, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20076     

Role of host susceptibility to toxicity and cancer caused by pesticides: cytochromes P450

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:184–186, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20080     

Biomarkers of thyroid function, genotoxicity and agricultural fungicide use

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:175, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20073     

Paraoxonase 1 (PON1) status and risk of insecticide exposure

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:182–183, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20079     

A study on immunological responses to exposures encountered in corn farming

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:172, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20071     

Pesticide metabolism and potential for metabolic interactions

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:276–277, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20077     

DNA replication and repair reactions relevant to the AHS

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:190–191, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20082     

Glutathione S-transferases as putative host susceptibility genes for cancer risk in agricultural workers

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:187–189, 2005; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20081     

Effect of egg‐phosphatidylcholine on the chilling sensitivity and lipid phase transition of Asian elephant (Elephas maximus) spermatozoa

This study was conducted in an effort to improve our understanding of the response of Asian elephant (Elephas maximus, Em) spermatozoa to chilling. Semen was collected from two elephant bulls by means of the manual rectal stimulation method. Five out of seven semen collections were deemed to be suitable for use based on motility (ranging from 20% to 60%) and membrane integrity. We evaluated the chilling sensitivity by incubating the sperm with a fluorescent dye (5‐carboxyfluorescein diacetate (cFDA)) at 16°C, 12°C, 4°C, and 22°C (control). Cells with an intact membrane retained the dye and were identified as viable. The membrane lipid phase transition (LPT) temperature curve was determined with a Fourier transform infrared (FTIR) spectrometer connected to an FTIR microscope. The LPT center, T_m, was determined by statistical analysis. The LPT and T_m were also assessed in fresh spermatozoa and spermatozoa incubated with egg yolk or egg‐phosphatidylcholine (EPC) liposomes at 16°C, 12°C, 4°C, and 26°C (control). The results show that the membrane integrity of spermatozoa incubated at 16°C, 12°C, and 4°C decreased by 39%, 62%, and 67%, respectively, compared to the control. The LPT temperatures were between room temperature (26°C) and 10°C, with T_m at 14–16°C. The T_m for sperm incubated with liposomes or egg‐yolk extender was below the measured range (2°C). Chilling sensitivity was found at a wide range of temperatures and transition temperatures, suggesting the presence of a wide variety of fatty acids (FAs) in the membrane with a high ratio of saturated‐to‐polyunsaturated FAs. Here we show that the protection afforded by the presence of egg yolk or liposomes in the extender is accomplished by shifting the T_m to below the 4°C point at which chilled semen is maintained for transport, or the point at which fast freezing begins to minimize cellular damage. Zoo Biol 0:1–13, 2005. © 2005 Wiley‐Liss, Inc.     

Purification and Characterization of a Cold-active Iron Superoxide Dismutase from a Psychrophilic Bacterium, Marinomonas sp. NJ522

Marinomonas sp. NJ522, isolated from Antarctic sea ice, produces a cold-active iron superoxide dismutase (SOD; EC 1.15.1.1). The purified SOD was dimeric and had an approx. Mr of 48 kDa. Highest activity was detected from pH 8 to 10 and at 40 °C (assayed over 10 min). Activity at 0 °C was nearly 35% of the maximum activity. Received 25 August 2005; Revisions requested 30 August 2005 and 26 September 2005; Revisions received 12 September 2005 and 25 October 2005; Accepted 1 November 2005     

Reconstructing the population history of Puerto Rico by means of mtDNA phylogeographic analysis

The haplogroup identities of 800 mtDNAs randomly and systematically selected to be representative of the population of Puerto Rico were determined by restriction fragment length polymorphism (RFLP), revealing maternal ancestries in this highly mixed population of 61.3% Amerindian, 27.2% sub‐Saharan African, and 11.5% West Eurasian. West Eurasian frequencies were low in all 28 municipalities sampled, and displayed no geographic patterns. Thus, a statistically significant negative correlation was observed between the Amerindian and African frequencies of the municipalities. In addition, a statistically highly significant geographic pattern was observed for Amerindian and African mtDNAs. In a scenario in which Amerindian mtDNAs prevailed on either side of longitude 66°16′ West, Amerindian mtDNAs were more frequent west of longitude 66°16′ West than east of it, and the opposite was true for African mtDNAs. Haplogroup A had the highest frequency among Amerindian samples (52.4%), suggesting its predominance among the native Taínos. Principal component analysis showed that the sub‐Saharan African fraction had a strong affinity to West Africans. In addition, the magnitudes of the Senegambian and Gulf of Guinea components in Puerto Rico were between those of Cape Verde and São Tomé. Furthermore, the West Eurasian component did not conform to European haplogroup frequencies. HVR‐I sequences of haplogroup U samples revealed a strong North African influence among West Eurasian mtDNAs and a new sub‐Saharan African clade. Am J Phys Anthropol 128:131‐155, 2005. © 2005 Wiley‐Liss, Inc.     

Synaptic integration in dendritic trees

The original article to which this Erratum refers has been published in Journal of Neurobiology J Neurobiol (2005)64(1)75–90 . © 2005 Wiley Periodicals, Inc.     

Discussion and conclusions

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:192–193, 2003; Published online in Wiley InterScience ( www.interscience.wiley.com ). DOI 10.1002/jbt.20083     

Manipulation and Investigation Activity in Seabirds: Behavioral Response to Artificial Objects Exposed to a Colony

Biology Bulletin - This study was conducted in 1987–1988 and 2008 on Talan Island (59°20′ N, 146°05′ E), Sea of Okhotsk; in 2005 and 2011 on the Medvezhii Island...     

Influences of mating groups on the reproductive success of the Southern Sichuan Red Panda (Ailurus fulgens styani)

The reproduction of female red pandas under three different husbandry conditions (monogamy, polygamy, and polyandry) was studied at the Chengdu Research Base for Giant Panda Breeding, and Chengdu Zoological Park, China. We monitored the fecal steroid profiles of seven females by radioimmunoassay in order to understand how the different mating groupings affect the animals' reproductive success. Of the seven females studied, all gave birth except the one that was kept in the polyandrous group. Although fecal estradiol metabolites exhibited several peaks during estrus, only one coincided with mating behavior. Fecal progesterone metabolites did not display a sustained rise in the absence of mating behavior, even though estradiol displayed a peak of secretion. This suggests that the red panda may be an induced ovulator. During gestation, fecal progesterone metabolites were maintained at a comparatively high level, and were much higher than those of nonpregnant females. The female in the polyandrous group showed an abnormal estradiol metabolite profile, with a level that was four to five times higher than those of the females in the polygynous groupings. It was observed that this female always escaped and hid in the trees to avoid courtships with males, and did not give birth. This phenomenon suggests that polyandrous groupings may be unsuitable for successful reproduction in captivity. Zoo Biol 24:169–176, 2005. © 2005 Wiley‐Liss, Inc.     

Increase in d-tagatose Production Rate by Site-directed Mutagenesis of l-arabinose Isomerase from Geobacillus thermodenitrificans

Among single-site mutations of l-arabinose isomerase derived from Geobacillus thermodenitrificans, two mutants were produced having the lowest and highest activities of d-tagatose production. Site-directed mutagenesis at these sites showed that the aromatic ring at amino acid 164 and the size of amino acid 475 were important for d-tagatose production. Among double-site mutations, one mutant converted d-galactose into d-tagatose with a yield of 58% whereas the wild type gave 46% d-tagatose conversion after 300 min at 65 °C. Received 31 August 2005; Revisions requested 27 September 2005; Revisions received 8 November 2005; Accepted 8 November 2005