Degradation of polycaprolactone at 50 °C by a thermotolerant Aspergillus sp.

A thermotolerant Aspergillus sp. strain ST-01 degrading poly(-caprolactone) films was isolated. The polyester was degraded and assimilated giving 36 mg of cell from 100 mg sample and 10 mg yeast extract after 6 days at 50 °C. The degradation products were identified as succinic acid, butyric acid, valeric acid, and caproic acid. The isolate also degraded more than 90% film samples of polyhydroxybutyrate (PHB) and poly(tetramethylene succinate-co-tetramethylene adipate) at 50 °C.     

Are short normal children at a disadvantage? The Wessex growth study.

OBJECTIVE: To examine whether short stature through childhood represents a disadvantage at around 12 years. DESIGN: Longitudinal non-intervention study of the physical and psychological development of children recruited from the community in 1986-7 after entry into primary school at age 5-6 years; this is the second psychometric assessment made in 1994-5 after entry into secondary school at age 11-13 years. SETTING: Southampton and Winchester health districts. SUBJECTS: 106 short normal children (< 3rd centile for height when recruited) and 119 controls of average stature (10th-90th centile). MAIN OUTCOME MEASURES: Psychometric measures of cognitive development, self concept development, behaviour, and locus of control. RESULTS: The short children did not differ significantly from the control children on measures of self esteem (19.4 v 20.2), self perception (104.2 v 102.4), parents'' perception (46.9 v 47.0), or behaviour (6.8 v 5.3). The short children achieved significantly lower scores on measures of intelligence quotient (IQ) (102.6 v 108.6; P < 0.005), reading attainment (44.3 v 47.9; P < 0.002), and basic number skills (40.2 v 43.5; P < 0.003) and displayed less internalisation of control (16.6 v 14.3; P < 0.001) and less satisfaction with their height (P < 0.0001). More short than control children, however, came from working class homes (P < 0.05). Social class was a better predictor than height of all measures except that of body satisfaction. Attainment scores were predicted by class and IQ together rather than by height. Height accounted for some of the variance in IQ and locus of control scores. CONCLUSIONS: These results provide only limited support for the hypothesis that short children are disadvantaged, at least up until 11-13 years old. Social class seems to have more influence than height on children''s psychological development.     

Looking back at a quarter-century of research at the Maurice E. Müller Institute for Structural Biology

The Maurice E. Müller Institute, embedded in the infrastructure of the Biozentrum, University of Basel, was founded in 1985 and financed by the Maurice E. Müller Foundation of Switzerland. For 26 years its two founders, Ueli Aebi and Andreas Engel, pursued the vision of integrated structural biology. This paper reviews selected publications issuing from the Maurice E. Müller Institute for Structural Biology and marks the end of this era.     

Methanopyrus kandleri,gen. and sp. nov. represents a novel group of hyperthermophilic methanogens,growing at 110°C

A novel group of hyperthermophilic rod-shaped motile methanogens was isolated from a hydrothermally heated deep sea sediment (Guaymas Basin, Gulf of California) and from a shallow marine hydrothermal system (Kolbeinsey ridge, Iceland). The grew between 84 and 110°C (opt: 98°C) and from 0.2% to 4% NaCl (opt. 2%) and pH 5.5 to 7 (opt: 6.5). The isolates were obligate chemolithoautotrophes using H₂/CO₂ as energy and carbon sources. In the presence of sulfur, H₂S was formed and cells tended to lyse. The cell wall consisted of a new type of pseudomurein containing ornithin in addition to lysine and no N-acetylglucosamine. The pseudomurein layer was covered by a detergent-sensitive protein surface layer. The core lipid consisted exclusively of phytanyl diether. The GC content of the DNA was 60 mol%. By 16S rRNA comparisons the new organisms were not related to any of the three methanogenic lineages. Based on the physiological and molecular properties of the new isolates, we describe here a new genus, which we name Methanopyrus (the methane fire). The type species is Methanopyrus kandleri (type strain: AV19; DSM 6324).This paper is dedicated to Otto Kandler on the occasion of his 70th birthday     

Pyrococcus furiosus sp. nov. represents a novel genus of marine heterotrophic archaebacteria growing optimally at 100°C

Ten strains representing a novel genus of marine thermophilic archaebacteria growing at between 70 and 103°C with an optimal growth temperature of 100°C and a doubling time of only 37 min were isolated from geothermally heated marine sediments at the beach of Porto di Levante, Vulcano, Italy. The organisms are spherical-shaped, 0.8 to 2.5 m in width and exhibit monopolar polytrichous flagellation. They are strictly anaerobic heterotrophs, growing on starch, maltose, peptone and complex organic substrates. Only CO₂ and H₂ could be detected as metabolic products, the latter being inhibitory to growth at high concentrations. Hydrogen inhibition can be prevented by the addition of S^o, whereupon H₂S is formed in addition, most likely as the result of a detoxification reaction. The GC-content of the DNA of isolate Vc 1 is 38 mol%. The new genus is named Pyrococcus, the fireball. Type species and strain is Pyrococcus furiosus Vc 1 (DSM 3638).     

Oramoeba fumarolia gen. nov., sp. nov., a new marine heterolobosean amoeboflagellate growing at 54 °C

An amoeba strain was isolated from marine sediment taken from the beach near a fumarole in Italy. The trophozoites of this new marine species transforms into flagellates with variable numbers of flagella, from 2 to 10. The strain forms round to oval cysts. This thermophilic amoeboflagellate grows at temperatures up to 54 °C. Molecular phylogenetic analysis of the small subunit ribosomal DNA (SSU rDNA) places the amoeboflagellate in the Heterolobosea. The closest relatives are Stachyamoeba sp. ATCC50324, a strain isolated from an ocean sample, and Vrihiamoeba italica, a recent isolate from a rice field. Like some other heterolobosean species, this new isolate has a group I intron in the SSU rDNA. Because of the unique place in the molecular phylogenetic tree, and because there is no species found in the literature with similar morphological and physiological characteristics, this isolate is considered to be a new genus and a new species, Oramoeba fumarolia gen. nov., sp. nov.     

CNS stem cells: Where's the biology (a.k.a. beef)?

Central nervous system (CNS) stem cells have become the subject of many laboratories' efforts, presentations, and publications. Yet, in the stem cell world, CNS cells are viewed with skepticism. This is likely due to a dearth of biology (in vivo function) to accompany a flurry of phenomenological and restorative neurology studies. In this article, we compare and contrast the biological knowledge of adult forebrain epidermal growth factor-responsive neural stem cells that has emerged from our laboratories with that of hematopoietic stem cells, using two recent papers in the latter field as specific examples. A comparison of stem cell location, lineage, and repopulation suggests that our understanding of CNS stem cell biology is immature. We conclude that a greater focus on in vivo biology will enhance our knowledge and understanding of CNS stem cells. © 1998 John Wiley & Sons, Inc. J Neurobiol 36: 307–314, 1998     

A. A. Ukhtomskiĭ and I. P. Pavlov: a controversy or a dialogue?

Pavlov's concept of conditioned reflexes and Ukhtomskii theory of dominanta fall within the biological line in physiology. They unravel the integral adaptive and active nature of the organism behavior in the environment. It is impossible to develop modern concepts about the determinants of goal-directed behavior of animals and voluntary activity of humans without in-depth study of the achievements of these Russian physiological schools which not only formed the methodological basis for the current studies but also directed the way for their further development.     

Grazing dynamics at different spatial and temporal scales: examples from the Swedish historical record a.d. 1620–1850

The aim of this paper is to discuss implications of different resolution scales of both time and space in studies of past land use and past vegetation, both historical and palaeoecological. The paper gives examples of short term-variation, long-term changes, small spatial scale differences and regional differences in land use, studied through historical sources in four regions in south central Sweden. It also discusses the difficulty of interpretation of forest vegetation in old cadastral maps. Historical sources can show dynamics on the fine temporal and spatial scales that are difficult to capture with pollen analysis. On the other hand, pollen analysis has unique possibilities for the study of time periods where historical records are lacking. Therefore the combination of several disciplines is likely to be productive in aiding understanding past land use and vegetation. However, there are important limitations in using the information in cadastral maps and other historical sources to interpret and quantify past vegetation.     

Abundance of terrestrial gymnamoebae at a northeastern U. S. site: a four-year study, including the El Niño winter of 1997-1998

ABSTRACT. The abundance, sizes, and when appropriate, diversity of gymnamoebae were documented at approximately monthly intervals for four years (1995–1998) at a grassy, terrestrial site slightly upslope from a freshwater pond. Soil samples were analyzed for viable gymnamoebae using a standard laboratory culturing protocol. The mean density of gymnamoebae based on the total data set was ca. 1,600/g (s.e. ± 190). Minimum densities of gymnamoebae (156/g) occurred in January 1995, and a maximum for the sampling period (5,838/g) occurred in July 1997, when a rainy period followed an extended period of drought. Among the environmental variables monitored (precipitation, soil moisture, organic content, and temperature) only precipitation correlated significantly with abundance of gymnamoebae (r= 0.34 , p = 0.02 ). During the mild, moist El Niño winter of 1997–1998, a larger than usual number of gymnamoebae was recorded at the site (～3,800/g) compared to a mean density of ～900/g for comparable periods in preceding years. The mean sizes were also larger. Since gymnamoebae are increasingly recognized as major members of soil microbial communities enhancing soil fertility through nutrient mineralization, it is important to document environmental variables that influence their abundance and activity in terrestrial ecosystems.     

The spliceosome: a ribozyme at heart?

The spliceosome, the multi-megadalton molecular machine that performs splicing, consists of over 200 different proteins and five small nuclear RNAs (snRNAs). Extensive mechanistic and structural similarities to self-splicing group II introns, large ribozymes found in prokaryotes and lower eukaryotes that catalyze an identical reaction, strongly suggest that the spliceosomal RNAs are in fact the catalytic components of the spliceosome. Of the five spliceosomal RNAs, U2 and U6 are the only ones that are absolutely required for both steps of splicing. These two snRNAs form an elaborate base-paired complex that might in fact constitute the active site of the spliceosome.     

Predation at a snail's pace: what's time to a gastropod?

Summary Predation by naticid gastropods shows evidence of adaptation to maximize the rate of energy intake. The predation rate of Polinices duplicatus feeding on artificially altered, thin-shelled Mercenaria mercenaria was faster than the predation rate on normal Mercenaria. The rate of energy intake was limited by handling time. The time saved by predation on thin-shelled prey was used to forage. Thus time was shown to be valuable to P. duplicatus, and cost-benefit functions using time and energy as currencies are appropriate for estimating dietary efficiency and predicting prey choice.Despite the clear superiority of thin-shelled prey, P. duplicatus did not learn to prefer this novel prey type, suggesting that predator choices are sterotyped, reflecting optima selected over evolutionary time.     

How does a small molecule bind at a cryptic binding site?

Protein-protein interactions (PPIs) are ubiquitous biomolecular processes that are central to virtually all aspects of cellular function. Identifying small molecules that modulate specific disease-related PPIs is a strategy with enormous promise for drug discovery. The design of drugs to disrupt PPIs is challenging, however, because many potential drug-binding sites at PPI interfaces are “cryptic”: When unoccupied by a ligand, cryptic sites are often flat and featureless, and thus not readily recognizable in crystal structures, with the geometric and chemical characteristics of typical small-molecule binding sites only emerging upon ligand binding. The rational design of small molecules to inhibit specific PPIs would benefit from a better understanding of how such molecules bind at PPI interfaces. To this end, we have conducted unbiased, all-atom MD simulations of the binding of four small-molecule inhibitors (SP4206 and three SP4206 analogs) to interleukin 2 (IL2)—which performs its function by forming a PPI with its receptor—without incorporating any prior structural information about the ligands’ binding. In multiple binding events, a small molecule settled into a stable binding pose at the PPI interface of IL2, resulting in a protein–small-molecule binding site and pose virtually identical to that observed in an existing crystal structure of the IL2-SP4206 complex. Binding of the small molecule stabilized the IL2 binding groove, which when the small molecule was not bound emerged only transiently and incompletely. Moreover, free energy perturbation (FEP) calculations successfully distinguished between the native and non-native IL2–small-molecule binding poses found in the simulations, suggesting that binding simulations in combination with FEP may provide an effective tool for identifying cryptic binding sites and determining the binding poses of small molecules designed to disrupt PPI interfaces by binding to such sites.