Biomolecular computing systems: principles, progress and potential

The task of information processing, or computation, can be performed by natural and man-made 'devices'. Man-made computers are made from silicon chips, whereas natural 'computers', such as the brain, use cells and molecules. Computation also occurs on a much smaller scale in regulatory and signalling pathways in individual cells and even within single biomolecules. Indeed, much of what we recognize as life results from the remarkable capacity of biological building blocks to compute in highly sophisticated ways. Rational design and engineering of biological computing systems can greatly enhance our ability to study and to control biological systems. Potential applications include tissue engineering and regeneration and medical treatments. This Review introduces key concepts and discusses recent progress that has been made in biomolecular computing.     

Early age cold conditioning in broiler chickens (Gallus domesticus): thermotolerance and growth responses

The influence of short repetitive cold exposure at an early age (cold conditioning—exposure to 15°C for 3 h at 3 and 4 days of age) on chickens’ thermotolerance during cold challenge (15°C) at 21 days of age was examined. The first cold exposure elicited a dramatic decline in body temperature (T_b) and a significant elevation in stress response (plasma corticosterone concentration); the second cold exposure resulted in moderate T_b and stress responses. Thereafter, the corticosterone concentration remained at a significantly lower level. Acute cold challenge of conditioned broilers at 21 days of age revealed better T_b and stress recovery during the first 24 h, and a significantly lower mortality rate thereafter. Conditioned chickens exposed to optimal conditions (22°C) achieved significantly higher body weights than others. It may be concluded that early cold conditioning improves thermotolerance in broiler chickens in later life.     

Polymorphisms in the human apolipoprotein-J/clusterin gene: ethnic variation and distribution in Alzheimer’s disease

Apolipoprotein-J/clusterin (APOJ/CLI) shares many biological properties with apolipoprotein-Ε (APOE) including, but not limited to, avid binding with β-amyloid peptide. Thus, APOJ/CLI warrants scrutiny as a candidate Alzheimer’s disease (AD) susceptibility gene. We identified seven nucleotide sequence polymorphisms in APOJ/ CLI, two of which, in exon 7, alter the predicted amino acid sequence. The JVIIB variant is an asparagine-to-histidine substitution, which deletes a glycosylation signal at amino acid 317; the JVIIC variant is an aspartate-to-asparagine substitution, which forms a new glycosylation signal at position 328. Both of these coding variants, as well as two neutral polymorphisms in exon 2, were more frequent in African-Americans than Hispanics and were rare in Caucasians. However, no individual coding or noncoding variant was consistently associated with AD. At the population level, APOJ/CLI polymorphisms are frequent among persons of African descent, but probably do not alter susceptibility to AD. Received: 14 February 1996 / Revised: 15 April 1996     

Histone modifications associated with drought tolerance in the desert plant <Emphasis Type="Italic">Zygophyllum dumosum</Emphasis> Boiss

Zygophyllum dumosum Boiss. is a perennial Saharo-Arabian phytogeographical element and a dominant shrub on the rocky limestone southeast-facing slopes of the Negev desert. The plant is highly active during the winter, and semideciduous during the dry summer, i.e., it sheds its leaflets, while leaving the thick, fleshy petiole green and rather active during the dry season. Being resistant to extreme perennial drought, Z. dumosum appears to provide an intriguing model plant for studying epigenetic mechanisms associated with drought tolerance in natural habitats. The transition from the wet to the dry season was accompanied by a significant decrease in nuclear size and with posttranslational modifications of histone H3 N-terminal tail. Dimethylation of H3 at lysine 4 (H3K4)—a modification associated with active gene expression—was found to be high during the wet season but gradually diminished on progression to the dry season. Unexpectedly, H3K9 di- and trimethylation as well as H3K27 di- and trimethylation could not be detected in Z. dumosum; H3K9 monomethylation appears to be prominent in Z. dumosum during the wet but not during the dry season. Contrary to Z. dumosum, H3K9 dimethylation was detected in other desert plants, including Artemisia sieberi, Anabasis articulata and Haloxylon scoparium. Taken together, our results demonstrate dynamic genome organization and unique pattern of histone H3 methylation displayed by Z. dumosum, which could have an adaptive value in variable environments of the Negev desert.     

Apoptotic cells represent a dynamic stem cell niche governing proliferation and tissue regeneration

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The effect of temperature on caecal fermentation processes in a poikilothermic mammal, Heterocephalus glaber

1. 1.|The effect of temperature on caecal function was examined in the naked mole-rat Heterocephalus glaber, a poikilothermic mammal, which consumes a high proportion of fibre in its natural diet.

2. 2.|The temperature of optimal caecal function was determined from fermentation data measure at three specifically chosen temperatures (28, 33 and 40°C).

3. 3.|There was no significant difference between gas production at 33 and 40°C, however, gas production was significantly lower at 28°C.

4. 4.|The relative proportions of the gases produced were markedly different at 33 and 40°C (P ≤ 0.01). More methane and hydrogen were produced at 33°C than at 40°C.

5. 5.|These data suggest that microbial organisms within the caecum were active and functioning more effectively at 33°C (the preferred body temperature of the naked mole-rat) than at the other two temperatures.

Non-shivering thermogenesis in winter-acclimatized and in long-scotophase and cold-acclimated Apodemus mystacinus (Rodentia)

1. 1.|Resistance to cold through non-shivering thermogenesis (the absolute increase in O₂ consumption caused by noradrenaline injection) was increased 3-fold in individuals of the broad-toothed mouse A. mystacinus, kept for 3 weeks under a short photoperiod (long scotophase 8L:16D) at an ambient temperature of 28°C, compared to control conditions (12L:12D; 28°C), and did not differ significantly from the winter-acclimatized group.

2. 2.|Acclimation of the same individuals to long scotophase and cold (8L:16d; 7°C) caused a significant (P < 0.01) increase in absolute O₂ consumption and maximal body temperature, as a response to noradrenaline injectin, when compared to long-scotophase individuals (8L:16D; 28°C).

3. 3.|The results of this study support the idea that winter acclimatization of heat-production mechanisims may be induced by the extension of scotophase, which cycles very regulary in nature and in the Mediterranean region occurs before the beginning of the cold season.