It is time to end the patenting of software

One of the most significant outcomes of genomics has been arapid increase in the rate that we as a community can generatedata on interesting biological systems. Rapid improvements intechnologies such as DNA microarrays and proteomics applicationshave produced a climate where the challenge is no longer collectinghigh quality data but rather managing and analyzing it. As wein the bioinformatics community have addressed this challenge,we have had to carefully consider the way in which the resultsof our intellectual efforts—the software tools that wedevelop—are made available to the wider research community.Increasingly, bioinformatics scientists are coming to call fordevelopment in an open source environment in which softwareis distributed with its underlying source code     

Physiological responses of the hyperthermophilic archaeon "Pyrococcus abyssi" to DNA damage caused by ionizing radiation

The mechanisms by which hyperthermophilic Archaea, such as "Pyrococcus abyssi" and Pyrococcus furiosus, survive high doses of ionizing gamma irradiation are not thoroughly elucidated. Following gamma-ray irradiation at 2,500 Gy, the restoration of "P. abyssi" chromosomes took place within chromosome fragmentation. DNA synthesis in irradiated "P. abyssi" cells during the DNA repair phase was inhibited in comparison to nonirradiated control cultures, suggesting that DNA damage causes a replication block in this organism. We also found evidence for transient export of damaged DNA out of irradiated "P. abyssi" cells prior to a restart of chromosomal DNA synthesis. Our cell fractionation assays further suggest that "P. abyssi" contains a highly efficient DNA repair system which is continuously ready to repair the DNA damage caused by high temperature and/or ionizing radiation.     

The question of threshold doses for radiation damage: Malformations induced by radiation exposure of unicellular or multicellular preimplantation stages of the mouse

Mouse embryos of the one-cell stage or the 32- to 64-cell stage were exposed to various X-ray doses (one-cell stage: 0.25-2 Gy; 32- to 64-cell stage: 1–3 Gy). It turned out that the shape of the dose-response curves is statistically compatible with the assumption derived from biological considerations that there is no threshold for radiation-induced malformations in the case of the exposure of one-cell embryos, whereas there is a threshold dose (close to 1 Gy) in the case of the exposure of 32- to 64-cell embryos.     

Genetic variation in male attractiveness: It is time to see the forest for the trees

Female choice based on multiple male traits, rather than on any single one, has been reported in many species and may well be a rule rather than an exception. However, the implications this has for selection acting on choosiness itself remain underappreciated. We argue that this constitutes one of the important impediments to our understanding of the evolution of mate choice. We discuss this issue primarily in the context of the Fisherian model of sexual selection. We review theory and empirical data, showing how the crucial parameter of the model—genetic variation in male attractiveness—can be estimated when attractiveness is a function of multiple traits. Based on the reviewed theory, we show how relying on individual male traits, instead of overall attractiveness, can produce biased estimates of Fisherian benefits of female choice. This bias can be substantial, especially when many traits contribute to male attractiveness. We discuss a number of methodological issues that, we hope, will stimulate future studies and help resolving the long‐standing mystery of mate choice.     

It is time to explore the impact of length of gestation and fetal health on the human lifespan

A recently proposed principal law of lifespan (PLOSP) proposes to extend the whole human lifespan by elongating different life stages. As the preborn stage of a human being, gestation is the foundation for the healthy development of the human body. The antagonistic pleiotropy (AP) theory of aging states that there is a trade-off between early life fitness and late-life mortality. The question is whether slower development during the gestation period would be associated with a longer lifespan. Among all living creatures, the length of the gestation period is highly positively correlated to the length of the lifespan, although such a correlation is thought to be influenced by the body sizes of different species. While examining the relationship between lifespan length and body size within the same species, dogs exhibit a negative correlation between lifespans and body sizes, while there is no such correlation among domestic cats. For humans, most adverse gestational environments shorten the period of gestation, and their impacts are long-term. While many issues remain unsolved, various developmental features have been linked to the conditions during the gestation period. Given that the length of human pregnancies can vary randomly by as long as 5 weeks, it is worth investigating whether a slow steady healthy gestation over a longer period will be related to a longer and healthier lifespan. This article discusses the potential benefits, negative impacts, and challenges of the relative elongation of the gestation period.     

MiR-21 is continually elevated long-term in the brain after exposure to ionizing radiation

Ionizing radiation stimulates miR-21 expression in different types of mammalian cells in culture. However, it remains unclear whether radiation could stimulate miR-21 expression in brain cells and tissue and, if so, how long the upregulation of miR-21 would be maintained after exposure to different types of radiation. To answer these questions, we examined the miR-21 levels in irradiated mouse hippocampal cells and brain tissue from mice at different times up to 1 year after whole-body exposure to 0.5 Gy of X rays [low linear energy transfer (LET)] or (56)Fe ions (high LET). The results showed that radiation stimulated miR-21 expression in mouse hippocampal cells and upregulation of EGFR, which is similar to that in human hepatocytes, as we reported previously. Interestingly, the miR-21 levels gradually increased within 1 year after irradiation, although there was no significant difference in the miR-21 low- and high-LET irradiated mice. The high expression of miR-21 in the brain was also associated with high expression of EGFR in irradiated mice; thus our data strongly support that EGFR and miR-21 are in a positive regulatory loop, because it is known that radiation stimulates miR-21 through the EGFR/Stat3 pathway and miR-21 activates the EGFR pathway. Since the brain is relatively resistant to radiation-induced histomorphological changes, our findings may provide a new way to explore radiation-induced pathological changes in the brain by investigating miR-21 and its multiple targets.     

A possibility to predict the severity of individual damage following the exposure to supralethal radiation dosage. Prediction by early radiation response

The experiments on dogs and monkeys have shown that the severity of radiation sickness following the exposure to supralethal radiation doses can be predicted by early response of an individual. For such prediction, the most informative criteria include general severity of clinical manifestations during primary radiation response and evaluated within a few post-damage hours, the degree of tension in cardiac rhythm control, the cortisol level, the endocrine status index.