Unlike previous methods that often use custom approaches that are organism specific, our method uses generalized linear models and extensions of standard reversible jump Markov chain Monte Carlo methods that can be readily extended to other organisms for a variety of biological inference problems relating to cell fate specification.
"The more we learn, the more it is clear that even though we might be able to tailor organisms to specification in the future, that is a long way from where we are now, which is the early stages of arranging genes at will, regardless of provenance.
These findings suggest that lineage specification programs may be dependent on but a few immutable genetic regulatory elements, while tolerating considerable epigenetic variation at numerous additional organism-specific lineage-specific elements.
Nevertheless the higher rate of adaptation in the young genes might be consistent with the ideas that lineage-specific genes may drive morphological specification, enabling organisms to adapt to changing conditions (Khalturin et al. 2009) and also with the observation that young genes tend to be less functionally important.
Furthermore, a KGML document may contain references to entries, which are not physically present in the actual organism and the KGML specification even allows entries to be reactions.
The current specification includes support for organism, organism part (tissue), cell type, the specific biological environment in which the evidence was proven and the type of the experiment used to gather evidence.
Patterns are specific and in their specification they are viable for organisms.
Many cellular processes in living organisms, including sex determination, lineage specification, cell differentiation, proliferation, and apoptosis, are irreversible, all-or-none (binary) phenomena.
In light of the robust expression of Sall1 in neural PCs and its role in neural specification in other organisms (de Celis et al., 1999; Ott et al., 2001; Rusten et al., 2001), we investigated the role of Sall1 in the development of the CNS.
Mechanical forces are critical to embryogenesis, specifically, in the lineage-specification gastrulation phase, whereupon the embryo is transformed from a simple spherical ball of cells to a multi-layered organism, containing properly organized endoderm, mesoderm, and ectoderm germ layers.
