Why genomics is more than genomes

A report on the 2004 meeting on Molecular Genetics of Bacteria and Bacteriophages, Cold Spring Harbor, USA, 25-29 August 2004.     

Sarcopenia is more than a muscular deficit

Sarcopenia is a complex process that appears in aged muscle associated with a decrease in mass, strength, and velocity of contraction. This process is the result of many molecular, cellular and functional alterations. It has been suggested that sarcopenia may be triggered by reactive oxygen species (ROS) that have accumulated throughout one's lifetime. We found a significant increase in oxidation of DNA and lipids in the elderly muscle, more evident in males, and a reduction in catalase and glutathione transferase activities. Experiments on Ca2+ transport showed an abnormal functional response of aged muscle after exposure to caffeine, which increases the opening of Ca2+ channels, as well a reduced activity of the Ca2+ pump in elderly males. From these results we concluded that oxidative stress play an important role in muscle aging and that oxidative damage is much more evident in elderly males, suggesting a gender difference may be related to hormonal factors. The progression of sarcopenia is directly related to a significant reduction of the regenerative potential of muscle normally due to a type of adult stem cells, known as satellite cells, which lie outside the sarcolemma and remain quiescent until external stimuli trigger as growth factors (IGF-1 or mIGF-1) their re-entry into the cell cycle. One possibility is that the anti oxidative capacity of satellite cells could also be altered and this, in turn, determines the decrease of their regenerative capacity. Data concerning this hypothesis are discussed     

There is more to autophagy than induction

Considerable attention has been paid to the topic of autophagy induction. In part, this is because of the potential for modulating this process for therapeutic purposes. Of course we know that induced autophagy can also be problematic—for example, when trying to eliminate an established tumor that might be relying on autophagy for its own cytoprotective uses. Accordingly, inhibitory mechanisms have been considered; however, the corresponding studies have tended to focus on the pathways that block autophagy under noninducing conditions, such as when nutrients are available. In contrast, relatively little is known about the mechanisms for inhibiting autophagy under inducing conditions. Yet, this type of regulation must be occurring on a routine basis. We know that dysregulation of autophagy, e.g., due to improper activation of Beclin 1 leading to excessive autophagy activity, can cause cell death.¹ Pattingre S, Tassa A, Qu X, Garuti R, Liang XH, Mizushima N, et al. Bcl-2 antiapoptotic proteins inhibit Beclin 1-dependent autophagy. Cell 2005; 122:927 - 39; http://dx.doi.org/10.1016/j.cell.2005.07.002; PMID: 16179260 [Crossref], [PubMed], [Web of Science ®] , [Google Scholar] Accordingly, we assume that during starvation or other inducing conditions there must be a mechanism to modulate autophagy. That is, once you turn it on, you do not want to let it continue unchecked. But how is autophagy downregulated when the inducing conditions still exist?     

The thalamus is more than just a relay

The lateral geniculate nucleus and pulvinar are examples of two different types of relay: the former is a first order relay, transmitting information from a subcortical source (retina), while the latter is mostly a higher order relay, transmitting information from layer 5 of one cortical area to another cortical area. First and higher order thalamic relays can also be recognized for much of the rest of thalamus, and most of thalamus seems to be comprised of higher order relays. Higher order relays seem especially important to general corticocortical communication, and this challenges and extends the conventional view that such communication is based on direct corticocortical connections.     

Procollagen is more stable in cellulo than in vitro

The thermal denaturation of both intracellular and freshly secreted chick embryo tendon type I procollagen was investigated using susceptibility to proteolysis by trypsin and chymotrypsin as a probe for triple-helical conformation. Freshly secreted procollagen from the medium of matrix-free tendon cells in suspension or procollagen within the cells and in the pericellular environment melted at 45 degrees C. In contrast, if freshly secreted procollagen was subjected to the melting procedure after dialysis of the medium against 0.4 M NaCl, 0.1 M Tris HCl, pH 7.4 the protein melted at 42 degrees C, the melting temperature of purified procollagen dissolved in the same buffer. In each of these cases, the thermal denaturation profile was narrow, with a width of 1.0-1.5 degrees C. These results demonstrate that, in situ, procollagen is more stable toward thermal denaturation than was previously thought. This extra margin of thermal stability partially resolves the dilemma of how tissues are able to assemble triple-helical procollagen molecules at body temperatures that closely approach the melting temperature of the purified protein.     

The CXXC motif is more than a redox rheostat

The CXXC active-site motif of thiol-disulfide oxidoreductases is thought to act as a redox rheostat, the sequence of which determines its reduction potential and functional properties. We tested this idea by selecting for mutants of the CXXC motif in a reducing oxidoreductase (thioredoxin) that complement null mutants of a very oxidizing oxidoreductase, DsbA. We found that altering the CXXC motif affected not only the reduction potential of the protein, but also its ability to function as a disulfide isomerase and also impacted its interaction with folding protein substrates and reoxidants. It is surprising that nearly all of our thioredoxin mutants had increased activity in disulfide isomerization in vitro and in vivo. Our results indicate that the CXXC motif has the remarkable ability to confer a large number of very specific properties on thioredoxin-related proteins.     

Life is more than a computer running DNA software

In his recent interview for the Guardian Craig Venter is elaborating about a household appliance for the future, Digital Biological Converter(DBC). Current prototype, which can produce DNA, is a box attached to the computer which receives DNA sequences over the internet to synthesize DNA; later in future also viruses, proteins, and living cells. This would help the household members to produce, e.g., insulin, virus vaccines or phages that fight antibiotic resistant bacteria. In more distant future, Craig Venter's hope is that the DBC will generate living cells via so-called Universal Recipient Cell. This platform will allow digitally transformed genomes, downloaded from the internet, to form new cells fitted for the particular needs such as therapeutics, food, fuel or cleaning water. In contrast to this, the authors propose that DNA sequences of genomes do not represent 1:1 depictions of unequivocal coding structures such as genes. In light of the variety of epigenetic markings, DNA can store a multitude of further meanings hidden under the superficial grammar of nucleic acid sequences.     

Luciferase-based transgenic recombination assay is more sensitive than beta-glucoronidase-based

Study of the DNA repair and genome stability in plants is directly dependent on the availability of an easy, inexpensive, and reliable assay. Marker gene-based homologous recombination (HR) assays were introduced more than a decade ago and have been intensively used ever since. Here, we compared several transgenic Arabidopsis and tobacco lines that carried in their genome the luciferase (LUC) or the beta-glucoronidase (uidA or GUS) substrates for HR. The average recombination frequency detected with the luciferase transgene was nearly 9.0-fold higher in Arabidopsis and 12.4-fold higher in tobacco plants. Importantly, both transgenes were under the control of 35S promoter and had similar expression levels throughout the plants. Irradiation with UVC increased the HR frequency similarly in both transgenes. The actual difference in the frequency of HR in Arabidopsis and tobacco possibly results from differing sensitivity to detection of transgene activity. Thus, we could suggest that luciferase recombination assay, due to its higher sensitivity, should be the assay of choice when plant genome stability is studied.     

Stretching skin: undermining is more important than intraoperative expansion

The efficacy of intraoperative expansion in reducing the tension of wound closure was tested in young pigs. The young piglet as a model for studying human skin was characterized by finding a close similarity between the modulus of elasticity of young piglet skin and human abdominoplasty and mammaplasty skin (range 12.8 to 23.7 N/mm2 for piglet skin, 14.3 to 19 N/mm2 for human skin). The tension required to close a standardized wound was determined before undermining, after undermining, and finally after intraoperative expansion. These measurements were performed in 10 young pigs with an average weight of 11.5 kg. Undermining the wound edges resulted in a significant decrease in the force required to close the wounds (p less than 0.0001). Intraoperative expansion did not significantly decrease the tension. Previous work showing the importance of site and direction of pull on the tension for wound closure was confirmed in this study. Analysis of variance demonstrated that the tension required to close a standard wound is greater high on the pig's back than near the belly and near the shoulder as opposed to the hip for midflank wounds (p less than 0.0001). Increasing the extent of undermining from 62 to 136 cm2 significantly decreased the tension for wound closure (p less than 0.05). Further undermining did not result in a significant decrease in wound closure tension. In this model, intraoperative expansion offers no advantage over simple undermining. We suggest that the benefit reported by clinicians using intraoperative expansion may derive from an increase in the extent of undermining required to place expanders under the wound margins.     

Neomycin is more efficient than streptomycin in suppressing frameshift mutations

The effects of streptomycin and neomycin on the phenotypic suppression of frameshift mutations in the lacZ gene of Escherichia coli and on the efficiency of suppression of amber mutations in T4 phage by the informational supE tRNA nonsense suppressor were compared. Neomycin stimulated much more efficiently than streptomycin the phenotypic suppression of frameshift mutations. Because neomycin favors mismatches of the central codon base whereas streptomycin favors mismatches of the first codon base, this result suggests that mismatching of the central codon base pair and shifting of the reading frame are two correlated phenomena. In contrast, both streptomycin and neomycin stimulated about equally the efficiency of the tRNA nonsense suppressor, an effect probably related to their interference with the proofreading control in tRNA selection.     

The patch clamp is more useful than anyone had expected

The patch clamp was developed into its present form by Neher and Sakmann for recording the currents through individual ionic channels in excitable membranes. Recent advances now allow the patch-clamp technique to be used to record from cell-free membrane patches and from entire small cells. The technique has been used extensively for recordings from single channels that have provided new insights into their functioning; it is also being applied to a surprising variety of other physiological problems.     

Mechanomyography is more sensitive than EMG in detecting age-related sarcopenia

The aim of this work was to investigate the effects of age-related sarcopenia on the time and frequency domain properties of lower extremity muscles’ electromyographic and mechanomyographic activities. Healthy elderly (n=10, 64.5±4.5 yr) and young (n=10, 22.6±2.8 yr) were recruited as participants. Participants’ lean thigh volumes (LTV) and 1 RM (one repetition maximum) leg strength of quadriceps and maximum speed knee extension with different load levels (45%, 60% and 75% 1 RM) were recorded. The root mean square (RMS) and the mean frequency (MF) of the surface electromyography (EMG_RMS, EMG_MF) and mechanomyography (MMG_RMS, MMG_MF) signals were collected at vastus lateralis during concentric contraction with different intensity levels. Compared to the young, the elderly had significantly less LTV, absolute and relative maximal force, as well as absolute and relative maximal power (p<.05). EMG_MF of the elderly and the young increased monotonically from 45% to 75% 1 RM testing conditions. While the MMG_RMS of the young increased with testing intensities, the MMG_RMS of the elderly increased only from 45% to 60% but leveled off from 60% to 75% 1 RM testing conditions. The results indicate the declines of muscle mass, force and power production capacity with aging. The observations could be explained by neuromuscular performance and change of MU activation patterns may result from age-related sarcopenia. Aging affected muscle power more than muscle strength, which could be due to fast fiber reduction. This is supported by our observations that the MMG_RMS differences between the young and the elderly across all three intensity level where EMG_RMS was only different at the greatest intensity. We suggest that MMG could be used as an important measurement in studying muscle contraction in age-related sarcopenia.     

Cenp-F (mitosin) is more than a mitotic marker

Cenp-F (mitosin) is a large coiled-coil protein whose function has remained obscure since its identification a decade ago. It has been suggested that the protein plays a role in the kinetochore-mediated mitotic functions but until recently there was little evidence to support this postulation. Recent results from five laboratories have given insights on how Cenp-F may participate in the regulation of cell division. In this mini-review, we will summarize the current data regarding the mitotic tasks of Cenp-F as well as discuss how it is used as a proliferation marker of malignant cell growth in the clinic. Also, the protein’s post-translational modification by farnesylation and potential contribution to cell cycle effects of farnesyl transferase inhibitors will be addressed.