Synchronous protein cycling in batch cultures of the yeast Saccharomyces cerevisiae at log growth phase

The assumption that cells are temporally organized systems, i.e. showing relevant dynamics of their state variables such as gene expression or protein and metabolite concentration, while tacitly given for granted at the molecular level, is not explicitly taken into account when interpreting biological experimental data. This conundrum stems from the (undemonstrated) assumption that a cell culture, the actual object of biological experimentation, is a population of billions of independent oscillators (cells) randomly experiencing different phases of their cycles and thus not producing relevant coordinated dynamics at the population level. Moreover the fact of considering reproductive cycle as by far the most important cyclic process in a cell resulted in lower attention given to other rhythmic processes. Here we demonstrate that growing yeast cells show a very repeatable and robust cyclic variation of the concentration of proteins with different cellular functions. We also report experimental evidence that the mechanism governing this basic oscillator and the cellular entrainment is resistant to external chemical constraints. Finally, cell growth is accompanied by cyclic dynamics of medium pH. These cycles are observed in batch cultures, different from the usual continuous cultures in which yeast metabolic cycles are known to occur, and suggest the existence of basic, spontaneous, collective and synchronous behaviors of the cell population as a whole.     

Large TCR diversity of virus-specific CD8 T cells provides the mechanistic basis for massive TCR renewal after antigen exposure

Ex vivo analysis of virus-specific CD8 T cell populations by anchored PCR has shown that the CD8 TCR repertoire was less oligoclonal (seven to nine clonotypes per individual epitope) than previously thought. In the current study, TCR diversity was investigated by assessing both the overall TCR β-chain variable regions usage as well as the CDR3 regions in ex vivo-isolated CMV- and EBV-specific CD8 T cells from 27 healthy donors. The average number of clonotypes specific to most single viral epitopes comprised between 14 and 77. Changes in the CD8 TCR repertoire were also longitudinally assessed under conditions of HIV-1 chronic infection (i.e., in patients with suppressed virus replication and after treatment interruption and Ag re-exposure). The results showed that a large renewal (≤ 80%) of the TRB repertoire occurred after Ag re-exposure and was eventually associated with an increased T cell recognition functional avidity. These results demonstrate that the global CD8 TCR repertoire is much more diverse (≤ 9-fold) than previously estimated and provide the mechanistic basis for supporting massive repertoire renewal during chronic virus infection and Ag re-exposure.     

The Acoustic Codes: How Animal Sign Processes Create Sound-Topes and Consortia via Conflict Avoidance

In this essay we argue for the possibility to describe the co-presence of species in a community as a consortium built by acoustic codes, using mainly the examples of bird choruses. In this particular case, the consortium is maintained via the sound-tope that different bird species create by singing in a chorus. More generally, the formation of acoustic codes as well as cohesive communicative systems (the consortia) can be seen as a result of plastic adaptational behaviour of the specimen who can solve and avoid conflicts both with conspecifics and with other species in the vicinity. Thus, sign-relations appear to resolve potential conflicts, and as a foundation for symbiotic aggregations. The spatio-temporal configuration of consortia—their chronotope—includes several eco-fields as respective to different functions of the participating organisms. Biological study is combined with a semiotic approach that, as we suggest, should be more often used together to effectively describe ecological processes.     

Elevated blood Hsp60, its structural similarities and cross-reactivity with thyroid molecules,and its presence on the plasma membrane of oncocytes point to the chaperonin as an immunopathogenic factor in Hashimoto's thyroiditis

The role Hsp60 might play in various inflammatory and autoimmune diseases is under investigation, but little information exists pertaining to Hashimoto’s thyroiditis (HT). With the aim to fill this gap, in the present work, we directed our attention to Hsp60 participation in HT pathogenesis. We found Hsp60 levels increased in the blood of HT patients compared to controls. The chaperonin was immunolocalized in thyroid tissue specimens from patients with HT, both in thyrocytes and oncocytes (Hurthle cells) with higher levels compared to controls (goiter). In oncocytes, we found Hsp60 not only in the cytoplasm but also on the plasma membrane, as shown by double immunofluorescence performed on fine needle aspiration cytology. By bioinformatics, we found regions in the Hsp60 molecule with remarkable structural similarity with the thyroglobulin (TG) and thyroid peroxidase (TPO) molecules, which supports the notion that autoantibodies against TG and TPO are likely to recognize Hsp60 on the plasma membrane of oncocytes. This was also supported by data obtained by ELISA, showing that anti-TG and anti-TPO antibodies cross-react with human recombinant Hsp60. Antibody-antigen (Hsp60) reaction on the cell surface could very well mediate thyroid cell damage and destruction, perpetuating inflammation. Experiments with recombinant Hsp60 did not show stimulation of cytokine production by peripheral blood mononuclear cells from HT patients. All together, these results led us to hypothesize that Hsp60 may be an active player in HT pathogenesis via an antibody-mediated immune mechanism.     

Hybrid neuromusculoskeletal modeling to best track joint moments using a balance between muscle excitations derived from electromyograms and optimization

Current electromyography (EMG)-driven musculoskeletal models are used to estimate joint moments measured from an individual?s extremities during dynamic movement with varying levels of accuracy. The main benefit is the underlying musculoskeletal dynamics is simulated as a function of realistic, subject-specific, neural-excitation patterns provided by the EMG data. The main disadvantage is surface EMG cannot provide information on deeply located muscles. Furthermore, EMG data may be affected by cross-talk, recording and post-processing artifacts that could adversely influence the EMG?s information content. This limits the EMG-driven model?s ability to calculate the multi-muscle dynamics and the resulting joint moments about multiple degrees of freedom. We present a hybrid neuromusculoskeletal model that combines calibration, subject-specificity, EMG-driven and static optimization methods together. In this, the joint moment tracking errors are minimized by balancing the information content extracted from the experimental EMG data and from that generated by a static optimization method. Using movement data from five healthy male subjects during walking and running we explored the hybrid model?s best configuration to minimally adjust recorded EMGs and predict missing EMGs while attaining the best tracking of joint moments. Minimally adjusted and predicted excitations substantially improved the experimental joint moment tracking accuracy than current EMG-driven models. The ability of the hybrid model to predict missing muscle EMGs was also examined. The proposed hybrid model enables muscle-driven simulations of human movement while enforcing physiological constraints on muscle excitation patterns. This might have important implications for studying pathological movement for which EMG recordings are limited.     

Epidermal growth factor modulation of prostaglandins and nitrite biosynthesis in rat fetal membranes

The production of prostaglandins (PGs) and nitric oxide (NO) by amnion tissue may play a significant role in parturition. It is thought that epidermal growth factor (EGF) may be one of the fetal signals that governs the initiation of labor. The aim of the present study was to investigate the effect of EGF in vivo on the PGs and nitrite production of rat fetal membranes. We have evaluated the regulation of PGs and nitrite production in rat fetal membranes ex vivo. The intra-uterine administration of EGF 500 ng in day 21 of pregnancy induced increases in PGE(2) (P<0.001) and PGF(2alpha) (P<0.01) compared to the control fetal membranes from pregnant rats on day 22. Also, this dose of EGF diminished nitrate production significantly (P<0.01). We found that fetal membranes at term (days 18-22 of gestation) expressed EGF-R. The NO donor, nitroprussiate 300 and 600 microM, elicited an inhibitory effect on the PGE(2) and PGF(2alpha) stimulated synthesis. On the other hand, indomethacin 10(-6) and 10(-7)M, a non-selective cyclooxygenase inhibitor, reverted the inhibitory effect exerted by EGF. Hence, rat fetal membranes were found to express epidermal growth factor receptors and, under the effect of EGF, PGs and nitrites production pathways interact probably to prevent a toxic effect caused by an exacerbated synthesis of these mediators.     

Post-translational modifications in MeHg-induced neurotoxicity

Mercury (Hg) exposure remains a major public health concern due to its widespread distribution in the environment. Organic mercurials, such as MeHg, have been extensively investigated especially because of their congenital effects. In this context, studies on the molecular mechanism of MeHg-induced neurotoxicity are pivotal to the understanding of its toxic effects and the development of preventive measures. Post-translational modifications (PTMs) of proteins, such as phosphorylation, ubiquitination, and acetylation are essential for the proper function of proteins and play important roles in the regulation of cellular homeostasis. The rapid and transient nature of many PTMs allows efficient signal transduction in response to stress. This review summarizes the current knowledge of PTMs in MeHg-induced neurotoxicity, including the most commonly PTMs, as well as PTMs induced by oxidative stress and PTMs of antioxidant proteins. Though PTMs represent an important molecular mechanism for maintaining cellular homeostasis and are involved in the neurotoxic effects of MeHg, we are far from understanding the complete picture on their role, and further research is warranted to increase our knowledge of PTMs in MeHg-induced neurotoxicity.