Field Hypothesis on the Self-regulation of Gene Expression

The mechanism of the self-regulation of gene expression in living cells is generally explained by considering complicated networks of key-lock relationships, and in fact there is a large body of evidence on a hugenumber of key-lock relationships. However, in the present article we stress that with the network hypothesis alone it is impossible to fully explain the mechanism of self-regulation in life. Recently, it has been established that individual giant DNA molecules, larger than several tens of kilo base pairs, undergo a large discrete transition in their higher-order structure. It has become clear that nonspecific weak interactions with various chemicals, suchas polyamines, small salts, ATP and RNA, cause on/off switching in the higher-order structure of DNA. Thus, the field parameters of the cellular environment should play important roles in the mechanism of self-regulation, in addition to networks of key and locks. This conformational transition induced by field parameters may be related to rigid on/off regulation, whereas key-lock relationships may be involved in a more flexible control of gene expression.     

Geographic isolation and evolution of Mediterranean endemic Cyclamen: insights from chloroplast trnL (UAA) intron sequence variation

 In this study we construct a phylogenetic hypothesis for the relatedness among disjunct subspecies of Cyclamen repandum and its two allopatric congeners, C. creticum and C. balearicum in order to examine the evolutionary divergence of currently isolated populations across the western Mediterranean. The most parsimonious phylogenetic tree obtained from sequencing the cpDNA trnL (UAA) intron suggests a major phylogeographic divide in southern Greece between two clades. The first clade comprises samples of C. repandum subsp. peloponnesiacum (from the Peloponnese) and C. creticum (from Crete). The second comprises samples of C. repandum subsp. repandum (from Croatia, Italy, southern France, Corsica, Sardinia and Sicily), C. repandum subsp. rhodense (from Rhodes and Kos) and C. balearicum (from the Balearic Islands and southern France). These data suggest that C. creticum has evolved in allopatry from C. repandum subsp. peloponnesiacum and that C. balearicum and C. repandum ssp. rhodense have diverged from C. repandum subsp. repandum at its western and eastern distribution limits. At one small site on Corsica, a population of C. repandum may have introgressed with relictual populations of C. balearicum. These divergence patterns illustrate how a phylogenetic perspective can be used to better understand the evolution of endemism in the Mediterranean flora. Received February 19, 2001 Accepted August 22, 2001     

Spectral composition of shade light in coastal-zone oak forests in SE Bulgaria,and relationships with leaf area index: a first overview

Major knowledge gaps exist with respect to light-quality regimes in the coastal-zone Strandzha Quercus frainetto (Q.f.) forest region adjoining the southern Bulgarian Black Sea. This paper presents preliminary results that help narrow these gaps. In conjunction with leaf area index (LAI) field campaigns we undertook measurements with an array of 7 broad-band (ca 40 nm) sensors covering the range 0.40–0.94 μm, plus 1 sensor for UVB (0.297 μm peak) and 1 for photosynthetically active radiation (PAR). Measurements focused on inside-forest shade conditions at sites 0 to ca 15 km from the Black Sea and at altitudes up to ca 120 m above sea level. Some of the sites were also studied using a high-resolution spectroradiometer. A sequential measuring strategy was necessary. This involves potentially large uncertainties, here addressed through estimations of the variability around the sinusoidal course of daylight. Light-quality regimes were found to be in general support of earlier studies of deciduous forests. Our data from the broad-band sensors and from the spectroradiometer are mutually supportive. They indicate a stronger red-shift below Q.f. canopies than below canopies in enclaves dominated by Fagus orientalis and Pinus sylvestris. Transmission in the range 0.50–0.55 μm increases beneath the three types of canopies, most pronounced in the Q.f. case. Analysis of relationships between the inside-forest to open-field irradiance ratio and LAI supports the use of Beer’s Law. We found a fairly strong relationship between the red (0.66 μm) to far-red (0.73 μm) irradiance ratios (R/FR) and LAI for the Q.f. forest. In quantitative terms, the result is new for this Q.f. region, and suggests further research to explore whether a two-sensor approach (0.66 and 0.73 μm) might offer possibilities for further low-cost mapping of the spatio-temporal patterns of R/FR and LAI in Strandzha. Such mapping would assist in further studies of the region’s forest biogeochemistry and vitality.     

An overview of indexes to evaluate terrestrial plants for phytoremediation purposes (Review)

This paper reviews the various factors, coefficients and indexes developed to evaluate terrestrial plant performance in respect to phytoremediation.A brief list of indexes includes the Accumulation factor, Bioabsorption coefficient, Bioaccumulation coefficient, Bioaccumulation factor, Bioconcentration, Bioconcentration coefficient, Bioconcentration factor, Biological absorption coefficient, Biological accumulation coefficient, Biological concentration factor, Biological transfer coefficient, Concentration factor, Enrichment coefficient, Enrichment factor, Extraction coefficient, Index of bioaccumulation, Mobility index, Shoot accumulation factor, Soil host transfer factor, Soil-plant transfer coefficient, Soil-plant transfer factor, Transfer factor and Translocation factor.These indexes represent the result of a ratio calculation between element concentrations in plant parts to that of substrata. In other cases indexes arise from the ratio calculation of element concentrations in two distinct plant parts.In the literature different terms have been attributed to the same ratio and this often represents an overlap in terminology. On the other hand the same term corresponds to several different ratios and this could create confusion and misinterpretation in data comparison.Furthermore, the evaluation of hyperaccumulation, phytostabilization or phytoextraction of plant species is not always performed in the same way. Different plant parts are considered as well as different extraction procedures for both plant and substrata element assessment. As a consequence, a direct comparison between obtained data is not always reliable and possible.In this paper the various available indexes are reviewed, highlighting both the similarity and differences between them with the aim of helping the community in choosing the appropriate term for both data evaluation and comparison. In this author’s opinion there is no need of new terms to define indexes. I would stress the need for conformity to the original definitions and criteria.     

ERK/MAPK and PI3K/AKT signal channels simultaneously activated in nerve cell and axon after facial nerve injury

BackgroundThe in-vitro study indicated that ERK/MAPK and PI3K/AKT signal channels may play an important role in reparative regeneration process after peripheral nerve injury. But, relevant in-vivo study was infrequent. In particular, there has been no report on simultaneous activation of ERK/MAPK and PI3K/AKT signal channels in facial nerve cell and axon after facial nerve injury.ResultsThe expression of P-ERK enhanced in nerve cells at the injury side on the 1 d after the rat facial nerve was cut and kept on a higher level until 14 d, but decreased on 28 d. The expression of P-AKT enhanced in nerve cells at the injury side on 1 d after injury, and kept on a higher level until 28 d. The expression of P-ERK enhanced at the near and far sections of the injured axon on 1 d, then increased gradually and reached the maximum on 7 d, but decreased on 14 d, until down to the level before the injury on 28 d. The expression of P-AKT obviously enhanced in the injured axon on 1 d, especially in the axon of the rear section, but decreased in the axon of the rear section on 7 d, while the expression of axon in the far section increased to the maximum and kept on till 14 d. On 28 d, the expression of P-AKT decreased in both rear and far sections of the axon.ConclusionThe facial nerve simultaneously activated ERK/MAPK and PI3K/AKT signal channels in facial nerve cells and axons after the cut injury, but the expression levels of P-ERK and P-AKT varied as the function of the time. In particular, they were quite different in axon of the far section. It has been speculated that two signal channels might have different functions after nerve injury. However, their specific regulating effects should still be testified by further studies in regenerative process of peripheral nerve injury.     

DNA replication stress: Causes,resolution and disease

DNA replication is a fundamental process of the cell that ensures accurate duplication of the genetic information and subsequent transfer to daughter cells. Various pertubations, originating from endogenous or exogenous sources, can interfere with proper progression and completion of the replication process, thus threatening genome integrity. Coordinated regulation of replication and the DNA damage response is therefore fundamental to counteract these challenges and ensure accurate synthesis of the genetic material under conditions of replication stress. In this review, we summarize the main sources of replication stress and the DNA damage signaling pathways that are activated in order to preserve genome integrity during DNA replication. We also discuss the association of replication stress and DNA damage in human disease and future perspectives in the field.     

Endoplasmic reticulum stress in insulin resistance and diabetes

The endoplasmic reticulum is the main intracellular Ca²⁺ store for Ca²⁺ release during cell signaling. There are different strategies to avoid ER Ca²⁺ depletion. Release channels utilize first Ca²⁺-bound to proteins and this minimizes the reduction of the free luminal [Ca²⁺]. However, if release channels stay open after exhaustion of Ca²⁺-bound to proteins, then the reduction of the free luminal ER [Ca²⁺] (via STIM proteins) activates Ca²⁺ entry at the plasma membrane to restore the ER Ca²⁺ load, which will work provided that SERCA pump is active. Nevertheless, there are several noxious conditions that result in decreased activity of the SERCA pump such as oxidative stress, inflammatory cytokines, and saturated fatty acids, among others. These conditions result in a deficient restoration of the ER [Ca²⁺] and lead to the ER stress response that should facilitate recovery of the ER. However, if the stressful condition persists then ER stress ends up triggering cell death and the ensuing degenerative process leads to diverse pathologies; particularly insulin resistance, diabetes and several of the complications associated with diabetes. This scenario suggests that limiting ER stress should decrease the incidence of diabetes and the mobility and mortality associated with this illness.     

How to deal with oxygen radicals stemming from mitochondrial fatty acid oxidation

Oxygen radical formation in mitochondria is an incompletely understood attribute of eukaryotic cells. Recently, a kinetic model was proposed, in which the ratio between electrons entering the respiratory chain via FADH₂ or NADH determines radical formation. During glucose breakdown, the ratio is low; during fatty acid breakdown, the ratio is high (the ratio increasing—asymptotically—with fatty acid length to 0.5, when compared with 0.2 for glucose). Thus, fatty acid oxidation would generate higher levels of radical formation. As a result, breakdown of fatty acids, performed without generation of extra FADH₂ in mitochondria, could be beneficial for the cell, especially in the case of long and very long chained ones. This possibly has been a major factor in the evolution of peroxisomes. Increased radical formation, as proposed by the model, can also shed light on the lack of neuronal fatty acid oxidation and tells us about hurdles during early eukaryotic evolution. We specifically focus on extending and discussing the model in light of recent publications and findings.