Overlapping genes and the proteins they encode differ significantly in their sequence composition from non-overlapping genes.

Overlapping genes represent a fascinating evolutionary puzzle, since they encode two functionally unrelated proteins from the same DNA sequence. They originate by a mechanism of overprinting, in which point mutations in an existing frame allow the expression (the "birth") of a completely new protein from a second frame. In viruses, in which overlapping genes are abundant, these new proteins often play a critical role in infection, yet they are frequently overlooked during genome annotation. This results in erroneous interpretation of mutational studies and in a significant waste of resources. Therefore, overlapping genes need to be correctly detected, especially since they are now thought to be abundant also in eukaryotes. Developing better detection methods and conducting systematic evolutionary studies require a large, reliable benchmark dataset of known cases. We thus assembled a high-quality dataset of 80 viral overlapping genes whose expression is experimentally proven. Many of them were not present in databases. We found that overall, overlapping genes differ significantly from non-overlapping genes in their nucleotide and amino acid composition. In particular, the proteins they encode are enriched in high-degeneracy amino acids and depleted in low-degeneracy ones, which may alleviate the evolutionary constraints acting on overlapping genes. Principal component analysis revealed that the vast majority of overlapping genes follow a similar composition bias, despite their heterogeneity in length and function. Six proven mammalian overlapping genes also followed this bias. We propose that this apparently near-universal composition bias may either favour the birth of overlapping genes, or/and result from selection pressure acting on them

Influence of thylakoid protein phosphorylation on photosystem I photochemistry

AbstractThe influence of the phosphorylation of thylakoid proteins on photosystem I photochemistry has been measured under conditions of linear dependence of the rate of electron transport to NADP on light intensity. It was found that the phosphorylation by ATP of light harvesting chlorophyll protein complex (LHC) II and other polypeptides stimulates the rate up to ∼ 40%; the stimulation is larger when the wavelength of actinic light corresponds to the main absorption of LHC II

Dissecting stochasticity in the temporal progression of translation: What exactly “can be otherwise”?

With a few exceptions, biological research dealing with stochasticity in molecular and cellular biology have focused on transcriptional processes (e.g., Elowitz et al 2002; Lipniacki et al 2006). Consequently, philosophical analyses have also centered on its role in transcription (e.g., Casali and Merlin 2020). Nonetheless, recent empirical evidence clearly shows that stochasticity is pervasive in translation too (e.g., Boersma et al 2019). Focusing on a noncanonical case of translation (i.e., start codon selection), this paper aims to disentangle two ways in which stochasticity can intervene in this intracellular process. Having provided a definition of what we mean by stochasticity, we first focus on the parameter of time. By introducing two temporal models, we show where and how stochasticity can make a difference in the timing of translation process. Second, we show how this difference can be biologically relevant for cell physiology. We conclude that, from an explanatory point of view, it is thus worth dissecting stochasticity when studying translation, gene expression and, more generally, biological processes at the molecular level

Overlapping genes and the proteins they encode differ significantly in their sequence composition from non-overlapping genes.

Overlapping genes represent a fascinating evolutionary puzzle, since they encode two functionally unrelated proteins from the same DNA sequence. They originate by a mechanism of overprinting, in which point mutations in an existing frame allow the expression (the "birth") of a completely new protein from a second frame. In viruses, in which overlapping genes are abundant, these new proteins often play a critical role in infection, yet they are frequently overlooked during genome annotation. This results in erroneous interpretation of mutational studies and in a significant waste of resources. Therefore, overlapping genes need to be correctly detected, especially since they are now thought to be abundant also in eukaryotes. Developing better detection methods and conducting systematic evolutionary studies require a large, reliable benchmark dataset of known cases. We thus assembled a high-quality dataset of 80 viral overlapping genes whose expression is experimentally proven. Many of them were not present in databases. We found that overall, overlapping genes differ significantly from non-overlapping genes in their nucleotide and amino acid composition. In particular, the proteins they encode are enriched in high-degeneracy amino acids and depleted in low-degeneracy ones, which may alleviate the evolutionary constraints acting on overlapping genes. Principal component analysis revealed that the vast majority of overlapping genes follow a similar composition bias, despite their heterogeneity in length and function. Six proven mammalian overlapping genes also followed this bias. We propose that this apparently near-universal composition bias may either favour the birth of overlapping genes, or/and result from selection pressure acting on them

A summated rating scale for measuring city image

The literature about cities' marketing is replete with articles on the subject of city branding. Included in this literature are articles dealing with the subject of measuring city image, which is a precursor to the development of a city brand. However, many of the image studies lack validity or generalization. This paper presents a methodology for measuring city image, grounded on the development of a scale for this purpose. Based on convergent and discriminant reliability and validity analyses, factors were identified that comprise a city's image among residents and tourists in three cities: Jerusalem, Rome and Trieste. Four factors identified by residents are Municipal Facilities, Leisure, Security and Public Services. Among tourists five factors were identified: Caring, Tourism and Recreation, Security, Public Services and Leisure and Entertainment. Three corresponding factors were identified in both tourists' and residents' replies. The scale validation process indicated that residents and tourists have similarities and differences in their perception of a city. As such, the current finding suggests that the scales developed in this paper may be used when surveying both groups

Fluorescence and Absorption Detected Magnetic Resonance of Chlorosomes from Green Bacteria <i>Chlorobium tepidum</i> and <i>Chloroflexus aurantiacus</i>. A Comparative Study

A comparative study on the isolated chlorosomes from Chloroflexus aurantiacus, a green filamentous photosynthetic bacterium and Chlorobium tepidum, a green sulfur photosynthetic bacterium, was done by ODMR (optically detected magnetic resonance). Correlation between the results obtained by fluorescence and absorption detection is shown to be a source of information about the functional interactions among pigments. Analogies and differences are pointed out between the light-harvesting systems of the two species. Triplet states are easily detected in both bacteria at 1.8 K under steady-state illumination and are assigned to BChl c, BChl a, and carotenoid molecules. Carotenoids are found to be able to quench BChl a triplet states, but no evidence of BChl c triplet states quenching by this triplet−triplet transfer mechanism is found in both systems. Then from the data it appears that some carotenoids are in close contact with BChl a molecules. The relevance of this finding to the localization of carotenoids in the chlorosomes is discussed. In Cb. tepidum three different pools of BChl c oligomers connected to BChl a were found by detection of their triplet state, while only one pool of BChl c was evidenced in Cf. aurantiacus. The latter appears to be unconnected, at least at 1.8 K, to BChl a. On the other hand, heterogeneity in the BChl a triplet population was detected in Cf. aurantiacus. Even though the two bacteria show common features in the way the light excitation induces triplet formation at low temperature, the detected triplet states show spectroscopic properties that strongly depend on the system. The results clearly indicate that differences in pigment organization exist both in the core and in the baseplate of the chlorosomes from the two different bacteria.</p