Imena metoda i akronimi - duhovita strana znanosti

The name of a method usually contains its basic principles. To simplify the name of a method and make it easier to remember, an acronym is often used. However, sometimes the name of a method and its acronym are formed in such a way that the result often has quite a different or even humorous meaning. Here we have sorted out acronyms of scientific methods that have unusual or humorous meaning. The summation is a list of representative methods that represent the true face of science: an interesting, skillful and joyful human activity.Ime metode najčešće sadrži opis njenih osnovnih načela. Kako bi se pojednostavio naziv metode, a samim time i olakšalo pamćenje naziva, redovito se upotrebljavaju akronimi. Međutim, često se događa da su ime metode i njezin akronim osmišljeni tako da dobiveni naziv ima potpuno drugačije značenje te ponekad i humorističnu konotaciju. Izdvojeni su akronimi znanstvenih metoda koji imaju neuobičajena i često humoristična značenja. Pregled ovih akronima je zbir reprezentativnih metoda koje prikazuju znanost u njezinom pravom svjetlu kao zahtjevnu, zanimljivu i zabavnu ljudsku aktivnost

A New Approach To Predict the Biological Activity of Molecules Based on Similarity of Their Interaction Fields and the logP and logD Values: Application to Auxins

The activity of a biological compound is dependent both on specific binding to a target receptor and its ADME (Absorption, Distribution, Metabolism, Excretion) properties. A challenge to predict biological activity is to consider both contributions simultaneously in deriving quantitative models. We present a novel approach to derive QSAR models combining similarity analysis of molecular interaction fields (MIFs) with prediction of logP and/or logD. This new classification method is applied to a set of about 100 compounds related to the auxin plant hormone. The classification based on similarity of their interaction fields is more successful for the indole than the phenoxy compounds. The classification of the phenoxy compounds is however improved by taking into account the influence of the logP and/or the logD values on biological activity. With the new combined method, the majority (8 out of 10) of the previously misclassified derivatives of phenoxy acetic acid are classified in accord with their bioassays. The recently determined crystal structure of the auxin-binding protein 1 (ABP1) enabled validation of our approach. The results of docking a few auxin related compounds with different biological activity to ABP1 correlate well with the classification based on similarity of MIFs only. Biological activity is, however, better predicted by a combined similarity of MIFs + logP/logD approach

AUXIN BINDING-PROTEIN1 (ABP1), a receptor to regulate auxin transport and early auxin genes in an interlocking system with PIN proteins and the receptor TIR1

Compared to the past 10 years, a flurry of publications, reviews and experimental papers on ABP1 have appeared in the last couple of years. Certainly, the reason is that new methods and conceptual approaches appeared to tackle the questions posed by this enigmatic auxin-binding protein. Part of the enigma is the obvious central importance of ABP1, documented by the embryo-lethal property of the homozygous T-DNA insertion into this gene.1 At the same time, this very property hindered progress in studying ABP1. Another delaying influence on ABP1 research was the fact that regulation of early auxin genes was fully explained by the mechanism provided by TRI1, the second auxin receptor.2–

Streptomyces coelicolor macrodomain hydrolase SCO6735 cleaves thymidine-linked ADP-ribosylation of DNA

ADP-ribosylation is an ancient, highly conserved, and reversible covalent modification critical for a variety of endogenous processes in both prokaryotes and eukaryotes. ADP-ribosylation targets proteins, nucleic acids, and small molecules (including antibiotics). ADP-ribosylation signalling involves enzymes that add ADP-ribose to the target molecule, the (ADP-ribosyl)transferases; and those that remove it, the (ADP-ribosyl)hydrolases. Recently, the toxin/antitoxin pair DarT/DarG composed of a DNA ADP-ribosylating toxin, DarT, and (ADP-ribosyl)hydrolase antitoxin, DarG, was described. DarT modifies thymidine in single-stranded DNA in a sequence-specific manner while DarG reverses this modification, thereby rescuing cells from DarT toxicity. We studied the DarG homologue SCO6735 which is highly conserved in all Streptomyces species and known to be associated with antibiotic production in the bacterium S. coelicolor. SCO6735 shares a high structural similarity with the bacterial DarG and human TARG1. Like DarG and TARG1, SCO6735 can also readily reverse thymidine-linked ADP-ribosylation catalysed by DarT in vitro and in cells. SCO6735 active site analysis including molecular dynamic simulations of its complex with ADP-ribosylated thymidine suggests a novel catalytic mechanism of DNA-(ADP-ribose) hydrolysis. Moreover, a comparison of SCO6735 structure with ALC1-like homologues revealed an evolutionarily conserved feature characteristic for this subclass of macrodomain hydrolases

The influence of demogeographic development on spatial contents and models of primary education in Istria

This work explores the influence of demographic processes, especially birth rate’s movements, on the changes in the features and organisation of primary education in Istria between years 2001 and 2017. The analyses were implemented on the level of municipalities and cities, and greater spatial units of Istria – coastal area, the inland and the city of Pula. We analysed the changes in population and student contingent, fluctuations of birth rate, net migration and the changes in primary education (number of students and classes, number of teachers and schools). The results have pointed out to the existence of a positive connection between birth rate’s change and number of students in primary schools, but also that birth rate has a postponed effect on the size of the student contingent. Spatial disparities between the Istria’s inland and coast are determined also in the features of primary education that generally adapts to demographic processes more slowl

Computational Study of the DNA-Binding Protein Helicobacter pylori NikR: The Role of Ni2+

An integrated approach, combining atomistic molecular dynamics simulations, coarsegrained models, and solution NMR, was used to characterize the internal dynamics of HpNikR, a Ni-dependent transcription factor. Specifically, these methods were used to ascertain how the presence of bound Ni2+ ions affects the stability of the known open, cis, and trans forms observed in the crystal structures of this protein as well as their interconversion capability. The consensus picture emerging from all the collected data hint at the interconversion of NikR among the three types of conformations, regardless of content of bound Ni2+. On the basis of atomistic and coarse-grained simulations, we suggest that the interconversion capability is particularly effective between the cis and the open forms and appreciably less so between the trans conformer and the other two forms. The presence of the bound Ni2+ ions does, however, affect significantly the degree of the correlations on the two DNA-binding domains of NikR, which is significantly suppressed as compared to the apo form. Overall, the findings suggest that the binding of HpNikR to DNA occurs through a sophisticated multistep process that might involve both a conformational selection and an induced fit