Mechanism of RNA 2'-O-methylation: evidence that the catalytic lysine acts to steer rather than deprotonate the target nucleophile

The weight of current evidence suggests that RNA 2'-O-MTases employ an S(N)2 mechanism with an in-line attack of the target nucleophile upon the methyl group of the AdoMet cofactor. It has been suggested that, like the phosphohydrolytic enzymes, ribozymes, and nucleic acid polymerases, the RNA 2'-O-MTases initially activate the substrate's attacking hydroxyl oxygen by deprotonation. Here, evidence is presented that the vaccinia virus mRNA cap specific 2'-O-MTase VP39 does not promote RNA 2'-oxyanion formation but that instead it acts by steering a hydroxyl oxygen orbital toward the cofactor methyl center.     

Leveraging AI tools to develop the writer rather than the writing

Scientific writing can prove challenging, particularly for those who are non-native English speakers writing in English. Here, we explore the potential of advanced artificial intelligence (AI) tools, guided by principles of second-language acquisition, to help scientists improve their scientific writing skills in numerous contexts.     

Hox gene complexity in medaka fish may Be similar to that in pufferfish rather than zebrafish.

Changes in number and the genomic organization of Hox genes have played an important role in metazoan body-plan evolution. They make cluster(s), and in vertebrates, each cluster contains different number of Hox genes that have been classified into 13 groups. There are 39 Hox genes in four clusters on different chromosomes in the mammalian genome. In the fish, while 31 Hox genes in four clusters have been identified in pufferfish Fugu rubripes, 47 Hox genes in seven clusters exist in the zebrafish Danio rerio. To estimate the evolutionary origin of Hox organization in ray-finned fishes, we searched for Hox genes in the medaka fish Oryzias latipes, with a taxon thought to be widely separated from those of pufferfish and zebrafish. We synthesized various mixed oligonucleotides that can work as group-specific primers for PCR, then cloned and sequenced amplified fragments. Numbers of Hox genes identified in the present study were 2 for group 1, 2 for group 2, 1 for group 3, 3 for group 4, 6 for groups 5-7, 2 for group 8, 4 for group 9, 3 for group 10, 1 for group 12, and 3 for group 13. The primers specific for group 11 did not function in this study. Thus, at least 27 Hox genes are present in medaka genome, suggesting that the Hox gene complexity of the medaka genome is similar to that of the pufferfish rather than the zebrafish.     

Evidence that substance P may be a modulator rather than a transmitter of noxious mechanical stimulation

Substance P (SP), injected intrathecally, produced a dose-related increase in responsiveness (hyperalgesia) in a pressure test for nociceptive thresholds. Pretreatment with two doses of SP produced complete desensitization to this response but did not alter base-line responsiveness. The hyperalgesic response to SP and the lack of change in base line following desensitization to SP suggest a modulator rather than a transmitter role for SP in the transmission of noxious mechanical stimulation.     

Evidence that accumulation of mutants in a biofilm reflects natural selection rather than stress-induced adaptive mutation

The accumulation of mutant genotypes within a biofilm evokes the controversy over whether the biofilm environment induces adaptive mutation or whether the accumulation can be explained by natural selection. A comparison of the virulence of two strains of the dental pathogen Streptococcus mutans showed that rats infected with one of the strains accumulated a high proportion (average, 22%) of organisms that had undergone a deletion between two contiguous and highly homologous genes. To determine if the accumulation of deletion mutants was due to selection or to an increased mutation rate, accumulations of deletion mutants within in vitro planktonic and biofilm cultures and within rats inoculated with various proportions of deletion organisms were quantified. We report here that natural selection was the primary force behind the accumulation of the deletion mutants.     

Toxin-assisted micropredation: experimental evidence shows that contact micropredation rather than exotoxicity is the role of Prymnesium toxins

Blooms of Prymnesium parvum can severely harm fish and zooplankton, presumably through the release of allelopathic exotoxins that offer advantages for Prymnesium in its interactions with competitors and prey. We show that Prymnesium attaches to zooplankton and fish, causing mortality, whereas exposure of these organisms to Prymnesium across a permeable membrane does not cause mortality. We also show that Prymnesium exotoxins are released independently of contact toxicity only in response to experimental procedures or natural causes of stress. Our results are consistent with the idea that toxins have evolved for release during cell-to-cell contact in support of heterotrophy. The evolution of toxin-assisted micropredation would be consistent with mechanisms of natural selection favouring individual fitness as opposed to broadcast allelopathy from which the benefits are more dispersed. Research into the toxicity of Prymnesium and other harmful algal species may profit from focus on processes following physical contact with potential prey.     

Selective binding of zinc ions to heparin rather than to other glycosaminoglycans.

The relative binding affinity of Zn2+ to several glycosaminoglycans was determined by gel-filtration chromatography. Binding was observed only between Zn2+ and heparin. No binding was observed between Zn2+ and chondroitin 4-sulphate, chondroitin 6-sulphate, dermatan sulphate of hyaluronic acid. All of the glycosaminoglycans contained carboxy groups, but only heparin bound Zn2+. This observation suggests that, contrary to a previously proposed hypothesis, simple electrostatic interactions between the negatively charged carboxy groups of the glycosaminoglycans and the positively charged Zn2+ cannot explain the observed binding.     

Evidence that sex chromosome asynapsis, rather than excess Y gene dosage, is responsible for the meiotic impairment of XYY mice

There is extensive evidence for the existence of a meiotic checkpoint that acts to eliminate spermatocytes that fail to achieve full sex chromosome synapsis at the pachytene stage of the first meiotic prophase. XYY mice are nearly always sterile, with clear signs of meiotic impairment, and sex chromosome asynapsis has been proposed to underlie this impairment. However, a study of XYY*(X) mice (mice having three sex chromosomes but only a single dose of Y genes) revealed that these mice are fertile, and thus implicated Y gene dosage as a major factor in the sterility of XYY mice. To address this question further, sex chromosome synapsis and spermatogenic proficiency were compared between XYY*(X) and XYY mice generated in the same litters. This established that differences in spermatogenic proficiency within and between the two genotypes correlated with the frequency of radial trivalent formation (full sex chromosome synapsis); XYY*(X) males, as a group, had double the radial trivalent frequency of XYY males. This observation provides strong support for the view that sex chromosome asynapsis (or some consequence thereof), rather than Y gene dosage, is the major factor leading to the meiotic impairment of XYY mice.     

Alfred Newton's contribution to ornithology: a conservative quest for facts rather than grand theories

Alfred Newton (1829–1907) was a founding member of the British Ornithologists’ Union, served as editor of The Ibis, and became one of the best‐known British ornithologists of the nineteenth‐century. Between 1855 and 1864 he travelled in Europe and North America, making a trip to Iceland in 1858 with John Wolley in search of information about the Great Auk Pinguinus impennis. In 1866 Newton obtained the chair of Zoology and Comparative Zoology at the University of Cambridge, where he remained for rest of his career. An unenthusiastic teacher, Newton nevertheless encouraged successive generations of young ornithologists through the soirées he held in his college rooms. Newton published extensively, but his most significant publication was the Dictionary of Birds (1896). Newton's death marked the beginning of the end of a long period in which scientific ornithology comprised little more than taxonomy and nomenclature, although Newton was also instrumental in initiating conservation legislation. Extremely conservative in most aspects of his life, Newton was nevertheless the first ornithologist to appreciate the significance of natural selection. He therefore constitutes an important figure in an era of ornithology that immediately precedes the current interest in field ornithology.     

Tree species composition rather than diversity triggers associational resistance to the pine processionary moth

The reduction of insect herbivory is one of the services provided by tree diversity in forest ecosystems. While it is increasingly acknowledged that the compositional characteristics of tree species assemblages play a major role in triggering associational resistance to herbivores, underlying mechanisms are less well known. We addressed this question in the ORPHEE experiment by assessing pine processionary moth infestations (Thaumetopoea pityocampa) across a tree diversity gradient from pine monocultures to five species mixtures. We showed that tree species richness per se had no effect on the probability of attack by this pest. By contrast, the infestation rate was strongly dependent on plot composition. Mixtures of pines (Pinus pinaster) and birches (Betula pendula) were less prone to T. pityocampa infestations, whereas mixtures of pines and oaks (Quercus spp.) were more often attacked than pine monocultures. By taking into account the relative height of pines and associated broadleaved species, this effect could be explained by pine apparency. Pines were on average 343 ± 5 cm height. Birches, as fast growing trees, were slightly taller than pines (363 ± 6 cm), while oak trees were significantly smaller (74 ± 1 cm). Host trees of T. pityocampa were then partly hidden in mixtures of pines and birches but more apparent in mixtures with oaks. We suggest that reduced pine apparency disrupted visual cues used by female moths to select host trees prior to oviposition. This study highlights the need to take into account tree traits such as growth rate when selecting the tree species that have to be associated in order to improve forest resistance to pest insects.     

One type of gamma-turn, rather than the other gives rise to chain-reversal in proteins

Gamma-turns may be defined by a hydrogen bond between the carbonyl group of one amino acid residue and the amino group of the acid two residues ahead in the sequence. They occur as two types, inverse gamma-turns and classic gamma-turns (classic gamma-turns are usually called just gamma-turns but we prefer to add the adjective classic to distinguish them from the word gamma-turn, referring collectively to both). Of the two, classic gamma-turns are less common and are considered by all authors to be extreme rarities in proteins. However, we find that a number do occur in a sample of proteins of known three-dimensional structure. One occurs at the edge of the second hypervariable region of the light chain in some immunoglobulins. All classic gamma-turns except one are associated with a reversal in the main chain direction. In most cases, the turn lies at the loop end of a beta-hairpin. By contrast, inverse gamma-turns, although giving rise to a kink in the chain, rarely occur within beta-hairpins and are seldom situated at a position of reversal, by 180 degrees, in chain direction.     

Longevity of orders is related to the longevity of their constituent genera rather than genus richness

Longevity of a taxonomic group is an important issue in understanding the dynamics of evolution. In this respect a key observation is that genera, families or orders can each be assigned a characteristic average lifetime (Van Valen in Evol Theory 1:1–30, 1973). Using the fossil marine animal genera database (Sepkoski in Bull Am Paleontol 363, pp 563, 2002) we here examine the relationship between longevity of a higher taxonomic group (orders) and the longevity of its lower taxonomic groups (genera). We find insignificant correlation between the size of an order and its longevity, whereas we observe large correlation between the lifetime of an order and the lifetime of its constituent genera. These observations suggest that longevity of taxonomic groups is heritable intrinsically or on the grounds of environmental preferences.     

Inactivation of active thrombin-activable fibrinolysis inhibitor takes place by a process that involves conformational instability rather than proteolytic cleavage

Thrombin-activable fibrinolysis inhibitor (TAFI) is present in the circulation as an inactive zymogen. Thrombin converts TAFI to a carboxypeptidase B-like enzyme (TAFIa) by cleaving at Arg(92) in a process accelerated by the cofactor, thrombomodulin. TAFIa attenuates fibrinolysis. TAFIa can be inactivated by both proteolysis by thrombin and spontaneous temperature-dependent loss of activity. The identity of the thrombin cleavage site responsible for loss of TAFIa activity was suggested to be Arg(330), but site-directed mutagenesis of this residue did not prevent inactivation of TAFIa by thrombin. In this study we followed TAFI activation and TAFIa inactivation by thrombin/thrombomodulin in time and characterized the cleavage pattern of TAFI using matrix-assisted laser desorption ionization mass spectrometry. Mass matching of the fragments revealed that TAFIa was cleaved at Arg(302). Studies of a mutant R302Q-TAFI confirmed identification of this thrombin cleavage site and, furthermore, suggested that inactivation of TAFIa is based on its conformational instability rather than proteolytic cleavage at Arg(302).     

Studying the mechanism that enables paullones to selectively inhibit glycogen synthase kinase 3 rather than cyclin-dependent kinase 5 by molecular dynamics simulations and free-energy calculations

Glycogen synthase kinase 3 (GSK-3) is an attractive target for the treatment of diabetes, and paullones have been reported to be effective inhibitors of GSK-3. However, it is still a challenging task to improve selectivity among protein kinases, especially cyclin-dependent kinases (CDKs). Here we investigated the mechanism that enables paullones to selectively inhibit GSK-3 rather than cyclin-dependent kinase 5 (CDK5) using sequence alignment, molecular dynamics simulations, free-energy calculations and free-energy decomposition analysis. The results indicate that the interaction between paullones and Val135 of GSK-3 is obviously stronger than that between paullones and Cys83 of CDK5, suggesting that paullones could be utilized as potent selective inhibitors. Meanwhile, we observed that the decrease in the interaction between paullones and the Asp86 of CDK5 favors their selectivity towards GSK-3 rather than CDK5, as demonstrated using 1-azakenpaullone as an example. Although substitution at position 9 and replacement at position 2 may influence the activity of GSK-3, they only have a minor effect on the selectivity. We expect that the information obtained here could prove useful for developing specific paullone inhibitors of GSK-3.