Free energy calculations on the stability of the 14-3-3ζ protein

Mutations of cysteine are often introduced to e.g. avoid formation of non-physiological inter-molecular disulfide bridges in in-vitro experiments, or to maintain specificity in labeling experiments. Alanine or serine is typically preferred, which usually do not alter the overall protein stability, when the original cysteine was surface exposed. However, selecting the optimal mutation for cysteines in the hydrophobic core of the protein is more challenging. In this work, the stability of selected Cys mutants of 14-3-3ζ was predicted by free-energy calculations and the obtained data were compared with experimentally determined stabilities. Both the computational predictions as well as the experimental validation point at a significant destabilization of mutants C94A and C94S. This destabilization could be attributed to the formation of hydrophobic cavities and a polar solvation of a hydrophilic side chain. A L12E, M78K double mutant was further studied in terms of its reduced dimerization propensity. In contrast to naïve expectations, this double mutant did not lead to the formation of strong salt bridges, which was rationalized in terms of a preferred solvation of the ionic species. Again, experiments agreed with the calculations by confirming the monomerization of the double mutants. Overall, the simulation data is in good agreement with experiments and offers additional insight into the stability and dimerization of this important family of regulatory proteins.     

Mineralization and non-ideality: on nature’s foundry

Understanding how ions, ion-clusters and particles behave in non-ideal environments is a fundamental question concerning planetary to atomic scales. For biomineralization phenomena wherein diverse inorganic and organic ingredients are present in biological media, attributing biomaterial composition and structure to the chemistry of singular additives may not provide a holistic view of the underlying mechanisms. Therefore, in this review, we specifically address the consequences of physico-chemical non-ideality on mineral formation. Influences of different forms of non-ideality such as macromolecular crowding, confinement and liquid-like organic phases on mineral nucleation and crystallization in biological environments are presented. Novel prospects for the additive-controlled nucleation and crystallization are accessible from this biophysical view. In this manner, we show that non-ideal conditions significantly affect the form, structure and composition of biogenic and biomimetic minerals.     

Is the chromanol head group of vitamin E nature’s final truth on chain-breaking antioxidants?

Tocopherol is believed to be the most potent naturally occurring chain-breaking antioxidant. Hence, its refined phenolic head group chromanol may represent an optimum evolutionary solution to the problem of free-radical chain reactions in the lipid bilayer. To test the universal validity of this assumption beyond phenolic head groups, we have synthesized aromatic amine analogues of vitamin E and trolox with otherwise closely matching physicochemical properties: NH-toc and NH-trox. We have found that NH-toc and NH-trox were significantly more potent free radical scavengers, lipid peroxidation inhibitors and cytoprotective agents than their phenolic templates, tocopherol and trolox. In a chemical sense, thus, the chromanol head group does not constitute a global optimum for the design of chain-breaking antioxidants.     

The impacts of the Free Semester program on students’ exam nervousness

I examine the impacts of the Free Semester (FS) program, which is an exam-free semester for middle school students in South Korea, on students’ level of exam nervousness. I use a difference-in-differences approach that exploits the variation in FS-implementation across middle schools to estimate these impacts. I find that the FS program has statistically significant impacts on relieving exam nervousness during the semester in which it is run. In contrast, I find no statistically significant average medium-run impacts of the program. My subgroup analyses suggest that the reduction in exam nervousness during the FS is driven largely by high-achieving students.     

Loss of nervous system complexity – Morphological analyses shed light on the neuronal evolution in Myzostomida (Annelida)

Myzostomida are putatively nested within the errant Annelida and exhibit a unique morphology. The latter fact might possibly be related to their long host-dependent radiation. Hence, an incomplete segmentation, lack of prominent sensory structures in adults and a dorso-ventrally flattened body are just some examples. Although numerous investigations of the nervous system exist for myzostomids, detailed ultrastructural as well as histological examinations of neuronal structures are lacking so far. Therefore, we investigate the nervous system of Myzostoma cirriferum Leuckart, 1836 using a comparative approach including paraffin histology, serial semi-thin sections, immunohistochemistry and ultrastructural investigations. Our analyses reveal a lack of complexity within the anterior-most neuronal condensation (herein called brain) of adult specimens. Hence, prominent tracts or glomeruli are absent, and a glial layer surrounding the brain or radial-like glial cells are lacking. Nevertheless, the ultrastructure of the ventral nervous system is comparable to other Errantia. Therefore, our investigations hint towards a reduction of neuronal complexity in Myzostomida. Additionally, an ontogenetic simplification seems plausible, although further investigations are necessary to verify such a hypothesis. A simplification of neuronal structures due to a drastic change in lifestyle was so far mainly observed for basally branching annelid clades.     

If at first you don't succeed… Studies of ontogeny shed light on the cognitive demands of habitual tool use

Many species use tools, but the mechanisms underpinning the behaviour differ between species and even among individuals within species, depending on the variants performed. When considering tool use ‘as adaptation’, an important first step is to understand the contribution made by fixed phenotypes as compared to flexible mechanisms, for instance learning. Social learning of tool use is sometimes inferred based on variation between populations of the same species but this approach is questionable. Specifically, alternative explanations cannot be ruled out because population differences are also driven by genetic and/or environmental factors. To better understand the mechanisms underlying routine but non-universal (i.e. habitual) tool use, we suggest focusing on the ontogeny of tool use and individual variation within populations. For example, if tool-using competence emerges late during ontogeny and improves with practice or varies with exposure to social cues, then a role for learning can be inferred. Experimental studies help identify the cognitive and developmental mechanisms used when tools are used to solve problems. The mechanisms underlying the route to tool-use acquisition have important consequences for our understanding of the accumulation in technological skill complexity over the life course of an individual, across generations and over evolutionary time.     

Does progressive nuclear staining with hemalum (alum hematoxylin) involve DNA,and what is the nature of the dye-chromatin complex?

Previous investigators have disagreed about whether hemalum stains DNA or its associated nucleoproteins. I review here the literature and describe new experiments in an attempt to resolve the controversy. Hemalum solutions, which contain aluminum ions and hematein, are routinely used to stain nuclei. A solution containing 16 Al³⁺ ions for each hematein molecule, at pH 2.0–2.5, provides selective progressive staining of chromatin without cytoplasmic or extracellular “background color.” Such solutions contain a red cationic dye-metal complex and an excess of Al³⁺ ions. The red complex is converted to an insoluble blue compound, assumed to be polymeric, but of undetermined composition, when stained sections are blued in water at pH 5.5–8.5. Staining experiments with DNA, histone and DNA + histone mixtures support the theory that DNA, not histone, is progressively colored by hemalum. Extraction of nucleic acids, by either a strong acid or nucleases at near neutral pH, prevented chromatin staining by a simple cationic dye, thionine, pH 4, and by hemalum, with pH adjustments in the range, 2.0–3.5. Staining by hemalum at pH 2.0–3.5 was not inhibited by methylation, which completely prevented staining by thionine at pH 4. Staining by hemalum and other dye-metal complexes at pH ≤ 2 may be due to the high acidity of DNA-phosphodiester (pK_a ~ 1). This argument does not explain the requirement for a much higher pH to stain DNA with those dyes and fluorochromes not used as dye-metal complexes. Sequential treatment of sections with Al₂(SO₄)₃ followed by hematein provides nuclear staining that is weaker than that attainable with hemalum. Stronger staining is seen if the pH is raised to 3.0–3.5, but there is also coloration of cytoplasm and other materials. These observations do not support the theory that Al³⁺ forms bridges between chromatin and hematein. When staining with hematein is followed by an Al₂(SO₄)₃ solution, there is no significant staining. Taken together, the results of my study indicate that the red hemalum cation is electrostatically attracted to the phosphate anion of DNA. The bulky complex cation is too large to intercalate between base pairs of DNA and is unlikely to fit into the minor groove. The short range van der Waals forces that bind planar dye cations to DNA probably do not contribute to the stability of progressive hemalum staining. The red cation is precipitated in situ as a blue compound, insoluble in water, ethanol and water-ethanol mixtures, when a stained preparation is blued at pH > 5.5.     

Mitochondrial permeability transition pore: a promising target for the treatment of Parkinson’s disease

Among the neurodegenerative diseases (ND), Parkinson’s disease affects 6.3 million people worldwide characterized by the progressive loss of dopaminergic neurons in substantia nigra. The mitochondrial permeability transition pore (mtPTP) is a non-selective voltage-dependent mitochondrial channel whose opening modifies the permeability properties of the mitochondrial inner membrane. It is recognized as a potent pharmacological target for diseases associated with mitochondrial dysfunction and excessive cell death including ND such as Parkinson’s disease (PD). Imbalance in Ca²⁺ concentration, change in mitochondrial membrane potential, overproduction of reactive oxygen species (ROS), or mutation in mitochondrial genome has been implicated in the pathophysiology of the opening of the mtPTP. Different proteins are released by permeability transition including cytochrome c which is responsible for apoptosis. This review aims to discuss the importance of PTP in the pathophysiology of PD and puts together different positive as well as negative aspects of drugs such as pramipexole, ropinirole, minocyclin, rasagilin, and safinamide which act as a blocker or modifier for mtPTP. Some of them may be detrimental in their neuroprotective nature.     

Comparison of the activation energy barrier for succinimide formation from α- and β-aspartic acid residues obtained from density functional theory calculations

The l-α-Asp residues in peptides or proteins are prone to undergo nonenzymatic reactions to form l-β-Asp, d-α-Asp, and d-β-Asp residues via a succinimide five-membered ring intermediate. From these three types of isomerized aspartic acid residues, particularly d-β-Asp has been widely detected in aging tissue. In this study, we computationally investigated the cyclization of α- and β-Asp residues to form succinimide with dihydrogen phosphate ion as a catalyst (H₂PO₄⁻). We performed the study using B3LYP/6-31 + G(d,p) density functional theory calculations. The comparison of the activation barriers of both residues is discussed. All the calculations were performed using model compounds in which an α/β-Asp-Gly sequence is capped with acetyl and methylamino groups on the N- and C-termini, respectively. Moreover, H₂PO₄⁻ catalyzes all the steps of the succinimide formation (cyclization-dehydration) acting as a proton-relay mediator. The calculated activation energy barriers for succinimide formation of α- and β-Asp residues are 26.9 and 26.0 kcal mol^− 1, respectively. Although it was experimentally confirmed that β-Asp has higher stability than α-Asp, there was no clear difference between the activation barriers. Therefore, the higher stability of β-Asp residue than α-Asp residue may be caused by an entropic effect associated with the succinimide formation.     

Effects of oxysterols on the blood–brain barrier: Implications for Alzheimer’s disease

Altered brain cholesterol homeostasis plays a key role in neurodegenerative diseases such as Alzheimer’s disease (AD). For a long time, the blood–brain barrier (BBB) was basically considered as a barrier isolating the brain from circulating cholesterol, however, several lines of evidence now suggest that the BBB strictly regulates the exchanges of sterol between the brain and the peripheral circulation. Oxysterols, synthesized by neurons or by peripheral cells, cross the BBB easily and modulate the expression of several enzymes, receptors and transporters which are involved not only in cholesterol metabolism but also in other brain functions. This review article deals with the way oxysterols impact BBB cells. These perspectives open new routes for designing certain therapeutical approaches that target the BBB so that the onset and/or progression of brain diseases such as AD may be modulated.     

Seasonal morphophysiological variations in the prostatic complex of the Tarabul’s gerbil (Gerbillus tarabuli)

Gerbillus tarabuli is a nocturnal Saharan rodent which has an annual reproductive cycle characterized by the reproductive activity in spring and a long phase of sexual quiescence in other seasons. We describe the morphology and hormonal regulation of the prostatic complex of this rodent in the two periods, based on anatomical, histological, morphometric, and immunohistochemical analyses. The organisation of this prostatic complex is similar to that reported for Meriones unguiculatus, but different from the prostate of Psammomys obesus, the rat, and the mouse. In addition to the anterior lobes, ventral lobes, and dorsal lobes, the prostatic complex of Gerbillus tarabuli, also includes dorsolateral lobe. Each lobe is composed of a fibro-muscular stroma surrounding a glandular epithelium. Dorsolateral lobes are easily distinguishable by their big volume. The prostate grows and regresses cyclically throughout the year. During the resting season, ventral lobes and anterior lobes showed atrophy, with a significant decrease in both epithelial height and supranuclear area size, and a strong thickening of the fibro-muscular compartment. In dorsal lobes, the epithelial and stromal compartments atrophied and regenerated simultaneously, whereas in dorsolateral lobe the thickness of the epithelium, the supranuclear zone and the stroma increased during resting period. Furthermore, seasonal variations were observed in the distribution and expression of both androgen receptors, and estrogens receptors. Expression patterns of all receptors were lobe-specific. In conclusion, both androgens and estrogens are involved in the homeostasis and regulation of the prostate in Gerbillus tarabuli. Dorsolateral lobe seems to be controlled by a different mechanism than other lobes.     

Free amino acid and dipeptide changes in the body fluids from Alzheimer’s disease subjects

Summary. Our aim was to determine changes in free amino acid (FAA) and dipeptide (DP) concentrations in probable Alzheimer’s disease (pAD) subjects compared with control (CT) subjects using liquid chromatography and electrospray ionization tandem mass spectrometry (LCMS²). We recruited gender- and age-matched study participants based on neurological and neuropsychological assessments. We measured FAAs and DPs in cerebrospinal fluid (CSF), plasma and urine using LCMS² with selected reaction monitoring (SRM). Imidazole-containing FAAs (histidine, methyl-histidine), catecholamines (L-DOPA and dopamine), citrulline, ornithine, glycine and antioxidant DPs (carnosine and anserine) accounted for the major changes between CT and pAD. Carnosine levels were significantly lower in pAD (328.4 ± 91.31 nmol/dl) than in CT plasma (654.23 ± 100.61 nmol/dl). In contrast, L-DOPA levels were higher in pAD (1400.84 ± 253.68) than CT (513.10 ± 121.61 nmol/dl) plasma. These data underscore the importance of FAA and DP metabolism in the pathogenesis of AD. Since our data show changes in antioxidants, neurotransmitters and their precursors, or FAA associated with urea metabolism in pAD compared with CT, we propose that manipulation of these metabolic pathways may be important in preventing AD progression.     

Investigations on the effect of „light break” on the nature of the endogenous rhythm in the flowering response of Biloxi soybean (Glycine,Max, L. merr.)

Zusammenfassung Biloxi-Soja-Bohnen (Glycine max. L. Merr) erhielten photoperiodische Cyclen, die aus 8-oder 9stündigen Lichtperioden und unterschiedlich langen Dunkelperioden bestanden. Die Dunkelperioden wurden zu verschiedenen Zeitpunkten durch halbstündiges Störlicht unterbrochen. Die Wirkung dieser unterschiedlichen Behandlungen wurde durch Messung der Blühreaktionen bestimmt.Ein Störlicht, welches in frühen Abschnitten der langen Dunkelperiode geboten wird, verhindert die Blütenbildung unabhängig von der Länge des Gesamtcyclus, dem die Pflanzen ausgesetzt werden. Diese Unterdrückung erreicht ihr Maximum mit einem Störlicht, welches 8 Std nach dem Beginn der Dunkelperiode wirkt; die Hemmung ist schwächer, wenn das Störlicht früher geboten wird. Ein Störlicht, das gegen Ende der Dunkelperiode geboten wird, reduziert die Blütenbildung ebenfalls. Dieser Effekt erreicht sein Maximum mit einem Störlicht, welches ungefähr 8 Std vor dem Ende der Dunkelperiode geboten wird, er wird mit abnehmender Länge der nach dem Störlicht folgenden Dunkelperiode kleiner. Die Wirkung von Störlicht, das zu anderen Zeiten während der Dunkelperiode geboten wird, hängt von der Länge des Gesamtcyclus ab. Bei Cycluslängen, die für Blütenbildung ungünstig sind, kann solches Störlicht blühfördernd wirken.

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Supported in part by a National Science Foundation grant toKarl C. Hamner.     

Influence of the facial ruff on the sound-receiving characteristics of the barn owl’s ears

The barn owl, a nocturnal predator, derives its German name (“Schleiereule”, direct English translation “veil owl”) from the conspicuous ruff that covers the ear openings and gives the head a face-like appearance. The ruff is a specialization for the perception of sound. The densely-ramified reflector feathers forming the border of the ruff direct sound to the ear-openings. We studied the influence of the ruff on the behaviorally relevant sound-localization parameters interaural time difference (ITD) and interaural level difference (ILD). The directionality of the ear was much greater when the ruff was intact than when the reflector feathers were removed. With ruff intact, the distribution of ILDs was oblique and the maximum ITD occurred around 110° of azimuth. When all head feathers were removed, the steepest ILD gradient was much closer to the horizontal axis and ITD was maximal at 90°. Many effects were frequency specific. Thus, the ruff reflects some properties of the human pinna. However, by shifting the point where ITD becomes maximal beyond 90°, the ruff also introduces a break of the front–back symmetry of ITD.