CFTR: what's it like inside the pore?

The Cystic Fibrosis Conductance Regulator (CFTR) functions as a cAMP-activated, anion-selective channel, but the structural basis for anion permeation is not well understood. Here we summarize recent studies aimed at understanding how anions move through the CFTR channel, and the nature of the environment anions experience inside the pore. From these studies it is apparent that anion permeability selectivity and anion binding selectivity of the pore are consistent with a model based on a "dielectric tunnel." The selectivity pattern for halides and pseudohalides can be predicted if it is assumed that permeant anions partition between bulk water and a polarizable space that is characterized by an effective dielectric constant of about 19. Covalent labeling of engineered cysteines and pH titration of engineered cysteines and histidines lead to the conclusion that the CFTR anion conduction path includes a positively charged outer vestibule. A residue in transmembrane segment 6 (TM6) (R334) appears to reside in the outer vestibule of the CFTR pore where it creates a positive electrostatic potential that enhances anion conduction.     

Actin' like actin?

The most biologically significant property of actin is its ability to self-associate and form two-stranded polymeric microfilaments. In living cells, these micro filaments form the actin cytoskeleton, essential for maintenance of the shape, passive mechanical properties and active motility of eukaryotic cells. Recently discovered actin-related proteins (ARPs) appear to share a common ancestor with conventional actin. At present, six classes of ARPs have been discovered, three of which have representatives in diverse species across eukaryotic phyla and may share functional characteristics with conventional actin. The three most ubiquitous ARPs are predicted to share a common core structure with actin and contain all the residues required for ATP binding. Surface residues involved in protein protein interactions, however, have diverged. Models of these proteins based on the atomic structure of actin provide some clues about how ARPs interact with each other, with conventional actin and with conventional actin-binding proteins.     

Parataenidium,a new taenidium‐like ichnogenus from the carboniferous of Ireland

The new ichnogenus Parataenidium is erected for backfilled tubular trace fossils that can appear superficially similar to Taenidium, but are divided horizontally into two distinct levels. Two ichnospecies are recognised: Parataenidium mullaghmorensis isp. nov. and Parataenidium moniliformis (Tate 1859). The latter ichnospecies is transferred from Eione Tate 1859, which is a junior homonym of Eione Rafinesque 1814, and therefore unavailable for Tate's ichnotaxon. The ichnogenus is an important component of late Paleozoic shallow‐water siliciclastic sediments, and can be considered as a “guide”; indicator for the Carboniferous.     

Is bisphenol A a weak carcinogen like the natural estrogens and diethylstilbestrol?

Bisphenol A (BPA) displays weak estrogenic properties and could be a weak carcinogen by a mechanism similar to that of estrone (E(1)), estradiol (E(2)) and the synthetic estrogen diethylstilbestrol, a human carcinogen. A wide variety of scientific evidence supports the hypothesis that certain estrogen metabolites, predominantly catechol estrogen-3,4-quinones, react with DNA to cause mutations that can lead to the initiation of cancer. One of the major pathways of estrogen metabolism leads to the 4-catechol estrogens, 4-OHE(1)(E(2)), which are oxidized to their quinones, E(1)(E(2))-3,4-Q. The quinones react with DNA to form predominantly the depurinating adducts 4-OHE(1)(E(2))-1-N3Ade and 4-OHE(1)(E(2))-1-N7Gua. This process constitutes the predominant pathway in the initiation of cancer by estrogens. One pathway of BPA metabolism is hydroxylation of one of its symmetric benzene rings to form its catechol, 3-OHBPA. Subsequent oxidation to BPA-3,4-quinone would lead to reaction with DNA to form predominantly the depurinating adducts 3-OHBPA-6-N3Ade and 3-OHBPA-6-N7Gua. The resulting apurinic sites in the DNA could generate mutations in critical genes that can initiate human cancers. The catechol of BPA may also alter expression of estrogen-activating and deactivating enzymes, and/or compete with methoxylation of 4-OHE(1)(E(2)) by catechol-O-methyltransferase, thereby unbalancing the metabolism of estrogens to increase formation of E(1)(E(2))-3,4-Q and the depurinating estrogen-DNA adducts leading to cancer initiation. Thus, exposure to BPA could increase the risk of developing cancer by direct and/or indirect mechanisms. Knowledge of these mechanisms would allow us to begin to understand how BPA may act as a weak carcinogen and would be useful for regulating its use.     

Is the bovine lysosomal phospholipase B‐like protein an amidase?

The main function of lysosomal proteins is to degrade cellular macromolecules. We purified a novel lysosomal protein to homogeneity from bovine kidneys. By gene annotation, this protein is defined as a bovine phospholipase B‐like protein 1 (bPLBD1) and, to better understand its biological function, we solved its structure at 1.9 Å resolution. We showed that bPLBD1 has uniform noncomplex‐type N‐glycosylation and that it localized to the lysosome. The first step in lysosomal protein transport, the initiation of mannose‐6‐phosphorylation by a N‐acetylglucosamine‐1‐phosphotransferase, requires recognition of at least two distinct lysines on the protein surface. We identified candidate lysines by analyzing the structural and sequentially conserved N‐glycosylation sites and lysines in bPLBD1 and in the homologous mouse PLBD2. Our model suggests that N408 is the primarily phosphorylated glycan, and K358 a key residue for N‐acetylglucosamine‐1‐phosphotransferase recognition. Two other lysines, K334 and K342, provide the required second site for N‐acetylglucosamine‐1‐phosphotransferase recognition. bPLBD1 is an N‐terminal nucleophile (Ntn) hydrolase. By comparison with other Ntn‐hydrolases, we conclude that the acyl moiety of PLBD1 substrate must be small to fit the putative binding pocket, whereas the space for the rest of the substrate is a large open cleft. Finally, as all the known substrates of Ntn‐hydrolases have amide bonds, we suggest that bPLBD1 may be an amidase or peptidase instead of lipase, explaining the difficulty in finding a good substrate for any members of the PLBD family. Proteins 2014; 82:300–311. © 2013 Wiley Periodicals, Inc.     

DnaJ—like蛋白研究进展

ＤｎａＪ－ｌｉｋｅ蛋白由Ｎ－端保守的Ｊ区域、富含Ｇｌｙ和Ｐｈｅ区域,富含Ｇｙｓ区域和Ｃ－端低同源区域组成。Ｊ功能域能调节ＨＳＰ７０分子伴侣的ＡＴＰａｓｅ活性,Ｃ－端不保守域能调节与多肽的关系。直核细胞中存在着多种结构不同的ＤｎａＪ－ｌｉｋｅ蛋白,但都含有一个Ｊ功能域。ＤｎａＪ－ｌｉｋｅ蛋白通过Ｊ功能域调节ＨＳＰ７０功能而参与蛋白的折叠,装配和运输过程。     

DuaJ—like蛋白研究进展

DuaJ-like蛋白由N-端保守的J区域、富含Gly和Phe区域、富含Cys区域和C-端低同源区域组成。J功能域能调节HSP70分子伴侣的ATPase活性,C-端不保守区域能调节与多肽的关系。真核细胞中存在着多种结构不同的DuaJ-like蛋白,但都含有一个J功能域。DuaJ-like蛋白通过J功能域调节HSP70功能而参与蛋白的折叠、装配和运输过程。     

Characteristics of established KSG cells derived from the scorpionfish Sebastiscus marmoratus: what happens under the hydrostatic pressure like the deep sea?

Advances in cell biology depend, partly, on the development of new cell lines and culture methods. Our research focused on a fibroblast-like cell line, “KSG,” which is derived from scorpionfish fin tissue (Sebastiscus marmoratus). Cells were grown in Leibovitz’s L-15 medium with 10% fetal bovine serum following standard procedures. The optimum growth temperatures for these lines ranged from 15°C to 25°C. All cells survived storage for at least 3 yr at ?80°C. Subsequently, they were continuously cultured until the 78th generation without evident changes in their morphology. Moreover, we were able to culture KSG cells in the absence of fetal bovine serum in a culture medium containing the fish serum “SeaGrow.” Optimum SeaGrow concentrations for these cells ranged from 5% to 20%. The growth rate of KSG cells decreased when the concentration of SeaGrow was reduced to 1%. However, this decrease could be partially reversed by adding 0.5% “Hy-Fish.” In addition, the inclusion of Hy-Fish improved cell adhesion. KSG cells that were cultured in serum-free culture media containing 0.5% and 1% Hy-Fish had been added and were able to survive at low densities. Furthermore, we successfully transfected this cell line with a commercial plasmid vector coding a fluorescent protein using the cationic lipid. Finally, the analyses of cell behavior under hydrostatic pressure showed that some pressures (10 MPa) helped the cells to proliferate more.     

Noradrenaline as a putative neurotransmitter mediating hypotension—induced FOs—like immunoreactivity in the supraoptic nucleus of the rat

Hemorrhage or hypotension induces extensive Fos-like immunoreactivity in the magnocellular neurosecretory cells in the supraoptic nucleus of the hypothalamus in rat,especially in the vasopressin neurons.The present study was to explore the neurotransmitter mediating this effect,Microinfusion of the alpha-adrenergic blocker into the supraoptic nucleus reduced the hypotension-induced FOs.whereas beta-antagonist did not affect it significantly.Alaha1-and alpha2-antagonist,prazosin and yohimbine,both reduced the Fos-Positive cell counts.However,the effective dosage of yohimbine was much larger,Alpha1-agonist,methoxamine,induced abundant Fos-like immunoreactivity in the vasopressin cells in this nucleus,while beta-and alpha2-agonist did not elicit such effect.Administration of the noradrenergic re-uptake inhibitor desipramine,to this nucleus to locally accumulate the spontaneously released noradrenaline from the nerve terminals also induced Fos expression,mostly in the vasopressin cells.     

TssA forms a gp6‐like ring attached to the type VI secretion sheath

The type VI secretion system (T6SS) is a supra‐molecular bacterial complex that resembles phage tails. It is a killing machine which fires toxins into target cells upon contraction of its TssBC sheath. Here, we show that TssA1 is a T6SS component forming dodecameric ring structures whose dimensions match those of the TssBC sheath and which can accommodate the inner Hcp tube. The TssA1 ring complex binds the T6SS sheath and impacts its behaviour in vivo. In the phage, the first disc of the gp18 sheath sits on a baseplate wherein gp6 is a dodecameric ring. We found remarkable sequence and structural similarities between TssA1 and gp6 C‐termini, and propose that TssA1 could be a baseplate component of the T6SS. Furthermore, we identified similarities between TssK1 and gp8, the former interacting with TssA1 while the latter is found in the outer radius of the gp6 ring. These observations, combined with similarities between TssF and gp6N‐terminus or TssG and gp53, lead us to propose a comparative model between the phage baseplate and the T6SS.     

¿I like the way you move¿: how hormonal changes across the menstrual cycle affect female perceptions of gait

ABSTRACT: BACKGROUND: Variations in hormone concentrations across the menstrual cycle affect human female mate preferences. It has been shown that around the time of ovulation human females prefer more masculine male voices, faces, and bodies while simultaneously preferring less faces that are more feminine. They prefer also displays of male dominance, males with more symmetrical faces, and the scent of males with high levels of body symmetry. The aim of the experiments reported here was to investigate whether there are changes in female preferences for walking gaits across the menstrual cycle. RESULTS: Experiment 1 showed female observers could discriminate between point-light walkers with low and high levels of fluctuating asymmetries in their gaits. Female observers were more sensitive to asymmetries in female gaits than they were for asymmetries in male gaits. Experiment 2 showed that level of gait asymmetry did not affect the abilities of observers to discriminate female from male walkers. Experiment 3 showed that female observers did not change their preference for low and high asymmetry walkers across their menstrual cycles. However, females showed a decreased preference for all female walkers at the time during which it was estimated observers were at peak fertility. That same change in preference was not observed for male walkers. CONCLUSIONS: These data suggest female observers may not value gait asymmetry, as a mate selection cue, in the same way that they value asymmetries in faces and bodies. While only "average" gaits were used in these experiments, rather than the gaits of individual walkers, the types of asymmetries in gait tested here were not used in the same way as static cues for judging the apparent healthiness of individuals. Females do discriminate well average female gait asymmetries and do change their preferences for those gaits across their menstrual cycle. Doing so may reflect the operation of processes that equip females with an advantage when competing for mates at times of peak fertility.     

Crystalline actin tubes. I. Is the conformation of the lanthanide-induced actin tube monomer more like F-actin than G-actin?

Actin, isolated from rabbit skeletal muscle, forms highly-ordered aggregates when it binds six moles of the lanthanide ion, Gd3+. In the presence of 0.1 M KCl, these aggregates are referred to as actin tubes. The monomer contained in the repeating subunit of these tubes possess a number of functional characteristics which include: (i) binding to myosin or subfragment-1 of myosin; (ii) rapid conversion into filamentous Gd-actin which can activate myosin ATPase activity; (iii) a slow rate of exchange of the bound nucleotide; (iv) a slow rate of exchange of the metal cation; (v) a resistance to digestion by proteolytic enzymes. Additionally, the monomer of the Gd-actin tube structures appears to stoichiometrically bind ATP and exhibit a lower minimum protein concentration for tube formation than is needed for the formation of F-actin. The properties listed above suggest that the actin monomer, which comprises the Gd-actin tubes, bears little resemblance to either the G-actin monomer or the recently-described actin monomer conformation that exists under conditions that favour polymerization. The data suggest that the actin molecules which comprise the Gd-actin tube structures contain sites which bind myosin, nucleotide and metal cations and that these sites are similar to the sites on F-actin.     

A rice tubulin tyrosine ligase‐like 12 protein affects the dynamic and orientation of microtubules

The detyrosination/retyrosination cycle is the most common post‐translational modification of α‐tubulin. Removal of the conserved C‐terminal tyrosine of α‐tubulin by a still elusive tubulin tyrosine carboxypeptidase, and religation of this tyrosine by a tubulin tyrosine ligase (TTL), are probably common to all eukaryotes. Interestingly, for plants, the only candidates qualifying as potential TTL homologs are the tubulin tyrosine ligase‐like 12 proteins. To get insight into the biological functions of these potential TTL homologs, we cloned the rice TTL‐like 12 protein (OsTTLL12) and generated overexpression OsTTLL12‐RFP lines in both rice and tobacco BY‐2 cells. We found, unexpectedly, that overexpression of this OsTTLL12‐RFP increased the relative abundance of detyrosinated α‐tubulin in both coleoptile and seminal root, correlated with more stable microtubules. This was independent of the respective orientation of cortical microtubule, and followed by correspondingly changing growth of coleoptiles and seminal roots. A perturbed organization of phragmoplast microtubules and disoriented cell walls were further characteristics of this phenotype. Thus, the elevated tubulin detyrosination in consequence of OsTTLL12 overexpression affects structural and dynamic features of microtubules, followed by changes in the axiality of cell plate deposition and, consequently, plant growth.     

Chemical shift assignments of the fibronectin III like domains 7–8 of type VII collagen

Type VII collagen (Col7) is important for skin stability. This is underlined by the severe skin blistering phenotype in the Col7 related diseases dystrophic epidermolysis bullosa and epidermolysis bullosa acquisita (EBA). Col7 has a large N-terminal non-collagenous domain (NC1) that is followed by the triple helical collagenous domain. The NC1 domain has subdomains with homology to adhesion molecules and mediates important interactions within the extracellular matrix. An 185 amino acid long part of the NC1-subdomain termed fibronectin III like domains 7 and 8 (FNIII7-8) was investigated. Antibodies against this region are pathogenic in a mouse model of EBA and one reported missense mutations of Col7 lies within these domains. The nearly complete NMR resonance assignment of recombinant FNIII7-8 of Col7 is reported.     

Just like the USA? Critical notes on Alba and Foner’s cross-Atlantic research agenda

ABSTRACT

A critical review of Alba and Foner's Strangers No More (2015 Foner, Nancy. 2015. “Is Islam in Western Europe Like Race in the United States?” Sociological Forum 30 (4): 885–899. [Google Scholar]) which focuses on questioning their comparative assimilation of European cases of immigrant integration to the North American, specifically U.S., experience. While this may work in terms of how national immigrant integration has mitigated over time racial discrimination for older, post-colonial migrants, it misrepresents the complex differentiations involved in the super-diversity of recent ‘new’ migrations within and to Europe. In particular, the variety of types and origins of recent migration is lost in their understanding of the U.K. case, with problems linked to their interpretation of data about minorities and foreigners in the country.     

Do some corals like it hot?

Global increases in sea temperatures threaten coral reef resilience because thermal stress can cause corals to bleach; that is, to lose their photosynthetic microalgal symbionts. Recent evidence suggests that some corals associate with genotypes of microalgae that resist future thermal stress, however, these genotypes might provide less energy for growth when thermal stresses are curtailed. Coral reef resilience depends on whether phenotypic and genotypic changes in host-symbiont associations can match projected increases in the frequency and severity of thermal stress, as well as on our ability to ameliorate continuing human impacts.     

Formation of α-synuclein Lewy neurite–like aggregates in axons impedes the transport of distinct endosomes

Aggregates of α-synuclein (α-syn) accumulate in neurons in Parkinson''s disease and other synucleinopathies. These inclusions predominantly localize to axons even in the early stages of the disease, but their affect on axon function has remained unknown. Previously we established a model in which the addition of preformed α-syn fibrils to primary neurons seeds formation of insoluble α-syn inclusions built from endogenously expressed α-syn that closely recapitulate the neuropathological phenotypes of Lewy neurites found in human diseased brains. Here we show, using live-cell imaging, that immobile α-syn inclusions accumulate in axons from the recruitment of α-syn located on mobile α-syn–positive vesicles. Ultrastructural analyses and live imaging demonstrate that α-syn accumulations do not cause a generalized defect in axonal transport; the inclusions do not fill the axonal cytoplasm, disrupt the microtubule cytoskeleton, or affect the transport of synaptophysin or mitochondria. However, the α-syn aggregates impair the transport of Rab7 and TrkB receptor–containing endosomes, as well as autophagosomes. In addition, the TrkB receptor–associated signaling molecule pERK5 accumulates in α-syn aggregate–bearing neurons. Thus α-syn pathology impairs axonal transport of signaling and degradative organelles. These early effects of α-syn accumulations may predict points of intervention in the neurodegenerative process.