Host–microbe interactions: fungi/viruses/parasites

A selection of World Wide Web sites relevant to papers published in this issue of Current Opinion in Microbiology.     

Phylogeny of the Rhizobium–Allorhizobium–Agrobacterium clade supports the delineation of Neorhizobium gen. nov.

The genera Agrobacterium, Allorhizobium, and Rhizobium belong to the family Rhizobiaceae. However, the placement of a phytopathogenic group of bacteria, the genus Agrobacterium, among the nitrogen-fixing bacteria and the unclear position of Rhizobium galegae have caused controversy in previous taxonomic studies. To resolve uncertainties in the taxonomy and nomenclature within this family, the phylogenetic relationships of generic members of Rhizobiaceae were studied, but with particular emphasis on the taxa included in Agrobacterium and the “R. galegae complex” (R. galegae and related taxa), using multilocus sequence analysis (MLSA) of six protein-coding housekeeping genes among 114 rhizobial and agrobacterial taxa. The results showed that R. galegae, R. vignae, R. huautlense, and R. alkalisoli formed a separate clade that clearly represented a new genus, for which the name Neorhizobium is proposed. Agrobacterium was shown to represent a separate cluster of mainly pathogenic taxa of the family Rhizobiaceae. A. vitis grouped with Allorhizobium, distinct from Agrobacterium, and should be reclassified as Allorhizobium vitis, whereas Rhizobium rhizogenes was considered to be the proper name for former Agrobacterium rhizogenes. This phylogenetic study further indicated that the taxonomic status of several taxa could be resolved by the creation of more novel genera.     

低剂量弱激光疗法调节ApoE–/–小鼠模型动脉粥样硬化效应的研究

动脉粥样硬化是一种慢性炎症疾病,是由于机体内脂质代谢异常从而导致富含胆固醇的脂蛋白在动脉壁中大量积累,进而造成动脉壁增厚、变硬、弹性减退和管腔狭窄的病理改变.据报道,低剂量弱激光疗法(LDLT)具有保护心血管的作用,但其发挥作用的机制尚未明确.本研究旨在探索LDLT是否可以延缓动脉粥样硬化疾病的发展.用高脂饮食(HFD...     

The PCM–basal body/primary cilium coalition

The centrosome is an organelle that acts as a microtubule-organizing center (MTOC) throughout the cell cycle. Within the centrosome are often two components that each have an ability to organize microtubule structures: the centriole that has the potential to function as a basal body and nucleate a cilium or a flagellum and a mass of protein material that in the presence of a centriole is commonly referred to as the pericentriolar material (PCM) that organizes cytoplasmic and spindle microtubule arrays. One characteristic of a large variety of cells is the ability to express a non-motile primary cilium. It is now appreciated that the function of the primary cilium is integral to a variety of essential cell functions and defects affecting this structure underlie a variety of human disease. While the function of the primary cilium and manner in which a basal body organizes a primary cilium has received extensive attention there is now a need to explore the inter-relationship between the PCM and the basal body/primary cilium. It is this latter topic that is the focus of this review where we show that the PCM is integrated with the centriole to form a coalition that is essential for both the expression and function of the primary cilium as well as the organization and function of the cellular environment that surrounds it.     

Critical evaluation of electron transfer kinetics in P700–FA/FB, P700–FX, and P700–A1 Photosystem I core complexes in liquid and in trehalose glass

This work aims to fully elucidate the effects of a trehalose glassy matrix on electron transfer reactions in cyanobacterial Photosystem I (PS I). Forward and backward electron transfer rates from A_1A^? and A_1B^? to F_X, and charge recombination rates from A₀^?, A_1B^?, A_1A^?, F_X^?, and [F_A/F_B]^? to P₇₀₀⁺ were measured in P₇₀₀–F_A/F_B complexes, P₇₀₀–F_X cores, and P₇₀₀–A₁ cores, both in liquid and in a trehalose glassy matrix at 11% humidity. By comparing CONTIN-resolved kinetic events over 6 orders of time in increasingly simplified versions of PS I at 480?nm, a wavelength that reports primarily A_1A^?/A_1B^? oxidation, and over 9 orders of time at 830?nm, a wavelength that reports P₇₀₀⁺ reduction and A₀^? oxidation, assignments could be made for nearly all of the resolved kinetic phases. Trehalose-embedded PS I samples demonstrated partially arrested forward electron transfer. The fractions of complexes in which electron transfer did not proceed beyond A₀, A₁ and F_X were 53%, 16% and 22%, respectively, with only 10% of electrons reaching the terminal F_A/F_B clusters. The ~10?μs and ~150?μs components in both liquid and trehalose-embedded PS I were assigned to recombination between A_1B^? and P₇₀₀⁺ and between A_1A^? and P₇₀₀⁺, respectively. The kinetics and amplitudes of these resolved kinetic phases in liquid and trehalose-embedded PS I samples could be well-fitted by a kinetic model that allowed us to calculate the asymmetrical contribution of the A_1A^? and A_1B^? quinones to the electrochromic signal at 480?nm. Possible reasons for these effects are discussed.     

SETD8~(–/–)抑制人胚胎干细胞向造血分化

表观遗传调控作为一种广泛的基因表达调控方式,已被报道可以参与干细胞多能性、谱系分化等生物学过程。虽然许多表观遗传调控因子的功能已被解析,但仍有一些并未被深入研究。SETD8(赖氨酸甲基转移酶5A, lysine methyltransferase 5A)作为一种甲基化转移酶,已被证实能够介导组蛋白H4第20位赖氨酸的单甲基化,并且可以参与细胞周期、P53介导的DNA损伤等过程。但是, SETD8是否可以直接调控人胚胎干细胞的多能性及其谱系分化还没有报道。该研究首先利用CRISPR/Cas9基因编辑技术在人的胚胎干细细胞中敲除SETD8。功能研究表明,敲除SETD8显著降低了多能性基因OCT4和NANOG的表达水平,并且抑制了体外造血发育过程。接着利用了siRNA在造血发育不同时期敲低STED8,发现均可以抑制造血发育过程,进一步证实了SETD8可以在各个阶段调控体外造血发育。     

Galangin ameliorates cardiac remodeling via the MEK1/2–ERK1/2 and PI3K–AKT pathways

Cardiac remodeling is associated with inflammation and apoptosis. Galangin, as a natural flavonol, has the potent function of regulating inflammation and apoptosis, which are factors related to cardiac remodeling. Beginning 3 days after aortic banding (AB) or Sham surgery, mice were treated with galangin for 4 weeks. Cardiac remodeling was assessed according to echocardiographic parameters, histological analyses, and hypertrophy and fibrosis markers. Our results showed that galangin administration attenuated cardiac hypertrophy, dysfunction, and fibrosis response in AB mice and angiotensin II-treated H9c2 cells. The inhibitory action of galangin in cardiac remodeling was mediated by MEK1/2–extracellular-regulated protein kinases 1/2 (ERK1/2)–GATA4 and phosphoinositide 3-kinase (PI3K)–protein kinase B (AKT)–glycogen synthase kinase 3β (GSK3β) activation. Furthermore, we found that galangin inhibited inflammatory response and apoptosis. Our findings suggest that galangin protects against cardiac remodeling through decreasing inflammatory responses and apoptosis, which are associated with inhibition of the MEK1/2–ERK1/2–GATA4 and PI3K–AKT–GSK3β signals.     

Evolution of the miR-290–295/miR-371–373 Cluster Family Seed Repertoire

Expression of the mouse miR-290–295 cluster and its miR-371–373 homolog in human is restricted to early embryos, primordial germ cells, the germ line stem cell compartment of the adult testis and to stem cell lines derived from the early embryonic lineages. Sequencing data suggest considerable seed diversification between the seven homologous pre-miRNAs of miR-290–295 but it is not clear if all of the implied miR-290–295 seeds are also conserved in the human miR-371–373 cluster, which consists of only three homologous pre-miRNAs. By employing miRNA target reporters we show that most, if not all, seeds in miR-290–295 are represented in miR-371–373. In the mouse, pre-miR-290, pre-miR-292 and pre-miR-293 express subsets of the miRNA isoforms processed from the single human pre-miR-371. Comparison of the possible miR-290–295/miR-371–373 seed repertoires in placental mammals suggests a model for the evolution of this miRNA cluster family, which would be otherwise difficult to deduce based solely on pre-miRNA sequence comparisons. The conservation of co-expressed seeds that is characteristic of miR-290–295/miR-371–373 should be taken into account in models of the corresponding miRNA-target interaction networks.     

Direct electrochemistry of hemoglobin based on chitosan–ionic liquid–ferrocene/graphene composite film

This paper described an ingenious approach for the fabrication of a promising biosensor, hemoglobin (Hb)/chitosan (Chit)–ionic liquid (IL)–ferrocene (Fc)/graphene (Gr)/glassy carbon electrode (GCE), that exploited the synergistic beneficial characteristics of Fc, Gr and IL for Hb. The proposed biosensor showed a strong electrocatalytic activity toward the reduction of H₂O₂, which could be attributed to the favored orientation of Hb in the well-confined surface as well as the high electrical conductivity of the resulting Chit–IL–Fc/Gr inorganic hybrid composite. The developed biosensor exhibited a fast amperometric response (2 s), a good linear response toward H₂O₂ over a wide range of concentration from 50 μM to 1200 μM, and a low detection limit of 3.8 μM. The apparent Michaelis–Menten constant (K_m) of Hb on the composite medium was 0.16 mM, showing high bioelectrocatalytic activity of immobilized protein toward H₂O₂ reduction. High sensitivity and stability, technically simple and possibility of preparation at short period of time are of great advantages of the developed biosensors.     

Dynamic relocation of the TORC1–Gtr1/2–Ego1/2/3 complex is regulated by Gtr1 and Gtr2

TORC1 regulates cellular growth, metabolism, and autophagy by integrating various signals, including nutrient availability, through the small GTPases RagA/B/C/D in mammals and Gtr1/2 in budding yeast. Rag/Gtr is anchored to the lysosomal/vacuolar membrane by the scaffold protein complex Ragulator/Ego. Here we show that Ego consists of Ego1 and Ego3, and novel subunit Ego2. The ∆ego2 mutant exhibited only partial defects both in Gtr1-dependent TORC1 activation and Gtr1 localization on the vacuole. Ego1/2/3, Gtr1/2, and Tor1/Tco89 were colocalized on the vacuole and associated puncta. When Gtr1 was in its GTP-bound form and TORC1 was active, these proteins were preferentially localized on the vacuolar membrane, whereas when Gtr1 was in its GDP-bound form, they were mostly localized on the puncta. The localization of TORC1 to puncta was further facilitated by direct binding to Gtr2, which is involved in suppression of TORC1 activity. Thus regulation of TORC1 activity through Gtr1/Gtr2 is tightly coupled to the dynamic relocation of these proteins.     

Unravelling the interface of Co–Pi/Ag/Fe2O3 and Ni–Pi/Ag/Fe2O3 heterostructures for enhanced solar water splitting

Recently, a new type of haematite-based (a-Fe₂O₃) photoanode has achieved a considerable catalytic performance through simply depositing Ag and cobalt phosphate (Co–Pi) nanoparticles (NPs) onto haematite nanosheets. However, there is no detailed mechanism study on the reason for high-performance catalysis. In view of this, we conduct first-principles calculations and our results indicate that there is a further accumulation of positive charge on Ag NPs on the heterogeneous interfaces with the addition of Co–Pi NPs than that of haematite modified only by Ag NPs. Also, there is a slight increase of the adsorption energy of water molecules.     

In memoriam: Gustaf Bolinder 19/12 1888–16/7 1957

Veena Das's work on suffering suggests that the appropriate approach to the subject is one that grounds research in social experience. To honor this pitch of anthropology, I examine the global mediatization of the trauma of political violence and its moral implications. I also describe the professional appropriation of suffering that transforms political economic conditions into medical realities. Because social experience is itself undergoing a profound alteration in the present period of disordered capitalism, the very phenomenological conditions that we have assumed as an ‘existential’ basis for responding to human misery are also being ominously transformed.     

Expression of HvHMA2 in tobacco modifies Zn–Fe–Cd homeostasis

HvHMA2 is a plasma membrane P_1B-ATPase from barley that functions in Zn/Cd root-to-shoot transport. To assess the usefulness of HvHMA2 for modifying the metal content in aerial plant parts, it was expressed in tobacco under the CaMV35S promoter. Transformation with HvHMA2 did not produce one unique pattern of Zn and Cd accumulation; instead it depended on external metal supply. Thus Zn and Cd root-to-shoot translocation was facilitated, but not at all applied Zn/Cd concentrations. Metal uptake was restricted in HvHMA2-transformed plants and the level in the shoot was not enhanced. It was shown that HvHMA2 localizes to the plasma membrane of tobacco cells, and overloads the apoplast with Zn, which could explain the overall decrease in metal uptake observed. Despite the lower levels in the shoot, HvHMA2 transformants showed increased Zn sensitivity. Moreover, introduction of HvHMA2 into tobacco interfered with Fe metabolism and Fe accumulation was modified in HvHMA2-transformants in a Zn- and Cd-concentration dependent manner. The results indicate that ectopic expression of the export protein HvHMA2 in tobacco interferes with tobacco metal Zn–Cd–Fe cross-homeostasis, inducing internal mechanisms regulating metal uptake and tolerance.     

Inter-laboratory reproducibility of fast gas chromatography–electron impact–time of flight mass spectrometry (GC–EI–TOF/MS) based plant metabolomics

The application of gas chromatography–mass spectrometry (GC–MS) to the ‘global’ analysis of metabolites in complex samples (i.e. metabolomics) has now become routine. The generation of these data-rich profiles demands new strategies in data mining and standardisation of experimental and reporting aspects across laboratories. As part of the META-PHOR project’s (METAbolomics for Plants Health and OutReach: ) priorities towards robust technology development, a GC–MS ring experiment based upon three complex matrices (melon, broccoli and rice) was launched. All sample preparation, data processing, multivariate analyses and comparisons of major metabolite features followed standardised protocols, identical models of GC (Agilent 6890N) and TOF/MS (Leco Pegasus III) were also employed. In addition comprehensive GC×GC–TOF/MS was compared with 1 dimensional GC–TOF/MS. Comparisons of the paired data from the various laboratories were made with a single data processing and analysis method providing an unbiased assessment of analytical method variants and inter-laboratory reproducibility. A range of processing and statistical methods were also assessed with a single exemplary dataset revealing near equal performance between them. Further investigations of long-term reproducibility are required, though the future generation of global and valid metabolomics databases offers much promise.     

Evidence for water-mediated triplet–triplet energy transfer in the photoprotective site of the peridinin–chlorophyll a–protein

Experimental and theoretical studies indicate that water molecules between redox partners can significantly affect their electron-transfer and possibly also the triplet–triplet energy transfer (TTET) properties when in the vicinity of chromophores. In the present work, the interaction of an intervening water molecule with the peridinin triplet state in the peridinin–chlorophyll a–protein (PCP) from Amphidinium carterae is studied by using orientation selective ²H electron spin echo envelope modulation (ESEEM) spectroscopy, in conjunction with quantum mechanical calculations. This water molecule is located at the interface between the chlorophyll and peridinin pigments involved in the photoprotection mechanism (Chl601(602)–Per614(624), for nomenclature see reference [1]), based on TTET. The characteristic deuterium modulation pattern is observed in the electron spin-echo envelopes for the PCP complex exchanged against ²H₂O. Simulations of the time- and frequency-domain two-pulse and three-pulse ESEEM require two types of coupled ²H. The more strongly coupled ²H has an isotropic coupling constant (a_iso) of − 0.4 MHz. This Fermi contact contribution for one of the two water protons and the precise geometry of the water molecule at the interface between the chlorophyll and peridinin pigments, resulting from the analysis, provide experimental evidence for direct involvement of this structured water molecule in the mechanism of TTET. The PCP antenna, characterised by a unity efficiency of the process, represents a model for future investigations on protein- and solvent-mediated TTET in the field of natural/artificial photosynthesis.     

Calculation of the Three-Dimensional Structures of Two Antigenic Sequences, Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp–Pro and Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp–Pro–Pro–Pro, of the Circumsporozoite Protein From a Malaria-Causing Plasmodium

Using the chain build-up procedure based on the program ECEPP, we have computed the lowest energy structures for two terminally blocked subsequences from the antigenic circumsporozoite protein of Plasmodium berghei, that is known to cause malaria in animals. The full antigenic sequence is an octapeptide proline-rich tandem repeat, (Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp)₂. We computed the structures for the first octapeptide plus one Pro from the second octapeptide, terminally blocked CH₃CO–Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp–Pro–NHCH₃ as well as the first octpeptide with an additional three Pro residues from the adjoining unit, i.e., CH₃CO–Pro–Pro–Pro–Pro–Asn–Pro–Asn–Asp–Pro–Pro–Pro–NHCH₃. We find that the first sequence adopts a number of different low energy structures, the most probable of which has a probability of occurrence of 56 %. Addition of two more Pro residues results in the adoption a single, unique lowest energy structure that has a probability of occurrence of over 95 % without solvation effects and 86 % when solvation effects are included in the calculations. We predict that this structure may be the one recognized as a major antigenic determinant.