Does a light-harvesting protochlorophyllide a/b-binding protein complex exist?

Recent in vitro studies have led to speculation that a novel light-harvesting protochlorophyllide a/b-binding protein complex (LHPP) might exist in dark-grown angiosperms. Structurally, it has been suggested that LHPP consists of a 5:1 ratio of dark-stable ternary complexes of the light-dependent NADPH: protochlorophyllide oxidoreductases A and B containing nonphotoactive protochlorophyllide b and photoactive protochlorophyllide a, respectively. Functionally, LHPP has been hypothesized to play major roles in establishing the photosynthetic apparatus, in protecting against photo-oxidative damage during greening, and in determining etioplast inner membrane architecture. However, the LHPP model is not compatible with other studies of the pigments and the pigment-protein complexes of dark-grown angiosperms. Protochlorophyllide b, which is postulated to be the major light-harvesting pigment of LHPP, has, for example, never been detected in etiolated seedlings. This raises the question: does LHPP exist?     

Alternative mating type configurations (a/α versus a/a or α/α) of Candida albicans result in alternative biofilms regulated by different pathways

Similar multicellular structures can evolve within the same organism that may have different evolutionary histories, be controlled by different regulatory pathways, and play similar but nonidentical roles. In the human fungal pathogen Candida albicans, a quite extraordinary example of this has occurred. Depending upon the configuration of the mating type locus (a/α versus a/a or α/α), C. albicans forms alternative biofilms that appear similar morphologically, but exhibit dramatically different characteristics and are regulated by distinctly different signal transduction pathways. Biofilms formed by a/α cells are impermeable to molecules in the size range of 300 Da to 140 kDa, are poorly penetrated by human polymorphonuclear leukocytes (PMNs), and are resistant to antifungals. In contrast, a/a or α/α biofilms are permeable to molecules in this size range, are readily penetrated by PMNs, and are susceptible to antifungals. By mutational analyses, a/α biofilms are demonstrated to be regulated by the Ras1/cAMP pathway that includes Ras1→Cdc35→cAMP(Pde2-|)→Tpk2(Tpk1)→Efg1→Tec1→Bcr1, and a/a biofilms by the MAP kinase pathway that includes Mfα→Ste2→ (Ste4, Ste18, Cag1)→Ste11→Hst7→Cek2(Cek1)→Tec1. These observations suggest the hypothesis that while the upstream portion of the newly evolved pathway regulating a/a and α/α cell biofilms was derived intact from the upstream portion of the conserved pheromone-regulated pathway for mating, the downstream portion was derived through modification of the downstream portion of the conserved pathway for a/α biofilm formation. C. albicans therefore forms two alternative biofilms depending upon mating configuration.     

Pseudomonas aeruginosa Cif defines a distinct class of α/β epoxide hydrolases utilizing a His/Tyr ring-opening pair

The Gram-negative bacterium Pseudomonas aeruginosa is an opportunistic pathogen that secretes a multitude of virulence factors during the course of infection. Among these is Cif, an epoxide hydrolase (EH) that reduces the functional localization of the cystic fibrosis transmembrane conductance regulator in epithelial cells. In addition to being the first reported EH virulence factor, Cif possesses unique sequence deviations from canonical EH motifs. Foremost among these is the substitution of a histidine for the first epoxide ring-opening tyrosine in the active site. To test the functional equivalence of Tyr and His side chains at this position, we have generated the mutant Cif-H177Y. Structural analysis confirms that both the WT His and mutant Tyr side chains can be accommodated without large-scale conformational changes. However, the Tyr mutant is functionally inactive. Based on a detailed analysis of the structure of the Tyr mutant, it appears that Cif's main-chain conformation imposes a functional requirement for a His at this position. Comparison with canonical EH structures reveals additional conformational differences, which are coupled to divergent sequence characteristics. When used to probe the genomes of other opportunistic pathogens, these sequence-structure criteria uncover candidate sequences that appear to form a distinct subfamily of Cif-like epoxide hydrolases characterized by a conserved His/Tyr ring-opening pair.     

Dinophysis norvegica (Dinophyceae), more a predator than a producer?

Several studies have proved that some Dinophysis species are capable of ingesting particulate organic matter besides of being photosynthetic, a form of nutrition termed mixotrophy. Phagotrophy may be an important aspect of the life history of the genus Dinophysis and the key to understand its ecology. We used modern techniques coupling flow cytometry and acidotropic probes to detect and score food vacuolated Dinophysis norvegica cells in natural samples. In addition, feeding experiments were conduced under controlled conditions to observe if D. norvegica would grow feeding on the cryptophyte Teleaulax amphioxeia. The results of the field observations showed a frequency of phagotrophy between 25 and 71% in a natural D. norvegica population from the Baltic Sea, which is higher than previous reports (1–20%). Although molecular methods have proved that the kleptoplastids of the D. norvegica from the Baltic Sea are from T. amphioxeia, the laboratory experiments showed that the presence of T. amphioxeia in the cultures did not enhance the survival rate of D. norvegica neither in phototrophic nor in heterotrophic conditions. We suggest that the D. norvegica Kleptoplats are obtained through a heterotrophic or mixotrophic protist, which have been feeding on cryptophytes, as it has recently been shown for Dinophysis acuminata. Our main conclusion is that D. norvegica, and probably all other species from the genus Dinophysis, is mainly phagotrophic and feeds on a larger prey than T. amphioxeia. Autotrophy through kleptoplastidy would be a secondary feature used as a complementary or short-term survival strategy.     

Excision of a Ds-like maize transposable element (AcΔ) in a transient assay in Petunia is enhanced by a truncated coding region of the transposable element Ac

Summary The excision of a Ds-like transposable element (Ac) is mediated in trans by the transposable element Ac or its derivatives in Petunia protoplasts cotransfected with two plasmid DNAs. Excision restores the activity of the -glucuronidase (GUS) gene that is otherwise shut off by the presence of Ac in its leader sequence. A transient expression assay (histochemical test) is used to detect the -glucuronidase activity at the protoplast level. The number of blue-stained protoplasts is a measure of the excision frequency. With Ac alone a near-zero background of GUS activity is detected, which is weakly enhanced by the presence, in trans, of either the wild-type Ac or the coding region (ORF_a) transcribed from the 2 promoter of Agrobacterium tumefaciens TR-DNA. A strong enhancement is observed when a truncated Ac coding region, also under the control of the 2 promoter, is supplied in trans. The truncated version has ATG₁₀ at codon 103 in frame with ORF_a and is preceded by 7 out-of-frame ATGs. The assay is quick and well suited for detection of excision frequencies above the value obtained with the wild-type Ac. The presence of empty donor sites following excision can be demonstrated by PCR amplification and direct sequencing of the appropriate DNA fragment.     

SnoN/SkiL,a TGFβ signaling mediator

Effective treatment of cancer cells with chemotherapeutic drugs relies on their ability to induce cell death, making the discovery of their mechanisms of action crucial. Arsenic trioxide (As₂O₃), used in the treatment of promyelocytic leukemia (PML), triggers cell death in several solid tumor cell lines including ovarian carcinomas. While As₂O₃ is remarkably cytotoxic in human ovarian cancer cells, its mechanism of action is poorly understood. We recently investigated the effects of As₂O₃ on several transforming growth factor-β (TGFβ) signaling mediators to better understand its cell death mechanism. Indeed, dysregulated (TGFβ) signaling is typical of ovarian cancers. Based on our findings, we propose that As₂O₃ induces a Beclin 1-independent autophagic pathway in ovarian carcinoma cells by modulating SnoN/SkiL expression, implicating SnoN as a novel therapeutic target for ovarian cancers.     

Drosophila as a lipotoxicity model organism — more than a promise?

Looking back over the century long research career of the fruit fly, Drosophila melanogaster has frequently been in the scientific spotlight with respect to fundamental discoveries in biology. The last decade witnessed the increasing importance of the fly as a human disease model but studies on energy homeostasis and lipometabolism remain in their infancy. This perspective, addressing readers largely unfamiliar with the Drosophila model system, aims to highlight the starting points for which the fly could be employed to gain a deeper understanding of lipotoxicity and possibly contribute to strategies for the identification of novel drug targets relevant to type 2 diabetes mellitus and the metabolic syndrome.     

SIRPα/CD172a regulates eosinophil homeostasis

Eosinophils are abundant in the lamina propria of the small intestine, but they rarely show degranulation in situ under steady-state conditions. In this study, using two novel mAbs, we found that intestinal eosinophils constitutively expressed a high level of an inhibitory receptor signal regulatory protein α (SIRPα)/CD172a and a low, but significant, level of a tetraspanin CD63, whose upregulation is closely associated with degranulation. Cross-linking SIRPα/CD172a on the surface of wild-type eosinophils significantly inhibited the release of eosinophil peroxidase induced by the calcium ionophore A23187, whereas this cross-linking effect was not observed in eosinophils isolated from mice expressing a mutated SIRPα/CD172a that lacks most of its cytoplasmic domain (SIRPα Cyto(-/-)). The SIRPα Cyto(-/-) eosinophils showed reduced viability, increased CD63 expression, and increased eosinophil peroxidase release with or without A23187 stimulation in vitro. In addition, SIRPα Cyto(-/-) mice showed increased frequencies of Annexin V-binding eosinophils and free MBP(+)CD63(+) extracellular granules, as well as increased tissue remodeling in the small intestine under steady-state conditions. Mice deficient in CD47, which is a ligand for SIRPα/CD172a, recapitulated these phenomena. Moreover, during Th2-biased inflammation, increased eosinophil cell death and degranulation were obvious in a number of tissues, including the small intestine, in the SIRPα Cyto(-/-) mice compared with wild-type mice. Collectively, our results indicated that SIRPα/CD172a regulates eosinophil homeostasis, probably by interacting with CD47, with substantial effects on eosinophil survival. Thus, SIRPα/CD172a is a potential therapeutic target for eosinophil-associated diseases.     

Dissimilatory nitrate uptake in Paracoccus denitrificans via a Δ\̃gmH+-dependent system and a nitrate-nitrite antiport system

Respiration-driven proton translocation has been studied with the oxidant pulse method for cells of denitrifying Paracoccus denitrificans oxidizing H₂ during reduction of O₂, NO^?₃, NO^?₂ or N₂O. A simplified scheme of anaerobic electron transport and associated proton translocation is shown that is consistent with the measured $\text{H}{}^{\mathrm{+}}\text{oxidant ratios}$. Furthermore, the kinetics and energetics of NO^?₃ uptake in whole cells of P. denitrificans were studied. For this purpose, we measured H₂ consumption or N₂O production after addition of NO^?₃ to a cell suspension, which indirectly gave information about uptake (and reduction) of NO^?₃. It was found that a lag phase in H₂ consumption or N₂O production appeared whenever the membrane potential was dissipated by addition of thiocyanate, carbonyl cyanide m-chlorophenylhydrazone or triphenyl-methylphosphonium bromide. However, these lag phases were not observed when NO^?₂ was present at the moment of introduction of NO^?₃. On the basis of these findings we conclude that there are two uptake systems for NO^?₃. One system is dependent on the proton-motive force and is probably used for initiation of NO^?₃ uptake. The other is an $\text{NO}{}^{\mathrm{?}}{}_3\text{NO}{}^{\mathrm{?}}{}_2$ antiport and its function is to take over NO^?₃ uptake from the first system.     

Studies of a pelleted growth form of Rhizopus nigricans as a biocatalyst for progesterone 11α-hydroxylation

The noncoagulative type of pellet formation can be induced in submerged cultivation of the filamentous fungus Rhizopus nigricans. The size and constitution of the hyphal agglomerates obtained varied with changes in inoculum size and agitation speed for given media composition and cultivation conditions. The physiological state of mycelium, used for a further process of biotransformation, was estimated by following the growth kinetics, pH value and substrate utilization during submerged cultivation. Namely, differences in pellet morphology and physiology affect the ability of R. nigricans to hydroxylate progesterone at the 11α position. A repeated batch procedure revealed the best maintenance of biotransformation capacity for pellets, obtained from the growth phase of cultivation at high agitation speed and with low inoculum size.     

Folding Simulations of a De Novo Designed Protein with a βαβ Fold

βαβ structural motifs are commonly used building blocks in protein structures containing parallel β-sheets. However, to our knowledge, no stand-alone βαβ structure has been observed in nature to date. Recently, for the first time that we know of, a small protein with an independent βαβ structure (DS119) was successfully designed in our laboratory. To understand the folding mechanism of DS119, in the study described here, we carried out all-atom molecular dynamics and coarse-grained simulations to investigate its folding pathways and energy landscape. From all-atom simulations, we successfully observed the folding event and got a stable folded structure with a minimal root mean-square deviation of 2.6 Å with respect to the NMR structure. The folding process can be described as a fast collapse phase followed by rapid formation of the central helix, and then slow formation of a parallel β-sheet. By using a native-centric Gō-like model, the cooperativity of the system was characterized in terms of the calorimetric criterion, sigmoidal transitions, conformation distribution shifts, and free-energy profiles. DS119 was found to be an incipient downhill folder that folds more cooperatively than a downhill folder, but less cooperatively than a two-state folder. This may reflect the balance between the two structural elements of DS119: the rapidly formed α-helix and the slowly formed parallel β-sheet. Folding times estimated from both the all-atom simulations and the coarse-grained model were at microsecond level, making DS119 another fast folder. Compared to fast folders reported previously, DS119 is, to the best of our knowledge, the first that exhibits a parallel β-sheet.     

Langerhans cell histiocytosis: a cytokine/chemokine-mediated disorder?

Langerhans cell histiocytosis (LCH) is a rare disorder characterized by an abnormal accumulation and/or proliferation of cells with a Langerhans cell phenotype. Although no clear cause of LCH has been identified, it has been postulated that LCH might be the consequence of an immune dysregulation, causing Langerhans cells to migrate to and accumulate at various sites. Production of cytokines and chemokines is a central feature of immune regulation. Cytokines are abundantly present within LCH lesions. We review here the potential role of cytokines and chemokines in the pathogenesis of LCH. The type, distribution, and number of different cytokines released within lesions can provide clues to the possible aetiology of LCH and, ultimately, might offer therapeutic possibilities using recombinant cytokines or antagonists for this disorder.     

SIRT1/PGC-1: a neuroprotective axis?

Neurodegenerative diseases are more and more prevalent in our aging societies. A rapid overview of the etiology of many neurodegenerative diseases like Alzheimer, Parkinson, Huntington disease and amyotrophic lateral sclerosis suggests a tight link with mitochondrial dysfunction. Since it has been recently demonstrated that activation of the SIRT1/PGC-1 pathway, in a metabolic context promotes mitochondrial function, we performed a detailed literature review on the implication of this pathway in neurodegeneration. Interestingly, transgenic mice with impaired PGC-1 expression have neurodegenerative lesions and show behavioural abnormalities. As evidenced from independent investigations, enhanced SIRT1 activity has been demonstrated to protect against axonal degeneration and to decrease the accumulation of amyloid beta peptides, the hallmark of Alzheimer disease, in cultured murine embryonic neurons. In addition, several studies suggest that resveratrol, a specific activator of SIRT1, could have protective effects in animal models of neurodegenerative diseases. Taken together, these results strongly suggest that the modulation of the SIRT1/PGC-1 pathway, which has not been well documented in the central nervous system, could become the cornerstone for new therapeutical approaches to combat neurodegeneration.     

How does a Psittacanthus robustus Mart. population structure relate to a Vochysia thyrsoidea Pohl. host population?

Distribution of parasitic plants is directly linked with the distribution of host species and behavioral patterns of seed dispersers. Psittacanthus robustus (Loranthaceae) is a neotropical hemiparasite that mainly colonizes species of the family Vochysiaceae. Vochysia thyrsoidea is the main host of P. robustus and is commonly found in areas of cerrado rupestre (rocky savanna), an abundant vegetation in our study site. We conducted the study in the ecological park Parque Ecológico Quedas do Rio Bonito (PEQRB), over an area of 2.82 ha of cerrado rupestre. The objective of this work was to investigate population structure, parasitic behavior (mistletoe grip height and circumference of host branch), and spatial distribution of Psittacanthus robustus on a population of Vochysia thyrsoidea. We sampled 267 V. thyrsoidea individuals and found that the population had a random distribution pattern. Seventy-nine individuals (29.6% of the sample population) hosted the hemiparasite, to a total of 193 P. robustus individuals. The number of mistletoe individuals per host plant ranged between 1 and 12. The V. thyrsoidea individuals most infested with mistletoes were those reaching greater heights. The correlation between height of host plant and preferred grip height was highly significant, with the preferred grip height being the uppermost portions of host plants. The crown size of P. robustus individuals ranged between 10 and 230 cm. The main disperser of P. robustus fruit was found to be swallow-tanager Tersina viridis viridis. Its activities led to a clumped pattern of spatial distribution of the hemiparasite along with higher infestation in larger trees.     

miR-146a/b在动脉粥样硬化疾病中的研究进展

动脉粥样硬化是冠心病等心血管疾病的病理学基础。血管内皮细胞、血管平滑肌细胞和单核/巨噬细胞是参与动脉粥样硬化发生发展的重要因素。microRNA是一类内源性、长约22个核苷酸的非编码RNA,能够参与调控众多生物学过程,与许多疾病密切相关。miR-146a/b广泛表达于血管内皮细胞、平滑肌细胞和单核/巨噬细胞中,并通过作用于不同靶基因发挥其多样化的生物学功能,参与调控动脉粥样硬化。现就miR-146a/b与动脉粥样硬化发生发展的关系作一综述。