Cell compartmentalisation in planctomycetes: novel types of structural organisation for the bacterial cell

The organisation of cells of the planctomycete species Pirellula marina, Isosphaera pallida, Gemmata obscuriglobus, Planctomyces maris and "Candidatus Brocadia anammoxidans" was investigated based on ultrastructure derived from thin-sections of cryosubstituted cells, freeze-fracture replicas, and in the case of Gemmata obscuriglobus and Pirellula marina, computer-aided 3-D reconstructions from serial sections of cryosubstituted cells. All planctomycete cells display a peripheral ribosome-free region, termed here the paryphoplasm, surrounding the perimeter of the cell, and an interior region including any nucleoid regions as well as ribosome-like particles, bounded by a single intracytoplasmic membrane (ICM), and termed the pirellulosome in Pirellula species. Immunogold labelling and RNase-gold cytochemistry indicates that in planctomycetes all the cell DNA is contained wholly within the interior region bounded by the ICM, and the paryphoplasm contains no DNA but at least some of the cell's RNA. The ICM in Isosphaera pallida and Planctomyces maris is invaginated such that the paryphoplasm forms a major portion of the cell interior in sections, but in other planctomycetes it remains as a peripheral zone. In the anaerobic ammonium-oxidising ("anammox" process) chemoautotroph "Candidatus Brocadia anammoxidans" the interior region bounded by ICM contains a further internal single-membrane-bounded region, the anammoxosome. In Gemmata obscuriglobus, the interior ICM-bounded region contains the nuclear body, a double-membrane-bounded region containing the cell's nucleoid and all genomic DNA in addition to some RNA. Shared features of cell compartmentalisation in different planctomycetes are consistent with the monophyletic nature of the planctomycetes as a distinct division of the Bacteria. The shared organisational plan for the planctomycete cell constitutes a new type not known in cells of other bacteria.     

Isolation of Gemmata-like and Isosphaera-like planctomycete bacteria from soil and freshwater.

New cultured strains of the planctomycete division (order Planctomycetales) of the domain Bacteria related to species in the genera Gemmata and Isosphaera were isolated from soil, freshwater, and a laboratory ampicillin solution. Phylogenetic analysis of the 16S rRNA gene from eight representative isolates showed that all the isolates were members of the planctomycete division. Six isolates clustered with Gemmata obscuriglobus and related strains, while two isolates clustered with Isosphaera pallida. A double-membrane-bounded nucleoid was observed in Gemmata-related isolates but not in Isosphaera-related isolates, consistent with the ultrastructures of existing species of each genus. Two isolates from this study represent the first planctomycetes successfully cultivated from soil.     

Assembly of a complete genome sequence for <Emphasis Type="Italic">Gemmata obscuriglobus</Emphasis> reveals a novel prokaryotic rRNA operon gene architecture

Gemmata obscuriglobus is a Gram-negative bacterium with several intriguing biological features. Here, we present a complete, de novo whole genome assembly for G. obscuriglobus which consists of a single, circular 9 Mb chromosome, with no plasmids detected. The genome was annotated using the NCBI Prokaryotic Genome Annotation pipeline to generate common gene annotations. Analysis of the rRNA genes revealed three interesting features for a bacterium. First, linked G. obscuriglobus rrn operons have a unique gene order, 23S–5S–16S, compared to typical prokaryotic rrn operons (16S–23S–5S). Second, G. obscuriglobus rrn operons can either be linked or unlinked (a 16S gene is in a separate genomic location from a 23S and 5S gene pair). Third, all of the 23S genes (5 in total) have unique polymorphisms. Genome analysis of a different Gemmata species (SH-PL17), revealed a similar 23S–5S–16S gene order in all of its linked rrn operons and the presence of an unlinked operon. Together, our findings show that unique and rare features in Gemmata rrn operons among prokaryotes provide a means to better define the evolutionary relatedness of Gemmata species and the divergence time for different Gemmata species. Additionally, these rrn operon differences provide important insights into the rrn operon architecture of common ancestors of the planctomycetes.     

Whole-genome reciprocal BLAST analysis reveals that planctomycetes do not share an unusually large number of genes with Eukarya and Archaea

The genome sequences of Rhodopirellula baltica, formerly Pirellula sp. strain 1, Blastopirellula marina, Gemmata obscuriglobus, and Kuenenia stuttgartiensis were used in a series of pairwise reciprocal best-hit analyses to evaluate the contested evolutionary position of Planctomycetes. Contrary to previous reports which suggested that R. baltica had a high percentage of genes with closest matches to Archaea and Eukarya, we show here that these Planctomycetes do not share an unusually large number of genes with the Archaea or Eukarya, compared with other Bacteria. Thus, best-hit analyses may assign phylogenetic affinities incorrectly if close relatives are absent from the sequence database.     

Unraveling the extent of diversity within the order Planctomycetales.

The phylogenetic positions of 22 isolates that morphologically resemble members of the family Planctomycetaceae were determined by sequence analysis of genes coding for 16S rRNA. While nine and eight isolates could be assigned to the genera Planctomyces and Pirellula, respectively, three strains grouped near Isosphaera pallida and one strain was closely related to Gemmata obscuriglobus. No isolate was found to be related to a previously described species of any of the four genera at the species level. Morphological characters and sequence idiosyncrasies of genes coding for 16S rRNA of the isolates generally correlated with features described for the four genera to which the isolates could be assigned. One strain stands phylogenetically isolated and may be representative of a novel genus of the family. Comparison with environmental clone sequences representing planctomycetes in soil and water revealed that three of the novel isolates were related to one clone of soil origin, but no close relationships between clones and the other new strains were found. The study reveals that the biodiversity of planctomycetes is significantly greater than was previously determined.     

Detection of representatives of the Planctomycetes in Sphagnum peat bogs by molecular and cultivation methods

By means of fluorescence in situ hybridization with 16S rRNA-targeted oligonucleotide probes (FISH), it has been shown that members of the phylum Planctomycetes represent a numerically significant bacterial group in boreal Sphagnum peat bogs. The population size of planctomycetes in oxic layers of the peat bog profile was in the range of 0.4-2.0 x 10(7) cells per g of wet peat, comprising 4 to 13% of the total bacterial cell number. A novel effective approach that combined a traditional cultivation technique with FISH-mediated monitoring of the target organism during the isolation procedure has been developed for the isolation of planctomycetes. Using this approach, we succeeded in isolating several peat-inhabiting planctomycetes in a pure culture. Sequencing of the 16S rRNA genes from two of these isolates, strains A10 and MPL7, showed that they belonged to the planctomycete lineages defined by the genera Gemmata and Planctomyces, respectively. The 16S rRNA gene sequence similarity between strains A10 and MPL7 and the phylogenetically closest organisms, namely, Gemmata obscuriglobus and Planctomyces limnophilus, was only 90%. These results suggest that the indigenous planctomycetes inhabiting Sphagnum peat bogs are so far unknown organisms.     

Isolation and molecular identification of planctomycete bacteria from postlarvae of the giant tiger prawn, Penaeus monodon.

Bacteria phenotypically resembling members of the phylogenetically distinct planctomycete group of the domain Bacteria were isolated from postlarvae of the giant tiger prawn, Penaeus monodon. A selective medium designed in the light of planctomycete antibiotic resistance characteristics was used for this isolation. Planctomycetes were isolated from both healthy and monodon baculovirus-infected prawn postlarvae. The predominant colony type recovered from postlarvae regardless of viral infection status was nonpigmented. Other, less commonly observed types were pink or orange pigmented. A planctomycete-specific 16S rRNA-directed probe was designed and used to screen the isolates for their identity as planctomycetes prior to molecular phylogenetic characterization. 16S rRNA genes from nine prawn isolates together with two planctomycete reference strains (Planctomyces brasiliensis and Gemmata obscuriglobus) were sequenced and compared with reference sequences from the planctomycetes and other members of the domain Bacteria. Phylogenetic analyses and sequence signatures of the 16S rRNA genes demonstrated that the prawn isolates were members of the planctomycete group. Five representatives of the predominant nonpigmented colony type were members of the Pirellula group within the planctomycetes, as were three pink-pigmented colony type representatives. Homology values and tree topology indicated that representatives of the nonpigmented and pink-pigmented colony types formed two discrete clusters within the Pirellula group, not identical to any known Pirellula species. A sole representative of the orange colony type was a member of the Planctomyces group, virtually identical in 16S rDNA sequence to P. brasiliensis, and exhibited distinctive morphology.     

Enrichment of microbial electrolysis cell biocathodes from sediment microbial fuel cell bioanodes

Electron-accepting (electrotrophic) biocathodes were produced by first enriching graphite fiber brush electrodes as the anodes in sediment-type microbial fuel cells (sMFCs) using two different marine sediments and then electrically inverting the anodes to function as cathodes in two-chamber bioelectrochemical systems (BESs). Electron consumption occurred at set potentials of -439 mV and -539 mV (versus the potential of a standard hydrogen electrode) but not at -339 mV in minimal media lacking organic sources of energy. Results at these different potentials were consistent with separate linear sweep voltammetry (LSV) scans that indicated enhanced activity (current consumption) below only ca. -400 mV. MFC bioanodes not originally acclimated at a set potential produced electron-accepting (electrotrophic) biocathodes, but bioanodes operated at a set potential (+11 mV) did not. CO(2) was removed from cathode headspace, indicating that the electrotrophic biocathodes were autotrophic. Hydrogen gas generation, followed by loss of hydrogen gas and methane production in one sample, suggested hydrogenotrophic methanogenesis. There was abundant microbial growth in the biocathode chamber, as evidenced by an increase in turbidity and the presence of microorganisms on the cathode surface. Clone library analysis of 16S rRNA genes indicated prominent sequences most similar to those of Eubacterium limosum (Butyribacterium methylotrophicum), Desulfovibrio sp. A2, Rhodococcus opacus, and Gemmata obscuriglobus. Transfer of the suspension to sterile cathodes made of graphite plates, carbon rods, or carbon brushes in new BESs resulted in enhanced current after 4 days, demonstrating growth by these microbial communities on a variety of cathode substrates. This report provides a simple and effective method for enriching autotrophic electrotrophs by the use of sMFCs without the need for set potentials, followed by the use of potentials more negative than -400 mV.     

Determinants of the higher order association of the restriction factor TRIM5alpha and other tripartite motif (TRIM) proteins

Many tripartite motif (TRIM) proteins self-associate, forming dimers and higher order complexes. For example, dimers of TRIM5α, a host factor that restricts retrovirus infection, assemble into higher order arrays on the surface of the viral capsid, resulting in an increase in avidity. Here we show that the higher order association of different TRIM proteins exhibits a wide range of efficiencies. Homologous association (self-association) was more efficient than the heterologous association of different TRIM proteins, indicating that specificity determinants of higher order self-association exist. To investigate the structural determinants of higher order self-association, we studied TRIM mutants and chimeras. These studies revealed the following: 1) the RING domain contributes to the efficiency of higher order self-association, which enhances the binding of TRIM5α to the human immunodeficiency virus (HIV-1) capsid; 2) the RING and B-box 2 domains work together as a homologous unit to promote higher order association of dimers; 3) dimerization is probably required for efficient higher order self-association; 4) the Linker 2 region contributes to higher order self-association, independently of effects of Linker 2 changes on TRIM dimerization; and 5) for efficiently self-associating TRIM proteins, the B30.2(SPRY) domain is not required for higher order self-association. These results support a model in which both ends of the core TRIM dimer (RING-B-box 2 at one end and Linker 2 at the other) contribute to the formation of higher order arrays.     

神农架川金丝猴投食群的取食优先序

为探讨人工补食条件下川金丝猴的取食优先序,2007年7月至9月,采用直接观察法对神农架自然保护区大龙潭投食猴群的取食顺序进行研究。结果表明,单元内有明显的取食顺序,但单元间没有。单元内取食顺序不仅与等级和年龄有关,还与单元结构变动相关。     

Within-subject differences in degree of delay discounting as a function of order of presentation of hypothetical cash rewards

Procedural variants in estimating delay discounting (DD) have been shown to yield significant differences in estimated degree of DD as well as variations in individual patterns of choice. For example, a recent study found significantly different degrees of DD between groups assessed using either an ascending or descending order of presentation of the immediately available rewards. The purpose of this study was to test for within-subject effects of order of presentation of the immediate rewards in a DD task. In a single session, college students (N = 29) were asked to complete two DD tasks, one with the immediate rewards presented in ascending order and one in descending order. Consistent with previous results, significantly larger mean area under the discounting curve (AUC) was observed when the descending sequence was used compared to the ascending order of presentation; and the correlation between both measurements was moderate. These results suggest that some DD assessment tasks may be sensitive to contextual variables such as order and range of the reward and delay values.     

The relationship between parental age and birth order with the percentage of low birth-weight infants

Birthweight, birth order, and parental age were abstracted from 1,515,443 New York State birth certificates to study the association between the birth of an infant weighing less than 2501 g and parental age. The percentage of premature infants was greatest for birth order 1 and 6+ and showed a minimum at birth order 3. When maternal age and birth order were analyzed jointly, a strong interaction was found. Young mothers showed a tendency to have an increasing proportion of low birthweight infants with increasing birth order, whereas, the exact opposite was true for mothers older than 45. The intermediate maternal age categories reflected this change from an association of increasing proportion of low birthweight infants with increasing birth order to a pattern of decreasing proportion of premature imfants with increasing birth order. In data stratified to eliminate the influence of maternal age and to some extent birth order, paternal age was shown to affect the percentage of infants weighing less than 2501 g. This association was described by a flat n-shaped curve that was significantly different from a horizontal line (P.01) in 6 of 7 maternal age categories.     

Order and fluidity of lipid membranes as determined by fluorescence anisotropy decay

The fluorescence anisotropy decay of four different probes in bilayers of dimyristoylphosphatidylcholine was measured. The probes are diphenylhexatriene, diphenyloctatetraene, trimethylaminodiphenylhexatriene, and trans-parinaric acid. The data for each probe were analyzed in terms of two orientational order parameters, the ordinary order parameter and a higher one, and two rotational diffusion coefficients. The order parameters are largely independent of probe size, but depend on the position of the probes along the membrane normal, thus reflecting the profile of lipid order. If a probe is located in the plateau region of lipid order, its order parameters are interpreted as representing the rigid-body order of lipids. According to this interpretation, the total lipid order in the plateau region originates about equally from rigid-body order and conformational order. The two order parameters obtained for each probe are used to derive approximate angular distributions of the probe molecules. The diffusion coefficient for rotation about the long molecular axis is found to be infinitely large, indicating unhindered rotation about this axis. The diffusion coefficient for rotation about the short molecular axes is evaluated for a viscosity which results as 0.2 poise. This viscosity for rotational diffusion is an order of magnitude smaller than the viscosity for lateral diffusion indicating that at least two viscosities are required to characterize the fluidity of a lipid membrane.Abbreviations FAD fluorescence anisotropy decay - DMR deuterium magnetic resonance - ESR electron spin resonance - DMPC dimyristoylphosphatidylcholine - DPPC dipalmitoylphosphatidylcholine - DPH 1,6-diphenyl-1,3,5-hexatriene - DPO 1,6-diphenyl-1,3,5,7-octatetraene - TMA-DPH 1-[4-(trimethylamino)phenyl]-6-phenyl-1,3,5-hexatriene - tPnA trans-parinaric acid - NPN N-phenyl-1-naphthylamine - BBO 2,5-bis(4-biphenylyl)oxazole     

Application of selected partial order tools to analyze fate and toxicity indicators of environmentally hazardous chemicals

Studies on fate and toxicity are important aspects in environmental impact assessments of chemicals. In order to elucidate “what is worst” a ranking of the chemicals under investigation is of significant interest, which obviously constitutes a multi-indicator system (MIS). Partial order methodologies turn out to be advantageous tools for analyses of such systems.In the present paper we focus on QSAR generated fate and toxicity indicators of 30 chemicals, comprising of a variety of chemical structures. In many risk assessment studies the level of a multi-indicator system is abandoned and the data are aggregated in order to obtain a composite index. However, such aggregation techniques are far from being trivial. The present paper describes an alternative strategy to handle MIS, i.e., applying partial order methodology leading to useful information. The paper demonstrate how partial order techniques lead to a weak order of the 30 chemicals as well as to the relative importance of the single indicators included in the study. Specifically, the paper addresses the topics on the “relations between the indicators” and “do chemical structures constitute a valid basis for ranking chemicals according to their environmental impact?”.     

Origin of polar order in dense suspensions of phototactic micro-swimmers

A main question for the study of collective motion in living organisms is the origin of orientational polar order, i.e., how organisms align and what are the benefits of such collective behaviour. In the case of micro-organisms swimming at a low Reynolds number, steric repulsion and long-range hydrodynamic interactions are not sufficient to explain a homogeneous polar order state in which the direction of motion is aligned. An external symmetry-breaking guiding field such as a mechanism of taxis appears necessary to understand this phonemonon. We have investigated the onset of polar order in the velocity field induced by phototaxis in a suspension of a motile micro-organism, the algae Chlamydomonas reinhardtii, for density values above the limit provided by the hydrodynamic approximation of a force dipole model. We show that polar order originates from a combination of both the external guiding field intensity and the population density. In particular, we show evidence for a linear dependence of a phototactic guiding field on cell density to determine the polar order for dense suspensions and demonstrate the existence of a density threshold for the origin of polar order. This threshold represents the density value below which cells undergoing phototaxis are not able to maintain a homogeneous polar order state and marks the transition to ordered collective motion. Such a transition is driven by a noise dominated phototactic reorientation where the noise is modelled as a normal distribution with a variance that is inversely proportional to the guiding field strength. Finally, we discuss the role of density in dense suspensions of phototactic micro-swimmers.     

Modeling the onset of symptoms of COVID-19: Effects of SARS-CoV-2 variant

Identifying order of symptom onset of infectious diseases might aid in differentiating symptomatic infections earlier in a population thereby enabling non-pharmaceutical interventions and reducing disease spread. Previously, we developed a mathematical model predicting the order of symptoms based on data from the initial outbreak of SARS-CoV-2 in China using symptom occurrence at diagnosis and found that the order of COVID-19 symptoms differed from that of other infectious diseases including influenza. Whether this order of COVID-19 symptoms holds in the USA under changing conditions is unclear. Here, we use modeling to predict the order of symptoms using data from both the initial outbreaks in China and in the USA. Whereas patients in China were more likely to have fever before cough and then nausea/vomiting before diarrhea, patients in the USA were more likely to have cough before fever and then diarrhea before nausea/vomiting. Given that the D614G SARS-CoV-2 variant that rapidly spread from Europe to predominate in the USA during the first wave of the outbreak was not present in the initial China outbreak, we hypothesized that this mutation might affect symptom order. Supporting this notion, we found that as SARS-CoV-2 in Japan shifted from the original Wuhan reference strain to the D614G variant, symptom order shifted to the USA pattern. Google Trends analyses supported these findings, while weather, age, and comorbidities did not affect our model’s predictions of symptom order. These findings indicate that symptom order can change with mutation in viral disease and raise the possibility that D614G variant is more transmissible because infected people are more likely to cough in public before being incapacitated with fever.     

Organization of the mitochondrial genomes of whiteflies,aphids, and psyllids (Hemiptera,Sternorrhyncha)

Background  

With some exceptions, mitochondria within the class Insecta have the same gene content, and generally, a similar gene order allowing the proposal of an ancestral gene order. The principal exceptions are several orders within the Hemipteroid assemblage including the order Thysanoptera, a sister group of the order Hemiptera. Within the Hemiptera, there are available a number of completely sequenced mitochondrial genomes that have a gene order similar to that of the proposed ancestor. None, however, are available from the suborder Sternorryncha that includes whiteflies, psyllids and aphids.     

Birth order and its association with the onset of chronic fatigue syndrome

Chronic fatigue syndrome (CFS) is a medically unexplained illness that is diagnosed on the basis of a clinical case definition; so it probably is an illness with multiple causes producing the same clinical picture. One way of dealing with this heterogeneity is to stratify patients based on illness onset. We hypothesized that either the whole group of CFS patients or that group which developed CFS gradually would show a relation with birth order, while patients who developed CFS suddenly, probably due to a viral illness, would not show such a relation. We hypothesized the birth order effect in the gradual onset group because those patients have more psychological problems, and birth order effects have been shown for psychological characteristics. We compared birth order in our CFS patients to that in a comparison group derived from U.S. demographic data. We found a tendency that did not reach formal statistical significance for a birth order effect in the gradual onset group, but not in either the sudden onset or combined total group. However, the birth order effect we found was due to relatively increased rates of CFS in second-born children; prior birth order studies of personality characteristics have found such effects to be skewed toward first-born children. Thus, our data do support a birth order effect in a subset of patients with CFS. The results of this study should encourage a larger multicenter study to further explore and understand this relation.     

Estimation of the mean waiting time of a customer subject to balking: a simulation study

To a customer, the waiting time for order processing for a product or service is important information for order placement. If the time foreseen for order fulfillment is long, the order might be lost to a competitor. In particular, modern principles of supply chain management highly suggest information sharing between entities in the chain and information technology has enabled customers to conveniently consider the waiting time for a potential balking decision. To help determine the design and operation of a manufacturing or service system in which a customer may balk based on the foreseen waiting time, this paper develops procedures to estimate the average waiting time of an order. Either the procedures allow the maximum waiting time for a balking decision to be random or do not require knowledge of the arrival process of customers before balking if the balking limit is known. For generality of the model, this paper considers general inter-arrival and service time distributions, and uses the simulation and regression approach.     

Slow decomposition of lower order roots: a key mechanism of root carbon and nutrient retention in the soil

Among tree fine roots, the distal small-diameter lateral branches comprising first- and second-order roots lack secondary (wood) development. Therefore, these roots are expected to decompose more rapidly than higher order woody roots. But this prediction has not been tested and may not be correct. Current evidence suggests that lower order roots may decompose more slowly than higher order roots in tree species associated with ectomycorrhizal (EM) fungi because they are preferentially colonized by fungi and encased by a fungal sheath rich in chitin (a recalcitrant compound). In trees associated with arbuscular mycorrhizal (AM) fungi, lower order roots do not form fungal sheaths, but they may have poorer C quality, e.g. lower concentrations of soluble carbohydrates and higher concentrations of acid-insolubles than higher order roots, thus may decompose more slowly. In addition, litter with high concentrations of acid insolubles decomposes more slowly under higher N concentrations (such as lower order roots). Therefore, we propose that in both AM and EM trees, lower order roots decompose more slowly than higher order roots due to the combination of poor C quality and high N concentrations. To test this hypothesis, we examined decomposition of the first six root orders in Fraxinus mandshurica (an AM species) and Larix gmelinii (an EM species) using litterbag method in northeastern China. We found that lower order roots of both species decomposed more slowly than higher order roots, and this pattern appears to be associated mainly with initial C quality and N concentrations. Because these lower order roots have short life spans and thus dominate root mortality, their slow decomposition implies that a substantial fraction of the stable soil organic matter pool is derived from these lower order roots, at least in the two species we studied.