Safety and Tolerability of GRF6019 Infusions in Severe Alzheimer's Disease: A Phase II Double-Blind Placebo-Controlled Trial.

BACKGROUND: The plasma fraction GRF6019 shows multiple benefits on brain aging in mice, including enhanced cognition, neurogenesis, and synaptic density, as well as reduced neuroinflammation. OBJECTIVE: To evaluate the safety, tolerability, and preliminary efficacy of GRF6019 in patients with severe Alzheimer's disease (AD). METHODS: A phase II, double-blind, placebo-controlled study in patients with severe AD (Mini-Mental State Examination score 0-10). Patients were randomized 2 : 1 to GRF6019 (N = 18) or placebo (N = 8) and received daily 250 mL intravenous infusions over 5 days. The primary endpoints were the rates of adverse events (AEs) and the tolerability of GRF6019 as assessed by the number of patients completing the study. Change from baseline in cognitive and functional assessments was also evaluated. RESULTS: All patients completed 100%of study visits and infusions. The rate of AEs was similar in the GRF6019 (8/18 patients [44.4%]) and placebo (3/8 patients [37.5%]) groups, and there were no deaths or serious AEs. The most common AEs considered related to treatment were mild, transient changes in blood pressure in the GRF6019 group (hypotension: 2 patients [11.1%]; hypertension: 1 patient [5.6%]); there were no related AEs in the placebo group. The trial was not powered to detect statistically significant differences between treatment groups. At the end of the study, patients in both treatment groups remained stable or improved on all cognitive and functional endpoints. CONCLUSION: GRF6019 demonstrated excellent safety, feasibility, and tolerability. Future trials designed to characterize the potential functional benefits of GRF6019 and related plasma fractions in severe AD are warranted.

Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains.

The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project to sequence about 250 bacterial and archaeal genomes of elevated phylogenetic diversity. Herein, we propose to extend this approach to type strains of prokaryotes associated with soil or plants and their close relatives as well as type strains from newly described species. Understanding the microbiology of soil and plants is critical to many DOE mission areas, such as biofuel production from biomass, biogeochemistry, and carbon cycling. We are also targeting type strains of novel species while they are being described. Since 2006, about 630 new species have been described per year, many of which are closely aligned to DOE areas of interest in soil, agriculture, degradation of pollutants, biofuel production, biogeochemical transformation, and biodiversity.

International interlaboratory study comparing single organism 16S rRNA gene sequencing data: Beyond consensus sequence comparisons.

This study presents the results from an interlaboratory sequencing study for which we developed a novel high-resolution method for comparing data from different sequencing platforms for a multi-copy, paralogous gene. The combination of PCR amplification and 16S ribosomal RNA gene (16S rRNA) sequencing has revolutionized bacteriology by enabling rapid identification, frequently without the need for culture. To assess variability between laboratories in sequencing 16S rRNA, six laboratories sequenced the gene encoding the 16S rRNA from Escherichia coli O157:H7 strain EDL933 and Listeria monocytogenes serovar 4b strain NCTC11994. Participants performed sequencing methods and protocols available in their laboratories: Sanger sequencing, Roche 454 pyrosequencing(®), or Ion Torrent PGM(®). The sequencing data were evaluated on three levels: (1) identity of biologically conserved position, (2) ratio of 16S rRNA gene copies featuring identified variants, and (3) the collection of variant combinations in a set of 16S rRNA gene copies. The same set of biologically conserved positions was identified for each sequencing method. Analytical methods using Bayesian and maximum likelihood statistics were developed to estimate variant copy ratios, which describe the ratio of nucleotides at each identified biologically variable position, as well as the likely set of variant combinations present in 16S rRNA gene copies. Our results indicate that estimated variant copy ratios at biologically variable positions were only reproducible for high throughput sequencing methods. Furthermore, the likely variant combination set was only reproducible with increased sequencing depth and longer read lengths. We also demonstrate novel methods for evaluating variable positions when comparing multi-copy gene sequence data from multiple laboratories generated using multiple sequencing technologies.

Non-prenylatable, cytosolic Rac1 alters neurite outgrowth while retaining the ability to be activated.

Rac1 is an important regulator of axon extension, cell migration and actin reorganization. Like all Rho guanine triphosphatases (GTPases), Rac1 is targeted to the membrane by the addition of a geranylgeranyl moiety, an action thought to result in Rac1 guanosine triphosphate (GTP) binding. However, the role that Rac1 localization plays in its activation (GTP loading) and subsequent activation of effectors is not completely clear. To address this, we developed a non-prenylatable emerald green fluorescent protein (EmGFP)-Rac1 fusion protein (EmGFP-Rac1(C189A)) and assessed how expressing this construct affected neurite outgrowth, Rac1 localization and activation in neuroblastoma cells. Expression of EmGFP-Rac1(C189A) increased localization to the cytosol and induced cell clustering while increasing neurite initiation. EmGFP-Rac1(C189A) expression also increased Rac1 activation in the cytosol, compared to cells expressing wild-type Rac1 (EmGFP-Rac1). These results suggest that activation of Rac1 may not require plasma membrane localization, potentially leading to differential activation of cytosolic signaling pathways that alter cell morphology. Understanding the consequences of differential localization and activation of Rho GTPases, including Rac1, could lead to new therapeutic targets for treating neurological disorders.

The Development of a Microbial Challenge Test with Acholeplasma laidlawii To Rate Mycoplasma-Retentive Filters by Filter Manufacturers.

Mycoplasma are bacteria that can penetrate 0.2 and 0.22 µm rated sterilizing-grade filters and even some 0.1 µm rated filters. Primary applications for mycoplasma filtration include large scale mammalian and bacterial cell culture media and serum filtration. The Parenteral Drug Association recognized the absence of standard industry test parameters for testing and classifying 0.1 µm rated filters for mycoplasma clearance and formed a task force to formulate consensus test parameters. The task force established some test parameters by common agreement, based upon general industry practices, without the need for additional testing. However, the culture medium and incubation conditions, for generating test mycoplasma cells, varied from filter company to filter company and was recognized as a serious gap by the task force. Standardization of the culture medium and incubation conditions required collaborative testing in both commercial filter company laboratories and in an Independent laboratory (Table I). The use of consensus test parameters will facilitate the ultimate cross-industry goal of standardization of 0.1 µm filter claims for mycoplasma clearance. However, it is still important to recognize filter performance will depend on the actual conditions of use. Therefore end users should consider, using a risk-based approach, whether process-specific evaluation of filter performance may be warranted for their application. LAY ABSTRACT: Mycoplasma are small bacteria that have the ability to penetrate sterilizing-grade filters. Filtration of large-scale mammalian and bacterial cell culture media is an example of an industry process where effective filtration of mycoplasma is required. The Parenteral Drug Association recognized the absence of industry standard test parameters for evaluating mycoplasma clearance filters by filter manufacturers and formed a task force to formulate such a consensus among manufacturers. The use of standardized test parameters by filter manufacturers, including the preparation of the culture broth, will facilitate the end user's evaluation of the mycoplasma clearance claims provided by filter vendors. However, it is still important to recognize filter performance will depend on the actual conditions of use; therefore end users should consider, using a risk-based approach, whether process-specific evaluation of filter performance may be warranted for their application.

Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project.

The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project with the objective of sequencing 250 bacterial and archaeal genomes. The two major goals of that project were (a) to test the hypothesis that there are many benefits to the use the phylogenetic diversity of organisms in the tree of life as a primary criterion for generating their genome sequence and (b) to develop the necessary framework, technology and organization for large-scale sequencing of microbial isolate genomes. While the GEBA pilot project has not yet been entirely completed, both of the original goals have already been successfully accomplished, leading the way for the next phase of the project. Here we propose taking the GEBA project to the next level, by generating high quality draft genomes for 1,000 bacterial and archaeal strains. This represents a combined 16-fold increase in both scale and speed as compared to the GEBA pilot project (250 isolate genomes in 4+ years). We will follow a similar approach for organism selection and sequencing prioritization as was done for the GEBA pilot project (i.e. phylogenetic novelty, availability and growth of cultures of type strains and DNA extraction capability), focusing on type strains as this ensures reproducibility of our results and provides the strongest linkage between genome sequences and other knowledge about each strain. In turn, this project will constitute a pilot phase of a larger effort that will target the genome sequences of all available type strains of the Bacteria and Archaea.

The status of coral reefs and associated fishes and invertebrates of commercial importance in Pedro Bank, Jamaica / Estado de los arrecifes de coral y comunidades de peces e invertebrados con interés comercial asociadas al Banco de Pedro, Jamaica

The coral reefs located off the north coast of the Jamaican mainland are some of the best and most studied reefs in the world. Coral reefs of Pedro Bank, Jamaica were assessed in March, 2012 as part of the KSLOF Global Reef Expedition using a modified Atlantic and Gulf Rapid Reef Assessment (AGRRA) protocol. The main objectives were to: 1) characterize the distribution, structure and health of coral reefs; and 2) evaluate the population status of commercially important reef fishes and invertebrates. This work was conducted to assist in characterizing coral reef habitats within and outside a proposed fishery reserve, and identify other possible conservation zones. Within 20 reefs, live coral cover ranged from 4.9% to 19.2%. Coral communities were dominated by small corals (esp. Agaricia, Porites and Siderastrea) although many sites had high abundances of large colonies of Montastraea annularis and M. faveolata, and these were generally in good condition. A single area, within the proposed fishery reserve, had extensive Acropora cervicornis thickets, and several shallow locations had small, but recovering A. palmata stands. Macroalgal cover at all sites was relatively low, with only three sites having greater than 30% cover; crustose coralline algae (CCA) was high, with eight sites exceeding 20% cover. Fish biomass at all sites near the Cays was low, with a dominance of herbivores (parrotfish and surgeonfish) and a near absence of groupers, snappers and other commercially important species. While parrotfish were the most abundant fish, these were all extremely small (mean size= 12cm; <4% over 29cm), and they were dominated by red band parrotfish (Sparisoma aurofrenatum) followed by striped parrotfish (Scarus iseri). While coral communities remain in better condition than most coastal reefs in Jamaica, intense fishing pressure using fish traps (main target species: surgeonfish) and hookah/spear fishing (main target: parrotfish) is of grave concern to the future persistence of these reefs. The proposed fishery reserve encompasses some of the best coral reef habitat near the Cays, but this MPA should be expanded to encompass other habitats and MPAs should be considered for bank reefs at the northwestern end, as well as Banner Reef and Blowers Rock.

Los arrecifes de coral ubicados en la costa norte de Jamaica son los mejores y mas estudiados corales del mundo. Los corales de arrecife del Banco de Pedro, Jamaica, fueron evaluados en marzo 2012 como parte de la expedición global KSLOF utilizando una modificación del protocolo de estimación rápida de arrecifes para el Atlántico y el Caribe (AGRRA). Los objetivos principales fueron: 1) caracterizar la distribución, estructura y salud de los arrecifes de coral; y 2) evaluar la condición de las poblaciones de peces arrecifales e invertebrados de interés comercial. Este trabajo fue realizado con el propósito de colaborar en la caracterización de hábitats arrecifales, tanto dentro como fuera de un área sugerida como reserva marina, e identificar otras áreas de conservación. Para los 20 arrecifes, la cobertura de coral vivo varió entre 4.9% y 19.2%. Las comunidades de corales son dominadas por corales pequeños (Agaricia, Porites y Siderastrea), aunque en varias localidades se presentó una mayor abundancia de colonias grandes de M. annularis y M. faveolata, y estos se encontraban por lo general en buenas condiciones. Dentro de la reserva pesquera propuesta, una sola área presentó fragmentos de A. cervicornis, y varias localidades someras presentaron pequeños fragmentos de A. palmata, pero en proceso de recuperación. La cobertura de macroalgas en todas las áreas fue relativamente baja, solo tres lugares presentaron más de un 30%; la cobertura de algas coralinas calcárea (CCA) fue alta, ocho lugares excedieron el 20%. La biomasa de peces fue baja en todos los sitios cercanos a los cayos, y hubo dominancia de herbívoros (pez loro y cirujanos), y en general ausencia de chernas, pargos y otras especies de peces de interés comercial. Aunque los peces loro fueron los más abundantes, estos presentaron tamaños extremadamente pequeños (tamaño promedio = 12cm; <4% por encima de 29cm), y estuvieron dominados por el pez loro de banda roja (Sparisoma aurofrenatum), y por el pez loro de rayas (Scarus iseri). Mientras que las comunidades de coral permanecen en mejor condición que muchos de los arrecifes costeros de Jamaica, existe una intensa presión pesquera usando trampas de pesca (principal objetivo: cirujanos) y de compresores de aire (hookah)/ pesca con arpón (principal objetivo: pez loro) es preocupante, y compromete la persistencia y el futuro de estos arrecifes. La reserva marina (MPA) que se sugiere incluye algunos de los mejores hábitats de arrecife coralino cerca de los cayos, pero es recomendable que se amplíe para incluir otros hábitats y que se consideren áreas marinas protegidas en los bancos de arrecife del extremo noroeste, así como el arrecife Banner y Blowers Rock.

Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.

Patient outcomes and surgical complications in coccidioidomycosis-related hydrocephalus: an institutional review.

OBJECTIVES: Coccidioidomycosis is a common fungal infection in the southwestern US. Hydrocephalus is a serious complication of cranial coccidioidomycosis, and the surgical management of coccidioidomycosis-related hydrocephalus has unique challenges. The authors reviewed their institutional experience with hydrocephalus in the setting of coccidioidomycosis. METHODS: The authors retrospectively identified 44 patients diagnosed with coccidioidomycosis-related hydrocephalus at their institution since 1990, who underwent a total of 99 shunting procedures. The authors examined patient demographics, type of shunt and valve used, pressure settings, failure rates, medical treatment, ventricular response to shunting, and other variables. RESULTS: The majority of patients were young (average age 37 years) men (male/female ratio 28:16) with a mean follow-up of 63 months. Patients of Asian and African descent were overrepresented in the cohort compared with regional demographic data. The overall shunt failure rate during follow-up was 50%, and the average number of revisions required if the shunt failed was 2.5 (range 1-8). Low to moderate draining pressures (mean 88 mm H2O) were used in this cohort. Fourteen patients received intrathecal antifungals, and a trend of initiating intrathecal therapy after need for a shunt revision was observed (p = 0.051). The majority of shunt failures (81%) were due to mechanical blockages in the drainage system. Most patients (59%) had at least partial persistent postoperative ventriculomegaly despite successful CSF diversion. Four patients (9%) died due to coccidioidomycosis during the follow-up period. CONCLUSIONS: Coccidioidomycosis-related hydrocephalus more often affected young males in the study's cohort, especially those of African and Asian descent. Despite the best medical therapy, there was a high rate of shunt failure due to clogged catheters or valves due to the underlying disease process. Many patients continued to have ventriculomegaly even with adequate CSF diversion. The morbidity and mortality of this chronic disease process must be recognized by the treatment team, and patients should be appropriately counseled.

Protein-protein interface detection using the energy centrality relationship (ECR) characteristic of proteins.

Specific protein interactions are responsible for most biological functions. Distinguishing Functionally Linked Interfaces of Proteins (FLIPs), from Functionally uncorrelated Contacts (FunCs), is therefore important to characterizing these interactions. To achieve this goal, we have created a database of protein structures called FLIPdb, containing proteins belonging to various functional sub-categories. Here, we use geometric features coupled with Kortemme and Baker's computational alanine scanning method to calculate the energetic sensitivity of each amino acid at the interface to substitution, identify hotspots, and identify other factors that may contribute towards an interface being FLIP or FunC. Using Principal Component Analysis and K-means clustering on a training set of 160 interfaces, we could distinguish FLIPs from FunCs with an accuracy of 76%. When these methods were applied to two test sets of 18 and 170 interfaces, we achieved similar accuracies of 78% and 80%. We have identified that FLIP interfaces have a stronger central organizing tendency than FunCs, due, we suggest, to greater specificity. We also observe that certain functional sub-categories, such as enzymes, antibody-heavy-light, antibody-antigen, and enzyme-inhibitors form distinct sub-clusters. The antibody-antigen and enzyme-inhibitors interfaces have patterns of physical characteristics similar to those of FunCs, which is in agreement with the fact that the selection pressures of these interfaces is differently evolutionarily driven. As such, our ECR model also successfully describes the impact of evolution and natural selection on protein-protein interfaces. Finally, we indicate how our ECR method may be of use in reducing the false positive rate of docking calculations.

Collaborative study report: evaluation of the ATCC experimental mycoplasma reference strains panel prepared for comparison of NAT-based and conventional mycoplasma detection methods.

The main goal of this collaborative study was to evaluate the experimental panel of cryopreserved mycoplasma reference strains recently prepared by the American Type Culture Collection (ATCC(®)) in order to assess the viability and dispersion of cells in the mycoplasma stocks by measuring the ratio between the number of genomic copies (GC) and the number of colony forming units (CFU) in the reference preparations. The employment of microbial reference cultures with low GC/CFU ratios is critical for unbiased and reliable comparison of mycoplasma testing methods based on different methodological approaches, i.e., Nucleic Acid Testing (NAT) and compendial culture-based techniques. The experimental panel included ten different mycoplasma species known to represent potential human and animal pathogens as well as common contaminants of mammalian and avian cell substrates used in research, development, and manufacture of biological products. Fifteen laboratories with expertise in field of mycoplasma titration and quantification of mycoplasmal genomic DNA participated in the study conducted from February to October of 2012. The results of this study demonstrated the feasibility of preparing highly viable and dispersed (possessing low GC/CFU ratios) frozen stocks of mycoplasma reference materials, required for reliable comparison of NAT-based and conventional mycoplasma detection methods.

Proposal of Zygosaccharomyces parabailii sp. nov. and Zygosaccharomyces pseudobailii sp. nov., novel species closely related to Zygosaccharomyces bailii.

Twenty-three yeast strains traditionally identified as Zygosaccharomyces bailii were studied in order to clarify their taxonomy and phylogenetic relationships. The molecular phylogeny from rRNA gene sequences showed that these yeasts were well divided into three major groups, and two of the groups could be clearly distinguished from the type strain of Z. bailii at the species level. Therefore, we propose Zygosaccharomyces parabailii sp. nov. (type strain ATCC 56075(T)  = NBRC 1047(T)  = NCYC 128(T)  = CBS 12809(T)) and Zygosaccharomyces pseudobailii sp. nov. (type strain ATCC 56074(T)  = NBRC 0488(T)  = CBS 2856(T)) to accommodate the yeasts belonging to the two groups. By conventional physiological tests, Z. bailii and the two novel species are not clearly distinguished from one another, as variations exist more frequently between individual strains and are not species-specific. However, the conclusions from rRNA gene sequence analyses are well supported by genome fingerprinting patterns as well as other protein-coding gene sequence comparisons.

Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names.

High quality 16S ribosomal RNA (rRNA) gene sequences from the type strains of all species with validly published names, as defined by the International Code of Nomenclature of Bacteria, are a prerequisite for their accurate affiliations within the global genealogical classification and for the recognition of potential new taxa. During the last few years, the Living Tree Project (LTP) has taken care to create a high quality, aligned 16S and 23S rRNA gene sequence database of all type strains. However, the manual curation of the sequence dataset and type strain information revealed that a total of 552 "orphan" species (about 5.7% of the currently classified species) had to be excluded from the reference trees. Among them, 322 type strains were not represented by an SSU entry in the public sequence repositories. The remaining 230 type strains had to be discarded due to bad sequence quality. Since 2010, the LTP team has coordinated a network of researchers and culture collections in order to improve the situation by (re)-sequencing the type strains of these "orphan" species. As a result, we can now report 351 16S rRNA gene sequences of type strains. Nevertheless, 201 species could not be sequenced because cultivable type strains were not available (121), the cultures had either been lost or were never deposited in the first place (66), or it was not possible due to other constraints (14). The International Code of Nomenclature of Bacteria provides a number of mechanisms to deal with the problem of missing type strains and we recommend that due consideration be given to the appropriate mechanisms in order to help solve some of these issues.

Post-ictal, lateralized hyperkinetic motor behavior.

Recognition of a transient, focal neurologic dysfunction after a seizure is important when evaluating patients with idiopathic epilepsy. Todd's palsy, a transient focal weakness after a seizure, is a highly accurate clinical sign indicative of a contralateral, cerebral epileptic focus. In contrast, a transient, lateralized hyperkinetic motor behavior from a contralateral, hemispheric ictal focus has not been emphasized as a localizing clinical sign. The following case demonstrates that transient hyperkinetic behavior occurs as a post-ictal phenomenon and may have a localizing value, as in Todd's palsy.

Equatorial decline of reef corals during the last Pleistocene interglacial.

The Last Interglacial (LIG; ca. 125,000 y ago) resulted from rapid global warming and reached global mean temperatures exceeding those of today. The LIG thus offers the opportunity to study how life may respond to future global warming. Using global occurrence databases and applying sampling-standardization, we compared reef coral diversity and distributions between the LIG and modern. Latitudinal diversity patterns are characterized by a tropical plateau today but were characterized by a pronounced equatorial trough during the LIG. This trough is governed by substantial range shifts away from the equator. Range shifts affected both leading and trailing edges of species range limits and were much more pronounced in the Northern Hemisphere than south of the equator. We argue that interglacial warming was responsible for the loss of equatorial diversity. Hemispheric differences in insolation during the LIG may explain the asymmetrical response. The equatorial retractions are surprisingly strong given that only small temperature changes have been reported in the LIG tropics. Our results suggest that the poleward range expansions of reef corals occurring with intensified global warming today may soon be followed by equatorial range retractions.

Lactobacillus brantae sp. nov., isolated from faeces of Canada geese (Branta canadensis).

Three strains of lactic acid bacteria (LAB) were isolated from the faeces of apparently healthy wild Canada geese (Branta canadensis) in 2010 by cultivating faecal LAB on Rogosa SL agar under aerobic conditions. These three isolates were found to share 99.9 % gene sequence similarity of their 16S rRNA, their 16S-23S intergenic transcribed spacer region (ITS), partial 23S rRNA, rpoB, rpoC, rpoA and pheS gene sequences. However, the three strains exhibited lower levels of sequence similarity of these genetic targets to all known LAB, and the phylogenetically closest species to the geese strains were Lactobacillus casei, Lactobacillus paracasei, Lactobacillus rhamnosus and Lactobacillus saniviri. In comparison to L. casei ATCC 393(T), L. paracasei ATCC 25302(T), L. rhamnosus ATCC 7469(T) and L. saniviri DSM 24301(T), the novel isolates reacted uniquely in tests for cellobiose, galactose, mannitol, citric acid, aesculin and dextrin, and gave negative results in tests for l-proline arylamidase and l-pyrrolydonyl-arylamidase, and in the Voges-Proskauer test. Biochemical tests for cellobiose, aesculin, galactose, gentiobiose, mannitol, melezitose, ribose, salicin, sucrose, trehalose, raffinose, turanose, amygdalin and arbutin could be used for differentiation between L. saniviri and the novel strains. On the basis of phenotypic and genotypic characteristics, and phylogenetic data, the three isolates represent a novel species of the genus Lactobacillus, for which the name Lactobacillus brantae sp. nov. is proposed. The type strain is SL1108(T) (= ATCC BAA-2142(T) = LMG 26001(T) = DSM 23927(T)) and two additional strains are SL1170 and SL60106.

Fanconi anemia D2 protein is an apoptotic target mediated by caspases.

FANCD2, a key factor in the FANC-BRCA1 pathway is monoubiquitinated and targeted to discrete nuclear foci following DNA damage. Since monoubiquitination of FANCD2 is a crucial indicator for cellular response to DNA damage, we monitored the fate of FANCD2 and its monoubiquitination following DNA damage. Disappearance of FANCD2 protein was induced following DNA damage in a dose-dependent manner, which correlated with degradation of BRCA1 and poly-ADP ribose polymerase (PARP), known targets for caspase-mediated apoptosis. Disappearance of FANCD2 was not affected by a proteasome inhibitor but was blocked by a caspase inhibitor. DNA damage-induced disappearance of FANCD2 was also observed in cells lacking FANCA, suggesting that disappearance of FANCD2 does not depend on FANC-BRCA1 pathway and FANCD2 monoubiquitination. In keeping with this, cells treated with TNF-α, an apoptotic stimulus without causing any DNA damage, also induced disappearance of FANCD2 without monoubiquitination. Together, our data suggest that FANCD2 is a target for caspase-mediated apoptotic pathway, which may be an early indicator for apoptotic cell death.

Biochemical characterization of metnase's endonuclease activity and its role in NHEJ repair.

Metnase (SETMAR) is a SET-transposase fusion protein that promotes nonhomologous end joining (NHEJ) repair in humans. Although both SET and the transposase domains were necessary for its function in DSB repair, it is not clear what specific role Metnase plays in the NHEJ. In this study, we show that Metnase possesses a unique endonuclease activity that preferentially acts on ssDNA and ssDNA-overhang of a partial duplex DNA. Cell extracts lacking Metnase poorly supported DNA end joining, and addition of wt-Metnase to cell extracts lacking Metnase markedly stimulated DNA end joining, while a mutant (D483A) lacking endonuclease activity did not. Given that Metnase overexpression enhanced DNA end processing in vitro, our finding suggests a role for Metnase's endonuclease activity in promoting the joining of noncompatible ends.

Complete genome sequence of Isosphaera pallida type strain (IS1B).

Isosphaera pallida (ex Woronichin 1927) Giovannoni et al. 1995 is the type species of the genus Isosphaera. The species is of interest because it was the first heterotrophic bacterium known to be phototactic, and it occupies an isolated phylogenetic position within the Planctomycetaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the genus Isosphaera and the third of a member of the family Planctomycetaceae. The 5,472,964 bp long chromosome and the 56,340 bp long plasmid with a total of 3,763 protein-coding and 60 RNA genes are part of the Genomic Encyclopedia of Bacteria and Archaea project.

Arginine-dependent acid-resistance pathway in Shigella boydii.

Ability to survive the low pH of the human stomach is considered be an important virulent determinant. It was suggested that the unique acid tolerance of Shigella boydii 18 CDPH, the strain implicated in a 1998 outbreak, may have played an important role in surviving the acidic food (bean salad). The strain was capable of inducing arginine-dependent acid-resistance (ADAR) pathway. This pathway was assumed to be absent in Shigella sp. Here, we have examined occurrence and efficacy of ADAR pathway in 21 S. boydii strains obtained from the American Type Culture Collection (ATCC) along with strains of S. flexneri (n = 7), S. sonnei (n = 4), and S. dysenteriae (n = 2). The eight S. boydii strains were able to induce ADAR to survive the acid challenge at pH 2.0; additional 8 strains could tolerate acid challenge at pH 2.5 but not at pH 2.0. The remaining five S. boydii strains were not able to induce ADAR pathway and could not survive acid challenge even at pH 2.5. ADAR pathway also appears to be present in all four Shigella sp. Shigella ADAR pathway was induced when cells were grown under partial oxygen pressure while its expression in E. coli required mere fermentative growth on glucose.